diff options
| author |   Justin Lecher <jlec@gentoo.org> | 2011-08-14 09:53:01 +0200 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2011-08-14 09:53:01 +0200 |
| commit | 7bb0a1f4eb11cce9e5343a2f1277e715c9be6c65 (patch) | |
| tree | 70dc061e23500190b9fa9db6e0a8eba594258b98 | |
| parent | Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci (diff) | |
| parent | Update use.local.desc (diff) | |
| download | sci-7bb0a1f4eb11cce9e5343a2f1277e715c9be6c65.tar.gz sci-7bb0a1f4eb11cce9e5343a2f1277e715c9be6c65.tar.bz2 sci-7bb0a1f4eb11cce9e5343a2f1277e715c9be6c65.zip | |
Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci: (79 commits)
Update use.local.desc
Fix categories
[sys-cluster/open-mx] Add different mtu support
[sys-cluster/open-mx] Add new version of open-mx
Masked live builds, librecad and brlcad
media-gfx/brlcad: fixed libpng-1.5, added version 9999 back
media-gfx/brlcad: No need to include cmake in deps
manifest
adjusting boehm-gc source file
[sci-visualization/gri] newer version in tree
round of manifest
[app-admin/eselect] Add prefix ~amd64-linux
[sci-libs/atlas] Add prefix ~amd64-linux
numbench depends on btl
Added BTL.
Restored atlas-3.8.4 from bicatali.
Version bump atlas
updating skel files
manifest
cleaning
...
211 files changed, 6329 insertions, 1927 deletions
diff --git a/app-admin/eselect/ChangeLog b/app-admin/eselect/ChangeLog new file mode 100644 index 000000000..cde504e23 --- /dev/null +++ b/app-admin/eselect/ChangeLog @@ -0,0 +1,739 @@ +# ChangeLog for app-admin/eselect +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/app-admin/eselect/ChangeLog,v 1.179 2011/01/22 21:38:52 ulm Exp $ + +*eselect-1.2.16-r1 + + 03 Aug 2011; Andrea Arteaga <andyspiros@gmail.com> + Imported from dev/bicatali + + 22 Jan 2011; Ulrich Mueller <ulm@gentoo.org> -eselect-1.2.10.ebuild, + -eselect-1.2.13.ebuild: + Remove old. + + 22 Jan 2011; Kacper Kowalik <xarthisius@gentoo.org> eselect-1.2.11.ebuild: + ppc64 stable wrt #344537 + +*eselect-1.2.14 (14 Jan 2011) + + 14 Jan 2011; Ulrich Mueller <ulm@gentoo.org> +eselect-1.2.14.ebuild: + Version bump. + +*eselect-1.2.13 (27 Nov 2010) + + 27 Nov 2010; Ulrich Mueller <ulm@gentoo.org> -eselect-1.2.12.ebuild, + +eselect-1.2.13.ebuild: + Version bump, fixes bug 346837. Remove intermediate version. + +*eselect-1.2.12 (21 Nov 2010) + + 21 Nov 2010; Ulrich Mueller <ulm@gentoo.org> +eselect-1.2.12.ebuild: + Version bump. + + 14 Nov 2010; Raúl Porcel <armin76@gentoo.org> eselect-1.2.11.ebuild: + alpha/ia64/m68k/s390/sh/sparc stable wrt #344537 + + 09 Nov 2010; Markus Meier <maekke@gentoo.org> eselect-1.2.11.ebuild: + arm stable, bug #344537 + + 09 Nov 2010; Jeroen Roovers <jer@gentoo.org> eselect-1.2.11.ebuild: + Stable for PPC (bug #344537). + + 09 Nov 2010; Jeroen Roovers <jer@gentoo.org> eselect-1.2.11.ebuild: + Stable for HPPA (bug #344537). + + 08 Nov 2010; Markos Chandras <hwoarang@gentoo.org> eselect-1.2.11.ebuild: + Stable on amd64 wrt bug #344537 + + 08 Nov 2010; Christian Faulhammer <fauli@gentoo.org> + eselect-1.2.11.ebuild: + stable x86, bug 344537 + + 23 Oct 2010; Ulrich Mueller <ulm@gentoo.org> -eselect-1.2.9.ebuild: + Remove old. + + 23 Oct 2010; Mark Loeser <halcy0n@gentoo.org> eselect-1.2.10.ebuild: + Mark ppc64; bug #313829 + +*eselect-1.2.11 (27 Jul 2010) + + 27 Jul 2010; Ulrich Mueller <ulm@gentoo.org> -eselect-1.2.8.ebuild, + +eselect-1.2.11.ebuild: + Version bump. Remove old. + + 23 May 2010; Pacho Ramos <pacho@gentoo.org> eselect-1.2.10.ebuild: + stable amd64, bug 313829 + + 08 May 2010; Raúl Porcel <armin76@gentoo.org> eselect-1.2.10.ebuild: + alpha/arm/ia64/m68k/s390/sh stable wrt #313829 + + 16 Apr 2010; Brent Baude <ranger@gentoo.org> eselect-1.2.10.ebuild: + stable ppc, bug 313829 + + 09 Apr 2010; Tiago Cunha <tcunha@gentoo.org> eselect-1.2.10.ebuild: + stable sparc, bug 313829 + + 09 Apr 2010; Jeroen Roovers <jer@gentoo.org> eselect-1.2.10.ebuild: + Stable for HPPA (bug #313829). + + 08 Apr 2010; Christian Faulhammer <fauli@gentoo.org> + eselect-1.2.10.ebuild: + stable x86, bug 313829 + + 10 Feb 2010; Joseph Jezak <josejx@gentoo.org> eselect-1.2.9.ebuild: + Marked ppc stable for bug #302878. + + 06 Feb 2010; Raúl Porcel <armin76@gentoo.org> eselect-1.2.9.ebuild: + alpha/ia64/m68k/s390/sh/sparc stable wrt #302878 + +*eselect-1.2.10 (05 Feb 2010) + + 05 Feb 2010; Ulrich Mueller <ulm@gentoo.org> -eselect-1.2.3.ebuild, + +eselect-1.2.10.ebuild: + Version bump. Remove old. + + 04 Feb 2010; Markus Meier <maekke@gentoo.org> eselect-1.2.9.ebuild: + amd64/arm stable, bug #302878 + + 02 Feb 2010; Jeroen Roovers <jer@gentoo.org> eselect-1.2.9.ebuild: + Stable for HPPA (bug #302878). + + 01 Feb 2010; Tiago Cunha <tcunha@gentoo.org> eselect-1.2.9.ebuild: + stable sparc, bug 302878 + + 01 Feb 2010; Christian Faulhammer <fauli@gentoo.org> eselect-1.2.9.ebuild: + stable x86, bug 302878 + + 01 Feb 2010; Brent Baude <ranger@gentoo.org> eselect-1.2.9.ebuild: + stable ppc64, bug 302878 + + 11 Jan 2010; Raúl Porcel <armin76@gentoo.org> eselect-1.2.8.ebuild: + alpha/arm/ia64/m68k/s390/sh stable wrt #297496 + + 31 Dec 2009; Ulrich Mueller <ulm@gentoo.org> eselect-1.2.9.ebuild: + Inherit bash-completion.eclass, bug 299051. + + 31 Dec 2009; Brent Baude <ranger@gentoo.org> eselect-1.2.8.ebuild: + Marking eselect-1.2.8 ppc64 for bug 297496 + +*eselect-1.2.9 (31 Dec 2009) + + 31 Dec 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.2.7.ebuild, + +eselect-1.2.9.ebuild: + Version bump, fixes bugs 298742 and 298789. Remove old. + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> eselect-1.2.8.ebuild: + stable x86, bug 297496 + + 29 Dec 2009; Samuli Suominen <ssuominen@gentoo.org> eselect-1.2.8.ebuild: + amd64 stable wrt #297496 + + 28 Dec 2009; nixnut <nixnut@gentoo.org> eselect-1.2.8.ebuild: + ppc stable #297496 + + 28 Dec 2009; Tiago Cunha <tcunha@gentoo.org> eselect-1.2.8.ebuild: + stable sparc, bug 297496 + + 24 Dec 2009; Jeroen Roovers <jer@gentoo.org> eselect-1.2.8.ebuild: + Stable for HPPA (bug #297496). + +*eselect-1.2.8 (20 Nov 2009) + + 20 Nov 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.2.5.ebuild, + -eselect-1.2.6.ebuild, +eselect-1.2.8.ebuild: + Version bump, fixes bug 293317. Remove old. + +*eselect-1.2.7 (14 Nov 2009) + + 14 Nov 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.2.7.ebuild: + Version bump, fixes bug 289095. + +*eselect-1.2.6 (07 Nov 2009) + + 07 Nov 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.1.3.ebuild, + -eselect-1.2.4.ebuild, +eselect-1.2.6.ebuild: + Version bump. Remove old. + +*eselect-1.2.5 (04 Nov 2009) + + 04 Nov 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.2.5.ebuild: + Version bump; fixes bugs 280191 and 288527. + + 13 Oct 2009; Ulrich Mueller <ulm@gentoo.org> eselect-1.1.3.ebuild, + eselect-1.2.3.ebuild, eselect-1.2.4.ebuild: + Update dependency after realpath package move, bug 273968. + + 11 Oct 2009; Jeroen Roovers <jer@gentoo.org> eselect-1.2.3.ebuild: + Stable for HPPA (bug #287135). + + 09 Oct 2009; Fabian Groffen <grobian@gentoo.org> eselect-1.2.4.ebuild: + Added Prefix keywords and fixed the ebuild for Prefix + +*eselect-1.2.4 (09 Oct 2009) + + 09 Oct 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.0.12.ebuild, + -eselect-1.2.1.ebuild, +eselect-1.2.4.ebuild: + Version bump. Remove old. + + 08 Oct 2009; Raúl Porcel <armin76@gentoo.org> eselect-1.2.3.ebuild: + alpha/arm/ia64/m68k/s390/sh stable wrt #287135 + + 05 Oct 2009; Tiago Cunha <tcunha@gentoo.org> eselect-1.2.3.ebuild: + stable sparc, bug 287135 + + 03 Oct 2009; Christian Faulhammer <fauli@gentoo.org> eselect-1.2.3.ebuild: + stable x86, bug 287135 + + 03 Oct 2009; Brent Baude <ranger@gentoo.org> eselect-1.2.3.ebuild: + Marking eselect-1.2.3 ppc64 for bug 287135 + + 03 Oct 2009; Mounir Lamouri <volkmar@gentoo.org> eselect-1.2.3.ebuild: + Stable for ppc, bug 287135 + + 01 Oct 2009; Dawid Węgliński <cla@gentoo.org> eselect-1.2.3.ebuild: + Stable on amd64 (bug #287135) + +*eselect-1.2.3 (20 Sep 2009) + + 20 Sep 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.2.2.ebuild, + +eselect-1.2.3.ebuild: + Version bump, fixes bug 285762. Remove intermediate version. + +*eselect-1.2.2 (19 Sep 2009) + + 19 Sep 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.2.2.ebuild: + Version bump. + + 15 Sep 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.1.1.ebuild, + -eselect-1.2.ebuild: + Remove old. + + 15 Sep 2009; Jeroen Roovers <jer@gentoo.org> eselect-1.1.3.ebuild: + Stable for HPPA (bug #283079). + + 11 Sep 2009; Raúl Porcel <armin76@gentoo.org> eselect-1.1.3.ebuild: + arm/ia64/m68k/s390/sh/sparc stable wrt #283079 + +*eselect-1.2.1 (09 Sep 2009) + + 09 Sep 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.2.1.ebuild: + Version bump, fixes bug 283932. + + 07 Sep 2009; Markus Meier <maekke@gentoo.org> eselect-1.1.3.ebuild: + amd64/x86 stable, bug #283079 + + 31 Aug 2009; Brent Baude <ranger@gentoo.org> eselect-1.1.3.ebuild: + Marking eselect-1.1.3 ppc64 for bug 283079 + + 31 Aug 2009; Brent Baude <ranger@gentoo.org> eselect-1.1.1.ebuild: + Marking eselect-1.1.1 ppc64 for bug 277187 + + 30 Aug 2009; Tobias Klausmann <klausman@gentoo.org> eselect-1.1.3.ebuild: + Stable on alpha, bug #283079 + + 30 Aug 2009; nixnut <nixnut@gentoo.org> eselect-1.1.3.ebuild: + ppc stable #283079 + +*eselect-1.2 (27 Aug 2009) + + 27 Aug 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.1.2.ebuild, + -eselect-1.2_rc1.ebuild, +eselect-1.2.ebuild: + Version bump. Remove intermediate versions. + +*eselect-1.2_rc1 (19 Aug 2009) + + 19 Aug 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.2_rc1.ebuild: + Version bump; fixes bug 280598; enhancements from bugs 154511 and 274760. + +*eselect-1.1.3 (16 Aug 2009) + + 16 Aug 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.0.10.ebuild, + -eselect-1.0.11-r1.ebuild, + -files/eselect-1.0.11-fix-paludis-command.patch, +eselect-1.1.3.ebuild: + Version bump, fixes bug 279662. Remove old. + + 21 Jul 2009; <chainsaw@gentoo.org> eselect-1.1.1.ebuild: + Marked stable on AMD64 as requested by Ulrich Müller <ulm@gentoo.org> in + bug #277187. Tested with the profile module. + + 17 Jul 2009; Raúl Porcel <armin76@gentoo.org> eselect-1.1.1.ebuild: + alpha/arm/ia64/m68k/s390/sh stable wrt #277187 + + 16 Jul 2009; nixnut <nixnut@gentoo.org> eselect-1.1.1.ebuild: + ppc stable #277187 + + 09 Jul 2009; Jeroen Roovers <jer@gentoo.org> eselect-1.1.1.ebuild: + Stable for HPPA (bug #277187). + + 09 Jul 2009; Christian Faulhammer <fauli@gentoo.org> eselect-1.1.1.ebuild: + stable x86, bug 277187 + + 09 Jul 2009; Ferris McCormick <fmccor@gentoo.org> eselect-1.1.1.ebuild: + Sparc stable, Bug #277187. + + 28 Jun 2009; Brent Baude <ranger@gentoo.org> eselect-1.0.12.ebuild: + Marking eselect-1.0.12 ppc64 for bug 270138 + +*eselect-1.1.2 (27 Jun 2009) + + 27 Jun 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.1.2.ebuild: + Version bump. + + 12 Jun 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.0.11-r2.ebuild, + -files/eselect-1.0.11-parent-profiles.patch, + -files/eselect-1.0.11-relative-profiles.patch, -eselect-1.1.ebuild, + metadata.xml: + Remove intermediate versions. + +*eselect-1.1.1 (06 Jun 2009) + + 06 Jun 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.1.1.ebuild: + Version bump. Remove paludis USE flag since it doesn't make much sense + without the corresponding dependency; use app-admin/eselect-package-manager + for selection of a package manager instead. + + 02 Jun 2009; Ulrich Mueller <ulm@gentoo.org> eselect-1.1.ebuild, + -eselect-1.1_rc2.ebuild, -eselect-1.1_rc3.ebuild: + Don't depend on paludis, in order to avoid a circular dependency; thanks + to Ingmar Vanhassel for pointing this out. Print a warning message in + pkg_postinst instead. Remove release candidates. + +*eselect-1.1 (27 May 2009) + + 27 May 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.1.ebuild, + -eselect-9999.ebuild: + Version bump. Remove live ebuild. + + 24 May 2009; Ulrich Mueller <ulm@gentoo.org> eselect-1.0.10.ebuild, + eselect-1.0.11-r1.ebuild, eselect-1.0.11-r2.ebuild, eselect-1.0.12.ebuild, + eselect-1.1_rc2.ebuild, eselect-1.1_rc3.ebuild, eselect-9999.ebuild: + Fix dependencies: readlink/realpath are also needed at run time. + + 24 May 2009; Markus Meier <maekke@gentoo.org> eselect-1.0.12.ebuild: + amd64 stable, bug #270138 + + 21 May 2009; Brent Baude <ranger@gentoo.org> eselect-1.0.12.ebuild: + stable ppc, bug 270138 + + 21 May 2009; Raúl Porcel <armin76@gentoo.org> eselect-1.0.12.ebuild: + arm/ia64/m68k/s390/sh/sparc stable wrt #270138 + +*eselect-1.1_rc3 (21 May 2009) + + 21 May 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.1_rc3.ebuild: + Version bump. + + 20 May 2009; Ulrich Mueller <ulm@gentoo.org> eselect-1.1_rc2.ebuild, + eselect-9999.ebuild: + Create directory for news-tng module. Set proper group and permissions. + +*eselect-1.1_rc2 (19 May 2009) + + 19 May 2009; Ulrich Mueller <ulm@gentoo.org> -eselect-1.1_rc1.ebuild, + +eselect-1.1_rc2.ebuild: + Version bump, fixes bug 270406. Remove previous release candidate. + +*eselect-1.1_rc1 (18 May 2009) + + 18 May 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.1_rc1.ebuild: + Version bump; fixes bugs 155814 and 156866; enhancements from bugs 148578, + 153890, 180966, 190216, and 220473. + + 18 May 2009; Christian Faulhammer <fauli@gentoo.org> + eselect-1.0.12.ebuild: + stable x86, bug 270138 + + 18 May 2009; Jeroen Roovers <jer@gentoo.org> eselect-1.0.12.ebuild: + Stable for HPPA (bug #270138). + + 17 May 2009; Tobias Klausmann <klausman@gentoo.org> eselect-1.0.12.ebuild: + Stable on alpha, bug #270138 + + 28 Apr 2009; Ulrich Mueller <ulm@gentoo.org> metadata.xml, eselect-9999: + Add paludis USE flag for the live ebuild. + +*eselect-9999 (18 Apr 2009) +*eselect-1.0.12 (18 Apr 2009) + + 18 Apr 2009; Ulrich Mueller <ulm@gentoo.org> +eselect-1.0.12.ebuild, + +eselect-9999.ebuild: + Version bump to 1.0.12; fixes bugs 172636, 198461, 203114, 204937, 218557, + 219864, 232874, 240402, 248470, 248487, 260464, and 264734. Add live ebuild + for SVN trunk. Remove dependencies on editor modes, since only few users of + eselect will edit its source. + + 17 Apr 2009; Ulrich Mueller <ulm@gentoo.org> eselect-1.0.11-r1.ebuild, + eselect-1.0.11-r2.ebuild: + Clarify the elog message in pkg_postinst, bug 187263. Remove the dependency + on procps (added at 14 April) again, since it leads to problems on FreeBSD; + bug 266540. In fact, a working "pgrep" command is not essential, since it is + only called from the "die" function. See bug 264734 for details. + + 15 Apr 2009; Ulrich Mueller <ulm@gentoo.org> + -files/eselect-1.0.8-fix-parallel-install.patch: + Remove stale file. + + 14 Apr 2009; Ulrich Mueller <ulm@gentoo.org> eselect-1.0.11-r2.ebuild: + Add procps to RDEPEND, fixes bug 174354. + + 08 Apr 2009; Jeremy Olexa <darkside@gentoo.org> + +files/eselect-1.0.11-relative-profiles.patch, eselect-1.0.11-r2.ebuild: + Make 'eselect profile show' show the relative path. Patch by Thomas Bellman + in bug 248487 + +*eselect-1.0.11-r2 (08 Apr 2009) + + 08 Apr 2009; Jeremy Olexa <darkside@gentoo.org> + +files/eselect-1.0.11-parent-profiles.patch, -eselect-1.0.2.ebuild, + -eselect-1.0.7.ebuild, -eselect-1.0.8.ebuild, -eselect-1.0.9.ebuild, + -eselect-1.0.11.ebuild, +eselect-1.0.11-r2.ebuild: + Version bump to fix bug 248470, patch by Thomas Bellman. Allows parent + profiles to be selectable. Also, remove old versions + + 08 Apr 2009; Jeremy Olexa <darkside@gentoo.org> eselect-1.0.11-r1.ebuild: + fix postinst message to include instructions for enabling globally, bug 265168 + + 17 Mar 2009; Raúl Porcel <armin76@gentoo.org> eselect-1.0.11-r1.ebuild: + m68k stable wrt #208898, thanks to kolla for testing + + 29 Dec 2008; Raúl Porcel <armin76@gentoo.org> eselect-1.0.11-r1.ebuild: + s390/sh stable wrt #208898 + + 16 Dec 2008; Doug Goldstein <cardoe@gentoo.org> eselect-1.0.11-r1.ebuild: + amd64 stable + + 10 Dec 2008; Jeroen Roovers <jer@gentoo.org> eselect-1.0.11-r1.ebuild: + Stable for HPPA (bug #208898). + + 09 Dec 2008; Brent Baude <ranger@gentoo.org> eselect-1.0.11-r1.ebuild: + Marking eselect-1.0.11-r1 ppc64 and ppc for bug 208898 + + 08 Dec 2008; Raúl Porcel <armin76@gentoo.org> eselect-1.0.11-r1.ebuild: + alpha/arm/ia64/sparc/x86 stable wrt #208898 + + 25 May 2008; Markus Rothe <corsair@gentoo.org> eselect-1.0.11-r1.ebuild: + Stable on ppc64 + +*eselect-1.0.11-r1 (20 Mar 2008) + + 20 Mar 2008; Piotr Jaroszyński <peper@gentoo.org> + +files/eselect-1.0.11-fix-paludis-command.patch, + +eselect-1.0.11-r1.ebuild: + Add -r1 with a patch fixing paludis_command(). + +*eselect-1.0.11 (01 Dec 2007) + + 01 Dec 2007; Piotr Jaroszyński <peper@gentoo.org> +eselect-1.0.11.ebuild: + Add 1.0.11. + + 05 Aug 2007; nixnut <nixnut@gentoo.org> eselect-1.0.10.ebuild: + Stable on ppc wrt bug 185691 + + 01 Aug 2007; Joshua Kinard <kumba@gentoo.org> eselect-1.0.10.ebuild: + Stable on mips, per #185691. + + 01 Aug 2007; <metalgod@gentoo.org> eselect-1.0.10.ebuild: + Stable on amd64. See bug #185691. + + 30 Jul 2007; Raúl Porcel <armin76@gentoo.org> eselect-1.0.10.ebuild: + alpha/ia64 stable wrt #185691 + + 30 Jul 2007; Jeroen Roovers <jer@gentoo.org> eselect-1.0.10.ebuild: + Stable for HPPA (bug #185691). + + 30 Jul 2007; Gustavo Zacarias <gustavoz@gentoo.org> eselect-1.0.10.ebuild: + Stable on sparc wrt #185691 + + 30 Jul 2007; Markus Rothe <corsair@gentoo.org> eselect-1.0.10.ebuild: + Stable on ppc64; bug #185691 + + 30 Jul 2007; Christian Faulhammer <opfer@gentoo.org> + eselect-1.0.10.ebuild: + stable x86, bug 185691 + +*eselect-1.0.10 (17 Jun 2007) + + 17 Jun 2007; Danny van Dyk <kugelfang@gentoo.org> +eselect-1.0.10.ebuild: + Released 1.0.10 that fixes bugs #172472 and #172475. Thanks to Ulrich + Mueller <ulm@gentoo.org>. + + 06 May 2007; Mike Kelly <pioto@gentoo.org> eselect-1.0.9.ebuild: + Add vim-syntax USE flag to pull in eselect-syntax. + +*eselect-1.0.9 (28 Mar 2007) + + 28 Mar 2007; <pioto@gentoo.org> +eselect-1.0.9.ebuild: + Version bump. Fixes parallel install, improper use of DISTDIR, and some + issues with env.eselect. + + 07 Feb 2007; Simon Stelling <blubb@gentoo.org> eselect-1.0.7.ebuild: + stable on amd64; bug 160535 + + 26 Jan 2007; Bryan Østergaard <kloeri@gentoo.org> eselect-1.0.7.ebuild: + Stable on Alpha. + + 25 Jan 2007; Alexander H. Færøy <eroyf@gentoo.org> eselect-1.0.7.ebuild: + Stable on MIPS. + + 24 Jan 2007; Marius Mauch <genone@gentoo.org> eselect-1.0.2.ebuild, + eselect-1.0.7.ebuild, eselect-1.0.8.ebuild: + Replacing einfo with elog + + 16 Jan 2007; Jeroen Roovers <jer@gentoo.org> eselect-1.0.7.ebuild: + Stable for HPPA (bug #160535). + + 15 Jan 2007; Mike Kelly <pioto@gentoo.org> + +files/eselect-1.0.8-fix-parallel-install.patch, eselect-1.0.8.ebuild: + Add a patch to really really fix Bug #162008. + + 14 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> eselect-1.0.7.ebuild: + Marked stable on amd64. + +*eselect-1.0.8 (14 Jan 2007) + + 14 Jan 2007; Mike Kelly <pioto@gentoo.org> +eselect-1.0.8.ebuild: + Version bump. Really fixes Bug #162008. + + 14 Jan 2007; Mike Kelly <pioto@gentoo.org> eselect-1.0.7.ebuild: + Force non-parallel install for now until all the Makefile issues can be fixed. + + 14 Jan 2007; Joseph Jezak <josejx@gentoo.org> eselect-1.0.7.ebuild: + Marked ppc stable for bug #160535. + + 09 Jan 2007; Christian Faulhammer <opfer@gentoo.org> eselect-1.0.7.ebuild: + stable x86, bug #160535 + + 09 Jan 2007; Markus Rothe <corsair@gentoo.org> eselect-1.0.7.ebuild: + Stable on ppc64; bug #160535 + + 08 Jan 2007; Gustavo Zacarias <gustavoz@gentoo.org> eselect-1.0.7.ebuild: + Stable on sparc wrt #160535 + + 07 Jan 2007; Mike Kelly <pioto@gentoo.org> eselect-1.0.7.ebuild: + Mark ~amd64 again, since we need to stable a few other things first. See Bug + #160535. + + 06 Jan 2007; Mike Kelly <pioto@gentoo.org> eselect-1.0.7.ebuild: + Mark stable on amd64 (okayed by Kugelfang). + + 06 Jan 2007; Mike Kelly <pioto@gentoo.org> -eselect-1.0.6.ebuild: + Remove old and kinda buggy 1.0.6 version. + + 09 Nov 2006; Marien Zwart <marienz@gentoo.org> Manifest: + Fix Manifest. + + 09 Nov 2006; Marien Zwart <marienz@gentoo.org> +eselect-1.0.6.ebuild: + Put 1.0.6 back to avoid a downgrade while 1.0.7 is masked. + +*eselect-1.0.7 (08 Nov 2006) + + 08 Nov 2006; Danny van Dyk <kugelfang@gentoo.org> -eselect-1.0.ebuild, + -eselect-1.0.6.ebuild, +eselect-1.0.7.ebuild: + Removed obsolete version 1.0. Bumped eselect to version 1.0.7, which is a + bugfix release. + + 18 Oct 2006; Roy Marples <uberlord@gentoo.org> eselect-1.0.6.ebuild: + Added ~sparc-fbsd keyword. + +*eselect-1.0.6 (03 Oct 2006) + + 03 Oct 2006; Danny van Dyk <kugelfang@gentoo.org> -eselect-1.0.5.ebuild, + +eselect-1.0.6.ebuild: + Removed version 1.0.5. Added version 1.0.6. + + 04 Sep 2006; Joshua Kinard <kumba@gentoo.org> eselect-1.0.2.ebuild: + Marked stable on mips. + +*eselect-1.0.5 (26 Aug 2006) + + 26 Aug 2006; Danny van Dyk <kugelfang@gentoo.org> -eselect-1.0.4.ebuild, + +eselect-1.0.5.ebuild: + Removed version 1.0.4. Added version 1.0.5. + + 19 Aug 2006; Bryan Østergaard <kloeri@gentoo.org> eselect-1.0.2.ebuild: + Stable on alpha. + + 16 Aug 2006; Markus Rothe <corsair@gentoo.org> eselect-1.0.2.ebuild: + Stable on ppc64 + +*eselect-1.0.4 (02 Aug 2006) + + 02 Aug 2006; Danny van Dyk <kugelfang@gentoo.org> -eselect-1.0.3.ebuild, + +eselect-1.0.4.ebuild: + Removed release 1.0.3. Added release 1.0.4. + + 02 Aug 2006; Gustavo Zacarias <gustavoz@gentoo.org> eselect-1.0.2.ebuild: + Stable on hppa + + 29 Jul 2006; Fabian Groffen <grobian@gentoo.org> eselect-1.0.2.ebuild: + Marked ~ppc-macos + + 15 Jul 2006; Joshua Jackson <tsunam@gentoo.org> eselect-1.0.2.ebuild: + Stable x86; openoffice security bug + + 15 Jul 2006; Luis Medinas <metalgod@gentoo.org> eselect-1.0.2.ebuild: + Stable on amd64. + + 12 Jul 2006; Aron Griffis <agriffis@gentoo.org> eselect-1.0.2.ebuild: + Mark 1.0.2 stable on ia64 + + 12 Jul 2006; Gustavo Zacarias <gustavoz@gentoo.org> eselect-1.0.2.ebuild: + Stable on sparc + + 06 Jul 2006; Danny van Dyk <kugelfang@gentoo.org> eselect-1.0.ebuild, + eselect-1.0.2.ebuild, eselect-1.0.3.ebuild: + Added ChangeLog to the list of to-be-installed documents. + + 05 Jul 2006; Lars Weiler <pylon@gentoo.org> eselect-1.0.2.ebuild: + Stable on ppc; dependency for bug #139249. + + 03 Jul 2006; <malc@gentoo.org> files/digest-eselect-1.0, + files/digest-eselect-1.0.2, Manifest: + Fix broken digests - as reported in #gentoo-amd64 + +*eselect-1.0.3 (03 Jul 2006) + + 06 Jun 2006; Stephen Bennett <spb@gentoo.org> eselect-1.0.ebuild: + Mips stable for bug #125630 + + 19 Apr 2006; Diego Pettenò <flameeyes@gentoo.org> eselect-1.0.2.ebuild: + Add dependency over freebsd-bin as alternative to realpath, it does already + provide a realpath binary that works. + +*eselect-1.0.2 (14 Apr 2006) + + 14 Apr 2006; Danny van Dyk <kugelfang@gentoo.org> -eselect-1.0.1.ebuild, + +eselect-1.0.2.ebuild: + Added bugfix release 1.0.2. Removed 1.0.1 due to a slightly broken env.eselect. + +*eselect-1.0.1 (02 Apr 2006) + + 02 Apr 2006; Danny van Dyk <kugelfang@gentoo.org> -eselect-0.9.6.ebuild, + -eselect-1.0_rc1.ebuild, -eselect-1.0_rc2.ebuild, eselect-1.0.ebuild, + +eselect-1.0.1.ebuild: + Removed obsolete versions. Updated RDEPEND with sys-apps/file. Added 1.0.1 + release. + + 30 Mar 2006; Diego Pettenò <flameeyes@gentoo.org> eselect-1.0.ebuild: + Add ~x86-fbsd keyword, although the env module doesn't work, as other + modules are needed for other packages; most of this version works fine. + + 12 Mar 2006; Jason Wever <weeve@gentoo.org> eselect-1.0.ebuild: + Stable on SPARC wrt bug #125630. + + 10 Mar 2006; Fernando J. Pereda <ferdy@gentoo.org> eselect-1.0.ebuild: + Stable on alpha wrt bug #125630 + + 10 Mar 2006; Markus Rothe <corsair@gentoo.org> eselect-1.0.ebuild: + Stable on ppc64; bug #125630 + + 10 Mar 2006; Lars Weiler <pylon@gentoo.org> eselect-1.0.ebuild: + Stable on ppc wrt bug #125630. + + 10 Mar 2006; Michele Noberasco <s4t4n@gentoo.org> eselect-1.0.ebuild: + Stable for x86. See bug #125630. + + 09 Mar 2006; Aron Griffis <agriffis@gentoo.org> eselect-1.0.ebuild: + Mark 1.0 stable on ia64 + + 09 Mar 2006; Jeroen Roovers <jer@gentoo.org> eselect-1.0.ebuild: + Stable on hppa (bug #125630). + + 09 Mar 2006; Danny van Dyk <kugelfang@gentoo.org> eselect-1.0.ebuild: + Marked stable on amd64. + +*eselect-1.0 (09 Feb 2006) + + 09 Feb 2006; Ciaran McCreesh <ciaranm@gentoo.org> +eselect-1.0.ebuild: + New release. + + 19 Nov 2005; Markus Rothe <corsair@gentoo.org> eselect-0.9.6.ebuild, + eselect-1.0_rc1.ebuild, eselect-1.0_rc2.ebuild: + Added ~ppc64; bug #102649 + +*eselect-1.0_rc2 (16 Nov 2005) + + 16 Nov 2005; Danny van Dyk <kugelfang@gentoo.org> +eselect-1.0_rc2.ebuild: + Second release candidate for eselect-1.0. Fixes some bugs in BLAS and LAPACK + support. Adds support for MKL72. + +*eselect-1.0_rc1 (19 Oct 2005) + + 19 Oct 2005; Aaron Walker <ka0ttic@gentoo.org> +eselect-1.0_rc1.ebuild: + First release candidate for 1.0. Please test; the more testers we get, the + faster we'll get a stable eselect. This release fixes bugs #101898,#104354, + and #106540 as well as a sleu of others (see NEWS for a full list). + + 19 Sep 2005; Aaron Walker <ka0ttic@gentoo.org> -eselect-0.9.5.ebuild: + 0.9.5 has a broken digest; not worth keeping around, so removing it. + + 01 Aug 2005; Aaron Walker <ka0ttic@gentoo.org> eselect-0.9.5.ebuild, + eselect-0.9.6.ebuild: + Since I'm an idiot, use newins rather than doins for installing the bashcomp. + + 31 Jul 2005; Aaron Walker <ka0ttic@gentoo.org> eselect-0.9.5.ebuild, + eselect-0.9.6.ebuild: + Added ~hppa; updated ebuilds to not use bash-completion.eclass; also added + missing NEWS/AUTHORS to the list of dodoc'd files. + +*eselect-0.9.6 (25 Jul 2005) + + 25 Jul 2005; Danny van Dyk <kugelfang@gentoo.org> +eselect-0.9.6.ebuild: + Version bump. + +*eselect-0.9.5 (18 Jun 2005) + + 18 Jun 2005; Aaron Walker <ka0ttic@gentoo.org> -eselect-0.9.4.ebuild, + +eselect-0.9.5.ebuild: + Version bump. + +*eselect-0.9.4 (13 Jun 2005) + + 13 Jun 2005; Aaron Walker <ka0ttic@gentoo.org> +metadata.xml, + +eselect-0.9.4.ebuild: + Version bump; moved from app-admin/eclectic to app-admin/eselect. + + 04 Jun 2005; Stephen Bennett <spb@gentoo.org> eclectic-0.9.3.ebuild: + ~mips keywords + + 17 May 2005; Ciaran McCreesh <ciaranm@gentoo.org> eclectic-0.9.2.ebuild, + eclectic-0.9.3.ebuild: + Update homepage now that there's a proper website + + 16 May 2005; Ciaran McCreesh <ciaranm@gentoo.org> eclectic-0.9.3.ebuild: + Up the bash dependency to version 3. This is temporary and just for this + release. + +*eclectic-0.9.3 (16 May 2005) + + 16 May 2005; Ciaran McCreesh <ciaranm@gentoo.org> +eclectic-0.9.3.ebuild: + Version bump + + 15 May 2005; Fernando J. Pereda <ferdy@gentoo.org> eclectic-0.9.2.ebuild: + keyworded ~alpha + + 15 May 2005; Ciaran McCreesh <ciaranm@gentoo.org> metadata.xml, + eclectic-0.9.2.ebuild: + Added ~sparc, update metadata + + 12 May 2005; Danny van Dyk <kugelfang@gentoo.org> eclectic-0.9.2.ebuild: + Marked ~amd64. + + 12 May 2005; Aaron Walker <ka0ttic@gentoo.org> eclectic-0.9.2.ebuild: + Fix dohtml glob; default.css wasn't getting installed. + + 11 May 2005; Lars Weiler <pylon@gentoo.org> eclectic-0.9.2.ebuild: + Added ~ppc. + +*eclectic-0.9.2 (08 May 2005) + + 08 May 2005; Aaron Walker <ka0ttic@gentoo.org> -eclectic-0.9.1.ebuild, + +eclectic-0.9.2.ebuild: + Version bump. + +*eclectic-0.9.1 (08 May 2005) + + 08 May 2005; Aaron Walker <ka0ttic@gentoo.org> +metadata.xml, + +eclectic-0.9.1.ebuild: + Initial commit. + diff --git a/app-admin/eselect/Manifest b/app-admin/eselect/Manifest new file mode 100644 index 000000000..c5bfe0ecb --- /dev/null +++ b/app-admin/eselect/Manifest @@ -0,0 +1,45 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +- -----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +AUX eselect-alternatives.patch 21936 RMD160 0fc1c038dd2c01a400274e502a422d2cd50f8582 SHA1 b40b41a36ce72c623834c1fff23ac4c0ce817ab3 SHA256 97733d6b2284c60b04cdeee77bd7433b698ccea8ef93ab34dd515fbbdc43c274 +DIST eselect-1.2.16.tar.bz2 169671 RMD160 50d1171fcba4d5d708e7b9a1c756ed6e4bbdb2b3 SHA1 51e90eeb08b5e2357009c9d157aad70b636ebfdd SHA256 184d33c4f1ea030698614ee7bc2ba1398c91a03b9f4d31505af036f9b641b403 +EBUILD eselect-1.2.16-r1.ebuild 1791 RMD160 ab4ab6b322b6d23194d0f2403037e95bc508c7cb SHA1 10de5cbd7a3907d265a5398378ce9b9983658093 SHA256 c38b6be16d27f8d00be1806d846cca14fb06abbce3c487e854156ea1aa359bc3 +MISC ChangeLog 25638 RMD160 cccb2d4a03ba4af0f17a5f0fe26c3edd5e4f5cbf SHA1 d5c6b7f6c088499fa372b4d61c5f8cf6893c91d2 SHA256 3d7aa3de066bb3538e490729d36a32169f71461bb85d0299838dcf8194a0715d +MISC metadata.xml 223 RMD160 ad3a63ca53ae3d53a6be0caea0f00d5339415496 SHA1 c5430898aa8d251b7469d16f66dbd02018581bb9 SHA256 9bfa4e7551e380482c16cb288fa4f711543e15f6c00aabd2bb38fdbcbbc6dd26 +- -----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.18 (GNU/Linux) + +iQIcBAEBCAAGBQJOPUiuAAoJEOf+E+/4L5LmT3IP/i4caQz8X1buGpeBol1QSBeA +S8vfDrelE6P+oPre0GATHOLqFHw5mizgNPbPfN8ifXNbkUEwxMgECmvsRw4xJbD1 +BsxVvSNsQRu+yM8ipBdZXfVy4Fpbv546sr2/+Gcmmec7MPCHydHyHiSsh4uxbPik +GAW7cy7v/kGD4HH0wYl+ecd6vtwtElnH5bQtj+hYSC8bBiFskq9tmqhSYSrsU6FG +ORybpDOYuQZwAG1J0jnvduFOyswyJbA3jaAiK8lwwlvbAb5PbQvKFrKW9h2oFFc0 +GlcOxnDmK+bVy5HlNRmFSLAAYzCoZkOXM1CBxvFw2AWrZ9Cvi2rZ36XaC2tQNn3k +l88i/bhH5WuPDU/+ycDvyqY+L/yNgSz0kMByAYLWTTSh6NqAsRRt8wXYBhpQh6RL +NuLGoLKA4K9qbwqaWghin5BdSm3/ymLGTIR14e2iqVzA9eVX/PtbhEDcYeDUclIR +3bnHetjIOOTPlVI2AnSOuy4pSe1VCMek+O/vcNW50TWCskmkeXe2hLhancMw5ng9 +HDmbzUdbniwZ8BJtpiA0knw7ilbOF9h+jQC3Qxf1zc5fqfx7b0HGL/+bey0H6UFX +S8WBrBwqxvgm7eQBwZLs3Ect0o1UYVsjc4MdbOzfhwNGY3FiGd70Nzll1HuO0RO7 +krDHqSyK7F3rhHw6bsrA +=rzTc +- -----END PGP SIGNATURE----- +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.18 (GNU/Linux) + +iQIcBAEBCAAGBQJOPUjVAAoJEOf+E+/4L5Lm9fwP/jPgCjV6wAqdbYOTxV7Z0geA +RF+mYvREzpS3ivphJiwZssZwWbcYJxrGzFRz7EDLTaeupdPSzN9H/PsJmt04tIbW +YS+r90mRuZl5tSlx0II7pkSm00MMUt8DmwAPZrtqKZJys7a9EhjbsG88IYuDzYmO +W2nMqh0UcV+rNt15JmyGYY9HqGNyM3X3rjLb263ldkxP4NKEmVYoRDqzH99iGSJ+ +iyyv/kBDTGhKWV2VVyoUoPGpRnmC4wJzV+eew+SGg+wQEVQ1CxdkmsgFtX4XcJVJ +imh3esWZkPsr8BoS64zPVXL+mDIgkC4d3DKLB8gs/JnzeSD/CAQWNdtke7BjVPKA +Bf6hqb0Gd4Iwd1c6XiLaM2SvOLB+AHFIebmWeuZ/0MEfWJUuYAXLEzri9ElHISbC +ZEZ1Rvr7Dmf4r6MvXTy4bJ/LGYL+tOWwZzU/Rj0yPzQWDmOpJK4KwW4I1qNgTkEM +Gtk8NLPaDUGG+znrX9+0WGVxOfMkJnnada2mxh50/Vg2O9fD6z9NRlAOalqcpPiX +K8IdpSJ8nJZsybVkIEViEf6MPm+VS0vcFTRwgfnPfdl+dKzodWwpJBTNSCmR4L8a +pwtuNfxaVklXRw74YgDSCcd3yQf1iddgHVxwnjr/irvi/jEftgn9jJfEfiTrNAez +a6QsmTOd35w7HVK8YZxo +=iiLi +-----END PGP SIGNATURE----- diff --git a/app-admin/eselect/eselect-1.2.16-r1.ebuild b/app-admin/eselect/eselect-1.2.16-r1.ebuild new file mode 100644 index 000000000..d8a2ea579 --- /dev/null +++ b/app-admin/eselect/eselect-1.2.16-r1.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 +inherit eutils bash-completion autotools + +DESCRIPTION="Gentoo's multi-purpose configuration and management tool" +HOMEPAGE="http://www.gentoo.org/proj/en/eselect/" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~sparc-fbsd ~x86-fbsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" +IUSE="doc" + +RDEPEND="sys-apps/sed + || ( + sys-apps/coreutils + sys-freebsd/freebsd-bin + app-misc/realpath + )" +DEPEND="${RDEPEND} + doc? ( dev-python/docutils )" +RDEPEND="!app-admin/eselect-news + ${RDEPEND} + sys-apps/file + sys-libs/ncurses" + +# Commented out: only few users of eselect will edit its source +#PDEPEND="emacs? ( app-emacs/gentoo-syntax ) +# vim-syntax? ( app-vim/eselect-syntax )" +src_prepare() { + epatch "${FILESDIR}"/${PN}-alternatives.patch + eautoreconf +} + +src_compile() { + emake || die "emake failed" + + if use doc; then + make html || die "failed to build html" + fi +} + +src_install() { + emake DESTDIR="${D}" install || die "make install failed" + dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt + use doc && dohtml *.html doc/* + dobashcompletion misc/${PN}.bashcomp + + # needed by news module + keepdir /var/lib/gentoo/news +} + +pkg_postinst() { + # fowners in src_install doesn't work for the portage group: + # merging changes the group back to root + [[ -z ${EROOT} ]] && local EROOT=${ROOT} + chgrp portage "${EROOT}/var/lib/gentoo/news" \ + && chmod g+w "${EROOT}/var/lib/gentoo/news" + + bash-completion_pkg_postinst +} diff --git a/app-admin/eselect/files/eselect-alternatives.patch b/app-admin/eselect/files/eselect-alternatives.patch new file mode 100644 index 000000000..991498053 --- /dev/null +++ b/app-admin/eselect/files/eselect-alternatives.patch @@ -0,0 +1,601 @@ +Index: libs/Makefile.am +=================================================================== +--- libs/Makefile.am (revision 803) ++++ libs/Makefile.am (working copy) +@@ -1,6 +1,7 @@ + eselectlibsdir = $(datadir)/$(PACKAGE_NAME)/libs/ + + eselectlibs_DATA = \ ++ alternatives.bash \ + config.bash \ + core.bash \ + default.eselect \ +@@ -14,6 +15,7 @@ + tests.bash + + EXTRA_DIST = \ ++ alternatives.bash.in \ + config.bash.in \ + core.bash.in \ + default.eselect.in \ +@@ -30,7 +32,8 @@ + -e 's,\@SED\@,@SED@,g' \ + -e 's,\@PORTAGEQ\@,@PORTAGEQ@,g' \ + -e 's,\@ENV_UPDATE\@,@ENV_UPDATE@,g' \ +- -e 's,\@CANONICALISE\@,@CANONICALISE@,g' ++ -e 's,\@CANONICALISE\@,@CANONICALISE@,g' \ ++ -e 's,\@sysconfdir\@,@sysconfdir@,g' + + %.bash : %.bash.in + @$(dosed) $< > $@ +Index: bin/Makefile.am +=================================================================== +--- bin/Makefile.am (revision 803) ++++ bin/Makefile.am (working copy) +@@ -4,6 +4,7 @@ + dosed = @SED@ -e 's,\@BASH\@,$(BASH),g' \ + -e 's,\@DATADIR\@,$(datadir),g' \ + -e 's,\@EPREFIX\@,$(EPREFIX),g' \ ++ -e 's,\@LIBEXECDIR\@,$(datadir),g' \ + -e 's,\@VERSION\@,$(VERSION),g' + + % : %.in +Index: bin/eselect.in +=================================================================== +--- bin/eselect.in (revision 803) ++++ bin/eselect.in (working copy) +@@ -22,10 +22,15 @@ + # Where are modules installed by default? + ESELECT_DEFAULT_MODULES_PATH="${ESELECT_DATA_PATH}/modules" + ++# Where are auto-generated modules placed? (e.g. from alternatives-2.eclas) ++ESELECT_AUTO_GENERATED_MODULES_PATH="${ESELECT_DEFAULT_MODULES_PATH}/auto" ++ + # Look in these places for modules +-ESELECT_MODULES_PATH=( \ +- "${HOME}/.eselect/modules" \ +- "${ESELECT_DEFAULT_MODULES_PATH}" ) ++ESELECT_MODULES_PATH=( ++ "${HOME}/.eselect/modules" ++ "${ESELECT_DEFAULT_MODULES_PATH}" ++ "${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++) + + # Look in this place for libraries + ESELECT_CORE_PATH="${ESELECT_DATA_PATH}/libs" +--- libs/alternatives.bash.in.orig 1970-01-01 01:00:00.000000000 +0100 ++++ libs/alternatives.bash.in 2010-12-15 19:37:54.000000000 +0000 +@@ -0,0 +1,533 @@ ++# Copyright 2008 Mike Kelly ++# Copyright 2009 David Leverton ++# Copyright 2010 Bo Ørsted Andresen ++# 2010: Adapted to eselect Sebastien Fabbro (who doesn't like copyrights) ++# Distributed under the terms of the GNU General Public License v2 ++ ++inherit config output path-manipulation ++ ++ALTERNATIVESDIR_ROOTLESS="@sysconfdir@/env.d/alternatives" ++ALTERNATIVESDIR="${EROOT}${ALTERNATIVESDIR_ROOTLESS}" ++ ++get_current_provider() { ++ local dieprefix="Could not determine current provider for ${ALTERNATIVE}" ++ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then ++ local provider=$(readlink "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: readlink ${symlink} failed") ++ [[ ${provider} == */* ]] && die "${dieprefix}: malformed target for ${symlink}" ++ ++ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} || ++ ( -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} && ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ) ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} is not a directory" ++ fi ++ ++ echo "${provider}" ++ ++ elif [[ -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current is not a symlink" ++ fi ++} ++ ++compare_importance() { ++ local IFS=. ++ local a=( ${1} ) b=( ${2} ) ++ local -i i=0 ++ while (( i<${#a[@]} && i<${#b[@]} )); do ++ if (( a[i]<b[i] )); then ++ return 0 ++ elif (( a[i]>b[i] )); then ++ return 1 ++ fi ++ i+=1 ++ done ++ (( i<${#b[@]} )) ++} ++ ++sort_providers() { ++ local begin=${1:-0} ++ local count=${2:-${#providers[@]}} ++ [[ ${count} -le 1 ]] && return 0 ++ sort_providers ${begin} $((count/2)) ++ sort_providers $((begin+count/2)) $((count-count/2)) ++ local left=( "${providers[@]:begin:count/2}" ) ++ local right=( "${providers[@]:begin+count/2:count-count/2}" ) ++ local -i x i=0 j=0 ++ for (( x=begin; x<begin+count; ++x )); do ++ if (( j>=${#right[@]} )) || { (( i<${#left[@]} )) && compare_importance "${left[i]%%:*}" "${right[j]%%:*}"; }; then ++ providers[x]=${left[i++]} ++ else ++ providers[x]=${right[j++]} ++ fi ++ done ++} ++ ++get_providers() { ++ local p= importance providers=() ++ for p in "${ALTERNATIVESDIR}/${ALTERNATIVE}"/* ; do ++ [[ -d ${p} && ! -L ${p} ]] || continue ++ p=${p##*/} ++ ++ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") ++ importance=${importance:-0} ++ [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" ++ ++ providers+=( "${importance}:${p}" ) ++ done ++ ++ sort_providers ++ for (( p=${#providers[@]}-1 ; p>=0 ; --p )); do ++ echo "${providers[p]#*:}" ++ done ++} ++ ++### show action ### ++describe_show() { ++ echo "Show the current provider in use for ${ALTERNATIVE}" ++} ++ ++do_show() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local current="$(get_current_provider)" ++ if [[ -z "${current}" ]] ; then ++ echo "(none)" ++ return 2 ++ fi ++ echo "${current}" ++} ++ ++options_show() { ++ : ++} ++ ++### list action ### ++describe_list() { ++ echo "Lists all available providers for ${ALTERNATIVE}" ++} ++ ++do_list() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local n cur= providers=( $(get_providers) ) ++ write_list_start "Available providers for ${ALTERNATIVE}:" ++ ++ cur="$(get_current_provider)" ++ ++ if [[ -n "${providers[@]}" ]] ; then ++ for (( n = 0 ; n < ${#providers[@]} ; ++n )) ; do ++ [[ ${cur} == "${providers[${n}]}" ]] && \ ++ providers[${n}]="${providers[${n}]} $(highlight '*')" ++ done ++ write_numbered_list "${providers[@]}" ++ else ++ write_kv_list_entry "(none found)" "" ++ fi ++} ++ ++options_list() { ++ : ++} ++ ++### files action ### ++describe_files() { ++ echo "Lists symlinks provided by the currently selected provider" ++} ++ ++do_files() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local cur="$(get_current_provider)" p= ++ [[ -n "${cur}" ]] || die -q "No selected provider, hence no symlinks provided" ++ local dieprefix="Could not list symlinks provided for ${ALTERNATIVE}" ++ ++ local errors symlink rootsymlink ++ while read -r -d '' symlink; do ++ rootsymlink="${EROOT}${symlink}" ++ rootsymlink=${rootsymlink//+(\/)/\/} ++ echo "${rootsymlink}" ++ if [[ -L ${rootsymlink} ]]; then ++ if [[ ! -e ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} is dangling symlink" ++ errors=yes ++ fi ++ elif [[ -d ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} is a directory" ++ errors=yes ++ elif [[ -e ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} exists but is not a symlink" ++ errors=yes ++ else ++ write_error_msg "${rootsymlink} does not exist" ++ errors=yes ++ fi ++ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++} ++ ++options_files() { ++ : ++} ++ ++### set action ### ++ ++describe_set() { ++ echo "Sets a provider for ${ALTERNATIVE}" ++} ++ ++describe_set_parameters() { ++ echo "[ --force ] <provider>" ++} ++ ++describe_set_options() { ++ echo "--force : overwrite or remove existing non-symlink files (but not directories) if necessary" ++ echo "<provider> : the name of the provider to use" ++} ++ ++do_set() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local force= ++ if [[ ${1} == --force ]]; then ++ force=yes ++ shift ++ fi ++ ++ local provider="${1}" ++ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" ++ if is_number "${provider}" ; then ++ local providers=( $(get_providers) ) ++ (( ${provider} <= ${#providers[@]} )) || die -q "The given provider (${provider}) does not exist" ++ provider=${providers[${provider}-1]} ++ fi ++ local dieprefix="Could not set provider ${provider} for alternative ${ALTERNATIVE}" ++ ++ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] \ ++ || die -q "The given provider (${provider}) does not exist" ++ ++ local symlink newsymlinks=() oldsymlinks=() ++ ++ while read -r -d '' symlink; do ++ local nicesymlink=${symlink#.} ++ nicesymlink=${nicesymlink//+(\/)/\/} ++ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: bad symlink ${symlink}?" ++ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: bad symlink ${symlink}?" ++ ++ newsymlinks+=( "${nicesymlink}" ) ++ done < <( ++ cd "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || die "${dieprefix}: cd failed" ++ find . -type l -print0 | LC_ALL=C sort -r -u -z) ++ [[ ${#newsymlinks[@]} -gt 0 ]] || die "${dieprefix}: does not provide any symlinks?" ++ ++ if [[ -f ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then ++ while read -r -d '' symlink; do ++ local nicesymlink=${symlink//+(\/)/\/} ++ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" ++ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" ++ ++ oldsymlinks+=( "${nicesymlink}" ) ++ done < <(LC_ALL=C sort -r -u -z "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list") ++ [[ ${#oldsymlinks[@]} -gt 0 ]] || die "${dieprefix}: old provider ${oldcur} does not provide any symlinks?" ++ ++ elif [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list || -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list is not a file" ++ fi ++ ++ local pass errors= ++ for pass in check perform; do ++ local -i new_i=0 old_i=0 ++ while [[ -n ${newsymlinks[new_i]} || -n ${oldsymlinks[old_i]} ]]; do ++ ++ if ( LC_ALL=C; [[ ${newsymlinks[new_i]} < ${oldsymlinks[old_i]} ]] ); then ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT}${oldsymlinks[old_i]} ]]; then ++ : ++ elif [[ -d ${EROOT}${oldsymlinks[old_i]} ]]; then ++ write_error_msg "Can't remove ${EROOT}${oldsymlinks[old_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT}${oldsymlinks[old_i]} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Removing ${EROOT}${oldsymlinks[old_i]} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to remove ${EROOT}${oldsymlinks[old_i]}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ rm -f "${ROOT}${oldsymlinks[old_i]}" || die "${dieprefix}: rm failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ ++ old_i+=1 ++ ++ else ++ local target=${ALTERNATIVESDIR_ROOTLESS#/}/${ALTERNATIVE}/_current${newsymlinks[new_i]} dir=${newsymlinks[new_i]%/*} ++ while [[ -n ${dir} ]]; do ++ target=../${target} ++ dir=${dir%/*} ++ done ++ ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT}${newsymlinks[new_i]} ]]; then ++ : ++ elif [[ -d ${EROOT}${newsymlinks[new_i]} ]]; then ++ write_error_msg "Can't overwrite ${EROOT}${newsymlinks[new_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT}${newsymlinks[new_i]} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Overwriting ${EROOT}${newsymlinks[new_i]} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to overwrite ${EROOT}${newsymlinks[new_i]}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ mkdir -p "${EROOT}${newsymlinks[new_i]%/*}" || die "${dieprefix}: mkdir -p failed" ++ ln -snf "${target#/}" "${EROOT}${newsymlinks[new_i]}" || die "${dieprefix}: ln -snf failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ ++ [[ ${newsymlinks[new_i]} == ${oldsymlinks[old_i]} ]] && old_i+=1 ++ new_i+=1 ++ fi ++ done ++ ++ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" ++ done ++ ++ local oldcur="$(get_current_provider)" ++ ln -snf "${provider}" "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: ln -snf failed" ++ ++ : >"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: emptying/creating _current_list failed" ++ for symlink in "${newsymlinks[@]}"; do ++ echo -n -e "${symlink}\\0" >>"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: appending ${symlink} to _current_list failed" ++ done ++ return 0 ++} ++ ++_options_parameters() { ++ [[ -n ${2} && ${2} != --descriptions ]] && die -q "Unrecognised option ${2}" ++ local describe_func=describe_${1#options_}_options descriptions=${2} opt options oldifs=$IFS ++ if is_function ${describe_func}; then ++ IFS=$'\n' ++ options=( $(${describe_func}) ) ++ IFS=$oldifs ++ for opt in "${options[@]}"; do ++ [[ ${opt} == --* ]] || continue ++ if [[ -n ${descriptions} ]]; then ++ echo "${opt/ : /:}" ++ else ++ echo "${opt%% : *}" ++ fi ++ done ++ fi ++} ++ ++options_set() { ++ _options_parameters $FUNCNAME "$@" ++ get_providers ++} ++ ++### update action ### ++ ++describe_update() { ++ echo "Set a default provider if no valid one currently exists" ++} ++ ++describe_update_parameters() { ++ echo "[--ignore] <provider>" ++} ++ ++describe_update_options() { ++ echo "--ignore : update to any valid provider EXCEPT the specified provider" ++ echo "<provider> : the name of the provider to use" ++} ++ ++do_update() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local p cur=$(get_current_provider) providers=( $(get_providers) ) ignore ++ if [[ "--ignore" == ${1} ]] ; then ++ # Try everything except setting the provider to the given ++ # one. So, if it isn't the given one, we end up doing ++ # nothing. Bug #128 ++ shift ++ ignore=${1} ++ fi ++ ++ if [[ ${cur} == ${1} && -z ${ignore} ]]; then ++ # if current provider was just updated, reselect it since it could have changed ++ do_set "${cur}" && return 0 ++ elif [[ -n ${cur} && ${cur} != ${ignore} ]] ; then ++ # verify existing provider's symlinks ++ local p= bad=0 ++ while read -r -d '' p ; do ++ [[ -L "${EROOT}${p}" && -e "${EROOT}${p}" ]] || (( bad++ )) ++ done < "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++ ++ [[ "${bad}" -eq 0 ]] && return 0 ++ # fix existing provider if possible ++ has "${cur}" "${providers[@]}" && do_set "${cur}" && return 0 ++ elif has "${1}" "${providers[@]}" && [[ -z ${ignore} ]] ; then ++ # switch to new provider if none was set before or it can't be fixed ++ do_set "${1}" && return 0 ++ fi ++ ++ # if no valid provider has been selected switch to first available, valid ++ # provider, sorted according to importance ++ for p in "${providers[@]}"; do ++ [[ ${ignore} != ${p} ]] && do_set "${p}" && return 0 ++ done ++ ++ # if a provider is set but no providers are available anymore cleanup ++ cur=$(get_current_provider) ++ if [[ -n ${cur} ]]; then ++ do_unset "${cur}" && return 2 ++ fi ++ # if no provider is set and none are available that are not ignored, return 2 for cleanup ++ [[ -z ${providers[@]} || ${providers[@]} == ${ignore} ]] && return 2 ++ ++ # we tried everything to select a valid provider, but failed ++ return 1 ++} ++ ++options_update() { ++ _options_parameters $FUNCNAME "$@" ++ get_providers ++} ++ ++### unset action ### ++ ++describe_unset() { ++ echo "Unset any symlinks created for the current provider for ${ALTERNATIVE}." ++} ++ ++describe_unset_parameters() { ++ echo "[ --force ]" ++} ++ ++describe_unset_options() { ++ echo "--force : remove existing non-symlink files (but not directories) if necessary" ++} ++ ++do_unset() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local force= ++ if [[ ${1} == --force ]]; then ++ force=yes ++ shift ++ fi ++ ++ local cur="$(get_current_provider)" p= ++ [[ -n "${cur}" ]] || die -q "Nothing to unset" ++ local dieprefix="Could not unset provider for ${ALTERNATIVE}" ++ ++ local one=false symlink pass errors= ++ for pass in check perform; do ++ while read -r -d '' symlink; do ++ one=true ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT}${symlink} ]]; then ++ : ++ elif [[ -d ${EROOT}${symlink} ]]; then ++ write_error_msg "Can't remove ${EROOT}${symlink}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT}${symlink} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Removing ${EROOT}${symlink} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to remove ${EROOT}${symlink}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ rm -f "${EROOT}${symlink}" || die "${dieprefix}: rm failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++ ++ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" ++ done ++ ++ ${one} || die "${dieprefix}: does not provide any symlinks?" ++ ++ rm "${ALTERNATIVESDIR}/${ALTERNATIVE}"/{_current,_current_list} || die "${dieprefix}: rm failed" ++} ++ ++options_unset() { ++ _options_parameters $FUNCNAME "$@" ++ get_current_provider ++} ++ ++### script action ### ++ ++describe_script() { ++ echo "Output an evalable script fragment to set PATH, LD_LIBRARY_PATH and MANPATH to use the specified provider" ++} ++ ++describe_script_parameters() { ++ echo "[--sh | --csh] [<provider>]" ++} ++ ++describe_script_options() { ++ echo "--sh : use Bourne shell syntax (default)" ++ echo "--csh : use C shell syntax" ++ echo "<provider> : the provider to use (if not specified, use the system default)" ++} ++ ++do_script() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local syntax=sh ++ if [[ ${1} == --sh ]]; then ++ shift ++ elif [[ ${1} == --csh ]]; then ++ syntax=csh ++ shift ++ fi ++ local provider=${1} ++ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" ++ if is_number "${provider}" ; then ++ local providers=( $(get_providers) ) ++ (( ${provider} <= ${#providers[@]} )) || die -q "The given provider (${provider}) does not exist" ++ provider=${providers[${provider}-1]} ++ fi ++ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] || die -q "The given provider (${provider}) does not exist" ++ ++ local variables=( PATH LD_LIBRARY_PATH MANPATH ) ++ [[ -n ${!default_*} ]] && local ${!default_*} ++ local default_LD_LIBRARY_PATH=$(grep '^[^#]' "${EROOT}"/etc/ld.so.conf | tr '\n' ':')/lib:/usr/lib ++ local default_MANPATH=$(MANPATH= man -C"${EROOT}"/etc/man.conf -w) ++ ++ local var IFS=: ++ for var in "${variables[@]}"; do ++ local defvar=default_${var} path paths=( ) ++ for path in ${!var}; do ++ [[ ${path} == ${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/* ]] && continue ++ [[ -n ${provider} && -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) ++ paths+=( "${path}" ) ++ done ++ ++ [[ -n ${provider} ]] && for path in ${!defvar}; do ++ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) ++ done ++ ++ local newval=${paths[*]} ++ if [[ ${newval} != ${!var} ]]; then ++ newval=${newval//\'/\'\\\'\'} ++ if [[ ${syntax} == sh ]]; then ++ echo "${var}='${newval}'; export ${var}" ++ else ++ echo "setenv ${var} '${newval}'" ++ fi ++ fi ++ done ++} ++ ++options_script() { ++ _options_parameters $FUNCNAME "$@" ++ get_providers ++} ++ ++# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/app-admin/eselect/metadata.xml b/app-admin/eselect/metadata.xml new file mode 100644 index 000000000..dbaf8c806 --- /dev/null +++ b/app-admin/eselect/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>no-herd</herd> +<maintainer> + <email>eselect@gentoo.org</email> +</maintainer> +</pkgmetadata> diff --git a/app-benchmarks/autobench/ChangeLog b/app-benchmarks/autobench/ChangeLog deleted file mode 100644 index f4fd7a183..000000000 --- a/app-benchmarks/autobench/ChangeLog +++ /dev/null @@ -1,9 +0,0 @@ -# ChangeLog for app-benchmarks/autobench -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*autobench-9999 (14 Jul 2011) - - 14 Jul 2011; Andrea Arteaga <andyspiros@gmail.com> +autobench-9999.ebuild, - +metadata.xml: - Initial import diff --git a/app-benchmarks/autobench/Manifest b/app-benchmarks/autobench/Manifest deleted file mode 100644 index 59a8793d6..000000000 --- a/app-benchmarks/autobench/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -EBUILD autobench-9999.ebuild 698 RMD160 173b39a0cb55ea93e0acadc4010205759d29a050 SHA1 6dd32f8759d6c039a7ffe29d426d6049ed864370 SHA256 52325b2dbe5b6563fe63c67d2062914fe0856f6952403f0647de6f98a662ed5d -MISC ChangeLog 267 RMD160 c80899c9ce145474176e584d48df19857c20fccc SHA1 8ba840afea9f9f87b858d7c428fee7a6b119816e SHA256 8e56ba061730950daf09bcdb3ae00b45370d33b45bc4858b407aaba228069b8b -MISC metadata.xml 491 RMD160 c40e7016c3c45f26f0a238ae27c11b9f857b03a8 SHA1 f00ff537b0a3dcd7188a1902159c1b2b48502339 SHA256 ccad0894a024e39cdd6b46adaee89d95561ab8ca7c4512276e4f990f08bd071c diff --git a/app-benchmarks/btl/ChangeLog b/app-benchmarks/btl/ChangeLog new file mode 100644 index 000000000..afc6916af --- /dev/null +++ b/app-benchmarks/btl/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for app-benchmarks/btl +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*btl-9999 (06 Aug 2011) + + 06 Aug 2011; Andrea Arteaga <andyspiros@gmail.com> + Initial revision diff --git a/app-benchmarks/btl/Manifest b/app-benchmarks/btl/Manifest new file mode 100644 index 000000000..f698658ae --- /dev/null +++ b/app-benchmarks/btl/Manifest @@ -0,0 +1,3 @@ +EBUILD btl-9999.ebuild 404 RMD160 b08a32148d37af1192745c9132e49e4e4f3385d9 SHA1 ba0fd31b0ba3831bf11fc40458dea0fdd07b8ee2 SHA256 e32ab61bf1b91ba4d8a8583ff8f4e2113692a48373db49a6a8c5f27799f94d6a +MISC ChangeLog 216 RMD160 3b4649893c1169c7b0bcc9d9c4fa8fb7dce99f2e SHA1 c9028941598fde13593bd4e234c14c3401320aa4 SHA256 f8f744cd883a5f63fd1fe121fd0d34bfc437e25c6c8d68669ee6f7b47cb332df +MISC metadata.xml 274 RMD160 6b1d1c61077bf6b8e2a341731f17285fb20f59a9 SHA1 d1e8e65580b622f14455d77e7bcfb077ab27776b SHA256 c7ce59de08668a301465a504598d2087d897d42b3fa28bd3a15e061bdfb39516 diff --git a/app-benchmarks/btl/btl-9999.ebuild b/app-benchmarks/btl/btl-9999.ebuild new file mode 100644 index 000000000..8ca6fdef2 --- /dev/null +++ b/app-benchmarks/btl/btl-9999.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit mercurial + +DESCRIPTION="Bench Template Library" +HOMEPAGE="https://bitbucket.org/spiros/btl" +EHG_REPO_URI="https://bitbucket.org/spiros/btl" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +IUSE="" + +RDEPEND="" + +src_install() { + insinto /usr/include/btl + doins -r * +}
\ No newline at end of file diff --git a/app-benchmarks/btl/metadata.xml b/app-benchmarks/btl/metadata.xml new file mode 100644 index 000000000..a69552766 --- /dev/null +++ b/app-benchmarks/btl/metadata.xml @@ -0,0 +1,11 @@ +<pkgmetadata> +<herd>sci</herd> +<maintainer> +<name>Andrea Arteaga</name> +<email>andyspiros@gmail.com</email> +</maintainer> +<description>Bench Template Library</description> +<longdescription> +This package contains a modified copy of the BTL. +</longdescription> +</pkgmetadata> diff --git a/app-benchmarks/numbench/ChangeLog b/app-benchmarks/numbench/ChangeLog new file mode 100644 index 000000000..3035d15e1 --- /dev/null +++ b/app-benchmarks/numbench/ChangeLog @@ -0,0 +1,19 @@ +# ChangeLog for app-benchmarks/numbench +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*numbench-9999 (3 Aug 2011) + + 4 Aug 2011; Andrea Arteaga <andyspiros@gmail.com> + Updated ebuild RDEPEND + + 3 Aug 2011; Andrea Arteaga <andyspiros@gmail.com> +numbench-9999.ebuild -autobench-9999.ebuild + +metadata.xml: + Renamed to numbench in order to avoid conflicts + + +*autobench-9999 (14 Jul 2011) + + 14 Jul 2011; Andrea Arteaga <andyspiros@gmail.com> +autobench-9999.ebuild, + +metadata.xml: + Initial import diff --git a/app-benchmarks/numbench/Manifest b/app-benchmarks/numbench/Manifest new file mode 100644 index 000000000..adac41cc4 --- /dev/null +++ b/app-benchmarks/numbench/Manifest @@ -0,0 +1,3 @@ +EBUILD numbench-9999.ebuild 716 RMD160 80f449e94330630e13f8acd6ccdf17b5ce6c0b20 SHA1 4427e9d2481e7c3546623eb7da0a75aa2a402b9c SHA256 1c41b76b85e20bd4c157dc9cb29fea78ecb92ea2a50b50a4397531397ed65272 +MISC ChangeLog 539 RMD160 88824e5b0bf5fa21c920bec815c52fe04acb29ce SHA1 cb49f4af3a9d2f87e582765174d0abf467553492 SHA256 5a4e46d51589945d553fee4eef29c30fdbeed066e69101eee683b202063c86cb +MISC metadata.xml 509 RMD160 df9509318921d0115534db222663191d9479df8e SHA1 0add159d5641874b5e70b470b9fbb07ee6c9b7ad SHA256 245250ede4aa9526557c822c21be288ccc3b9b3c5a4d1f643a4eae3c644e2e57 diff --git a/app-benchmarks/autobench/metadata.xml b/app-benchmarks/numbench/metadata.xml index 37157bd6d..93bbb5514 100644 --- a/app-benchmarks/autobench/metadata.xml +++ b/app-benchmarks/numbench/metadata.xml @@ -6,6 +6,6 @@ </maintainer> <description>Automated bechmarks of numerical libraries</description> <longdescription> -This package contains a set of scripts and C++ sources developed during the Google Summer of Code 2011 project. It aims to benchmark numerical libraries, and more precisely implementations of the standard BLAS, CBLAS, LAPACK and the library FFTW. +This package contains a set of scripts and C++ sources developed during the Google Summer of Code 2011 project. It aims to benchmark numerical libraries, and more precisely implementations of the standard BLAS, CBLAS, LAPACK, PBLAS, ScaLAPACK and the library FFTW. </longdescription> </pkgmetadata> diff --git a/app-benchmarks/autobench/autobench-9999.ebuild b/app-benchmarks/numbench/numbench-9999.ebuild index fe0b51162..6610f57f0 100644 --- a/app-benchmarks/autobench/autobench-9999.ebuild +++ b/app-benchmarks/numbench/numbench-9999.ebuild @@ -20,12 +20,13 @@ RDEPEND="!app-admin/eselect-blas !app-admin/eselect-cblas !app-admin/eselect-lapack >=dev-python/matplotlib-1.0.0 - =app-admin/eselect-1.2.15-r1" + =app-admin/eselect-1.2.16-r1 + app-benchmarks/btl" src_install() { - insinto /usr/$(get_libdir)/autobench + insinto /usr/$(get_libdir)/numbench doins *.py doins -r btl accuracy - chmod +x "${D}"/usr/$(get_libdir)/autobench/main.py - dosym /usr/$(get_libdir)/autobench/main.py /usr/bin/autobench -}
\ No newline at end of file + chmod +x "${D}"/usr/$(get_libdir)/numbench/main.py + dosym /usr/$(get_libdir)/numbench/main.py /usr/bin/numbench +} diff --git a/app-doc/root-docs/ChangeLog b/app-doc/root-docs/ChangeLog new file mode 100644 index 000000000..8ae624428 --- /dev/null +++ b/app-doc/root-docs/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for app-doc/root-docs +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*root-docs-5.30 (02 Aug 2011) + + 02 Aug 2011; Andrew Savchenko <bircoph@gmail.com> +root-docs-5.30.ebuild, + +metadata.xml: + Version bump. + diff --git a/app-doc/root-docs/Manifest b/app-doc/root-docs/Manifest new file mode 100644 index 000000000..fb08b8b51 --- /dev/null +++ b/app-doc/root-docs/Manifest @@ -0,0 +1,4 @@ +DIST html530.tar.gz 855673363 RMD160 6a44697e956cc8583a4c33facc2dd8bc236cbb85 SHA1 8134ba74d75b43ebf0279d3a24a8c1d08052ad27 SHA256 ae0ab07f411c7cfb941c78e18dcee800d43c9796b522c97dbcb3480011a02141 +EBUILD root-docs-5.30.ebuild 644 RMD160 890e8ab96a7c1f88a909832918a4e20c08558b68 SHA1 1c480c2f82d522c6f06c93248776007ad0c4e272 SHA256 2f00f97a50db54e2284e1a940afac20ce4b99c1fdcbb487b3efddc4ce452e33d +MISC ChangeLog 259 RMD160 24a6219fbe8782ee318c111d06c6625e66a2122d SHA1 33a447d2e5e34b9ba07374130a6d49f4a1d37697 SHA256 9c054e0d4b4e065cb74ff3f3a6d12aecc33ada17c04874b841c7a1584d0d0bb5 +MISC metadata.xml 164 RMD160 6e4c63a6f70f174f40277eed39ac05fba4a49566 SHA1 e1af6f2028e69dee3c76e7e85353a144c83d3383 SHA256 9eddaccbdd2f6b3f93213d72782f07518dff1625fd8d63faf61dc97bd328b5e7 diff --git a/sci-visualization/gri/metadata.xml b/app-doc/root-docs/metadata.xml index b229aec85..131ee598c 100644 --- a/sci-visualization/gri/metadata.xml +++ b/app-doc/root-docs/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-physics</herd> </pkgmetadata> diff --git a/app-doc/root-docs/root-docs-5.30.ebuild b/app-doc/root-docs/root-docs-5.30.ebuild new file mode 100644 index 000000000..e9a7b43c9 --- /dev/null +++ b/app-doc/root-docs/root-docs-5.30.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.28-r1.ebuild,v 1.1 2011/05/17 17:51:07 bicatali Exp $ + +EAPI=3 +inherit versionator + +DESCRIPTION="An Object-Oriented Data Analysis Framework" +MYP=html$(replace_version_separator 1 '') + +SRC_URI="ftp://root.cern.ch/root/${MYP}.tar.gz" +HOMEPAGE="http://root.cern.ch/" + +SLOT="0" +LICENSE="as-is" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S=${WORKDIR}/htmldoc + +src_install() { + insinto /usr/share/doc/${PF}/html + # use mv, there is too much to copy + mv * "${ED}"/usr/share/doc/${PF}/html +} diff --git a/dev-lang/path64/ChangeLog b/dev-lang/path64/ChangeLog index 757595609..b462b718b 100644 --- a/dev-lang/path64/ChangeLog +++ b/dev-lang/path64/ChangeLog @@ -2,6 +2,20 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 29 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> + -path64-1.0.0_pre20110729.ebuild: + Moved to g-x86 + + 29 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> + path64-1.0.0_pre20110729.ebuild: + Fix SRC_URI for snapshot + +*path64-1.0.0_pre20110729 (29 Jul 2011) + + 29 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> + +path64-1.0.0_pre20110729.ebuild: + Add snapshot + 27 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> path64-9999.ebuild: Add missing LDPATH to env file diff --git a/dev-lang/path64/Manifest b/dev-lang/path64/Manifest index 5db061d52..818595508 100644 --- a/dev-lang/path64/Manifest +++ b/dev-lang/path64/Manifest @@ -1,3 +1,3 @@ EBUILD path64-9999.ebuild 3637 RMD160 2a6b69d2cc992a1eaf5c0cc380ba487c1679062a SHA1 5c9fdc7f5094d9157b5b0178aaa751738d96bab0 SHA256 5a04225dc103d33a433373f0acb8361ff35d64f990218cb5f6df64873a757f6d -MISC ChangeLog 1659 RMD160 17e3557ea54915f9906106d30878ce36861f180b SHA1 fb3eaf4b230e533ca4c498c013878d11e41707c9 SHA256 f22340c1c2fb726e97acc989c4c8204ae4178717f9fa5ecef225184756145302 +MISC ChangeLog 2031 RMD160 239738d04d5922686e12e66975143ead188931a3 SHA1 22374a13dcee92fab2445c6e1e52dea69f2e00fe SHA256 25f66a4c72e3a57b81cc07c4648e84b9f934f83127cfe2c8b7e6b7e073d2a433 MISC metadata.xml 723 RMD160 db0d2917268fd37e631f878b1f03b3d388a4b3f3 SHA1 fe4aaa16e9cb916611384197b4da25309cea3271 SHA256 91d773a1787cd749f0c98ce6bf088bf28e4dab3143d704afb5a7f3114f609c96 diff --git a/dev-perl/BTLib/BTLib-0.19.ebuild b/dev-perl/BTLib/BTLib-0.19.ebuild new file mode 100644 index 000000000..54ff640d6 --- /dev/null +++ b/dev-perl/BTLib/BTLib-0.19.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +MODULE_AUTHOR="" +inherit perl-module +SRC_URI="http://downloads.sourceforge.net/estscan/BTLib-0.19.tar.gz" + +DESCRIPTION=" A part of the estscan package" + +#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND}" + +SRC_TEST="do" diff --git a/dev-perl/BTLib/ChangeLog b/dev-perl/BTLib/ChangeLog new file mode 100644 index 000000000..3d57b6a86 --- /dev/null +++ b/dev-perl/BTLib/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for dev-perl/BTLib +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*BTLib-0.19 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BTLib-0.19.ebuild, + +metadata.xml: + dev-perl/BTLib: new package required by sci-biology/estscan + diff --git a/dev-perl/BTLib/Manifest b/dev-perl/BTLib/Manifest new file mode 100644 index 000000000..a02a12d57 --- /dev/null +++ b/dev-perl/BTLib/Manifest @@ -0,0 +1,4 @@ +DIST BTLib-0.19.tar.gz 36283 RMD160 14ae4a24c81a381e9a75ddcde7552a1f9dc301b8 SHA1 7a0545cb64976ee61e76a80a9ee1a87eb1747078 SHA256 0acd6446031222b8fd5bd11eb3ec6c3164bc50491feef765c052689d9c3ee302 +EBUILD BTLib-0.19.ebuild 414 RMD160 15d7e76febdf93c94f9edde338d99d1b943e2404 SHA1 e406122b24070ab95c667fd95bb13578fcdd4705 SHA256 cc254f5c636d7917ff6e3de2b930487e3365e5b5eb5f5fe4d7664e49e8cc50a9 +MISC ChangeLog 302 RMD160 3046b208df030e5b85db6e540f2c1b2318d02962 SHA1 69b7b4151dd065d6b4305814d049dc0fbc762063 SHA256 ba0e255c5b90e09769e1bc55de95c6407f45eed978d42db561cdb533ff6461ce +MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 diff --git a/sci-biology/go-db-perl/metadata.xml b/dev-perl/BTLib/metadata.xml index d4648212c..d4648212c 100644 --- a/sci-biology/go-db-perl/metadata.xml +++ b/dev-perl/BTLib/metadata.xml diff --git a/dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild b/dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild new file mode 100644 index 000000000..74d055422 --- /dev/null +++ b/dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +MODULE_AUTHOR="LDS" +inherit perl-module + +DESCRIPTION="BigWig and BigBed file perl-based interface for Gbrowse-2" + +#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="sci-biology/ucsc-genome-browser" +DEPEND="${RDEPEND} + virtual/perl-Module-Build" + +SRC_TEST="do" + +src_prepare(){ + epatch "${FILESDIR}"/Build.PL.patch || die "Failed to patch Build.PL" +} + +CFLAGS="${CFLAGS} -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64" diff --git a/dev-perl/Bio-BigFile/Manifest b/dev-perl/Bio-BigFile/Manifest new file mode 100644 index 000000000..2f1063527 --- /dev/null +++ b/dev-perl/Bio-BigFile/Manifest @@ -0,0 +1,4 @@ +AUX Build.PL.patch 1350 RMD160 74a62e75c72cce3b11eac3df94cba4347383a884 SHA1 3eb47d1d7aeaf31efdf3d7fba1356f7e2d0b7ec2 SHA256 2f9fc8d8eb469e7b5758e306f9933a69fa4347eba6d31e43d5469cba19369429 +DIST Bio-BigFile-1.06.tar.gz 603786 RMD160 4a8e0bf325ccb93c3d4e7a1e577815f6b908ed6f SHA1 5a9fd3149847fe30703f36658693bc6cd4e30004 SHA256 15f1ece2563096a301cff533a9ac91b8fc31af7643b4c4d7fd5d4fa75d4cb5ef +EBUILD Bio-BigFile-1.06.ebuild 639 RMD160 f134d8ec7052b996749a58161d639e8c99f8611e SHA1 da1ff4de41e53e8961800c5d432aad32cc90396d SHA256 dc0ada94ec2397a2ac26a30aae09016b278ddfe9c38791372a46f12f5d5b02c1 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/dev-perl/Bio-BigFile/files/Build.PL.patch b/dev-perl/Bio-BigFile/files/Build.PL.patch new file mode 100644 index 000000000..b6dc709d7 --- /dev/null +++ b/dev-perl/Bio-BigFile/files/Build.PL.patch @@ -0,0 +1,40 @@ +--- Bio-BigFile-1.06/Build.PL.ori 2011-07-14 01:36:32.000000000 +0200 ++++ Bio-BigFile-1.06/Build.PL 2011-07-14 02:01:27.000000000 +0200 +@@ -47,12 +47,10 @@ + sub find_jk { + my ($jk_include,$jk_lib); + +- if (my $jksrc = $ENV{KENT_SRC}) { +- $jk_include = "$jksrc/inc" +- if -e "$jksrc/inc/$HeaderFile"; +- $jk_lib = "$jksrc/lib/$ENV{MACHTYPE}" +- if -e "$jksrc/lib/$ENV{MACHTYPE}/$LibFile"; +- } ++ $jk_include = "/usr/include/ucsc-genome-browser" ++ if -e "/usr/include/ucsc-genome-browser/$HeaderFile"; ++ $jk_lib = "/usr/lib" ++ if -e "/usr/lib/$LibFile"; + + unless ($jk_include && $jk_lib) { + print STDERR <<END; +@@ -67,15 +65,15 @@ + + END + my $prompt = "Please enter the location of Kent source tree: "; +- my $found; ++ my $found = 1; + while (!$found) { + my $path = prompt($prompt); + print STDERR "\n"; + last unless $path; +- $jk_include = "$path/inc" +- if -e "$path/inc/$HeaderFile"; +- $jk_lib = "$path/lib/$ENV{MACHTYPE}" +- if -e "$path/lib/$ENV{MACHTYPE}/$LibFile"; ++ $jk_include = "/usr/include/ucsc-genome-browser" ++ if -e "/usr/include/ucsc-genome-browser/$HeaderFile"; ++ $jk_lib = "/usr/lib" ++ if -e "/usr/lib/$LibFile"; + $found = $jk_include && $jk_lib; + unless ($found) { + print STDERR "Can't find the $HeaderFile and $LibFile files at this location.\n"; diff --git a/sci-chemistry/ambertools/metadata.xml b/dev-perl/Bio-BigFile/metadata.xml index 20e218e23..07b525505 100644 --- a/sci-chemistry/ambertools/metadata.xml +++ b/dev-perl/Bio-BigFile/metadata.xml @@ -1,10 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> + <herd>sci-biology</herd> <maintainer> - <email>alexxy@gentoo.org</email> - <name>Alexey Shvetsov</name> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> - diff --git a/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.32.ebuild b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.32.ebuild new file mode 100644 index 000000000..073584505 --- /dev/null +++ b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.32.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +MODULE_AUTHOR="SCAIN" +inherit perl-module + +DESCRIPTION="A Chado database interface for Gbrowse-2" + +#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="dev-perl/DBD-Pg" +DEPEND="${RDEPEND} + virtual/perl-Module-Build" + +SRC_TEST="do" diff --git a/dev-perl/Bio-DB-Das-Chado/ChangeLog b/dev-perl/Bio-DB-Das-Chado/ChangeLog new file mode 100644 index 000000000..993e189af --- /dev/null +++ b/dev-perl/Bio-DB-Das-Chado/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for dev-perl/Bio-DB-Das-Chado +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*Bio-DB-Das-Chado-0.32 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +Bio-DB-Das-Chado-0.32.ebuild, +metadata.xml: + dev-perl/Bio-DB-Das-Chado: new package required by sci-biology/gbrowse + diff --git a/dev-perl/Bio-DB-Das-Chado/Manifest b/dev-perl/Bio-DB-Das-Chado/Manifest new file mode 100644 index 000000000..afeae8077 --- /dev/null +++ b/dev-perl/Bio-DB-Das-Chado/Manifest @@ -0,0 +1,4 @@ +DIST Bio-DB-Das-Chado-0.32.tar.gz 76578 RMD160 54463c5cb14b4c7b5c0385a1cc836742f234a003 SHA1 ecf97205854f2031ea3ee0841fddaf51d4c5a125 SHA256 086c84087fa0898ce4ad60b273685af181933410a3d0db7de070c1c449e2c209 +EBUILD Bio-DB-Das-Chado-0.32.ebuild 402 RMD160 aa41c2087b665d00cbd8aa85917130c74d725b41 SHA1 6d63d65a3147339791dd264a6194294ce67683f7 SHA256 c0dea37144712bc4f724268767393fa2ec8d3b7244574f53c7638e1b6ef11d3b +MISC ChangeLog 346 RMD160 d18c5c31b7ed7f0640d48606f7a2bad1f0464684 SHA1 067f32e81d46fce5fd5d554020e35f113fb10dd2 SHA256 5e5c9a4973813ef230b5a6b640de2a09846981d8d4211309a9b6722b507978dd +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/dev-perl/Bio-DB-Das-Chado/metadata.xml b/dev-perl/Bio-DB-Das-Chado/metadata.xml new file mode 100644 index 000000000..07b525505 --- /dev/null +++ b/dev-perl/Bio-DB-Das-Chado/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild new file mode 100644 index 000000000..1b985ff5b --- /dev/null +++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# This ebuild generated by g-cpan 0.16.4 + +EAPI="2" + +MODULE_AUTHOR="LDS" + +inherit perl-module + +DESCRIPTION="Bio::DB::Sam -- Read SAM/BAM database files" + +LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=">=sci-biology/bioperl-1.6.901 + virtual/perl-Module-Build + dev-lang/perl + >=sci-biology/samtools-0.1.16" + +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -i s'#HeaderFile = "bam.h#HeaderFile = "bam/bam.h#' "${WORKDIR}"/"${P}"/Build.PL || die "Failed to fix bam.h to bam/bam.h in Build.PL" + sed -i s'#include "bam.h#include "bam/bam.h#' "${WORKDIR}"/"${P}"/lib/Bio/DB/Sam.xs || die "Failed to fix bam.h to bam/bam.h in lib/Bio/DB/Sam.xs" + sed -i s'#include "khash.h#include "bam/khash.h#' "${WORKDIR}"/"${P}"/lib/Bio/DB/Sam.xs || die "Failed to fix khash.h to bam/khash.h in lib/Bio/DB/Sam.xs" + sed -i s'#include "faidx.h#include "bam/faidx.h#' "${WORKDIR}"/"${P}"/lib/Bio/DB/Sam.xs || die "Failed to fix faidx.h to bam/faidx.h in lib/Bio/DB/Sam.xs" +} diff --git a/dev-perl/Bio-SamTools/ChangeLog b/dev-perl/Bio-SamTools/ChangeLog new file mode 100644 index 000000000..f54409a3a --- /dev/null +++ b/dev-perl/Bio-SamTools/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for dev-perl/Bio-SamTools +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*Bio-SamTools-1.29 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +Bio-SamTools-1.29.ebuild, +metadata.xml: + dev-perl/Bio-SamTools: new package required by sci-biology/gbrowse + diff --git a/dev-perl/Bio-SamTools/Manifest b/dev-perl/Bio-SamTools/Manifest new file mode 100644 index 000000000..1b2d90813 --- /dev/null +++ b/dev-perl/Bio-SamTools/Manifest @@ -0,0 +1,4 @@ +DIST Bio-SamTools-1.29.tar.gz 331127 RMD160 e86b51bdd7ffdfd42076da11b19ab4cbb3a9a93a SHA1 2925e95fc77d70d1bd5dedb3e1f4d7f00b8facd6 SHA256 9f9a6ea320b581a4bc4f61372f17310d063b3c1a534fd2f756e967c44b0f4c06 +EBUILD Bio-SamTools-1.29.ebuild 1096 RMD160 d0f997e2024e0afa73b897993704c0137aeb0440 SHA1 bc529914e20f23f2c612788a2881bd862a9d3c57 SHA256 e2627f4380a52a9925a267235bf5912d28723a906df2ff44e7dc77ccc8cbd0e4 +MISC ChangeLog 330 RMD160 9573d481469c701ae4569e9c66d1b145cfb7d836 SHA1 9d4e08c3ab47342d320b16e6a5620ce2376bd8c1 SHA256 0593a57b076251bb53e1e278eb3f4ba5fbc57df54c16311f075c967733181e27 +MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 diff --git a/dev-perl/Bio-SamTools/metadata.xml b/dev-perl/Bio-SamTools/metadata.xml new file mode 100644 index 000000000..d4648212c --- /dev/null +++ b/dev-perl/Bio-SamTools/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/dev-perl/DBIx-DBStag/ChangeLog b/dev-perl/DBIx-DBStag/ChangeLog new file mode 100644 index 000000000..0d2382ad8 --- /dev/null +++ b/dev-perl/DBIx-DBStag/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for dev-perl/DBIx-DBStag +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*DBIx-DBStag-0.12 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +DBIx-DBStag-0.12.ebuild, +metadata.xml: + dev-perl/DBIx-DBStag: new package required by sci-biology/gbrowse + diff --git a/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild b/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild new file mode 100644 index 000000000..aaeebfbd5 --- /dev/null +++ b/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# This ebuild generated by g-cpan 0.16.4 + +EAPI="2" + +MODULE_AUTHOR="SCAIN" + +inherit perl-module + +DESCRIPTION="Relational Database to Hierarchical (Stag/XML) Mapping" + +LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=">=dev-perl/DBIx-DBSchema-0.39 + dev-perl/libxml-perl + >=dev-perl/Data-Stag-0.11 + dev-perl/DBI + dev-perl/Parse-RecDescent + dev-lang/perl" + +RDEPEND="${DEPEND}" diff --git a/dev-perl/DBIx-DBStag/Manifest b/dev-perl/DBIx-DBStag/Manifest new file mode 100644 index 000000000..ba2ba6380 --- /dev/null +++ b/dev-perl/DBIx-DBStag/Manifest @@ -0,0 +1,4 @@ +DIST DBIx-DBStag-0.12.tar.gz 142945 RMD160 5163a58fd03a9ef047c89c3e7b197d29bcf5747a SHA1 582505e67eefc184e18c742e69b9127a3b8e0606 SHA256 c2f07f42ffbbfb4256c1b66b4936bf9869acb7f4b058351290bbee4d719b1e67 +EBUILD DBIx-DBStag-0.12.ebuild 523 RMD160 84495609f5cd9e6dbc82a89954725eb8f39edaac SHA1 c9f1a8bdbae1d0c6458e4715a0d42c208ddac957 SHA256 cef97617ad8e4de981cbdaaeb9c55d5479bbdcfb102704a68bd71ef56da9518e +MISC ChangeLog 326 RMD160 4744ffb6a6b283565f87d1c4db2575e811d713f5 SHA1 b2dc4f06964e0bfca0645f64376563e96b8a9c12 SHA256 67657aca6bf19877b1867b0ad9cd4b9759151a49f89281667804304b77837c44 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/dev-perl/DBIx-DBStag/metadata.xml b/dev-perl/DBIx-DBStag/metadata.xml new file mode 100644 index 000000000..07b525505 --- /dev/null +++ b/dev-perl/DBIx-DBStag/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/dev-perl/Text-ParseWords/ChangeLog b/dev-perl/Text-ParseWords/ChangeLog new file mode 100644 index 000000000..21674a4ba --- /dev/null +++ b/dev-perl/Text-ParseWords/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for dev-perl/Text-ParseWords +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*Text-ParseWords-3.27 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +Text-ParseWords-3.27.ebuild, +metadata.xml: + dev-perl/Text-ParseWords: new package required by sci-biology/gbrowse + diff --git a/dev-perl/Text-ParseWords/Manifest b/dev-perl/Text-ParseWords/Manifest new file mode 100644 index 000000000..79bad7dd2 --- /dev/null +++ b/dev-perl/Text-ParseWords/Manifest @@ -0,0 +1,4 @@ +DIST Text-ParseWords-3.27.zip 9740 RMD160 0c3344087a5b8fe0270a9d6c8133358bacd5c99e SHA1 12ef6ce2a82cd595a0f50333b8beb9357a5efae2 SHA256 4d4bceae6a957941c758ebd5a47b680f0f8964934b766d13ba2adc3e62b6676d +EBUILD Text-ParseWords-3.27.ebuild 412 RMD160 bf36abfbefce52f3412e5932602242c4dc277c9e SHA1 fc324b5833d03a2e46a796fcf7c0a56690913cf2 SHA256 a8d5344a80262025d0cee264ee44ad04ebb016a3e2ddfd627aae4ccfe07110ac +MISC ChangeLog 342 RMD160 84887f191c1b3c3c9212e673f8ee405ee7e7ae86 SHA1 7385e983fb50ab3666f3b946897a4f0501ed0f58 SHA256 b3250cdfbe575f2924180f71ec402afcc8476f88241f84404bb817e2ad5a96d3 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild b/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild new file mode 100644 index 000000000..57f8bc5bb --- /dev/null +++ b/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# This ebuild generated by g-cpan 0.16.4 + +EAPI="2" + +MODULE_AUTHOR="CHORNY" +MODULE_A_EXT="zip" + +inherit perl-module + +DESCRIPTION="Parse strings containing shell-style quoting" + +LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="dev-lang/perl" + +RDEPEND="${DEPEND}" diff --git a/dev-perl/Text-ParseWords/metadata.xml b/dev-perl/Text-ParseWords/metadata.xml new file mode 100644 index 000000000..07b525505 --- /dev/null +++ b/dev-perl/Text-ParseWords/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/dev-perl/Time-Progress/ChangeLog b/dev-perl/Time-Progress/ChangeLog new file mode 100644 index 000000000..88eb8ecf5 --- /dev/null +++ b/dev-perl/Time-Progress/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for dev-perl/Time-Progress +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*Time-Progress-1.7 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +Time-Progress-1.7.ebuild, +metadata.xml: + dev-perl/Time-Progress: new package required by sci-biology/gbrowse + diff --git a/dev-perl/Time-Progress/Manifest b/dev-perl/Time-Progress/Manifest new file mode 100644 index 000000000..f420d0c01 --- /dev/null +++ b/dev-perl/Time-Progress/Manifest @@ -0,0 +1,4 @@ +DIST Time-Progress-1.7.tar.gz 4366 RMD160 6af7d39f3f4998ec7185608d26fc37fa7eab3fe7 SHA1 98e7d807141457089657f33f679a5f758552fe9c SHA256 7f823cfa9e294d3c45117ad2a82ef4830deb5689be6fe84fbd72cd37103b7a43 +EBUILD Time-Progress-1.7.ebuild 346 RMD160 85f1adcaf3ff392def9c9a0d13296aa14784b571 SHA1 66e1bd05fcb8d7f082cf5a994fbe176b9dc5ce9d SHA256 90b3b3b4a315ea59d09ed992ded218d63255bf6324d00116a4ec1fb479b1ba19 +MISC ChangeLog 332 RMD160 95cf46489e0dbce8468083f14b5f1019d2cc374a SHA1 3750f5e589475bcb08a00a243ac4e2851a0d003c SHA256 54bb7b06abf3735265779563913a78158ec0dc499ccea6c90ffbfc8111fb6d1c +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/dev-perl/Time-Progress/Time-Progress-1.7.ebuild b/dev-perl/Time-Progress/Time-Progress-1.7.ebuild new file mode 100644 index 000000000..7bb62ec26 --- /dev/null +++ b/dev-perl/Time-Progress/Time-Progress-1.7.ebuild @@ -0,0 +1,16 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# This ebuild generated by g-cpan 0.16.4 + +EAPI="2" + +MODULE_AUTHOR="CADE" + +inherit perl-module + +DESCRIPTION="Elapsed and estimated finish time reporting." + +LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" diff --git a/dev-perl/Time-Progress/metadata.xml b/dev-perl/Time-Progress/metadata.xml new file mode 100644 index 000000000..07b525505 --- /dev/null +++ b/dev-perl/Time-Progress/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/go-db-perl/Manifest b/dev-perl/go-db-perl/Manifest index 998dfce5f..15f150f07 100644 --- a/sci-biology/go-db-perl/Manifest +++ b/dev-perl/go-db-perl/Manifest @@ -1,3 +1,3 @@ DIST go-db-perl-0.04.tar.gz 512925 RMD160 3bd39c1600ea2a998851db434c953ada3cfcac8d SHA1 e4cbd7f7b6979402475d2ff72307e468d2c05477 SHA256 8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b -EBUILD go-db-perl-0.04.ebuild 402 RMD160 013dd06b7074ba688404a44a667b1068f67deaa6 SHA1 cef96fd10ad16b7df3eed44ac6f70b0a671314a1 SHA256 05ab1bf7c10e6dcdeb5ba98e2a7b1e4e72ff64125e13f47bd89b45a71c04b4b4 +EBUILD go-db-perl-0.04.ebuild 398 RMD160 72049d924baafd03586f7718fbc4586ddf45efae SHA1 9a9447a55453997cea430e962cbdbf148aa1eb58 SHA256 f40eb12b2cdcb3b52ab5629a88023534e0e008e5f24ff0f0e972d465bc994b0a MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 diff --git a/sci-biology/go-db-perl/go-db-perl-0.04.ebuild b/dev-perl/go-db-perl/go-db-perl-0.04.ebuild index f58a27e60..c90ab3b35 100644 --- a/sci-biology/go-db-perl/go-db-perl-0.04.ebuild +++ b/dev-perl/go-db-perl/go-db-perl-0.04.ebuild @@ -17,7 +17,7 @@ DEPEND="" RDEPEND="${DEPEND} dev-perl/FreezeThaw dev-perl/XML-LibXSLT - >=perl-gcpan/DBIx-DBStag-0.06 - perl-gcpan/go-perl" + >=dev-perl/DBIx-DBStag-0.06 + dev-perl/go-perl" SRC_TEST=do diff --git a/dev-perl/go-db-perl/metadata.xml b/dev-perl/go-db-perl/metadata.xml new file mode 100644 index 000000000..d4648212c --- /dev/null +++ b/dev-perl/go-db-perl/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/dev-perl/go-perl/ChangeLog b/dev-perl/go-perl/ChangeLog new file mode 100644 index 000000000..2e162b59e --- /dev/null +++ b/dev-perl/go-perl/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for dev-perl/go-perl +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*go-perl-0.13 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +go-perl-0.13.ebuild, +metadata.xml: + dev-perl/go-perl: new package required by sci-biology/gbrowse + diff --git a/dev-perl/go-perl/Manifest b/dev-perl/go-perl/Manifest new file mode 100644 index 000000000..e0e1ba940 --- /dev/null +++ b/dev-perl/go-perl/Manifest @@ -0,0 +1,4 @@ +DIST go-perl-0.13.tar.gz 806739 RMD160 e55c6b0f1647a4087d094b6e83fa3351f7f57624 SHA1 25fa3bda2b8f9654d0552e10c9f8b778de41d6fe SHA256 392835fe0dd201a11b4f257bc10b8774cadc30dd93ef972fb65382b2a3557541 +EBUILD go-perl-0.13.ebuild 426 RMD160 3503932329cfaed1bafba121ae4ba68793b531fa SHA1 49f57fd78eb0744ff29dfe8da5ca5734690dfcd3 SHA256 a23582388da5ec9a4f745d6fd74fd6eb2259c5fe72d6d469aa097442fc4210e2 +MISC ChangeLog 310 RMD160 982f68bb9757bb245e01355f9b3fb2e0b41f8f0d SHA1 5769f4b1c068d0a2bfc86c83bd52dab8d6cba51a SHA256 af7c57e97b6e3683829a21aab56ee98059aad6b26a855a76f2620fd9c5981927 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/dev-perl/go-perl/go-perl-0.13.ebuild b/dev-perl/go-perl/go-perl-0.13.ebuild new file mode 100644 index 000000000..ae9db233b --- /dev/null +++ b/dev-perl/go-perl/go-perl-0.13.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# This ebuild generated by g-cpan 0.16.4 + +EAPI="2" + +MODULE_AUTHOR="CMUNGALL" + +inherit perl-module + +DESCRIPTION="GO::Parser parses all GO files formats and types" + +LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=">=dev-perl/Data-Stag-0.11 + dev-lang/perl" + +RDEPEND="${DEPEND}" diff --git a/dev-perl/go-perl/metadata.xml b/dev-perl/go-perl/metadata.xml new file mode 100644 index 000000000..07b525505 --- /dev/null +++ b/dev-perl/go-perl/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/dev-python/asciidata/ChangeLog b/dev-python/asciidata/ChangeLog index 1320ff27e..69d7889af 100644 --- a/dev-python/asciidata/ChangeLog +++ b/dev-python/asciidata/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/asciidata -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + *asciidata-1.1.1-r1 (25 Jun 2010) 25 Jun 2010; Justin Lecher <jlec@gentoo.org> -asciidata-1.1.1.ebuild, diff --git a/dev-python/asciidata/Manifest b/dev-python/asciidata/Manifest index 2c31be953..5d39c1263 100644 --- a/dev-python/asciidata/Manifest +++ b/dev-python/asciidata/Manifest @@ -1,15 +1,5 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - DIST asciidata-1.1.1.tar.gz 482467 RMD160 d66edac0d1418d990de102e87f591d8c5905b9bf SHA1 815307ab8a4063d18a064778cda3c23b2dd7ef80 SHA256 4dfbf3145ddda8693fb82d97fbaf14ebcddf957557c4e97c789bc6fd1862f11e DIST asciidata_1.1.1.tar.gz 108025 RMD160 f3f65b4bde4cde3d32b7aeb9fcf61b882a861560 SHA1 e7fa97e35dea4f26c43639826d63b2a51d9294c4 SHA256 e2f3d50d25c9986246acb4feac255d88d3acae49408fbae091649be574ace0df EBUILD asciidata-1.1.1-r1.ebuild 790 RMD160 99a309c248f2362917e2d38013596573303ef50c SHA1 c3c44ca51150ddd5cf9001be8e48f6612ab8d5f3 SHA256 20f04b3426dcc6c930180a0e781678ddaacb038112e923e1ee3410e927d8db77 -MISC ChangeLog 711 RMD160 48f45f81d50567f5bbab37e41a5193e725a788e6 SHA1 a335b2e675bcb4da7862eb382877fe510ad579f8 SHA256 8d711d2fa246167b3a185210e3e05e32f0902ffdd45c8ddf3df4b0e6e3d99cbd -MISC metadata.xml 450 RMD160 f1fd6a7506bf4680e443c4444e838c920a47fab8 SHA1 59d2acea5be821cfee9f363273ad9b7822a989b6 SHA256 b9d5f1a73e94560204c68661bb3b14507a68d3058d78cb65ee121e87f7462557 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.15 (GNU/Linux) - -iEYEARECAAYFAkwk/VsACgkQgAnW8HDreRYVRgCghVRrr1/wCf9GEhGDFtBowKtb -5HMAoJZP3xhFSeXwiFfR9WtME6+xw3gN -=9+hs ------END PGP SIGNATURE----- +MISC ChangeLog 814 RMD160 e968f684530d454eb7ef7c8156d9cc7a3e072bb1 SHA1 652199674f52395897b79b6dbf7bcff0fb46721e SHA256 57a1ffbb47c91b029542ea54d9e55e9c2effbceb7e05882160939d7d3ba8a2bd +MISC metadata.xml 460 RMD160 125e6f064b24ac30b00c3422b8c9ee86c6bfc17f SHA1 cdcff5e2b4d6d84477dbb917d018e96e47884753 SHA256 d709319b8ad290c86fe1809817e50001df2a994616e3b71141ccc81c02dc8cbb diff --git a/dev-python/asciidata/metadata.xml b/dev-python/asciidata/metadata.xml index 4f6d8e18c..804a75129 100644 --- a/dev-python/asciidata/metadata.xml +++ b/dev-python/asciidata/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> AsciiData is a Python module to handle ASCII tables. With this module it is possible to: diff --git a/dev-python/astlib/ChangeLog b/dev-python/astlib/ChangeLog index a6c512b54..77cb925ac 100644 --- a/dev-python/astlib/ChangeLog +++ b/dev-python/astlib/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/astlib -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + *astlib-0.4.0 (15 Jul 2010) 15 Jul 2010; Sébastien Fabbro <bicatali@gentoo.org> +astlib-0.4.0.ebuild, diff --git a/dev-python/astlib/Manifest b/dev-python/astlib/Manifest index 812c758a1..7fc5ac73f 100644 --- a/dev-python/astlib/Manifest +++ b/dev-python/astlib/Manifest @@ -1,5 +1,5 @@ AUX astlib-0.4.0-wcstools.patch 3332 RMD160 6ae573643fe64857746000bfd4a46261780e02f0 SHA1 28963489edeace88216d85308c2f9b0d9205838e SHA256 588f7e8bd22f5dcf7e4eb0a324eceab076dcf1b6aba3dc015a72d29249ecc6cb DIST astLib-0.4.0.tar.gz 1002727 RMD160 9902f6a0704a495070ecc176998fe431ce8b7d13 SHA1 6d856c39a31f999ee88cd7baec1cc0cb23b85001 SHA256 c8d9f4b42716bbbd398040c9e8eaadca437cc2dd9dca020b36ac45144ac699db EBUILD astlib-0.4.0.ebuild 908 RMD160 f22d921430e8ad81946be31f72f97f21b25a6af4 SHA1 374aad305aa759285b0717f1a6bf21b09daad5c0 SHA256 0141b74ad5686ea9c71e7e3198e9f9c6a93dd78db380ecaeeb9cba4fcabe14c9 -MISC ChangeLog 295 RMD160 21f68cef49e095479ec7f4530c56f691f0b7361e SHA1 783da4280a9ee7b238468ce4589bd78e828a53fa SHA256 bec660fabc8f9fed417cd41dd53ad7db0ebce5d940830840824305911180de24 -MISC metadata.xml 671 RMD160 5e43200e338499bb1444277f1184af4ba420d106 SHA1 89facf43679f05f52731670fe115c0e032e52281 SHA256 68f9c9113770aaff9280e3c859f6e4da5ba54972939fb41ecd48812a0ffb754f +MISC ChangeLog 398 RMD160 2b2337b53e710ecd2515b3790fcff7d2278aac21 SHA1 6ee5cdea1d5660d723fcbe419587129256aa3d73 SHA256 487863b905a2d1b491cdab2efbab2eb8b53889fae6fa4e578ffdec01108d7596 +MISC metadata.xml 681 RMD160 65830d27707695afa1d887f3622aab183fefbef7 SHA1 cf0f5691f7b5de1750461e4628f886cf1e4777a2 SHA256 f91b838969a15279336b8b826ce752c456c541ed7f6eefd8dacaa7fa9a1f2f8d diff --git a/dev-python/astlib/metadata.xml b/dev-python/astlib/metadata.xml index 25f46bdc4..7f08aaee0 100644 --- a/dev-python/astlib/metadata.xml +++ b/dev-python/astlib/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> astLib is a set of Python modules that provides some tools for research astronomers. It can be used for simple plots, statistics, diff --git a/dev-python/astropysics/ChangeLog b/dev-python/astropysics/ChangeLog index 18ce76bab..9656cef6f 100644 --- a/dev-python/astropysics/ChangeLog +++ b/dev-python/astropysics/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + 15 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> astropysics-9999.ebuild: Update dependencies, move to git repo diff --git a/dev-python/astropysics/Manifest b/dev-python/astropysics/Manifest index f5c1b285c..04e525081 100644 --- a/dev-python/astropysics/Manifest +++ b/dev-python/astropysics/Manifest @@ -1,3 +1,3 @@ EBUILD astropysics-9999.ebuild 1002 RMD160 5b452eb4bfea4947a9d9942ed9d697d7007eb76f SHA1 9340949992d12c86d24ab1b2f14f748ab8b3d4d2 SHA256 a354085ce97fcf61c492ea47637821b376bf9845beef1336f8c10a24848e61aa -MISC ChangeLog 759 RMD160 32e5bd34df9693bcff95dd46bb7cb31c5241d09f SHA1 dfb170f8dba0dc4ac612b2bb53de0ecb3c34fcf4 SHA256 1c132fd19699b3284d6f9ea1919fbd4d044f6e58ad30fd1005abd046692a0eea -MISC metadata.xml 486 RMD160 d5e6a36e6d91a77898000adba8b28e7431abc794 SHA1 75bbc7323e13478dae304b0115aaf1cf5dd12bff SHA256 b5655d42282d201e0618314761e94eb6d433644425ce86287a360ffd53131d47 +MISC ChangeLog 862 RMD160 3b2c3433b3294e74102733ce420747020107c747 SHA1 c1fbc127ca893e9a7d11730dbf1aa7549c0cc8f6 SHA256 175f29b4bb7d29b4c622b21d258b34610119c897371bce4d6b39e6395a852c7e +MISC metadata.xml 496 RMD160 9936cd2795fcc2abb59fce88d24bf9f6ff62763a SHA1 0b790c2a4942bcef39c5ca295caf2d941e133ef2 SHA256 dae5c55a277811ed0288875d36b66b89b3144fb374735818dfaffcb4ca139d58 diff --git a/dev-python/astropysics/metadata.xml b/dev-python/astropysics/metadata.xml index db677d5dd..f344d8b22 100644 --- a/dev-python/astropysics/metadata.xml +++ b/dev-python/astropysics/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> Astropysics leverages a variety of tools already developed for python to simplify quick-and-dirty calculations and streamline really hard ones. When paired with diff --git a/dev-python/coords/ChangeLog b/dev-python/coords/ChangeLog index d75b7cef3..0c7e492e9 100644 --- a/dev-python/coords/ChangeLog +++ b/dev-python/coords/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> coords-0.37.ebuild, metadata.xml: Fixed malformat CVS line in header diff --git a/dev-python/coords/Manifest b/dev-python/coords/Manifest index ce65b9bef..f754e0786 100644 --- a/dev-python/coords/Manifest +++ b/dev-python/coords/Manifest @@ -1,14 +1,4 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 - DIST coords-0.37.tar.gz 736179 RMD160 bb273716fd4bd3f5df7558f5cdb19dde732ee5c3 SHA1 8de4563e2d2b43d9c1b308f6dad0dd702e795a1a SHA256 67ce4316e37a75b83a459e1103b497149d4fec9388ac042f756338fff1fc22b3 EBUILD coords-0.37.ebuild 736 RMD160 6b013f0857597eba71c9e8f5a96549321d472e89 SHA1 57fc05af48e7787ee5470b69ff8ba455310bc6a0 SHA256 ecc134f372dfe23dd7ec8e0738a6e5a5ed4764064f4274ccce72935f866aac8d -MISC ChangeLog 573 RMD160 d76c93db183b59073ccd84ec73abf9bc80cf7605 SHA1 aebd16cdd6527c4d465aa500b7b575832f5a1719 SHA256 1917a3261622a39a0706a0013569ca5fc69bde77c1a3fbd5fdde9b3c0a4d9543 -MISC metadata.xml 314 RMD160 e5366240b8eecf07bbcbaaa0e3102a70a439ae6d SHA1 ecdd6ca0f44aee7f6df2102639692c8b6e61fb1e SHA256 b5eecff4fb2537a471c6aebc9a9a30f5abfa0c9e2a8b8f59e234331e183e00ee ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEAREIAAYFAk4F6V0ACgkQgAnW8HDreRbTKQCgz1iCMZ57UDT1xQLK+xubDjLv -PZAAn3TlUTKlMvG1DY9kVCrumPmRuuOC -=WYdz ------END PGP SIGNATURE----- +MISC ChangeLog 676 RMD160 6f85e2f04b6983902cf8f094da8761b0ea0274e8 SHA1 89fa7ef3bc2ef640de83998c432efead6226685c SHA256 ab33cc4031dcd7f14ae0f7d082edebac93c1f1bab964f726cd44398aa2fc37c2 +MISC metadata.xml 324 RMD160 3fd22d42fe485a9102c16a0b575cd8956236e0ad SHA1 ea3df08b5626683cb4692bc37533a831dcad2cbe SHA256 4871be13c5042792c0aab870714eb4d3b51477a02e0c8e912098b95360acabb8 diff --git a/dev-python/coords/metadata.xml b/dev-python/coords/metadata.xml index 0cc1b5f15..f5a586e46 100644 --- a/dev-python/coords/metadata.xml +++ b/dev-python/coords/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> + <herd>sci-astronomy</herd> <longdescription lang="en"> coords is a part of Astrolib and provide a set of routines for managing astronomical coordinate systems diff --git a/dev-python/cosmocalc/ChangeLog b/dev-python/cosmocalc/ChangeLog index 0a5d0dcf9..345fa9b18 100644 --- a/dev-python/cosmocalc/ChangeLog +++ b/dev-python/cosmocalc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/cosmocalc -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + *cosmocalc-0.1.2 (16 Jul 2010) 16 Jul 2010; Sébastien Fabbro <bicatali@gentoo.org> diff --git a/dev-python/cosmocalc/Manifest b/dev-python/cosmocalc/Manifest index 3fde5d0d0..3dc56b87c 100644 --- a/dev-python/cosmocalc/Manifest +++ b/dev-python/cosmocalc/Manifest @@ -1,4 +1,4 @@ DIST cosmocalc-0.1.2.tar.gz 4830 RMD160 012d26ea9e2531770ef7db12cf1ce529d8874a6c SHA1 d0e333c0ea03fe9e528ef01d9090b8240f937fbc SHA256 6b0cff5809c5b13fcd6bcbc6c97924cc94e52e87d102f42425598f4b9a16da94 EBUILD cosmocalc-0.1.2.ebuild 371 RMD160 a92c1add8ea151fbf1d672f729ad6a35e1daf951 SHA1 6f1e32cff1de16959ece9493b19ddb7605603ea6 SHA256 191e7384441fdb81f33170519246de0e361002bc24e8de79798165e20ca8c28f -MISC ChangeLog 268 RMD160 99d0594a1a92b20fdacd58f1d1dce439ed46cc9f SHA1 016443eb77602d19e16fc0b95e7cd7611f454543 SHA256 2a8df30b3a48c0aeafd751cf6e47e75f1c004840ef113220cbe5392330751416 -MISC metadata.xml 383 RMD160 08930731cb12832736968763e9e3f45c958ac319 SHA1 93f4ad16ac8384ec392637ef4f8a06e2f76930f2 SHA256 94f52a90f4c62afc74945b62aabf2211840933837f990f8b66b7f313734ea6e9 +MISC ChangeLog 371 RMD160 cff28a16f5e490283ae5002922162ed99d5ffa55 SHA1 db6770e7bd76a81b3fe93319927f0065a83e7e58 SHA256 32dca3fdb6a960ff1aabc4d466c77408e06cae75d2994c882b4572668e552173 +MISC metadata.xml 393 RMD160 7cef3fa8e242355093e033f340ee303b2219f1d1 SHA1 aad8734d67b5ff2fba23aa3b01dd8e2b257c1edf SHA256 5666401aa19890d3641727b43679fef6883a121af6d07178b5fe1fdfb0934031 diff --git a/dev-python/cosmocalc/metadata.xml b/dev-python/cosmocalc/metadata.xml index 32c50574d..289b0e8ae 100644 --- a/dev-python/cosmocalc/metadata.xml +++ b/dev-python/cosmocalc/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> Calculate useful values for a given cosmology. This module uses code adapted from CC.py (James Schombert) which is a Python version of diff --git a/dev-python/pysolar/ChangeLog b/dev-python/pysolar/ChangeLog index a5193acbc..77b3ee2d0 100644 --- a/dev-python/pysolar/ChangeLog +++ b/dev-python/pysolar/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + *pysolar-0.4.3 (03 May 2011) 03 May 2011; Justin Lecher <jlec@gentoo.org> pysolar-0.4.2.ebuild, diff --git a/dev-python/pysolar/Manifest b/dev-python/pysolar/Manifest index abc405058..6bc2bf944 100644 --- a/dev-python/pysolar/Manifest +++ b/dev-python/pysolar/Manifest @@ -1,16 +1,4 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - -DIST pysolar-0.4.2.tar.gz 1861071 RMD160 003f8e7f404ac4953a0d7440bd2984355b2d5e68 SHA1 a5105fe6f4f7fcb7051c3d6411b8cfeea146e9fd SHA256 b72d53ea8931b902ce2f3d3b7e63ed1765a9497f0d88bc9d47560d12fad8c5cf DIST pysolar-0.4.3.tar.gz 1862462 RMD160 13e478c5b6df110f1dc7dc15166b5873a8875c65 SHA1 3b8f88f61772ba4fdd06c2d3ec94d185fd11441e SHA256 894a00559ec9840caa5763df6f8ba7cf3a8ad4d3bed96cca96dbd4113898160e -EBUILD pysolar-0.4.2.ebuild 1286 RMD160 4ee22120e434162e395b084168f6795ffa7aaef3 SHA1 6b9776aa12108aefd043c788f0a0f06bead3a946 SHA256 aa88e338a59c362c1ebfffffc6245e120b551c256c9efb47fb4f53a7f646d726 EBUILD pysolar-0.4.3.ebuild 1319 RMD160 addfab4d19ec588b483dfe2004887a5537cd8eaa SHA1 714438520dfa301d688cbffdc3dd25bfc273d377 SHA256 916759386dcf15b1733662e7b04cadb902f54a2d1606cacae00aedc0754305fc -MISC ChangeLog 538 RMD160 51e7fad94ba440406abe375f3af1d8380977345a SHA1 8cc4a79f0e47543c45d3365b8863295ef6ac4575 SHA256 af90d27ccd5f970df235c0480ad2fad7eae79c55f1f633588ab548c7e937bed1 -MISC metadata.xml 517 RMD160 a39bb85d484de830c6d0e01ae456ef6b7ded98e3 SHA1 2e79881da57cf326c900691cc2fa885fbe8d18c5 SHA256 ff9fc747f21fc437d9604d459d02add9fdb026e60ec86fd37ecedf3fb87a0b2e ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk3AXYMACgkQgAnW8HDreRabbACgws7tccVmoKJyJzLZTki3c1f5 -t0sAn2EYOqor+W5mJG42ni7eeuYjGEft -=nhzu ------END PGP SIGNATURE----- +MISC ChangeLog 641 RMD160 155c1d7cff2832872f6d04786eea37c59b6e1893 SHA1 fac0d24a419a63087585101afbd01e0c81a59c17 SHA256 d9d83b7ec7c342fa6e23c616e950badd38c76b6c5d1438bc95de1222cc7784e4 +MISC metadata.xml 530 RMD160 92abf1da8528f3ccd085e07a16e41de3bc58830d SHA1 079550f656fc707348db44e866656319b7ea411a SHA256 10c04280260eb319667d9cb12156ef3613c5842cc9c734c0383be8db63db616b diff --git a/dev-python/pysolar/metadata.xml b/dev-python/pysolar/metadata.xml index 085fa9944..40069ec01 100644 --- a/dev-python/pysolar/metadata.xml +++ b/dev-python/pysolar/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> -Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth -by the sun. It includes code for extremely precise ephemeris calculations, and more. Pysolar can -calculate the location of the sun or the shading percentage as a function of time for a row of -2-axis tracked panels + Pysolar is a collection of Python libraries for simulating the + irradiation of any point on earth by the sun. It includes code for + extremely precise ephemeris calculations, and more. Pysolar can + calculate the location of the sun or the shading percentage as a + function of time for a row of 2-axis tracked panels. </longdescription> </pkgmetadata> diff --git a/dev-python/pysolar/pysolar-0.4.2.ebuild b/dev-python/pysolar/pysolar-0.4.2.ebuild deleted file mode 100644 index 4c335dc3d..000000000 --- a/dev-python/pysolar/pysolar-0.4.2.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=2 - -PYTHON_DEPEND="2:2.5" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.*" - -inherit distutils python - -DESCRIPTION="A collection of Python libraries for simulating the Sun's irradiation" -HOMEPAGE="http://pysolar.org/ http://pypi.python.org/pypi/Pysolar/" -SRC_URI="http://github.com/pingswept/${PN}/tarball/${PV} -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc" - -DEPEND="doc? ( dev-python/numpydoc )" -RDEPEND=" - dev-python/imaging - dev-python/matplotlib - dev-python/numpy - dev-python/pygtk:2 - dev-python/pytz - sci-libs/scipy" - -S="${WORKDIR}"/pingswept-${PN}-a110543 - -PYTHON_MODNAME="constants.py horizon.py julian.py \ - poly.py query_usno.py radiation.py shade.py \ - simulate.py solar.py util.py" - -src_prepare() { - sed \ - -e "s:'testsolar', ::" \ - -e "s:'shade_test', ::" \ - -i setup.py || die -} - -src_compile() { - distutils_src_compile - - if use doc; then - cd doc - PYTHONPATH=".." emake html || die - fi -} - -src_test() { - testing() { - PYTHONPATH="build-${PYTHON_ABI}/abi" "$(PYTHON)" testsolar.py - } - python_execute_function testing -} - -src_install() { - distutils_src_install - if use doc; then - dohtml -r doc/.build/html/* || die - fi -} diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass new file mode 100644 index 000000000..bbbe6e081 --- /dev/null +++ b/eclass/alternatives-2.eclass @@ -0,0 +1,157 @@ +# Copyright 2008, 2009 Bo Ørsted Andresen +# Copyright 2008, 2009 Mike Kelly +# Copyright 2009 David Leverton +# 2010: Adapted for Gentoo by Sebastien Fabbro, who does not like copyrights +# Distributed under the terms of the GNU General Public License v2 + +# If your package provides pkg_postinst or pkg_prerm phases, you need to be +# sure you explicitly run alternatives_pkg_{postinst,prerm} where appropriate. + +ALTERNATIVES_DIR="/etc/env.d/alternatives" + +DEPEND=">=app-admin/eselect-1.2.15-r1" +RDEPEND="${DEPEND} + !app-admin/eselect-blas + !app-admin/eselect-cblas + !app-admin/eselect-lapack" + +# alternatives_for alternative provider importance source target [ source target [...]] +alternatives_for() { + #echo alternatives_for "${@}" + + (( $# >= 5 )) && (( ($#-3)%2 == 0)) || die "${FUNCNAME} requires exactly 3+N*2 arguments where N>=1" + local x dupl alternative=${1} provider=${2} importance=${3} index unique src target ret=0 + shift 3 + + # make sure importance is a signed integer + if [[ -n ${importance} ]] && ! [[ ${importance} =~ ^[0-9]+(\.[0-9]+)*$ ]]; then + eerror "Invalid importance (${importance}) detected" + ((ret++)) + fi + + [[ -d "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}" ]] || dodir "${ALTERNATIVES_DIR}/${alternative}/${provider}" + + # keep track of provided alternatives for use in pkg_{postinst,prerm}. keep a mapping between importance and + # provided alternatives and make sure the former is set to only one value + if ! has "${alternative}:${provider}" "${ALTERNATIVES_PROVIDED[@]}"; then + index=${#ALTERNATIVES_PROVIDED[@]} + ALTERNATIVES_PROVIDED+=( "${alternative}:${provider}" ) + ALTERNATIVES_IMPORTANCE[index]=${importance} + [[ -n ${importance} ]] && echo "${importance}" > "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}/_importance" + else + for((index=0;index<${#ALTERNATIVES_PROVIDED[@]};index++)); do + if [[ ${alternative}:${provider} == ${ALTERNATIVES_PROVIDED[index]} ]]; then + if [[ -n ${ALTERNATIVES_IMPORTANCE[index]} ]]; then + if [[ -n ${importance} && ${ALTERNATIVES_IMPORTANCE[index]} != ${importance} ]]; then + eerror "Differing importance (${ALTERNATIVES_IMPORTANCE[index]} != ${importance}) detected" + ((ret++)) + fi + else + ALTERNATIVES_IMPORTANCE[index]=${importance} + [[ -n ${importance} ]] && echo "${importance}" > "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}/_importance" + fi + fi + done + fi + + while (( $# >= 2 )); do + src=${1//+(\/)/\/}; target=${2//+(\/)/\/} + if [[ ${src} != /* ]]; then + eerror "Source path must be absolute, but got ${src}" + ((ret++)) + + else + local reltarget= dir=${ALTERNATIVES_DIR}/${alternative}/${provider}${src%/*} + while [[ -n ${dir} ]]; do + reltarget+=../ + dir=${dir%/*} + done + + reltarget=${reltarget%/} + [[ ${target} == /* ]] || reltarget+=${src%/*}/ + reltarget+=${target} + dodir "${ALTERNATIVES_DIR}/${alternative}/${provider}${src%/*}" + dosym "${reltarget}" "${ALTERNATIVES_DIR}/${alternative}/${provider}${src}" + + # say ${ED}/sbin/init exists and links to /bin/systemd (which doesn't exist yet) + # the -e test will fail, so check for -L also + if [[ -e ${ED}${src} || -L ${ED}${src} ]]; then + local fulltarget=${target} + [[ ${fulltarget} != /* ]] && fulltarget=${src%/*}/${fulltarget} + if [[ -e ${ED}${fulltarget} || -L ${ED}${fulltarget} ]]; then + die "${src} defined as provider for ${fulltarget}, but both already exist in \${ED}" + else + mv "${ED}${src}" "${ED}${fulltarget}" || die + fi + fi + fi + shift 2 + done + + [[ ${ret} -eq 0 ]] || die "Errors detected for ${provider}, provided for ${alternative}" +} + +cleanup_old_alternatives_module() { + local alt=${1} old_module="${EROOT}/usr/share/eselect/modules/${alt}.eselect" + if [[ -f "${old_module}" && "$(source "${old_module}" &>/dev/null; echo "${ALTERNATIVE}")" == "${alt}" ]]; then + local version="$(source "${old_module}" &>/dev/null; echo "${VERSION}")" + if [[ "${version}" == "0.1" || "${version}" == "20080924" ]]; then + echo rm "${old_module}" + rm "${old_module}" || eerror "rm ${old_module} failed" + fi + fi +} + +alternatives-2_pkg_postinst() { + local a alt provider module_version="20090908" + for a in "${ALTERNATIVES_PROVIDED[@]}"; do + alt="${a%:*}" + provider="${a#*:}" + if [[ ! -f "${EROOT}/usr/share/eselect/modules/auto/${alt}.eselect" \ + || "$(source "${EROOT}/usr/share/eselect/modules/auto/${alt}.eselect" &>/dev/null; echo "${VERSION}")" \ + -ne "${module_version}" ]]; then + #einfo "Creating alternatives module for ${alt}" + if [[ ! -d ${EROOT}/usr/share/eselect/modules/auto ]]; then + install -d "${EROOT}"/usr/share/eselect/modules/auto || eerror "Could not create eselect modules dir" + fi + cat > "${EROOT}/usr/share/eselect/modules/auto/${alt}.eselect" <<-EOF + # This module was automatically generated by alternatives.eclass + DESCRIPTION="Alternatives for ${alt}" + VERSION="${module_version}" + MAINTAINER="eselect@gentoo.org" + ESELECT_MODULE_GROUP="Alternatives" + + ALTERNATIVE="${alt}" + + inherit alternatives + EOF + fi + + #echo eselect "${alt}" update "${provider}" + einfo "Creating ${provider} alternative module for ${alt}" + eselect "${alt}" update "${provider}" + + cleanup_old_alternatives_module ${alt} + done +} + +alternatives-2_pkg_prerm() { + local a alt provider p ignore + [[ -n ${REPLACED_BY_ID} ]] || ignore=" --ignore" + for a in "${ALTERNATIVES_PROVIDED[@]}"; do + alt="${a%:*}" + provider="${a#*:}" + #echo "Making sure ${alt} has a valid provider" + #echo eselect "${alt}" update${ignore} "${provider}" + eselect "${alt}" update${ignore} "${provider}" && continue + einfo "Removed ${provider} alternative module for ${alt}, current is $(eselect ${alt} show)" + if [[ $? -eq 2 ]]; then + einfo "Cleaning up unused alternatives module for ${alt}" + echo rm "${EROOT}/usr/share/eselect/modules/auto/${alt}.eselect" + rm "${EROOT}/usr/share/eselect/modules/auto/${alt}.eselect" || + eerror rm "${EROOT}/usr/share/eselect/modules/auto/${alt}.eselect" failed + fi + done +} + +EXPORT_FUNCTIONS pkg_postinst pkg_prerm diff --git a/eclass/intel-sdp.eclass b/eclass/intel-sdp.eclass index be74bd114..6759185b9 100644 --- a/eclass/intel-sdp.eclass +++ b/eclass/intel-sdp.eclass @@ -64,7 +64,7 @@ intel-sdp_pkg_setup() { elif use amd64; then arch=x86_64 INTEL_ARCH="intel64" - if use multilib; then + if has_multilib_profile; then arch="x86_64 ${INTEL_X86:-i486}" INTEL_ARCH="intel64 ia32" fi diff --git a/media-gfx/brlcad/.brlcad-7.20.2-r1.ebuild.swo b/media-gfx/brlcad/.brlcad-7.20.2-r1.ebuild.swo Binary files differdeleted file mode 100644 index 9ce9b1c1e..000000000 --- a/media-gfx/brlcad/.brlcad-7.20.2-r1.ebuild.swo +++ /dev/null diff --git a/media-gfx/brlcad/ChangeLog b/media-gfx/brlcad/ChangeLog index eaddf8044..95fa30042 100644 --- a/media-gfx/brlcad/ChangeLog +++ b/media-gfx/brlcad/ChangeLog @@ -4,6 +4,12 @@ *brlcad-7.20.2 (15 Jul 2011) + 09 Aug 2011; Dongxu Li <dongxuli2011@gmail.com> +brlcad-9999.ebuild brlcad-7.20.2-r1.ebuild: + No need to depend on cmake explicitly, added patch for libpng-1.5, added the subversion version brlcad-9999.ebuild + + 15 Jul 2011; Dongxu Li <dongxuli2011@gmail.com> brlcad-7.20.2-r1.ebuild: + Patching of CMakeLists.txt still needed. Since upstream already fixed this problem, the patch won't be necessary after the current release + 15 Jul 2011; Dongxu Li <dongxuli2011@gmail.com> brlcad-7.20.2-r1.ebuild: Added back >=virtual/jre-1.5 dependency diff --git a/media-gfx/brlcad/Manifest b/media-gfx/brlcad/Manifest index 3a16b8460..19308c586 100644 --- a/media-gfx/brlcad/Manifest +++ b/media-gfx/brlcad/Manifest @@ -1,6 +1,9 @@ AUX brlcad-7.20.2-cmake.patch 855 RMD160 a5cdfe4f00113631c677662a6b05d9008ec96959 SHA1 4944966b897e3d89f6815db5164c975f432d0a0c SHA256 98f121ca6b78207f583ed70952ffa29c82787fd1febbaa781cf37a33a316d1f2 +AUX brlcad-9999-cmake.patch 488 RMD160 51c1eaa27d2248f186746ad1b1b9c5ee32a9abbf SHA1 8f1e9ec4860bd9212892a185eafcfcd20137d328 SHA256 0131261e5ca51aeef5381e528feda1b5b4e24510c65f93861cb4d2ab1e4032b1 +AUX png_patch.diff 1171 RMD160 6faea89e2fcd65b5dc48e82a3cd343e4aba5b104 SHA1 509a912d0114599dcc600601d4eac04e614946b3 SHA256 066d0aec82e7e72d51d7dd3f5b12ce722e21e2b79382256e7e09aeb9a6a2a7e0 DIST brlcad-7.20.2.tar.gz 56219423 RMD160 b366d6956aa63f22ea14ed03f212e1a184eee429 SHA1 6d465398740a67572cfd9a8c3c6771e0b263d806 SHA256 879d21ff87808bf60956eec915b5bd6f1af1b4869145c239345f2a00267434ca -EBUILD brlcad-7.20.2-r1.ebuild 3508 RMD160 2061e936a2bc329f674c1573df6be1d86925bac4 SHA1 0256793266c0a7866e703c18b70faec689fd22da SHA256 63e7601c1d23b1c2ba66c5d963c7418badee4c0bec5cc567ba450e7d57fb1843 +EBUILD brlcad-7.20.2-r1.ebuild 3548 RMD160 0bebb71647cc17c38b1b6a9dae19bd840437ef69 SHA1 758b59511d903251a42c09f1986fb167e77c170c SHA256 adaf01174244ecf5cb6b39adc3f42a21d06e45cca9023b857b5435b8bb808002 EBUILD brlcad-7.20.2.ebuild 2584 RMD160 b0e5363f18e894c77fdf18e340f3f354a977d782 SHA1 cb54a0b829fa9a433b37a185119a3c2568e7c42c SHA256 44d8d0987fab07c5e6b482649eb776fff4055bec021d6dbf8a2e8d66a430aec4 -MISC ChangeLog 3659 RMD160 8eca13b3a7afcc35c327993d97a6ed2965ae48d4 SHA1 7b9ee2e165ef64e41b7bd818ec50b2782722fa94 SHA256 818d7c58f11e5e2e1f134965f2af89e10f5b74ee8dbf32124a2b11324c16cb0a +EBUILD brlcad-9999.ebuild 3525 RMD160 d751d025c898a4b2af235e9cf0f47a4320e2f560 SHA1 e77768b4a4d078bb387b96ed90ef2bb016dd7fc2 SHA256 cbbfe6ca0ff4384cb7377b3e823171c6e00e68f15e41926d9d56a65e9e68de02 +MISC ChangeLog 4090 RMD160 8f8bc2eace4ec11bfa413f6a17d2da6cd22ee10c SHA1 60bf3d6ffe3df28dd8245ab93d527b7c78d9c742 SHA256 80fdceba558b4c4ca193177a1ff161282733af28da5eada53febcb5606a11806 MISC metadata.xml 1379 RMD160 7407a87496226206896ad41f07cbf1b4900faf05 SHA1 6fb2b9de93b48435f93a968de325d1b483160a63 SHA256 0374773ad63ea0e195813d44eeca951b9b756a73ad1fe034499532aef7e6078d diff --git a/media-gfx/brlcad/brlcad-7.20.2-r1.ebuild b/media-gfx/brlcad/brlcad-7.20.2-r1.ebuild index 066edbcec..4a42be013 100644 --- a/media-gfx/brlcad/brlcad-7.20.2-r1.ebuild +++ b/media-gfx/brlcad/brlcad-7.20.2-r1.ebuild @@ -8,6 +8,7 @@ inherit cmake-utils eutils DESCRIPTION="Constructive solid geometry modeling system" HOMEPAGE="http://brlcad.org/" SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +# CMAKE_MIN_VERSION="2.8" LICENSE="LGPL-2 BSD" SLOT="0" @@ -31,7 +32,6 @@ RDEPEND="media-libs/libpng #java? ( >=virtual/jre-1.5 )" DEPEND="${RDEPEND} - >=dev-util/cmake-2.8 sys-devel/bison sys-devel/flex dev-tcltk/tktable @@ -45,6 +45,7 @@ BRLCAD_DIR="${EPREFIX}/usr/${PN}" src_prepare() { epatch "${FILESDIR}/${P}-cmake.patch" + epatch "${FILESDIR}/png_patch.diff" } src_configure() { @@ -63,13 +64,12 @@ src_configure() { -DBRLCAD_BUILD_LOCAL_TKTABLE=OFF -DBRLCAD_BUILD_LOCAL_PNG=OFF -DBRLCAD_BUILD_LOCAL_REGEX=OFF - -DBRLCAD_BUILD_LOCAL_ZLIB=OFF -DBRLCAD_BUILD_LOCAL_TERMLIB=OFF -DBRLCAD_BUILD_LOCAL_UTAHRLE=OFF -DBRLCAD_BUILD_LOCAL_SCL=OFF -DBRLCAD-ENABLE_RTSERVER=OFF -DBRLCAD-ENABLE_JOVE=OFF - + -DBRLCAD_BUILD_LOCAL_ZLIB=OFF -DBRLCAD_BUILD_LOCAL_IWIDGETS_FORCE_ON=ON -DBRLCAD_BUILD_LOCAL_TCL_FORCE_ON=ON -DBRLCAD_BUILD_LOCAL_TK_FORCE_ON=ON diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild new file mode 100644 index 000000000..76d25444d --- /dev/null +++ b/media-gfx/brlcad/brlcad-9999.ebuild @@ -0,0 +1,122 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/media-gfx/brlcad/brlcad-7.18.4.ebuild,v 1.1 2011/04/18 22:47:37 dilfridge Exp $ + +EAPI=4 +inherit cmake-utils eutils subversion + +DESCRIPTION="Constructive solid geometry modeling system" +HOMEPAGE="http://brlcad.org/" +ESVN_REPO_URI="https://brlcad.svn.sourceforge.net/svnroot/${PN}/${PN}/trunk" + +LICENSE="LGPL-2 BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="benchmarks debug doc examples opengl smp" + +RDEPEND="media-libs/libpng + sys-libs/zlib + >=sci-libs/tnt-3 + sci-libs/jama + =dev-tcltk/itcl-3.4* + =dev-tcltk/itk-3.4* + dev-tcltk/iwidgets + dev-tcltk/tkimg + dev-tcltk/tkpng + sys-libs/libtermcap-compat + media-libs/urt + x11-libs/libXt + x11-libs/libXi + " + #java? ( >=virtual/jre-1.5 )" + +DEPEND="${RDEPEND} + sys-devel/bison + sys-devel/flex + dev-tcltk/tktable + >=virtual/jre-1.5 + doc? ( + dev-libs/libxslt + app-doc/doxygen + )" + +BRLCAD_DIR="${EPREFIX}/usr/${PN}" + +src_prepare() { + epatch "${FILESDIR}/${P}-cmake.patch" +} + +src_configure() { + #waiting for upstream to fix itck/itk issues for cmake + #have to enable tcl/tk local build, otherwise cmake won't be able to link for + # -litcl -litk + local mycmakeargs=( + -DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}" + -DBRLCAD-ENABLE_STRICT=OFF + -DBRLCAD_BUILD_LOCAL_OPENNURBS=ON + -DBUILD_STATIC_LIBS=OFF + -DBRLCAD-ENABLE_X11=ON + -DBRLCAD_BUILD_LOCAL_INCRTCL=OFF + -DBRLCAD_BUILD_LOCAL_TKHTML=OFF + -DBRLCAD_BUILD_LOCAL_TKPNG=OFF + -DBRLCAD_BUILD_LOCAL_TKTABLE=OFF + -DBRLCAD_BUILD_LOCAL_PNG=OFF + -DBRLCAD_BUILD_LOCAL_REGEX=OFF + -DBRLCAD_BUILD_LOCAL_ZLIB=OFF + -DBRLCAD_BUILD_LOCAL_TERMLIB=OFF + -DBRLCAD_BUILD_LOCAL_UTAHRLE=OFF + -DBRLCAD_BUILD_LOCAL_SCL=OFF + -DBRLCAD-ENABLE_RTSERVER=OFF + -DBRLCAD-ENABLE_JOVE=OFF + + -DBRLCAD_BUILD_LOCAL_IWIDGETS_FORCE_ON=ON + -DBRLCAD_BUILD_LOCAL_TCL_FORCE_ON=ON + -DBRLCAD_BUILD_LOCAL_TK_FORCE_ON=ON + -DBRLCAD_BUILD_LOCAL_ITCL_FORCE_ON=ON + -DBRLCAD_BUILD_LOCAL_ITK_FORCE_ON=ON + + ) + + # use flag triggered options + if use debug; then + mycmakeargs += "-DCMAKE_BUILD_TYPE=Debug" + else + mycmakeargs += "-DCMAKE_BUILD_TYPE=Release" + fi + mycmakeargs+=( + $(cmake-utils_use amd64 BRLCAD-ENABLE_64BIT) + $(cmake-utils_use aqua BRLCAD-ENABLE_AQUA) + $(cmake-utils_use examples BRLCAD-INSTALL_EXAMPLE_GEOMETRY) + $(cmake-utils_use doc BRLCAD-BUILD_EXTRADOCS) + $(cmake-utils_use doc BRLCAD-BUILD_EXTRADOCS_PDF) + $(cmake-utils_use doc BRLCAD-BUILD_EXTRADOCS_MAN) + $(cmake-utils_use opengl BRLCAD-ENABLE_OPENGL) + $(cmake-utils_use smp BRLCAD-ENABLE_SMP) + $(cmake-utils_use debug BRLCAD-ENABLE_VERBOSE_PROGRESS) +# $(cmake-utils_use !debug BRLCAD-ENABLE_OPTIMIZED_BUILD) +# $(cmake-utils_use !debug ) +# $(cmake-utils_use debug BRLCAD-ENABLE_DEBUG_BUILD) +# $(cmake-utils_use debug BRLCAD-ENABLE_RUNTIME_DEBUG) +# $(cmake-utils_use debug BRLCAD-ENABLE_COMPILER_WARNINGS_LABEL) + ) + cmake-utils_src_configure +} + +src_test() { + cmake-utils_src_test + #emake check || die "emake check failed" + if use benchmarks; then + emake benchmark || die "emake benchmark failed" + fi +} + +src_install() { + cmake-utils_src_install + rm -f "${D}"usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING} + dodoc AUTHORS NEWS README HACKING TODO BUGS ChangeLog + echo "PATH=\"${BRLCAD_DIR}/bin\"" > 99brlcad + echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad + doenvd 99brlcad || die + newicon misc/macosx/Resources/ReadMe.rtfd/brlcad_logo_tiny.png brlcad.png + make_desktop_entry mged "BRL-CAD" brlcad "Graphics;Engineering" +} diff --git a/media-gfx/brlcad/files/brlcad-9999-cmake.patch b/media-gfx/brlcad/files/brlcad-9999-cmake.patch new file mode 100644 index 000000000..d85af6954 --- /dev/null +++ b/media-gfx/brlcad/files/brlcad-9999-cmake.patch @@ -0,0 +1,11 @@ +--- a/CMakeLists.txt 2011-08-09 16:41:03.073611709 -0400 ++++ b/CMakeLists.txt 2011-08-09 16:41:22.943844346 -0400 +@@ -1221,7 +1221,7 @@ + ENDFOREACH() + FOREACH(path_label ${PATH_LABELS}) + SET(CURRENT_LABEL ${${path_label}_LABEL}) +- STRING(LENGTH ${CURRENT_LABEL} CURRENT_LENGTH) ++ STRING(LENGTH "${CURRENT_LABEL}" CURRENT_LENGTH) + WHILE(${PATH_LABEL_LENGTH} GREATER ${CURRENT_LENGTH}) + SET(CURRENT_LABEL " ${CURRENT_LABEL}") + STRING(LENGTH "${CURRENT_LABEL}" CURRENT_LENGTH) diff --git a/media-gfx/brlcad/files/png_patch.diff b/media-gfx/brlcad/files/png_patch.diff new file mode 100644 index 000000000..bdae6ba53 --- /dev/null +++ b/media-gfx/brlcad/files/png_patch.diff @@ -0,0 +1,48 @@ +Index: src/other/libpng.dist +=================================================================== +--- src/other/libpng.dist (revision 45616) ++++ src/other/libpng.dist (revision 45617) +@@ -8,7 +8,6 @@ + configure.ac + contrib + example.c +-libpng-1.4.5.txt + libpng-config.in + libpng.3 + libpng.pc.in +Index: src/libged/png.c +=================================================================== +--- src/libged/png.c (revision 45616) ++++ src/libged/png.c (revision 45617) +@@ -30,6 +30,7 @@ + #include <string.h> + #include "bio.h" + ++#include "zlib.h" + #include "png.h" + #include "bu.h" + #include "vmath.h" +Index: src/fb/fb-png.c +=================================================================== +--- src/fb/fb-png.c (revision 45616) ++++ src/fb/fb-png.c (revision 45617) +@@ -38,6 +38,7 @@ + # include <unistd.h> + #endif + ++#include "zlib.h" + #include "png.h" + #include "bu.h" + #include "fb.h" +Index: src/util/pix-png.c +=================================================================== +--- src/util/pix-png.c (revision 45616) ++++ src/util/pix-png.c (revision 45617) +@@ -36,7 +36,6 @@ + #include "bio.h" + + #include "zlib.h" +-#include "pngconf.h" + #include "png.h" + + #include "bu.h" diff --git a/media-gfx/librecad/Manifest b/media-gfx/librecad/Manifest index 321af0699..7396f8178 100644 --- a/media-gfx/librecad/Manifest +++ b/media-gfx/librecad/Manifest @@ -1,5 +1,5 @@ EBUILD librecad-1.0.0_beta5.ebuild 1026 RMD160 6f3911c70fa4fb9d7c567c59461043703f6361a9 SHA1 ecf63cbc86357ad8d4aab725069c781c0aa4c5a8 SHA256 8bf33da124d924a17e2de727107ecc582efe75c4f09569d32e873effa360f2fa EBUILD librecad-1.0.0_rc1.ebuild 1022 RMD160 65a83ae087ec90c8737157cc3f94628e18a5f2b1 SHA1 65e9382cf7a3df13685a9c345f96c2f066d13344 SHA256 ebabd9d622e584ac3ce9921469cb233c4d2e222d9ef75db3b5c299f6153701da -EBUILD librecad-9999.ebuild 995 RMD160 7e39a040f956931f9d3140c0bd21d13f8c71a8cf SHA1 adcb62ec9df2db7086bbec52f89b0f2d2482b6a0 SHA256 0162d4b7ca22086c0e9f9e8d3838f7cbafd2fac7e4cbc4e0054e61629b26d422 +EBUILD librecad-9999.ebuild 991 RMD160 823baf6530595b9f337ea45a32a1dd6c171e3a58 SHA1 d1fb05ede6aa78c11721e6150ecde68ff4837a84 SHA256 418da24f661bfe51a62e5ebe4b46420b58d6eebfcdf388527a34ab7be953c071 MISC ChangeLog 738 RMD160 8da5b642c518fbe646a1c47aff41d7d9dc463e62 SHA1 588c5f947c13ce5d85745775a97d27cb1a602f4e SHA256 bac2883e23376c1fe285f0bd031be01619000e0d5fccd32b1456727a7371f5c2 MISC metadata.xml 450 RMD160 62a6501cecfe47078279b48be9b1c658d40e59f9 SHA1 c4ea83204f0d636b89b362f43aa2f5f487b9d9c7 SHA256 891d496161866e9f329036a1a953bd667d7be70de7cb1da41eadbb4be21c7df8 diff --git a/media-gfx/librecad/librecad-9999.ebuild b/media-gfx/librecad/librecad-9999.ebuild index 8c3d065d1..b50de9b51 100644 --- a/media-gfx/librecad/librecad-9999.ebuild +++ b/media-gfx/librecad/librecad-9999.ebuild @@ -12,7 +12,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="debug doc" -EGIT_REPO_URI="https://github.com/LibreCAD/LibreCAD.git" +EGIT_REPO_URI="https://github.com/dxli/LibreCAD.git" RDEPEND="x11-libs/qt-gui[qt3support]" DEPEND="${RDEPEND} diff --git a/media-libs/OpenMOIV/Manifest b/media-libs/OpenMOIV/Manifest new file mode 100644 index 000000000..379dc3d4c --- /dev/null +++ b/media-libs/OpenMOIV/Manifest @@ -0,0 +1,23 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +DIST OpenMOIV.src.1.0.3a.tar.bz2 327168 RMD160 a5aa797458f87cd4dc0846c565e358577f094c31 SHA1 7af9fad07d57423c5c01ded9741d28bd5b92c337 SHA256 91c6b24aceb72d5884b0291ae28fca358a78e1590ccd0554ef7e7f8a3ef6dbe8 +EBUILD OpenMOIV-1.0.3a.ebuild 983 RMD160 b88c44ca2d039b1bf631c171f437a105c0fc007f SHA1 719c28e6444372364426222a2cabdb086a0d4292 SHA256 87340ea0545f178c22373ac16e13ea022046518fd2e755843ca7d6cadb541951 +MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iQIcBAEBCAAGBQJOOU7iAAoJEOf+E+/4L5Lma30P/0XPw7870fwAHmIeEOS4uwPO ++ipqD5l6QpeVh5cnBiXyDfimABxWO7/5/0gIn+MSSiqxgYM7B/uBw2mkCRGsJEC+ +tuMVJtt0OgM7LlKW55kl8J6useqI3K4Aiq1heA6RQhP8EaGr/ADtuIVRCIopYFjL +h8zNeK4/KcHLTxT9Gx4ExSvEko/8HjcxDaHGS5LUS5tRjhXyVxfDljXJh6HMgj85 +Wj//sQizCiDWd5gRNjaxlPXPpG9LfDonz+iDkcFqz4Q5nbRLXsF1X3v8pxL52x3i +wMSiIe1VTnQxQ8V4YWczGrTlUGjmIeA6QpyQMJhjd3R4bnIgr8yN110n9AHnueBs +hWucWu8ic8dIndHJpHVcutlrTLjc0XNdzj+aketW72+0kUoeHStd9+wXtyMMX+ac +4XQaeGA6SoWuIcVZEkZsL+4yEP9Klim4CaY2RHQG3Ww51vCLcszYKSCaBq2ilWk7 +ADwWHe0mPdQQBnB3rUDP4JvqLHcmKLcyR6Rt1GTwqzlCIZy/cv0uLW+bQemgayYe +Xn2AdHhZfXOd5XpcHFedLr0Hn/MVd9pjmy/lnuEXEsK2zG+UAWjK4tSuMUUYqhN9 +4e8ZD+Ba22xEy0jz2mW92A8C3X4j9nM5VCoE5e1ikZVvkcDfzwdHibSx3ntTMlHz +Y6LI8h60VlYqTCon6POj +=tc65 +-----END PGP SIGNATURE----- diff --git a/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild b/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild new file mode 100644 index 000000000..5c150c1b3 --- /dev/null +++ b/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="4" + +inherit cmake-utils + +DESCRIPTION="Object-oriented 3D toolkit that facilitates the rendering and interaction of chemical systems." +HOMEPAGE="http://www.tecn.upf.es/openMOIV/" +SRC_URI="http://www.tecn.upf.es/openMOIV/download/1.0.3/${PN}.src.${PV}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~x86 ~amd64" + +IUSE="" + +RDEPEND=" + media-libs/coin + " +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${PN}.src.${PV/a//}" + +src_prepare() { + sed -e 's:$ENV{OIV_DIR}/include:/usr/include/coin:g' \ + -i CMakeLists.txt || die +} + +src_configure() { + mycmakeargs="${mycmakeargs} -Dshared:int=1 -Dcoin:int=1 -Dsys_fonts:int=1" + cmake-utils_src_configure +} + +src_install() { + insinto "/usr/$(get_libdir)" + doins "${CMAKE_BUILD_DIR}/libChemKit2.so" || die "doins for libChemKit2 failed" + + insinto "/usr/include" + doins -r "${S}/include/ChemKit2" || die "include install failed" +} diff --git a/sys-devel/ucpp/metadata.xml b/media-libs/OpenMOIV/metadata.xml index efb490d78..efb490d78 100644 --- a/sys-devel/ucpp/metadata.xml +++ b/media-libs/OpenMOIV/metadata.xml diff --git a/profiles/categories b/profiles/categories index 964a77a1a..e1fb02460 100644 --- a/profiles/categories +++ b/profiles/categories @@ -1,3 +1,5 @@ +app-admin +app-benchmarks app-doc app-portage app-text @@ -30,6 +32,7 @@ sci-physics sci-visualization sys-cluster sys-devel -sys-infiniband +sys-fs +virtual www-apps x11-libs diff --git a/profiles/package.mask b/profiles/package.mask index 386ab9a92..75cd9d3fa 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -30,6 +30,18 @@ #--- END OF EXAMPLES --- +# Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011) +# Mask live version of librecad +>=media-gfx/librecad-9999 + +# Dongxu Li <dongxuli2011@gmail.com> (10 Aug 2011) +# Mask live version of brlcad +>=media-gfx/brlcad-9999 + +# Alexey Shvetsov <alexxy@gentoo.org> (30 Jul 2011) +# Mask live version of path64 +~dev-lang/path64-9999 + # Justin Lecher <jlec@gentoo.org> (24 Jun 2011) # fftw dep is masked sci-libs/pfft diff --git a/profiles/use.local.desc b/profiles/use.local.desc index ea6b8847c..597e7df73 100644 --- a/profiles/use.local.desc +++ b/profiles/use.local.desc @@ -1,74 +1,160 @@ -# Copyright 1999-2006 Gentoo Foundation. -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ +# This file is deprecated as per GLEP 56 in favor of metadata.xml. Please add +# your descriptions to your package's metadata.xml ONLY. +# * generated automatically using egencache * -# This file contains descriptions of local USE flags, and the ebuilds which -# contain them. -# Keep it sorted. - -# We keep here only the new USE flags introduced by packages in the overlay. -# Ultimately, they will be merged into the main tree. - -sci-biology/tgi-tools:pvm - Use sys-cluster/pvm (Parallel Virtual Machine) and build the pvmsx utility -sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats (sci-chemistry/gromacs) -sci-geosciences/libtcd:non-commercial - Install tide constituent database that is free for non-commercial use only +dev-java/hdf-java:hdf - Add support for the Hierarchical Data Format v.4 (sci-libs/hdf) +dev-lang/icc:eclipse - Install the dev-util/eclipse-sdk plugins +dev-lang/idb:eclipse - Install the dev-util/eclipse-sdk plugins +dev-lang/path64:debugger - Build PathDB +dev-lang/path64:native - Use EKOPath/Path64 for bootstraping +dev-libs/intel-common:compiler - Install the libraries needed for the icc and ifort compilers +dev-ml/mlgmpidl:mpfr - add support for mpfr, the library for multiple-precision floating-point computations with exact rounding +dev-python/cvxopt:glpk - Use GNU Linear Programming Kit +dev-python/ffnet:matplotlib - Use matplotlib for drawing +media-gfx/brlcad:benchmarks - Run benchmarks during test phase (need test option enabled) +net-misc/dhcp:client - Install the dhclient program +net-misc/dhcp:infiniband - Enable ipoib support +net-misc/dhcp:server - Install the dhcpd and dhcrelay programs +sci-astronomy/psfex:plplot - Build with sci-libs/plplot to allow diagnostic plots during processing +sci-biology/estscan:intel - Use intel compiler +sci-chemistry/avogadro:glsl - Enable glsl features via GLEW. +sci-chemistry/gromacs:double-precision - More precise calculations at the expense of speed +sci-chemistry/gromacs:fkernels - Enable building of Fortran Kernels for platforms that dont have assembly loops +sci-chemistry/gromacs:single-precision - Single precision version of gromacs (default) +sci-chemistry/jmol:client-only - Install the viewer only, no applet files for httpd +sci-chemistry/pymol:apbs - Pymol supprt for sci-chemistry/apbs +sci-chemistry/pymol:numpy - Enable numpy support for Pymol +sci-chemistry/pymol:vmd - Builds molfile plugin support +sci-chemistry/pymol:web - Install Pymodule needed for web app support +sci-chemistry/rosetta:boinc - compile rosetta as a rosetta@home client +sci-chemistry/rosetta:boost - compile rosetta with boost supported code +sci-chemistry/votca-csg:boost - Compile against external boost headers from dev-libs/boost +sci-chemistry/votca-csg:extras - Pull in extra applications from dev-libs/boost +sci-chemistry/votca-csg:gromacs - Add support for gromacs file formats through sci-chemistry/gromacs +sci-electronics/player:boost - Automatically generated description for boost +sci-electronics/player:festival - Automatically generated description for festival +sci-electronics/player:openssl - Automatically generated description for openssl +sci-electronics/player:sphinx2 - Automatically generated description for sphinx2 +sci-geosciences/libtcd:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only. +sci-geosciences/qgis:grass - Add support for sci-geosciences/grass +sci-geosciences/xtide:non-commercial - Allows the use of a tide constituent database that is available for non-commercial use only. +sci-libs/atlas:xblas - Build LAPACK with extra precision (needs sci-libs/xblas) +sci-libs/bigdft:cuda - Add cuda support sci-libs/calculix-ccx:arpack - Add sparse eigen value support via sci-libs/arpack -sci-libs/factory:singular - Add support for sci-mathematics/Singular +sci-libs/factory:singular - Enable support for sci-mathematics/singular +sci-libs/fox:dom - Automatically generated description for dom +sci-libs/fox:fast - Automatically generated description for fast +sci-libs/fox:sax - Automatically generated description for sax +sci-libs/fox:wcml - Automatically generated description for wcml +sci-libs/fox:wxml - Automatically generated description for wxml sci-libs/gmsh:cgns - Enables cgns output support sci-libs/gmsh:chaco - Enables chaco partitioner support +sci-libs/gmsh:med - Enables med support sci-libs/gmsh:metis - Enables metis support +sci-libs/gmsh:netgen - Enable 3D Frontal triangulation using netgen lib sci-libs/gmsh:opencascade - Enable OpenCASCADE support -sci-libs/libfac:singular - Add support for sci-mathematics/Singular +sci-libs/gmsh:petsc - Enable sci-mathematics/petsc support +sci-libs/gmsh:taucs - Enable sci-libs/taucs support +sci-libs/gmsh:tetgen - Enable 3D delauny triangulation using tetgen lib +sci-libs/libcmatrix:atlas - Use of atlas blas implementation +sci-libs/libfac:singular - Automatically generated description for singular +sci-libs/lwpr:octave - Add sci-mathematics/octave support +sci-libs/oasa:cairo - Add support for Cairo graphics library using dev-python/pycairo +sci-libs/openblas:dynamic - Build dynamic architecture detection at run time (for multi targets) +sci-libs/openblas:incblas - Build the CBLAS interface +sci-libs/openblas:int64 - Build the 64 bits integer library +sci-libs/openmm:cuda - Build Cuda lib +sci-libs/openmm:opencl - Build OpenCL lib +sci-libs/pagmo:kepler - Automatically generated description for kepler +sci-libs/pagmo:nlopt - Automatically generated description for nlopt sci-libs/votca-tools:boost - Compile against external boost headers (dev-libs/boost) -sci-mathematics/gap:xtom - extra tables of marks +sci-libs/xdrfile:dmalloc - Enable use of Debug Malloc +sci-mathematics/Macaulay2:optimization - Accept upstream's choices for -O option, i.e. -O3 almost everywhere. +sci-mathematics/algae:intel - Use icc as c compiler +sci-mathematics/apron:ppl - Enable optional interface to the Parma Polyhedra Library +sci-mathematics/dolfin:cgal - Adds support for geometric algorithms with sci-mathematics/cgal +sci-mathematics/dolfin:cholmod - Adds support for sparse Cholesky factorization with sci-libs/cholmod +sci-mathematics/dolfin:parmetis - Adds support for parallel graph partitioning with sci-libs/parmetis +sci-mathematics/dolfin:scotch - Adds support for graph partitioning with sci-libs/scotch +sci-mathematics/dolfin:umfpack - Adds support for sparse solving with sci-libs/umfpack +sci-mathematics/frama-c:apron - ?apron? +sci-mathematics/frama-c:gtk - ?gtk? +sci-mathematics/frama-c:why - ?why? +sci-mathematics/gambit:X - Enable gui support using wxWidgets. +sci-mathematics/gap:xtom - Automatically generated description for xtom +sci-mathematics/giac:fltk - ?fltk? sci-mathematics/netgen:opencascade - Enable OpenCASCADE support -sci-misc/opencascade:draw-harness - Enable building of draw-harness -sci-misc/opencascade:stlport - Build OpenCASCADE with STLPort -sci-misc/opencascade:wok - Enable building of WOK -sci-misc/opennlp-tools:models - Install prebuild ME models (requires a ton of disk space) -sci-misc/salome-component:openpbs - Enables openpbs support -sci-misc/salome-gui:corba - Enables corba support -sci-misc/salome-gui:glviewer - make glviewer module -sci-misc/salome-gui:occviewer - make occviewer module -sci-misc/salome-gui:plot2dviewer - make plot2dviewer module -sci-misc/salome-gui:pyconsole - make python console module -sci-misc/salome-gui:salomeobject - make salomeobject module -sci-misc/salome-gui:supervgraphviewer - make supervgraphviewer module -sci-misc/salome-gui:vtkviewer - make vtkviewer module -sci-misc/salome-kernel:openpbs - Enables openpbs support -sci-misc/salome-med:openpbs - Enables openpbs support -sci-visualization/nodemon:pbs - Adds support for PBS (Portable Batch System) queries -sys-cluster/openib-drivers:cxgb3 - make CXGB3 module -sys-cluster/openib-drivers:ehca - make EHCA module -sys-cluster/openib-drivers:hpage-patch - apply huge pages patch -sys-cluster/openib-drivers:ipath - make IPATH module -sys-cluster/openib-drivers:iser - make ISER module -sys-cluster/openib-drivers:madeye - make MADEYE module -sys-cluster/openib-drivers:memtrack - enable momory tracking -sys-cluster/openib-drivers:mlx4 - make MLX4 module -sys-cluster/openib-drivers:rds - make RDS module -sys-cluster/openib-drivers:srp - make SRP module -sys-cluster/openib-drivers:vnic - make VNIC module -sys-cluster/openib-files:ehca - load EHCA module -sys-cluster/openib-files:ipath - load IPATH module -sys-cluster/openib-files:iser - load ISER module -sys-cluster/openib-files:mlx4 - load MLX4 module -sys-cluster/openib-files:rds - load RDS module -sys-cluster/openib-files:srp - load SRP module -sys-cluster/openib-files:vnic - load VNIC module -sys-cluster/openib-mvapich2:large-cluster - build _LARGE_CLUSTER configuration -sys-cluster/openib-mvapich2:medium-cluster - build _MEDIUM_CLUSTER configuration -sys-cluster/openib-mvapich2:rdma - use rdmacm -sys-cluster/openib-mvapich2:romio - enable ROMIO support -sys-cluster/openib-userspace:cxgb3 - include libcxgb3 package -sys-cluster/openib-userspace:dapl - add DAPL (Direct Access Provider Library) support -sys-cluster/openib-userspace:ehca - include libehca package -sys-cluster/openib-userspace:ipath - add PathScale HCA support -sys-cluster/openib-userspace:mstflint - include mstflint package -sys-cluster/openib-userspace:opensm - add OpenSM Subnet Management support. -sys-cluster/openib-userspace:qlvnictools - include qlvnictools package -sys-cluster/openib-userspace:srptools - include srptools package -sys-cluster/openib-userspace:tvflash - include tvflash package -sys-cluster/openib:dapl - add DAPL (Direct Access Provider Library) support. -sys-cluster/openib:ipath - add PathScale HCA support. -sys-cluster/openib:opensm - add OpenSM Subnet Management support. +sci-mathematics/petsc:complex-scalars - Make scalars complex +sci-mathematics/petsc:hypre - Use HYPRE (sci-mathematics/hypre) for preconditioning +sci-mathematics/petsc:metis - Use METIS (sci-libs/parmetis) for partitioning +sci-mathematics/polybori:sage - Replace the standard python interface by sage's python interface for easy integration in sage. +sci-mathematics/scilab:gui - Build the Java base graphical interface +sci-mathematics/scilab:matio - Enable support for MATLAB file through sci-libs/matio +sci-mathematics/scilab:umfpack - Adds support for sparse solving with sci-libs/umfpack +sci-mathematics/scilab:xcos - Enable building hybrid dynamic systems modeler and simulator Xcos +sci-mathematics/why:apron - ?apron? +sci-mathematics/why:coq - ?coq? +sci-mathematics/why:gappa - ?gappa? +sci-mathematics/why:gtk - ?gtk? +sci-mathematics/why:jessie - ?jessie? +sci-mathematics/why:pff - ?pff? +sci-misc/hfst:openfst - Add optional support for openfst backend library (sci-misc/openfst) +sci-misc/hfst:sfst - Add optional support for sfst backend library (sci-misc/sfst) +sci-misc/nco:ncap2 - Build next generation netcdf arithmetic processor (needs dev-java/antlr) +sci-misc/nco:udunits - Add sci-libs/udunits files support +sci-misc/opennlp-tools:models - Automatically generated description for models +sci-misc/salome-kernel:numpy - Enable support for dev-python/numpy +sci-misc/salome-med:metis - Add support for metis +sci-misc/salome-med:scotch - Add support for scotch +sci-physics/abinit:cuda - Enable support for nVidia CUDA +sci-physics/abinit:fox - Enable support for FoX Fortran XML library +sci-physics/abinit:vdwxc - Activate van der Waals exchange-correlation +sci-physics/atompaw:libxc - Use libxc for something +sci-physics/elk:libxc - Use sci-libs/libxc library of exchange-correlation functionals by ETSF. +sci-physics/espresso:examples - Installs the examples +sci-physics/espresso:packages - Installs extra subpackages +sci-physics/fastjet:allcxxplugins - Build all C++ plugins. +sci-physics/fastjet:allplugins - Build all standard plugins. +sci-physics/fastjet:cgal - Use sci-mathematics/cgal instead of bundled algorithms. +sci-physics/root:clarens - Buld the Clarens and PEAC plug-ins, to use in a GRID enabled analysis. +sci-physics/root:fits - Support for images and data from FITS files with sci-libs/cfitsio +sci-physics/root:llvm - Build the new cling interactive interpreter based on sys-devel/llvm +sci-physics/root:math - Build all math related libraries plugins, needs sci-libs/gsl +sci-physics/root:pythia6 - Builds the interface to Pythia-6 (sci-physics/pythia) high energy physics generation events library +sci-physics/root:pythia8 - Builds the interface to Pythia-8 (sci-physics/pythia) high energy physics generation events library +sci-physics/root:reflex - Builds the reflection database for the C++ interpretor +sci-physics/root:xrootd - Build the xrootd low latency file server +sci-visualization/gnuplot:gd - Add support for media-libs/gd. Needed for GIF, JPEG, and PNG image output. +sci-visualization/gnuplot:qt4 - Build Qt4 terminal +sci-visualization/gnuplot:thin-splines - Enable thin plate splines +sci-visualization/nodemon:pbs - Enable support for the Portable Batch System. +sci-visualization/paraview:adaptive - Enable the adaptive paraview application +sci-visualization/paraview:cg - Add support for nvidia's cg shaders +sci-visualization/paraview:coprocessing - Enable the coprocessing infrastructure which is mainly useful in the context of clusters +sci-visualization/paraview:gui - Build paraview's gui not just the server +sci-visualization/paraview:mysql - Build support for MySQL data item in the XDMF format +sci-visualization/paraview:nvcontrol - Add NVCONTROL support for OpenGL options +sci-visualization/paraview:plugins - Build and install additional plugins +sci-visualization/paraview:streaming - Enable streaming paraview application +sci-visualization/paraview:webkit - Built support for qt-webkit in vtk +sci-visualization/v_sim:abinit - Add support for ABINIT file formats sci-physics/abinit +sci-visualization/v_sim:cube - Add support plug-in support for Cube files (densities and structures) +sci-visualization/v_sim:openbabel - Add support for ABINIT file formats sci-chemistry/openbabel +sci-visualization/v_sim:xsf - plug-in support for files that follow the XCrysDen format for structural positions and densities +sys-cluster/condor:classads - Enable the Condor's classified advertisement language +sys-cluster/condor:drmaa - Enable the Distributed Resource Management Application API +sys-cluster/condor:gcb - Enable condor to communicate over firewall/NAT +sys-cluster/condor:kbdd - Enable the Condor Keyboard Daemon to monitor logged in X users for activity +sys-cluster/mpich2:mpi-threads - Enable MPI_THREAD_MULTIPLE +sys-cluster/mpich2:romio - Build the ROMIO MPI-IO component +sys-cluster/mvapich2:large-cluster - Automatically generated description for large-cluster +sys-cluster/mvapich2:medium-cluster - Automatically generated description for medium-cluster +sys-cluster/mvapich2:romio - Automatically generated description for romio +sys-cluster/openmpi:heterogeneous - Enable features required for heterogeneous platform support +sys-cluster/openmpi:infiniband - Enable infiniband support +sys-cluster/openmpi:mpi-threads - Enable MPI_THREAD_MULTIPLE +sys-cluster/openmpi:pbs - Add support for the Portable Batch System (PBS) +sys-cluster/openmpi:romio - Build the ROMIO MPI-IO component +sys-cluster/openmpi:vt - Enable bundled VampirTrace support +sys-fs/ocfs2-tools:external - Enable external locking +virtual/mpi:romio - Enable romio, a high-performance portable MPI-IO diff --git a/sci-astronomy/casacore/ChangeLog b/sci-astronomy/casacore/ChangeLog index b66cfa96f..6ee2a4362 100644 --- a/sci-astronomy/casacore/ChangeLog +++ b/sci-astronomy/casacore/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> casacore-1.2.20110516.ebuild: Sort inherit and/or USE diff --git a/sci-astronomy/casacore/Manifest b/sci-astronomy/casacore/Manifest index cfca214ff..389f26104 100644 --- a/sci-astronomy/casacore/Manifest +++ b/sci-astronomy/casacore/Manifest @@ -1,17 +1,7 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - AUX 1.2.20110516-headers.patch 936 RMD160 0775642a72727df99130b41c484d69f034410992 SHA1 7ede5cb0f92cc5cf6ed9ce1d1beda191ad7d5c4e SHA256 34769b047fabff24e6da4069d040c6f5f44e393170831925c14d5391394d9444 AUX 1.2.20110516-implicits.patch 6423 RMD160 01569cd7ec3b5f4cb6498722945fb1a9eccf87a2 SHA1 512e292f7a9ea90ec87950a9a5c70e94cf91a020 SHA256 7f537b6a7404d185580b3ad12676f87a718f9e92ffab24229888959f323879f4 AUX 1.2.20110516-libdir.patch 8284 RMD160 dcecff84020fff3f7fb91386a3c338b5fda26c44 SHA1 1fdc9e7f8087918d6511d1ccdf717c1e078f1be7 SHA256 112112db01eca5657a08a492b923f96c183d6e77aa9d6ca1d2402fd7aedb72a2 DIST casacore-1.2.20110516.tar.bz2 4649168 RMD160 3d0f7df94b88b93a3cd36b5f76e01538f37b0877 SHA1 57e9b1b19a61c846d7ceeeeb575ff92998b011fc SHA256 d47a113038bf26a4431bbbeb4821b0e245a452fc1d63ffe4d9df2af0d3155ca7 EBUILD casacore-1.2.20110516.ebuild 1099 RMD160 16c1a52947aef05bb0b9e659b1186de0b4853bdc SHA1 d13dee016b957873fc9697890714f326a6890895 SHA256 304fd4e2bf4bd89aaa822a4fc416a5decc62dbe90620560b23aaccf17d3865dc -MISC ChangeLog 227 RMD160 0d357dccfeb0a6901a4ccc9c76b4c2504a6f9778 SHA1 7d6e4e2958d8c32529cf17799d0e3969f2af9de0 SHA256 bc19d04dfc4d26a88d22b044b6ef22dffa673a176740292d834020bbf7af336e -MISC metadata.xml 391 RMD160 2b9d91edfd432ddf16694c417d25e89eaa13da42 SHA1 c6300dc3bf52bdd055804ad2f2c2480cc2304dcb SHA256 58c9dd33f794ccc2a1243b05da6f787660e1d844ba29c62f264b780793ab01b8 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4EgYUACgkQgAnW8HDreRZWgQCdH+9ScWjLhwnS2K4iuHeSZQ94 -zVYAn2Saqxtf69UPwG1llHMrkeg2ND2t -=b+gh ------END PGP SIGNATURE----- +MISC ChangeLog 330 RMD160 3a044de690e5e20452bceab02e84bb6b2f3db4e2 SHA1 1ca58a798550d36c032c85c2997bbe2df2cd8bde SHA256 e2e4c73ad04adc66801639828e416e770d231480fd1286639720c13e7f53f6b0 +MISC metadata.xml 401 RMD160 efd1b8a1e74e6d9dc79c3cb13abee03ccef970d9 SHA1 4a0da15c2ff7b7e56dbe0a287eda71a8f0ddc16d SHA256 a6ea9973fb3220a7184017947301549159c774f66dd31bde902c52969aa8a985 diff --git a/sci-astronomy/casacore/metadata.xml b/sci-astronomy/casacore/metadata.xml index e83314833..0aaf75cda 100644 --- a/sci-astronomy/casacore/metadata.xml +++ b/sci-astronomy/casacore/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> A set of libraries for the the Common Astronomy Software Applications for radioastronomy. This project contains C++ libraries diff --git a/sci-astronomy/eye/ChangeLog b/sci-astronomy/eye/ChangeLog index 205be6502..7660b4938 100644 --- a/sci-astronomy/eye/ChangeLog +++ b/sci-astronomy/eye/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> eye-1.4.1.ebuild: Sort inherit and/or USE diff --git a/sci-astronomy/eye/Manifest b/sci-astronomy/eye/Manifest index 7f6594d04..ae90521d5 100644 --- a/sci-astronomy/eye/Manifest +++ b/sci-astronomy/eye/Manifest @@ -1,15 +1,5 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - AUX eye-1.4.1-configure.patch 1521 RMD160 4e21ded936e19e7745a815b02d5121a5de7e791d SHA1 b0a81827e9f052ccf91ac93571ef2ce2872a93c8 SHA256 426d54714b01cf7616e31401e6f36f93642a28e50f13bbb30718d5d949ae4e0b DIST eye-1.4.1.tar.gz 744173 RMD160 886d85638f099276d393dd14c841efb41c06d50a SHA1 73815581cb93c6c579f4a8c8de88f274890439e9 SHA256 f3b480be936ea8143d9f469d2901b227092ec8e7692fd2578b8ecdbcd8875824 EBUILD eye-1.4.1.ebuild 808 RMD160 e82521ff4555390253da4101a4f6611d6b58ce87 SHA1 e6847c2dd4f0b9d3f30413413036d7dbe1114bb5 SHA256 077abf77b9498f9523663c2a88ea87b5ff54fb4f3dd9bb451a18ac1e368d0623 -MISC ChangeLog 379 RMD160 1f5edf69d0645a9e4e313386c8700cedd8b6ed36 SHA1 05d2519b348918e5adb5b303fe1d7ce227c6f57c SHA256 85420060f74136642827d24c07b6ee0c30203bd1000a3feb3004229f2e9ef8ad -MISC metadata.xml 655 RMD160 fcec85388054934d37c4188bd508c00e00c281d2 SHA1 e51a4415f87217fbd8ade88e15fa2c10f1de83a2 SHA256 a4dca7403f21df6c4862cfd17549594c627b82633cb5cea7e808834f6c08959e ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4EglcACgkQgAnW8HDreRZx1QCgjHsaSmcpZQMsysuvjSEXlF/a -nycAoJyW/sXiWmudK29m4fBrTVeWTBtg -=Ry2X ------END PGP SIGNATURE----- +MISC ChangeLog 482 RMD160 c1a12d6f06746c5e0318de45f572257ee8259333 SHA1 e982b8ae27380d8bceed368f721a772ba8e6d327 SHA256 48cee6377e6845b5e343b922cb947f9ef4e7be67deb58d9b1f24c89885fac34a +MISC metadata.xml 665 RMD160 1f21fdf621c2cdc340b59494c816fa72c8083c77 SHA1 6ac594a48e784353cd1e414dfaa25bba50287dec SHA256 8c27e75a9236e5d15aefa6b535071159795f33e1aba8a3434a03c956559e18ef diff --git a/sci-astronomy/eye/metadata.xml b/sci-astronomy/eye/metadata.xml index cec9e15a3..9c2032f73 100644 --- a/sci-astronomy/eye/metadata.xml +++ b/sci-astronomy/eye/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> In EyE (Enhance Your Extraction) an artificial neural network connected to pixels of a moving window (retina) is trained to diff --git a/sci-astronomy/missfits/ChangeLog b/sci-astronomy/missfits/ChangeLog index 8a7e0eb1c..255e574d2 100644 --- a/sci-astronomy/missfits/ChangeLog +++ b/sci-astronomy/missfits/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> missfits-2.4.0.ebuild, metadata.xml: Cleaned ebuild, unused local USE-description: 'plplot' diff --git a/sci-astronomy/missfits/Manifest b/sci-astronomy/missfits/Manifest index 57320f9f5..bf0b00f6d 100644 --- a/sci-astronomy/missfits/Manifest +++ b/sci-astronomy/missfits/Manifest @@ -1,15 +1,5 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 - AUX missfits-2.4.0-configure.patch 3223 RMD160 7a3da312bf067a655202624cc1e156666b25dfd5 SHA1 a2652ebb1ad4e799308fbebadd47a70765a55d94 SHA256 57d8c51435573043c35b532e779f8f67eee54d8f17e63cb9fd3b892d7153fa35 DIST missfits-2.4.0.tar.gz 381606 RMD160 0cc4e7aa2d27607c5137e424581dc173ab692bcb SHA1 f2ff6fa889bcab66fffa3210a7d179b5f1d0b641 SHA256 40cd9de9d539ac95d34c108afa0ade4b26475adf4772a95ee42b0f9ab6edaf21 EBUILD missfits-2.4.0.ebuild 686 RMD160 479a50099efd2546a939186d2516b4baabf0afaf SHA1 71eb8d465aef1a4c279a4bf9f14a3a4cfb9d8126 SHA256 30f8d0024e63818852e0ae100d23909f341b5a90da23a36872cfd0e256646ac6 -MISC ChangeLog 451 RMD160 2a3817063c4b042617072685618ffb3c832c40d9 SHA1 ba5d8d96687be98cdb33419daa9988d45b8e069a SHA256 eda78d1d6a24df563ec11f957886d878976bed13a0f301c38500663949ff31cb -MISC metadata.xml 543 RMD160 0ba62e9208ce536ee9a2c08ed24b0ba0b8f02083 SHA1 65a101f1e363e77f9555655bc66458c514d193f3 SHA256 fcfb63c372b73a4553c56f39d6940a0cf8d8d8d15e5beef95ffcb5acab405d17 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEAREIAAYFAk4F7tQACgkQgAnW8HDreRZYtwCfczBxyOBZSaFSdizjB6Adaf30 -7zYAoIlovwtLBhTIDcftTq9+FPiuh4b/ -=bzQS ------END PGP SIGNATURE----- +MISC ChangeLog 554 RMD160 50affa4c5d095fd8efc19dea949a2b568ef142aa SHA1 6d0fa25c1033ed3c012c77feebcbe2d725979fa5 SHA256 56f9580afaf8e4d83bc49866202695ed2018dd8f5f4d30a1f52a9ae6cdf8b06c +MISC metadata.xml 553 RMD160 09e7a0be2e8ebe72d3bdc460e743f2eaead2333e SHA1 f138f24790241367693414abd82941ba1d1e796d SHA256 5cdac6b9202fd4b027141c89a05b5812f77fe547febd965b234502de674d9d51 diff --git a/sci-astronomy/missfits/metadata.xml b/sci-astronomy/missfits/metadata.xml index e8c098543..15e9db47e 100644 --- a/sci-astronomy/missfits/metadata.xml +++ b/sci-astronomy/missfits/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> + <herd>sci-astronomy</herd> <longdescription lang="en"> MissFITS is a program that performs basic maintenance and packaging tasks on FITS files using an optimised FITS library. MissFITS can: diff --git a/sci-astronomy/psfex/ChangeLog b/sci-astronomy/psfex/ChangeLog new file mode 100644 index 000000000..194a9b99f --- /dev/null +++ b/sci-astronomy/psfex/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-astronomy/psfex +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + diff --git a/sci-astronomy/psfex/Manifest b/sci-astronomy/psfex/Manifest index e38a380d7..9620f0611 100644 --- a/sci-astronomy/psfex/Manifest +++ b/sci-astronomy/psfex/Manifest @@ -1,13 +1,4 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - DIST psfex-3.9.1.tar.gz 2364495 RMD160 54c1a32c7f9305a91b973a974c4ae527a4dc3143 SHA1 af164b4e3d1bf61cdd738e8c52730f8564460ae0 SHA256 1758a1a40166ef59475d8fab6abda33ca0ed0a837531ff7ad577d8bce4e511f7 EBUILD psfex-3.9.1.ebuild 1183 RMD160 26f4f8c2c4e6e6bee033972d051f5ca949a58877 SHA1 88f82e87f8258be728318d1930dfcf93cec51022 SHA256 afe364cee799aabbe1a474fbd62f88db3288f7078292be05965f437e81083d55 -MISC metadata.xml 608 RMD160 16d7fe8c80598c89ae9a28647326731fa17579b5 SHA1 aa50c8cf441f11b93cf3cb133113d819cb55178b SHA256 11164a313edba70d4453e479bc6ee510c190f60dfe8ddaf6e1df74cde674d07b ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4EhyIACgkQgAnW8HDreRbrjACfStyPlJje9jUp1Iii4zNJzaVe -EAwAn0mOjSRI8gK34Pgnt2HxijHc5BIB -=zk3W ------END PGP SIGNATURE----- +MISC ChangeLog 223 RMD160 d0b003facb024aa6fdd256e22e4bc195fb869fad SHA1 88423e194987deee94f09e7bf83a2108fb5cdaf2 SHA256 e54455e8fe6b6c783abcba8ee9911786d19e3434881f11652617a007dd6d0036 +MISC metadata.xml 618 RMD160 4457a863e2920a162d35f06cb54131569b7a1570 SHA1 39b4dbb51a1b04df0638bbb35404970544d91531 SHA256 5d67566a70b08931f4df71183ef8c69d237af0c54d8544547fc8bd0712160e5f diff --git a/sci-astronomy/psfex/metadata.xml b/sci-astronomy/psfex/metadata.xml index 02991f4c0..4f00f5a6b 100644 --- a/sci-astronomy/psfex/metadata.xml +++ b/sci-astronomy/psfex/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> PSFEx (“PSF Extractor”) extracts models of the Point Spread Function (PSF) from FITS images processed with <pkg>sci-libs/sextractor</pkg>, and diff --git a/sci-astronomy/skymaker/ChangeLog b/sci-astronomy/skymaker/ChangeLog index 4c6602f9d..9ffd58d4e 100644 --- a/sci-astronomy/skymaker/ChangeLog +++ b/sci-astronomy/skymaker/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/skymaker -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + 17 Nov 2010; Sébastien Fabbro <bicatali@gentoo.org> skymaker-3.3.3.ebuild: License and web site changes diff --git a/sci-astronomy/skymaker/Manifest b/sci-astronomy/skymaker/Manifest index 5e57a4766..e71aea04e 100644 --- a/sci-astronomy/skymaker/Manifest +++ b/sci-astronomy/skymaker/Manifest @@ -1,15 +1,5 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - AUX skymaker-configure.patch 1152 RMD160 ac9808398cf1e2e0dcb17ca7a0e0e54814e1803c SHA1 1ddbe2391e66a48c5220a00a3500cb5a6cbfe356 SHA256 a27412b932426c28b61e98eb6eb9be8c83c8ad56c020b3892ecf4e6ae2235374 DIST skymaker-3.3.3.tar.gz 415740 RMD160 8f9809a1fcf6659a6d76b6d8f6cc1a9154306262 SHA1 781e4e1955a04bfadb74904243ddfd8f507839d5 SHA256 75ddcfcc577591b3ad430171fa867cc7a573bb93f541fd82ef6ebe873c1816f4 EBUILD skymaker-3.3.3.ebuild 698 RMD160 5086f36d06bdd0bcf82f1066233c1d6c2bfb324a SHA1 a78b52ddf0b7294864d08794b466815cc08605e3 SHA256 5c6ff7aae00edf2b7a61027a1cc258e30fe972cb5c457b9d2905e7d28f2e38f7 -MISC ChangeLog 504 RMD160 3278dbafae2c1350b3ee2132d40feb2884ad24d9 SHA1 9ad54a932a7d3dd7a237e095fa69e29eca1f81f2 SHA256 954c491b6107fe2867ecdb7a6ff89d89c45dd16220b88a31d76c8ba496f8b1fc -MISC metadata.xml 522 RMD160 82a2f56adf45447226214d63b733d5ee59a7a28f SHA1 f3fd9b95737eec4ac3bb5d7103b6237b21089d20 SHA256 d86351847a40cd61b3b7da6a9794b11a34de5192952dcb849d91cbc442b05646 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4EhycACgkQgAnW8HDreRYIKwCg0aUQ4uxJxWREhEsQkfzXoXWp -7XUAn2DgdbrunHDwK76kE9aJme7it8Jj -=k3Vm ------END PGP SIGNATURE----- +MISC ChangeLog 607 RMD160 e141894611a351790b1dde2468cecc25198d0b11 SHA1 2578334be5101f6b72337b3ce7b425610f03f682 SHA256 61f2f82121a15458bd6293e94dfbbdd26b89e7d8e372a4ecf075922e18e0107a +MISC metadata.xml 532 RMD160 2e8bf7d442e9cc6a9fce8f4e75323d16eb62119a SHA1 8433f6c78c17ba7040362b89edab27ba3eeb025b SHA256 6f8889a64e59fef92c964c20952cd1d3f0f91f478f871bf4f291430a690e57f3 diff --git a/sci-astronomy/skymaker/metadata.xml b/sci-astronomy/skymaker/metadata.xml index caa0b0596..6b3fd39d2 100644 --- a/sci-astronomy/skymaker/metadata.xml +++ b/sci-astronomy/skymaker/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> SkyMaker is a program that simulates astronomical images. It accepts object lists in ASCII generated by the Stuff program to produce diff --git a/sci-astronomy/stuff/ChangeLog b/sci-astronomy/stuff/ChangeLog index fb0f93482..2f967daf9 100644 --- a/sci-astronomy/stuff/ChangeLog +++ b/sci-astronomy/stuff/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/stuff -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + 18 Nov 2010; Sébastien Fabbro <bicatali@gentoo.org> stuff-1.19.ebuild: License and web site changes diff --git a/sci-astronomy/stuff/Manifest b/sci-astronomy/stuff/Manifest index a38923192..dd33d9305 100644 --- a/sci-astronomy/stuff/Manifest +++ b/sci-astronomy/stuff/Manifest @@ -1,15 +1,5 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - AUX stuff-configure.patch 1734 RMD160 cd80f40b8bf4757a7f30219a68393bc014dad63d SHA1 ba572bd637a09246ca2fcdb0f576ec183ce798b0 SHA256 7cdcd8b57aae0d2b80534794d3f9d34a72fde74e20cd6220f70e7d286fce11a9 DIST stuff-1.19.tar.gz 4017086 RMD160 c8ac8d3bbe7cd4a7e48b81b98de60b6c777e6e74 SHA1 acf5b26e5cc10eac757b55b8cca59d5ca3d3ab94 SHA256 592e6bfff704d1391b150a0820b52258ef69a99b698ac07eb0a8f04daf5b0210 EBUILD stuff-1.19.ebuild 690 RMD160 d131ccfb5b7ad8fe0a8f272ed3d8b2323f7190d7 SHA1 1321ff319e1d02027374dbaaf4404da7584b56d5 SHA256 a6a667a18447e04baeace961941cc8c7d114f0f39535b516b45211c9ce8060c0 -MISC ChangeLog 393 RMD160 1b8d57da8f964e6b587cb88039da9a7d096f7517 SHA1 b1224d92a265403f6473771b8887d9bc9b094a4c SHA256 49ac0889dbb5ce913e6f1068db7d490f3590071faec88b8ecc3b34c6e916a2f5 -MISC metadata.xml 397 RMD160 1b501841d3d65e5f322607b8f336e077ded9cb7e SHA1 5c5037a6ce527cf3c559426e9355fa804ad6e2db SHA256 69add15cada8ac23ffc005025d85d26e369d568ee8d3b88755d0a99571d6bd3f ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4EhywACgkQgAnW8HDreRayhgCfUDhqlPx5iUku6SQJpMNK8yZ/ -JX8AnApgK1ToA9ofIO/qUVr5FufOwh7w -=2Vnj ------END PGP SIGNATURE----- +MISC ChangeLog 496 RMD160 f17ec8801140d3aef210ee43a0fb58ba448aa919 SHA1 96018091c057e58dd228dac6d0d89050c738256c SHA256 7d188ca638ac97f9a42b5d6ba73f13a9ccadf605078cb7278d360264313bbb5f +MISC metadata.xml 407 RMD160 db2d2eebbc7437c87244eab05e9174be55e045fb SHA1 82d83009b5e6723f4529111445bd9776d07c237e SHA256 a9c3aedb664b1ff6e760aa802e938539c0e11ba5770e83ef8fc9e074a8dd5697 diff --git a/sci-astronomy/stuff/metadata.xml b/sci-astronomy/stuff/metadata.xml index 11798a28a..140cfac08 100644 --- a/sci-astronomy/stuff/metadata.xml +++ b/sci-astronomy/stuff/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-astronomy</herd> <longdescription lang="en"> Stuff is a program that simulates “perfect” astronomical catalogues. It generate object lists in ASCII which can read by the diff --git a/sci-astronomy/weightwatcher/ChangeLog b/sci-astronomy/weightwatcher/ChangeLog index b886eb169..7588f6b93 100644 --- a/sci-astronomy/weightwatcher/ChangeLog +++ b/sci-astronomy/weightwatcher/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Aug 2011; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + Switched herd to sci-astronomy + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> weightwatcher-1.8.10.ebuild, metadata.xml: Cleaned ebuild, no eauto* function called diff --git a/sci-astronomy/weightwatcher/Manifest b/sci-astronomy/weightwatcher/Manifest index 9826603bc..14ffe14b5 100644 --- a/sci-astronomy/weightwatcher/Manifest +++ b/sci-astronomy/weightwatcher/Manifest @@ -1,14 +1,4 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 - DIST weightwatcher-1.8.10.tar.gz 403372 RMD160 530b81d4b40354f85eb21bcd62b473457033ce4d SHA1 00c824fdc068299db04e48263558e1da223baeff SHA256 7f8a09deb586bb118c79d7ebcb8c6958d9ea49862f7d5a2dfdf229c550e8f740 EBUILD weightwatcher-1.8.10.ebuild 517 RMD160 cc2f96177bbb6af7bb746c85669e2616d50f1e70 SHA1 4bafd53f0944f6045c70370fd72f8a2619e275e9 SHA256 9a19a994c35259bfc6743fe13995b380c5c8368d670f3ab5b99d9ae07ffb2b1f -MISC ChangeLog 349 RMD160 1f074aee3274c53f77def751a5ef77754e44e58e SHA1 0051d0f751f75ce7e167e6c80a65aa3af9f0dd4d SHA256 4959c4d7230fb771495634b9c1416a5085750f08831fde056761f29725e3e341 -MISC metadata.xml 481 RMD160 3335871d604c67ce9b43c7d863f951b9e1735eb4 SHA1 31775493c9b40dfce2fb7aa638b6d325bf9911ce SHA256 af2d3375fefbb033ababcc44c8a2f9cd3765b3ec0d786bdb6d37d7dd356a141f ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEAREIAAYFAk4F7xoACgkQgAnW8HDreRaeOACfZ5L1wH10RAKUbSrEzywHmv7i -iJIAoLdCz8gJ36paAzfxnrmJAWzYyvqA -=KJ7w ------END PGP SIGNATURE----- +MISC ChangeLog 452 RMD160 fbfb633a3ac1cef7bfed8e55efba573f5f480f4a SHA1 abcef5bba226e6d9c9b4961e31282485dbd4203c SHA256 c02a52feb3409b9d3e838465a5161072f617aa142c9c236c1ea7363b51bd6a23 +MISC metadata.xml 491 RMD160 53afb12ba371c1b327b320bef61af663daf2195b SHA1 e7592ef72ae8062c96e58c153ae4050f889976fe SHA256 d0a9eef2ff53e78c15f9bc7aef2a62ae28937d65b9ff516b4b7d3383e452493d diff --git a/sci-astronomy/weightwatcher/metadata.xml b/sci-astronomy/weightwatcher/metadata.xml index 278512904..4cb96196d 100644 --- a/sci-astronomy/weightwatcher/metadata.xml +++ b/sci-astronomy/weightwatcher/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> + <herd>sci-astronomy</herd> <longdescription lang="en"> WeightWatcher is a program that combines weight-maps, flag-maps and polygon data in order to produce control maps which can directly be diff --git a/sci-biology/erpin/Manifest b/sci-biology/erpin/Manifest index ec46324dd..f2f720668 100644 --- a/sci-biology/erpin/Manifest +++ b/sci-biology/erpin/Manifest @@ -2,3 +2,5 @@ AUX erpincommand-5.5b.pl 8153 RMD160 90af7d4f81f16fbfda9eb6001096f25f64648ff4 SH DIST ErpinBatch.1.4.tar.gz 2195075 RMD160 a9044e42d41081fd72b6d072b94e4b2ce53dd38c SHA1 9344ce75ce4e751d3c82ee7ad87946f65b797124 SHA256 5da4c69d88092e79f4f5d73e7d67dfccbb3d4a8cbe38c74169548ef608f25808 DIST erpin5.5b.serv.tar.gz 1145698 RMD160 289b7b325b3f5dc45b93df4eefb7d56d08500f9e SHA1 b0a748b8761b2ac7be998f8498394cdc3f54d563 SHA256 0433ed25dd54491ddc4c025bb61d78d36797c2c83c61f260b5663c44cbad4d4d EBUILD erpin-5.5b.ebuild 1357 RMD160 7f1ce1e7b06a8de42f48fc378bdb248cb3e88055 SHA1 f7d265426d2e90cd5e0917af519fe6ec2eb5d03e SHA256 c0e44f71108216f0f8d7e0881b69e70a57261ebb456cad6c1d608708f78b061b +MISC ChangeLog 216 RMD160 bf895675eb7b110abc67d64b937ce103fa16c03e SHA1 3eb513509aeaed6f96d249785efb91481d83ce78 SHA256 d9f8edfd1857615662343519e908c66ded5fcef728f34adfbad092397aeee754 +MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/est2uni/ChangeLog b/sci-biology/est2uni/ChangeLog new file mode 100644 index 000000000..6c7cd1b03 --- /dev/null +++ b/sci-biology/est2uni/ChangeLog @@ -0,0 +1,23 @@ +# ChangeLog for sci-biology/est2uni +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch, + +est2uni-9999.ebuild: + ebuild cleanup est2uni-0.27.ebuild est2uni-9999.ebuild Manifest + files/9999-est_clustering.pm.patch files/9999-pipe_db.pm.patch + files/99est2uni files/est2uni files/est_annot.pm.patch + files/est_annot_go.pm.patch files/est_annot_psnp.pm.patch + files/est_annot_reciprocal_blast.pm.patch files/est_clustering.pm.patch + files/est_prepro.pm.patch files/installation_est2uni_perl.txt.patch + files/mysql_fixes.sql files/pipe_db.pm.patch files/tables.sql.patch + files/tgicl_files.patch metadata.xml + +*est2uni-9999 (05 Jul 2011) + + 05 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch, + +est2uni-9999.ebuild: + vim est2uni-9999.ebuild + diff --git a/sci-biology/est2uni/Manifest b/sci-biology/est2uni/Manifest index 211a599bd..fac903531 100644 --- a/sci-biology/est2uni/Manifest +++ b/sci-biology/est2uni/Manifest @@ -1,6 +1,5 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - +AUX 9999-est_clustering.pm.patch 1276 RMD160 4a54b28c9a67ae8476255a4063768a1c7b466357 SHA1 1d255394dad2f608bd91f6064232a3cd431e368d SHA256 c289866a862a18a9385db9931c3c0c9175334e829819f075cc7fbf7e8bbd83ce +AUX 9999-pipe_db.pm.patch 534 RMD160 8b2a5ef4de3a2c65eb65476cbb4decdad3eb8a74 SHA1 46509d05f01ae53764b4947ddb663edbb3bfee9d SHA256 11aa489e406bceabdd3b7d532fbca69ede1c0a116cc7a38ae9ea32dafc41f54c AUX 99est2uni 82 RMD160 4171612511e63f41fa57aa743a435e4e5ca811d1 SHA1 a51b17f763855cda65e3bf5f401dccab231e1593 SHA256 4317ba1309d2506682d5146f7fb52f388b368bfd2ab33b4a2cf95ec8b117341e AUX est2uni 82 RMD160 4171612511e63f41fa57aa743a435e4e5ca811d1 SHA1 a51b17f763855cda65e3bf5f401dccab231e1593 SHA256 4317ba1309d2506682d5146f7fb52f388b368bfd2ab33b4a2cf95ec8b117341e AUX est_annot.pm.patch 19656 RMD160 83c75544edf45b7dffe92b97ec1935ec4774241d SHA1 f6051670594093ba89cb259cb0427222bf4a3f02 SHA256 fdfb19e711a05b02016ffbe57f5d68f5d7b8746690445aafa2cab6ebf8ddd058 @@ -20,11 +19,6 @@ DIST UniVec_Core 542650 RMD160 a8cf42b9015622a8ac52839c7b794bbad4c1f92a SHA1 6eb DIST est2uni_0.27.tar.gz 4616613 RMD160 06ec260f79fe11f7779b75aad825e665f421d4eb SHA1 5ee9b5dc51f4829c5ed0d4ddd47bb68e7f3c43ee SHA256 33d2f2981ca70fa6707d3a2f310c0492cd12a430b6bb9b7ad8697a8fc3305cd4 DIST gene_ontology.obo 19990996 RMD160 b3584271ab0a05909cde9a92e6eb635b08fe23be SHA1 bdb9d396d4320bf639be310cf6f93b08b25ef0e9 SHA256 7f70c7a1dd4b75f6055f05c5e5445a49ecf20fed8172d54ec2d04722842ff19b EBUILD est2uni-0.27.ebuild 3292 RMD160 d676915e49ef8f3ec04da0391945441fd47028f1 SHA1 a349fbd92f6ec096f5cad8dbabb2769594531111 SHA256 e47c997ced2b2b01e4abc509349e389e9f1e3b272e696c606aa9d010984f2821 +EBUILD est2uni-9999.ebuild 3511 RMD160 355f09b04cc16424482896dd48b764066fdb68db SHA1 1cddcddb8f5c7ec0e8733258296df1c6c47856b4 SHA256 730bc309495d0be63208424c2fe18cd75fcb4410461f4100c0ec0cbe0affe706 +MISC ChangeLog 984 RMD160 87af050bbce9cf9611924edfd27c999183954591 SHA1 23aea083fd9d5eb9ccaa3e06bb4fca454ae5b7e1 SHA256 5d7413b010752dcc0cadc53633dc48d613e037f40ec946bc103be7f30e2b279d MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4EiSQACgkQgAnW8HDreRaZuwCfYMccT5NROdxtN7jg0sFQZ4vh -QE4AoLcFDH3moqCaBR2DMkuxrBu4i9NL -=ZlWM ------END PGP SIGNATURE----- diff --git a/sci-biology/est2uni/est2uni-9999.ebuild b/sci-biology/est2uni/est2uni-9999.ebuild new file mode 100644 index 000000000..5066917d9 --- /dev/null +++ b/sci-biology/est2uni/est2uni-9999.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +inherit webapp eutils perl-module + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface" +HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="git://gitolite@bioinfo.comav.upv.es:2203/est2uni.git" + KEYWORDS="" +else + SRC_URI="http://cichlid.umd.edu/est2uni/est2uni.tar.gz + ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec + ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core + http://www.geneontology.org/ontology/gene_ontology.obo + http://www.geneontology.org/doc/GO.terms_and_ids" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="GPL-3" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/lucy + sci-biology/cap3-bin + sci-biology/estscan + <sci-biology/hmmer-3.0 + sci-biology/phred + sci-biology/seqclean + sci-biology/repeatmasker + sci-biology/tgicl + sci-biology/ncbi-tools + sci-biology/bioperl + sci-biology/exonerate + dev-perl/go-perl + www-servers/apache + >=dev-db/mysql-4.1 + <dev-lang/php-5.3" + +S="${WORKDIR}"/est2uni + +src_prepare(){ + for f in "${FILESDIR}"/9999-*.pm.patch; do + cd perl; epatch $f || die "Failed to apply patch $f" + done +} + +src_compile(){ + "$(tc-getCC)" external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik +} + +src_install(){ + mkdir -p "${D}"/opt/est2uni + mv external_software/sputnik/sputnik "${D}"/opt/est2uni || die + + chmod a+rx perl/*.pl perl/*.pm || die + mv perl/* "${D}"/opt/est2uni || die + + doenvd "${FILESDIR}"/99est2uni || die + + mkdir -p "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs + cp -r php/* "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die + + mkdir -p "${D}"/opt/est2uni/test_data || die + mv test_data/* "${D}"/opt/est2uni/test_data || die + # mkdir -p "${D}"/usr/share/"${PN}" || die + # mv test_data "${D}"/usr/share/"${PN}" || die + perl-module_src_install || die + + webapp_src_preinst + webapp_postinst_txt en "${S}"/README + webapp_src_install + # mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/temp + # mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/blast + + # cp "${DISTDIR}"/UniVec_Core "${DISTDIR}"/UniVec "${D}"/usr/share/ncbi/data/ || die + + einfo "Please follow the pipeline installation and web configuration docs at" + einfo "http://cichlid.umd.edu/est2uni/install.php" + einfo "BEWARE the software is not maintained anymore by upstream but I do not" + einfo "know any better available (replaced by ngs_backbone which has no web" + einfo "interface yet). Consider using latest svn checkout instead of 0.27" + einfo "release from 2007 or so." + einfo "Possible fixes and stuff to read:" + einfo "https://listas.upv.es/pipermail/est2uni/2008-January/000069.html" + einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000103.html" + einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000101.html" + einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000135.html" + einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000131.html" + einfo "https://listas.upv.es/pipermail/est2uni/2008-February/000070.html" + einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000129.html" + einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000128.html" + einfo "https://listas.upv.es/pipermail/est2uni/2008-May/000139.html" + einfo "" + einfo "Current code is at http://bioinf.comav.upv.es/git///?p=est2uni;a=summary" +} + +pkg_postinst(){ + webapp_pkg_postinst || die "webapp_pkg_postinst failed" +} diff --git a/sci-biology/est2uni/files/9999-est_clustering.pm.patch b/sci-biology/est2uni/files/9999-est_clustering.pm.patch new file mode 100644 index 000000000..ec38e5208 --- /dev/null +++ b/sci-biology/est2uni/files/9999-est_clustering.pm.patch @@ -0,0 +1,29 @@ +--- perl/est_prepro.pm.ori 2011-02-23 10:56:06.000000000 +0100 ++++ perl/est_prepro.pm 2011-02-23 19:53:13.000000000 +0100 +@@ -499,15 +499,17 @@ + $sth->bind_param(5,$unique_seq_control); + # we get the clone names from the data file + # if not in the data file, we guess it following user specifications in config file +- unless (${%$clone}{$real_name}) { +- ${%$clone}{$real_name}=get_clone_from_est($config,$real_name); +- } +- $sth->bind_param(6,${%$clone}{$real_name}); +- $$seq_info{clone}=${%$clone}{$real_name}; +- if (!${%$clone}{$real_name}){ +- print localtime().": Unable to get clone name for EST $real_name\n"; +- return undef; +- } ++ #unless (${%$clone}{$real_name}) { ++ # ${%$clone}{$real_name}=get_clone_from_est($config,$real_name); ++ #} ++ #$sth->bind_param(6,${%$clone}{$real_name}); ++ #$$seq_info{clone}=${%$clone}{$real_name}; ++ #if (!${%$clone}{$real_name}){ ++ # print localtime().": Unable to get clone name for EST $real_name\n"; ++ # return undef; ++ #} ++ $sth->bind_param(6,'blah'); ++ $$seq_info{clone}='blah'; + } + if (not $qual and not ($unique_seq_control eq 'raw_est' or $unique_seq_control eq 'clean_est')) { + $sth->bind_param(5,$unique_seq_control) diff --git a/sci-biology/est2uni/files/9999-pipe_db.pm.patch b/sci-biology/est2uni/files/9999-pipe_db.pm.patch new file mode 100644 index 000000000..729c55099 --- /dev/null +++ b/sci-biology/est2uni/files/9999-pipe_db.pm.patch @@ -0,0 +1,15 @@ +--- perl/pipe_db.pm 2011-02-23 18:38:47.000000000 +0100 ++++ pipe_db.pm 2011-02-23 19:41:06.000000000 +0100 +@@ -1468,10 +1468,11 @@ + my $tables=shift; + my $ok=1; + ++ my %t = %$tables; # Can't use string ("38/64") as a HASH ref while "strict refs" in use at /opt/est2uni/pipe_db.pm line 1474. + my $table; + foreach $table(keys %$tables) { + if ($ok) { +- $ok=create_table($db,$table,${%{$tables}}{$table}); ++ $ok=create_table($db,$table,$t{$table}); + if ($ok) { + print localtime().": Table $table created\n"; + } else { diff --git a/sci-biology/estscan/ChangeLog b/sci-biology/estscan/ChangeLog index ff0f2e4b0..bce0bfa39 100644 --- a/sci-biology/estscan/ChangeLog +++ b/sci-biology/estscan/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + estscan-3.0.3.ebuild: + some ebuild cleanup estscan-3.0.3.ebuild + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> estscan-3.0.3.ebuild, metadata.xml: Streamlined fortran-2 eclass usage diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest index e41936f81..1fdd337f7 100644 --- a/sci-biology/estscan/Manifest +++ b/sci-biology/estscan/Manifest @@ -1,6 +1,3 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - DIST At.smat.gz 32314 RMD160 5c66e467d20e1ce43dce35cf20540649bbcf2879 SHA1 bd3e2d87be468e7d9c46557bce68e94bdd3f1aa2 SHA256 7f41329858b19ea13809becf58c7262b48dd8070dc38894b8ad7c55adcdd4c2a DIST BTLib-0.19.tar.gz 36283 RMD160 14ae4a24c81a381e9a75ddcde7552a1f9dc301b8 SHA1 7a0545cb64976ee61e76a80a9ee1a87eb1747078 SHA256 0acd6446031222b8fd5bd11eb3ec6c3164bc50491feef765c052689d9c3ee302 DIST Dm.smat.gz 31711 RMD160 1e77b7f743ea9198108dff3dec2e8fd64ba8751c SHA1 6dd589a2dac0d4ea51ad085a835a5100b5eab8e1 SHA256 1f741836aa2b4ed96ab9ea6adb883eaa4d8d95610bd7a1ac484193ab30afca1d @@ -10,13 +7,6 @@ DIST Mm.smat.gz 62711 RMD160 30cf8dd0d944afcae7dd05b30bc08820e303c7c4 SHA1 2d0d5 DIST Rn.smat.gz 32388 RMD160 4ff99c8502aa914c85aeaf19f98bc7362ab70cb0 SHA1 060e66141a19302e805323322ab219d990cf4592 SHA256 2e0a9b3347a8d216a026f98e38243d207e683bc50ac5be35c4c24f5ee1803cb8 DIST estscan-3.0.3.tar.gz 46412 RMD160 dc5e12e8196837585c405163f643e2da0c84bd79 SHA1 8af2128aaa02c50d1d3cfa75188fac038381975c SHA256 037dc8770681ed12406a789ea292462a4ce5d89b0e906a1a3340aa4debc71e2f DIST user_guide_fev_07.pdf 327005 RMD160 99f838a2c61c82a5078fb49e06ab8c8a7a8c1509 SHA1 335b3bacf0af8947db57324a702d335e72d58abd SHA256 416998f9fc282a53679fd56585b468ccebc4463e61ee5e989d9b426ed6f725fd -EBUILD estscan-3.0.3.ebuild 3627 RMD160 04e489ba6db85e382a3d55adbab168e46f09e791 SHA1 3412b7e3aa90ee4392a48b59fc3cd5712f0c3a1e SHA256 64c25c435fdaa15c814707ed13d3ad42ca7cac6f5cbb29d1d52ff432359aa4cc -MISC ChangeLog 362 RMD160 fd6d014788fd1c68fd8e1e58b37c2ac0585fdb4d SHA1 5079e398e369900824f8b7f4d3ed176df88a1fd2 SHA256 96f00043d927fffa618ad23bc67589ce75caff6294afd1f4e16795cb47b09082 +EBUILD estscan-3.0.3.ebuild 3934 RMD160 b30e11d2b638afeb8f400949e66d6e74701043f8 SHA1 f1c3fe99f57796cbc859a7e42d62d1d971372a6b SHA256 6eb53fcf71e6e9b5070f6d268143bb7f60038b064bd861a70882cac8b08ae2cf +MISC ChangeLog 490 RMD160 658879ed6fe982e758a447d2ab7db7d47e71702f SHA1 3d3cd938b76d67f655e5c81389517f1d5a53fe89 SHA256 9bf7dc9d26ab70d67a01b49de4991dda0633e1f67f218e4d13385458d328c424 MISC metadata.xml 326 RMD160 cdc20d05766f861cff6889339611ca1c22579631 SHA1 dddeeb441b46d5437d1883f7c44ea26ad704344e SHA256 530e03907f86440fdc52832f744b709dde2ee85492cad7b8a263544a93ea0bea ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4DAxcACgkQgAnW8HDreRYbrQCfRdlKYlwAQQu22Y741J7tR7t6 -jp0AoIpbBVtLAlueTxY2BLymUs2wbbGz -=zCkB ------END PGP SIGNATURE----- diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild index d2828605a..913303a8e 100644 --- a/sci-biology/estscan/estscan-3.0.3.ebuild +++ b/sci-biology/estscan/estscan-3.0.3.ebuild @@ -21,14 +21,16 @@ SRC_URI=" SLOT="0" LICENSE="estscan" -KEYWORDS="~x86 ~amd64" +KEYWORDS="" +#KEYWORDS="~x86 ~amd64" IUSE="intel" DEPEND=" virtual/fortran intel? ( dev-lang/icc - dev-lang/ifc )" + dev-lang/ifc ) + dev-perl/BTLib" RDEPEND="${DEPEND}" S="${WORKDIR}" @@ -74,40 +76,39 @@ src_prepare() { src_compile() { emake -C ${P} - - cd ../BTLib-0.19 - perl Makefile.PL || die "perl Makefile.PL failed" } src_install() { # FIXME: Some kind of documentation is in {P}/estscan.spec - cd ${P} + cd ${P} || die "Failed to chdir to "${P}" dobin \ build_model estscan evaluate_model extract_EST extract_UG_EST \ extract_mRNA makesmat maskred prepare_data winsegshuffle # the file build_model_utils.pl should go into some PERL site-packages dir # see {P}/estscan.spec - # install the doc (but is not in ${WORKDIR} because src_UNPACK() failed on it - cd "${WORKDIR}" + # install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension + cd "${DISTDIR}" || die "Failed to chdir to "${DISTDIR}" insinto /usr/share/doc/ESTscan # grab the file directly from ../distdir/ - doins ../distdir/user_guide_fev_07.pdf + doins "${DISTDIR}"/user_guide_fev_07.pdf # install the default precomputed matrices - cd "${WORKDIR}" + cd "${WORKDIR}" || die "Failed to chdir to "${WORKDIR}" insinto /usr/share/ESTscan doins *.smat # install BTlib (in perl) - cd BTLib-0.19 || die - dobin fetch indexer netfetch + # dobin fetch indexer netfetch insinto /usr/share/ESTscan/ - doins fetch.conf + # install the config file which is packed inside the BTLib tarball while is not + # being installed by dev-perl/BTLib + doins "${WORKDIR}"/BTLib-0.19/fetch.conf # FIXME: install the *.pm files from BTLib-0.19 - myinst="DESTDIR=${D}" - perl-module_src_install + # cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19 + # myinst="DESTDIR=${D}" + # perl-module_src_install einfo "Please edit /usr/share/ESTscan/fetch.conf to fit your local database layout." einfo "Also create your own scoring matrices and place them into /usr/share/ESTscan/." diff --git a/sci-biology/gbench/ChangeLog b/sci-biology/gbench/ChangeLog new file mode 100644 index 000000000..00fb7d502 --- /dev/null +++ b/sci-biology/gbench/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-biology/gbench +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*gbench-2.3.2 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +gbench-2.3.2.ebuild, +metadata.xml: + backbone of a new package, should probably use a lot of stuff from + ncbi-tools++ ebuild + diff --git a/sci-biology/gbench/Manifest b/sci-biology/gbench/Manifest new file mode 100644 index 000000000..31f0fbc28 --- /dev/null +++ b/sci-biology/gbench/Manifest @@ -0,0 +1,4 @@ +DIST gbench-src-2.3.2.tgz 23329652 RMD160 a4aedb72fe3814c98a69b8ffe21432e51058c15d SHA1 ab1ace68e50d6f7f547b2151dd0b18f82f7d7848 SHA256 ea45974d4b843a0033c587b575cb22388de96d2e300e1bedc8e16a11d9e154be +EBUILD gbench-2.3.2.ebuild 1381 RMD160 081ee7ff7100b0de79bae08d0ade9ad1aba8025d SHA1 ad299e02dac4292a329390bb85595aef08a59015 SHA256 fd6d79f202d1563c0f3a1658b34ba6612ada26a78c03de6c965bcc42961ccaf6 +MISC ChangeLog 339 RMD160 2da3436e35c53ed8d3fd41a9927f9a8e264d47e0 SHA1 ac3281b5eeb8eef528b1a39ef4c6e57bafe62299 SHA256 55c8cf2c1537ca7a26f65c50010d18db433c9dd9ba159df87f16a6af70e2aa99 +MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 diff --git a/sci-biology/gbench/gbench-2.3.2.ebuild b/sci-biology/gbench/gbench-2.3.2.ebuild new file mode 100644 index 000000000..e9bf5b57f --- /dev/null +++ b/sci-biology/gbench/gbench-2.3.2.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +inherit wxwidgets + +DESCRIPTION="View and analyze genome sequences" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/projects/gbench/" +SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/gbench/ver-2.3.2/gbench-src-"${PV}".tgz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="" +#KEYWORDS="~amd64 ~x86" +IUSE="xml ssl sybase-ct zlib lzo pcre gnutls freetds mysql berkdb python opengl glut icu expat sqlite hdf5 jpeg png tiff gif xpm sybase threads fltk cgi" + +DEPEND="sys-fs/fuse + app-arch/bzip2 + dev-libs/lzo + pcre? ( dev-libs/libpcre ) + net-libs/gnutls + ssl? ( dev-libs/openssl ) + sybase-ct? ( dev-db/freetds ) + mysql? ( virtual/mysql ) + sys-libs/db + dev-lang/python + dev-libs/boost + virtual/opengl + virtual/glut + media-libs/glew + x11-libs/wxGTK + dev-libs/icu + dev-libs/expat + app-text/sablotron + xml? ( dev-libs/libxml2 ) + dev-libs/libxslt + sqlite? ( dev-db/sqlite:3 ) + sci-libs/hdf5 + media-libs/tiff + media-libs/giflib + xpm? ( x11-libs/libXpm + virtual/jpeg + media-libs/libpng sys-libs/zlib ) + media-libs/freetype + x11-libs/fltk + dev-libs/xerces-c + dev-libs/xalan-c + dev-cpp/muParser + dev-util/cppunit" + +RDEPEND="${DEPEND}" + +# ensure in src_compile no --mandir=/usr/share/man is passed to configure, use the ebuild logic from ncbi-tools++ diff --git a/sci-biology/gbench/metadata.xml b/sci-biology/gbench/metadata.xml new file mode 100644 index 000000000..d4648212c --- /dev/null +++ b/sci-biology/gbench/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog index eaa41a45d..b64e88094 100644 --- a/sci-biology/gbrowse/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -2,6 +2,47 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $ + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + gbrowse-2.39.ebuild, +files/disable-gbrowse_metadb_config.pl.patch, + +files/gbrowse_metadb_config.pl.patch, +files/symlink.patch: + Make sure portage does not run gbrowse_metadb_config.pl otherwise sandbox + violation occurs when modifying /var/www/gbrowse2/databases/users.sqlite* + file, maybe we could copy these during src_install to the {}, fix there and + copy back to live filesystem? Improve error handling in + gbrowse_metadb_config.pl. Fix symlink creation during install procedure. + gbrowse-2.39.ebuild files/GBrowseInstall.pm-2.39.patch files/destdir.patch + files/disable-gbrowse_metadb_config.pl.patch files/fix-PNG-export.patch + files/gbrowse-slave.default files/gbrowse-slave.init.d + files/gbrowse.conf.vhosts.d files/gbrowse_metadb_config.pl.patch + files/symlink.patch + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + gbrowse-2.39.ebuild, +files/fix-PNG-export.patch: + sci-biology/gbrowse: add missing brackets cause a perl error while exporting + a PNG image gbrowse-2.39.ebuild files/fix-PNG-export.patch + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + gbrowse-2.39.ebuild, +files/destdir.patch: + added support for --destdir, patch sent to upstream gbrowse-2.39.ebuild + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + gbrowse-2.39.ebuild, +files/destdir.patch: + added support for --destdir, patch sent to upstream + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch, + +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch: + version bump but still need to rewrite upstream's install procedure to + prevent 'mkdir /var/lib/gbrowse2' from happening + +*gbrowse-2.39 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch, + +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch: + version bump but still need to rewrite upstream's install procedure to + prevent 'mkdir /var/lib/gbrowse2' from happening + 08 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> gbrowse-2.38.ebuild: Added dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest index b63129745..0946c2e34 100644 --- a/sci-biology/gbrowse/Manifest +++ b/sci-biology/gbrowse/Manifest @@ -1,8 +1,13 @@ -AUX GBrowseInstall.pm-2.38.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c +AUX GBrowseInstall.pm-2.39.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c +AUX destdir.patch 3481 RMD160 adc51869aac4802c968119702ca124b8a9a0d867 SHA1 769442ac0986a4a2ccb1327fca9fdd6984494234 SHA256 63665f69f5dd20bf13d0055faa41331d82baf8984197246988046e893d45bf90 +AUX disable-gbrowse_metadb_config.pl.patch 956 RMD160 a1c1d77eee0b63e19522071f92028ece79b51ade SHA1 8cf0c3dd22bb41b03dbaa91d025c6c312d88055f SHA256 ab637098935cd9ec81243a69236cee08ee43476dcbb9a4d22144a2e56a7d70db +AUX fix-PNG-export.patch 480 RMD160 4ef82dd9bfaa23a7d42aec1e2d2c7ed69b9b2fb2 SHA1 0fc39c21fd84d059110d9fc502b2486e9125262a SHA256 ac222c71d29843439c7aab6ffb7ce0c7a741eff68715e5bebdc3a19dd933f444 AUX gbrowse-slave.default 210 RMD160 77245190ab0d3a543f3103bb6f21864f73ea1cde SHA1 a19d60edd3fdc1f059ed8fa58f7e91fc47ec92dc SHA256 e4e6d68ade29681f442b2e1c7f8abbc7ff3255b3b8db3c59ed6368ba561d7d66 AUX gbrowse-slave.init.d 2196 RMD160 8b565d1be23c89cbae0f9fd5cd2201f47a564b94 SHA1 738bc8f06486a0e6caa72642f79f9b7dbb356524 SHA256 de511a92757153ee648eb6cd39e3c69c1e30fa2c2ed406f24c08571c72609219 AUX gbrowse.conf.vhosts.d 740 RMD160 e24f5132e37a84dd0bb9a39e2de99cd11d260844 SHA1 2c44fdcf04bef92eb6210d4e6667b994e5643a13 SHA256 8acd5a067ab3dd42cff0ab7cb0d783b2409ccb872590eba32ea55d4929f65f21 -DIST GBrowse-2.38.tar.gz 11966992 RMD160 dde50d49ee1b228103dffc9701e450ac9e3be3cd SHA1 4228a4938cbdbc409ddb23f81cd3186cdf15391d SHA256 acf7d3d0f32d0138640b2773ed580572ff63d646d4538f354dec8986607aa275 +AUX gbrowse_metadb_config.pl.patch 2305 RMD160 d567aa4402db58bf5c1ae3a84ea221feb24613db SHA1 9c6922dc8872bafd75f75bc51cd0022a1bcf1c9a SHA256 2e06c1fe2d02b03bcd36181c4c3a61a790d489841450341c50fd274575527971 +AUX symlink.patch 498 RMD160 ee64ebf5f3e63d77cb77d3e169f7e096e94fec79 SHA1 aabbe26f4eb36b58537ccf2e7582fbc0f57c9fa4 SHA256 7b33d386901c856b488d32a10264452c0a10e8476d059e9a7bd0b084ad92dd41 +DIST GBrowse-2.39.tar.gz 11969088 RMD160 47dd338a0b99632e77a532a3c27d0b9d9d514dca SHA1 2cc48cc1603aa3ae487c47259f9a896bec4eff8e SHA256 b4e76acfa1d8f64d5f227c3ba0258666928b4f357428549be85f05c944337d44 DIST README-gff-files 5309 RMD160 8ba184fa8a6b921f925143cf53de06e3da353023 SHA1 ad2d2b3133c73a05ace4a0107ff1a3a4221bc8f8 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a DIST Refseq_Genome_TBLASTX.tar.gz 56482234 RMD160 e188d9dfe12bed3fd299be4625f7e658f54bb8c4 SHA1 72ec3de9b9ca0e10c2dd8dcda24f9be74f98cf09 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af DIST fly.fasta.gz 37349852 RMD160 4bedfcc5d0ea3d325f3d3e446713251a8ce34ca3 SHA1 8f2c7a2f24dbab0f27c73009fe51efb8f41d6769 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea @@ -13,6 +18,6 @@ DIST worm.fasta.gz 30593662 RMD160 674ef3d09cdfaa5d748f18c0e769f0a5ca3d48cf SHA1 DIST worm.gff.gz 65789458 RMD160 ddced7c965963ce41a10bdecae949731ed305121 SHA1 ccfb0f287e27ff7849b099c81d811f468a7e617c SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f DIST yeast.fasta.gz 3801757 RMD160 5545054cf6ffa5381c7992141144107076fdf62e SHA1 c36fddc5fd2c79e01292f66644088654304bc438 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d DIST yeast.gff.gz 249814 RMD160 64538d18de23d930915938bd00ae4a94a52f3960 SHA1 ec753b1ae409e1377f568531a53be8985a7bfa2e SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1 -EBUILD gbrowse-2.38.ebuild 6381 RMD160 a8a14f370543197cde8816f4d0cc0797eba158b7 SHA1 6f67d008248a7fdef7848a55855788bc367c15d5 SHA256 1107ad4bd23e6c34d09d5e9bf026c64d302282d477fb6546936a0eee27b87de2 -MISC ChangeLog 2729 RMD160 de32f4faa78f55a913b316b8eea10e978e02a38b SHA1 7c533d5e014be35560270b678053679083160696 SHA256 a5190627f4800c65af6f0fb3cc8a97d3d54909ef83611bf0d346696a89e43583 +EBUILD gbrowse-2.39.ebuild 6789 RMD160 3ca4e5e6ede46a782366522a24682bb15236d99c SHA1 5ced83e7d9279ca76e1532d8bdc5fe4b2477f037 SHA256 a0edd5b51f24041f3c00f7ee324e8636a770c7422e1ecdd89a58d6442887de1a +MISC ChangeLog 4819 RMD160 d4f0b30e70617731d8b241f9c811d080c2dc4f8a SHA1 9496a9fd42fd5ccc1d9571f7d4af0a796c8b1f4c SHA256 a32da925e0544508a2f19dada64de6bbf57c12b4a268bc99497dc6da811ca53d MISC metadata.xml 572 RMD160 bc941571413238acb3d77e61d49b959737ed4f5a SHA1 0c05303509c0e2dd21b37fc93c936809db49e530 SHA256 89b9964a9404a95dbb622a91735348da8e66d34d7dd7e7f144ed8c0159c43e31 diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch index e91fe1634..e91fe1634 100644 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch diff --git a/sci-biology/gbrowse/files/destdir.patch b/sci-biology/gbrowse/files/destdir.patch new file mode 100644 index 000000000..655158c04 --- /dev/null +++ b/sci-biology/gbrowse/files/destdir.patch @@ -0,0 +1,92 @@ +--- install_util/GBrowseInstall.pm.ori 2011-07-30 16:06:18.000000000 +0200 ++++ install_util/GBrowseInstall.pm 2011-07-30 16:06:28.000000000 +0200 +@@ -419,6 +419,7 @@ + sub ACTION_install { + my $self = shift; + my $prefix = $self->install_base || $self->prefix || ''; ++ my $destdir = $self->destdir || ''; + GBrowseGuessDirectories->prefix($prefix); + + $self->depends_on('config_data'); +@@ -445,7 +446,7 @@ + + # fix some directories so that www user can write into them + my $tmp = $self->config_data('tmp') || GBrowseGuessDirectories->tmp; +- mkpath($tmp); ++ mkpath($destdir.$tmp); + my ($uid,$gid) = (getpwnam($user))[2,3]; + + # taint check issues +@@ -454,29 +455,29 @@ + $gid =~ /^(\d+)$/; + $gid = $1; + +- unless (chown $uid,$gid,$tmp) { ++ unless (chown $uid,$gid,$destdir.$tmp) { + $self->ownership_warning($tmp,$user); + } + + my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); + my $images = File::Spec->catfile($tmp,'images'); + my $htdocs = $self->install_path->{htdocs}; +- chown $uid,-1,$htdocs; ++ chown $uid,-1,$destdir.$htdocs; + { + local $> = $uid; + symlink($images,$htdocs_i); # so symlinkifowner match works! + } +- chown $>,-1,$self->install_path->{htdocs}; ++ chown $>,-1,$destdir.$self->install_path->{htdocs}; + + my $persistent = $self->install_path->{'persistent'}; + my $sessions = File::Spec->catfile($persistent,'sessions'); + my $userdata = File::Spec->catfile($persistent,'userdata'); +- mkpath([$sessions,$userdata],0711); ++ mkpath([$destdir.$sessions,$destdir.$userdata],0711); + + my $databases = $self->install_path->{'databases'}; + +- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { +- $self->ownership_warning($databases,$user); ++ unless (chown $uid,$gid,glob($destdir.File::Spec->catfile($databases,'').'*')) { ++ $self->ownership_warning($destdir.$databases,$user); + } + + # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); +@@ -490,7 +491,7 @@ + my $perl = $self->perl; + my @inc = map{"-I$_"} split ':',$self->added_to_INC; + system $perl,@inc,$metadb_script; +- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; ++ system 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.$userdata; + + # if (Module::Build->y_n( + # "It is recommended that you restart Apache. Shall I try this for you?",'y' +@@ -600,6 +601,7 @@ + my $self = shift; + + my $prefix = $self->install_base || $self->prefix || ''; ++ my $destdir = $self->destdir || ''; + GBrowseGuessDirectories->prefix($prefix); + my $install_path = GBrowseGuessDirectories->etc; + +@@ -647,7 +649,7 @@ + if ($self->config_data('installconf') =~ /^[yY]/ && !-e "${includes}/$file") { + warn "Creating include file for Apache config: $target\n"; + my $dir = dirname($target); +- mkpath([$dir]); ++ mkpath([$destdir.$dir]); + if (my $f = IO::File->new("blib${includes}/$file",'>')) { + $f->print($self->apache_conf); + $f->close; +@@ -935,8 +937,9 @@ + sub ownership_warning { + my $self = shift; + my ($path,$owner) = @_; ++ my $destdir = $self->destdir || ''; + warn "*** WARNING: Using sudo to change ownership of $path to '$owner'. You may be prompted for your login password ***\n"; +- system "sudo chown -R $owner $path"; ++ system "sudo chown -R $owner $destdir.$path"; + } + + sub cgiurl { diff --git a/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch b/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch new file mode 100644 index 000000000..1e96bb8c6 --- /dev/null +++ b/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch @@ -0,0 +1,19 @@ +--- install_util/GBrowseInstall.pm.ori 2011-07-30 20:42:02.000000000 +0200 ++++ install_util/GBrowseInstall.pm 2011-07-30 20:42:19.000000000 +0200 +@@ -486,11 +486,11 @@ + my $base = basename($self->install_path->{htdocs}); + + # Configure the databases, if needed. +- print STDERR "Updating user account database...\n"; +- my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); +- my $perl = $self->perl; +- my @inc = map{"-I$_"} split ':',$self->added_to_INC; +- system $perl,@inc,$metadb_script; ++# print STDERR "Updating user account database...\n"; ++# my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); ++# my $perl = $self->perl; ++# my @inc = map{"-I$_"} split ':',$self->added_to_INC; ++# system $perl,@inc,$metadb_script; + system 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.$userdata; + + # if (Module::Build->y_n( diff --git a/sci-biology/gbrowse/files/fix-PNG-export.patch b/sci-biology/gbrowse/files/fix-PNG-export.patch new file mode 100644 index 000000000..469f75202 --- /dev/null +++ b/sci-biology/gbrowse/files/fix-PNG-export.patch @@ -0,0 +1,11 @@ +--- lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm.ori 2011-07-30 17:14:28.000000000 +0200 ++++ lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm 2011-07-30 17:13:13.000000000 +0200 +@@ -30,7 +30,7 @@ + sub setting { + my $self = shift; + my ($label,$option,@rest) = @_ >= 2 ? @_ : ('general',@_); +- $label = 'general' if lc $label eq 'general'; # buglet ++ $label = 'general' if lc($label) eq 'general'; # buglet + $self->SUPER::setting($label,$option,@rest); + } + diff --git a/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch b/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch new file mode 100644 index 000000000..0f7d5d373 --- /dev/null +++ b/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch @@ -0,0 +1,55 @@ +--- bin/gbrowse_metadb_config.pl.ori 2011-07-30 19:57:33.000000000 +0200 ++++ bin/gbrowse_metadb_config.pl 2011-07-30 20:04:51.000000000 +0200 +@@ -703,9 +703,9 @@ + local $database->{AutoCommit} = 0; + local $database->{RaiseError} = 1; + eval { +- $database->do("delete from $table"); +- $database->do("insert into $table (schema_version) values ($version)"); +- $database->commit(); ++ $database->do("delete from $table") or warn "delete from $table failed with: $database->errstr"; ++ $database->do("insert into $table (schema_version) values ($version)") or warn "insert into $table (schema_version) values ($version) failed with: $database->errstr"; ++ $database->commit() or warn "commitfailed with: $database->errstr"; + }; + if ($@) { + warn "update failed due to $@. Rolling back"; +@@ -768,11 +768,11 @@ + $insert_user->finish; + # rename the current users table + $database->do('drop table users') +- or die "Couldn't drop old users table"; ++ or die "Couldn't drop old users table: $database->errstr"; + $database->do('alter table users_new rename to users') +- or die "Couldn't rename new users table"; ++ or die "Couldn't rename new users table: $database->errstr"; + $database->do('create index index_session on session(username)') +- or die "Couldn't index sessions table"; ++ or die "Couldn't index sessions table: $database->errstr"; + + # now do the uploads table + # this upgrades to latest version 0 +@@ -808,9 +808,9 @@ + $insert->finish(); + + $database->do('drop table uploads') +- or die "Couldn't drop old uploads table"; ++ or die "Couldn't drop old uploads table: $database->errstr"; + $database->do('alter table uploads_new rename to uploads') +- or die "Couldn't rename new uploads table"; ++ or die "Couldn't rename new uploads table: $database->errstr"; + + # now do the openid_users table + # this creates the new one +@@ -916,10 +916,10 @@ + $select->finish; + $insert->finish; + $database->do('drop table users') +- or die "Couldn't drop old users table"; ++ or die "Couldn't drop old users table: $database->errstr"; + + $database->do('alter table users_new rename to users') +- or die "Couldn't rename new users table"; ++ or die "Couldn't rename new users table: $database->errstr"; + $database->commit(); + }; + diff --git a/sci-biology/gbrowse/files/symlink.patch b/sci-biology/gbrowse/files/symlink.patch new file mode 100644 index 000000000..e6df771ee --- /dev/null +++ b/sci-biology/gbrowse/files/symlink.patch @@ -0,0 +1,11 @@ +--- install_util/GBrowseInstall.pm.ori 2011-07-30 19:41:55.000000000 +0200 ++++ install_util/GBrowseInstall.pm 2011-07-30 19:42:31.000000000 +0200 +@@ -465,7 +465,7 @@ + chown $uid,-1,$destdir.$htdocs; + { + local $> = $uid; +- symlink($images,$htdocs_i); # so symlinkifowner match works! ++ symlink($images,$destdir.$htdocs_i) or warn "symlink($images,$destdir.$htdocs_i) failed: $!\n"; # so symlinkifowner match works! + } + chown $>,-1,$destdir.$self->install_path->{htdocs}; + diff --git a/sci-biology/gbrowse/gbrowse-2.38.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild index ea981ca01..d4cee63ef 100644 --- a/sci-biology/gbrowse/gbrowse-2.38.ebuild +++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild @@ -28,17 +28,17 @@ SRC_URI=" LICENSE="Artistic" # webapp ebuilds do not set SLOT KEYWORDS="~x86 ~amd64" -IUSE="-minimal svg test" # lwp moby scf +IUSE="cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf S="${WORKDIR}/${MY_P}" # TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) -# TODO: make sure www-servers/apache +cgi +# how about mod_fcgi and dev-libs/fcgi and mod_scgi? DEPEND=" >=perl-core/Module-Build-0.380.0 >=dev-lang/perl-5.8.8 dev-perl/Capture-Tiny - >=sci-biology/bioperl-1.6 + >=sci-biology/bioperl-1.6.901 >=dev-perl/GD-2.07 dev-perl/IO-String virtual/perl-Digest-MD5 @@ -47,20 +47,18 @@ DEPEND=" >=dev-perl/Bio-Graphics-1.97 >=dev-perl/JSON-2.510.0 dev-perl/libwww-perl - svg? ( dev-perl/GD-SVG )" + svg? ( dev-perl/GD-SVG ) + pdf? ( media-gfx/inkscape ) + mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg ) + sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src # TODO: based on the following message in apache/error_log the list of deps should be longer # GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase -# TODO: implement ebuild checks for these version of packages -# ! Bio::Root::Version (1.006001) is installed, but we need version >= 1.0069 -# * Bio::DB::BigFile is not installed -# * Bio::DB::Sam is not installed, install http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.29 -# * DBD::Pg is not installed -# >=perl-gcpan/Text-ParseWords-3.27 - RDEPEND="${DEPEND} >=www-servers/apache-2.0.47 + fastcgi? ( dev-libs/fcgi ) www-apache/mod_fastcgi dev-perl/DBI || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) @@ -84,12 +82,20 @@ RDEPEND="${DEPEND} dev-perl/XML-Parser dev-perl/Bio-Das dev-perl/Text-Shellwords + postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 ) + >=dev-perl/Bio-SamTools-1.29 + >=dev-perl/Bio-BigFile-1.06 )" src_prepare() { sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die sed -i 's/process_/bp_process_/g' INSTALL || die - epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch" + epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch" + epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch" + epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch" + epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patch" + epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to apply gbrowse_metadb_config.pl.patch" + epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch" } src_configure() { @@ -143,8 +149,7 @@ src_install() { pkg_postinst() { webapp_pkg_postinst || die "webapp_pkg_postinst failed" - einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or the live database" - einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch" + einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database." } src_test() { diff --git a/sci-biology/genepop/Manifest b/sci-biology/genepop/Manifest index 8b2b7def8..3ff6e6b88 100644 --- a/sci-biology/genepop/Manifest +++ b/sci-biology/genepop/Manifest @@ -1,2 +1,4 @@ DIST genepop-4.0.10.zip 843785 RMD160 8d27e63681929f5cfceec90ce82763c32694cd2a SHA1 a2c4abf99c979197e516fda54a406714d9cfd697 SHA256 22c8134b6be30e9b6983e289ad97bc9e096cc5fed363d9650d9623e21d34a3d2 EBUILD genepop-4.0.10.ebuild 891 RMD160 1c2734b78bc5838e17770b774be3d6081e882463 SHA1 2b5addf43b8b7e2aa37542c1f9c4ce7b5a554634 SHA256 fef787e3ec6caa003b158f5c493e4e71852679ca7ba403d7cbde9c217a225c40 +MISC ChangeLog 218 RMD160 568adfec5156eeca1024dd40e035b257394a5979 SHA1 01158b792ad73647f0ac7b02c511e771baa8c4ef SHA256 33b81ae52ddb9e87ee8cf798f0f6e5cfcf48cf7acb86cf45a43994c825bbd1ba +MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/mreps/Manifest b/sci-biology/mreps/Manifest index f0df4f77c..6d97720d5 100644 --- a/sci-biology/mreps/Manifest +++ b/sci-biology/mreps/Manifest @@ -1,3 +1,4 @@ DIST mreps-2.5.tar.gz 28017 RMD160 11f43d34dad37d0c4037ffd1953cf9b6b6a71ba0 SHA1 48f6abd68fa2082bb1c2b259e93c37074e4b9f50 SHA256 fa39c37787311903ce93e1ab519dc00ca0b104285beae400aa5f72e148d17a58 EBUILD mreps-2.5.ebuild 490 RMD160 ec90ce9d2f0a3dfb49dbe11701bac99f7d7b3bf0 SHA1 cf1d14f7150f9cf881d5a2e22b995347f244a990 SHA256 72554c07857ae8e53467d6fa43f515736a3dbd725bd63e53074459c1f2129a5f +MISC ChangeLog 216 RMD160 497466b9dac3cdd72c2a66413927d975ab8d6f2b SHA1 2e4a136bbc18d7ba06c5823d1fb3f98ba06a0064 SHA256 dc5394c3b15d800a716ed142eaabc45ad82af552f882025427d10c37a97785a7 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog new file mode 100644 index 000000000..67fd8f4ba --- /dev/null +++ b/sci-biology/sra_sdk/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/sra_sdk +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + sra_sdk-2.0.1.ebuild: + backbone of a new package, should probably use a lot of stuff from + ncbi-tools++ ebuild + diff --git a/sci-biology/sra_sdk/Manifest b/sci-biology/sra_sdk/Manifest index 81d92e2a8..cc86577b3 100644 --- a/sci-biology/sra_sdk/Manifest +++ b/sci-biology/sra_sdk/Manifest @@ -1,3 +1,4 @@ DIST sra_sdk-2.0.1.tar.gz 1830293 RMD160 5ee0bbf61484c0afc374bd026792ca7b1f0e99d5 SHA1 cbf5e650c9cd779041a624b3a7e896bf01da1b43 SHA256 6bffbfd21a3e412dce74c26ca579cc9b9a0a66f541ecbce555b2600558f63da4 -EBUILD sra_sdk-2.0.1.ebuild 1498 RMD160 0cc4febbe45098b3900bc9b05f0e6ada561c0991 SHA1 10d46ac94359fe1dc83ee48cc5335e0f4023f587 SHA256 256342ef57d24a952a2872e3b2837550384a31ac3be77fc92e1b66846c5c07c4 +EBUILD sra_sdk-2.0.1.ebuild 1600 RMD160 461e2c47d431a81319b65e0fff50900fb5091fa2 SHA1 454fad14ac6a1f3b1a6bedd4009f77506269fec7 SHA256 ea1ed7ccdf2ecca7eb72fa8aa5bb5da1802569860f9ad7fce994782d820f339d +MISC ChangeLog 296 RMD160 405c2604a97eb9a00c95dc2ba4c1df7bec2a7716 SHA1 b97a47218446b00458b16b268b9152359a67a85b SHA256 26aa108198103be6dc46e3fad8256d5a1e567b5747aee9a64dcd1b8d9e0211df MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild index f8708e1be..5777c88ba 100644 --- a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild +++ b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild @@ -7,10 +7,12 @@ EAPI=3 DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit" HOMEPAGE="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_runs_v1&m=downloads&s=download_sra" SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz" +# http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-centos_linux64.tar.gz LICENSE="public-domain" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="" +#KEYWORDS="~amd64 ~x86" IUSE="" DEPEND="app-shells/bash diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog deleted file mode 100644 index d51fa1a46..000000000 --- a/sci-chemistry/ambertools/ChangeLog +++ /dev/null @@ -1,29 +0,0 @@ -# ChangeLog for sci-chemistry/ambertools -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 24 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild, - -files/ambertools-1.4-bugfix_1-18.patch, ambertools-1.5.ebuild, - -files/ambertools-1.5-bugfix_1-3.patch: - Cleaned ebuild - - 23 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild, - ambertools-1.5.ebuild: - Streamlined fortran-2 eclass usage - - 21 Jun 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild, - ambertools-1.5.ebuild: - Added fortran-2.eclass support - -*ambertools-1.5 (04 Jun 2011) - - 04 Jun 2011; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5.ebuild, - +files/ambertools-1.5-bugfix_1-3.patch, +files/ambertools-1.5-gentoo.patch: - Version bump. - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild: - Remove fortran.eclass - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> ambertools-1.4.ebuild: - Remove fortran.eclass removal - diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest deleted file mode 100644 index 98d79e2e3..000000000 --- a/sci-chemistry/ambertools/Manifest +++ /dev/null @@ -1,20 +0,0 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - -AUX ambertools-1.4-gentoo.patch 9926 RMD160 d84b121e1fa940cbf949855de3a5f0bee7566330 SHA1 08ea41b969bed5320230420d047e71a28333f76c SHA256 8f520c01146a704173ca31c68dc9440e2938263416f6d0c95de22d138426e01f -AUX ambertools-1.5-gentoo.patch 14083 RMD160 762c52626c4eda51839caf74c001bb660052706a SHA1 ab0afa1f5b73569539515dba4cf6638a594c7d6e SHA256 82a83f660701c192272e79f5bab17a8a8be945d78fdab454ade3918281749922 -DIST AmberTools-1.4.tar.bz2 67331137 RMD160 b499e18b583a0b454dd3a554986c19c111822e6a SHA1 ef0f9a44c8767ed35f942fd41afc636b67da0389 SHA256 af61da2f3643b4ec7f41620242b734a3cb4a79c5d422100fbd1fd1c402fecfc1 -DIST AmberTools-1.5.tar.bz2 121062582 RMD160 4a086b42c378f0904f7bf0b16adb042f1677be55 SHA1 92e47e7337fb4901a5a145d808c5ffd42c82d08d SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c -DIST ambertools-1.4-bugfix_1-18.patch.xz 48136 RMD160 83fe98ef2f4620cd4c85fc72147f830ddfa47b51 SHA1 7a5a2cba9172d017d83aed16ece06d6fed6a5196 SHA256 7ea936442ce1b29943e867adaeb69932d297ae50e0a63b0e03cfb18953e9f7c2 -DIST ambertools-1.5-bugfix_1-3.patch.xz 27268 RMD160 18a74e2e84e81d39417f656ef93e8ee4d4d4583d SHA1 bc52c0776d151a8db005bb7bfb40bf9e963bdeba SHA256 edec6ccc275ee0a70b2ecc9316c031249c4f32d89b1aa145cee32c862516049a -EBUILD ambertools-1.4.ebuild 3201 RMD160 b2f4331166bafc5093f04c4e7ad9bf2eee9ee0e5 SHA1 4033d6225f7e86d42292eed5ddecd7edeb6742ec SHA256 e3a77f1a006832c46117a5c6a6a641685965f8dfe0c949c0ec1e2f7e57f73835 -EBUILD ambertools-1.5.ebuild 3336 RMD160 d97fc7eade8bcf0d12596d42a512560671751d18 SHA1 0427a45349e95be91e274d0e12eb2eb484da6dd3 SHA256 8f8f33770cb12253fef10e9b651a567de36a2863d674b82ca3b1959ab8684353 -MISC ChangeLog 979 RMD160 02da25807e2c08495e5e6ed5803c8db37b6f0630 SHA1 086394d21356fb100929d5f86e86a098d34abe43 SHA256 c3cf8fabe0c249e1b500319df8296405392fa976fb599d941544af342d292aec -MISC metadata.xml 263 RMD160 9484584cc295931e963dc785e211261f68e48c82 SHA1 a2c5af57c8eb879a4249fc0240432a4fc5b91ca5 SHA256 0e94df6d8502bc41ccd18ec4d570490e245c08595e837fd116a255458939e69b ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4E9DkACgkQgAnW8HDreRa8NwCg0fxLgoMsWuqoreVAAV0tzOgb -Bp4An3RO97c8j9rzfFLDjx6ix2ySY7kE -=zAXR ------END PGP SIGNATURE----- diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemistry/ambertools/ambertools-1.4.ebuild deleted file mode 100644 index 5e75cdb63..000000000 --- a/sci-chemistry/ambertools/ambertools-1.4.ebuild +++ /dev/null @@ -1,133 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" -HOMEPAGE="http://ambermd.org/#AmberTools" -SRC_URI=" - AmberTools-${PV}.tar.bz2 - mirror://gentoo/${P}-bugfix_1-18.patch.xz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="mpi openmp X" - -RESTRICT="fetch" - -RDEPEND=" - virtual/cblas - virtual/lapack - sci-libs/arpack - sci-libs/cifparse-obj - sci-chemistry/mopac7 - sci-libs/netcdf - sci-chemistry/reduce - virtual/fortran" -DEPEND="${RDEPEND} - dev-util/byacc - dev-libs/libf2c - sys-devel/ucpp" -S="${WORKDIR}/amber11" - -pkg_nofetch() { - einfo "Go to ${HOMEPAGE} and get ${A}" - einfo "Place it in ${DISTDIR}" -} - -pkg_setup() { - fortran-2_pkg_setup - if use openmp; then - tc-has-openmp || \ - die "Please select an openmp capable compiler like gcc[openmp]" - fi - AMBERHOME="${S}" -} - -src_prepare() { - epatch \ - "${WORKDIR}/${P}-bugfix_1-18.patch" \ - "${FILESDIR}/${P}-gentoo.patch" - cd AmberTools/src - rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die -} - -src_configure() { - cd AmberTools/src - sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ - -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \ - -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ - -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ - -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ - -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \ - -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \ - -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \ - -e "s:fc=g77:fc=$(tc-getFC):g" \ - -e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=$(pkg-config netcdf --libs):g" \ - -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ - -e "s:-O3::g" \ - -i configure || die - sed -e "s:arsecond_:arscnd_:g" \ - -i sff/time.c \ - -i sff/sff.h \ - -i sff/sff.c || die - sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ - -i nss/Makefile || die - - local myconf - - use X || myconf="${myconf} -noX11" - - for x in mpi openmp; do - use ${x} && myconf="${myconf} -${x}" - done - - ./configure \ - ${myconf} \ - -nobintraj \ - gnu -# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') -} - -src_compile() { - cd AmberTools/src - emake || die -} - -src_install() { - for x in bin/* - do dobin ${x} || die - done - rm "${ED}/usr/bin/yacc" - dobin AmberTools/src/antechamber/mopac.sh - sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ - -i "${ED}/usr/bin/mopac.sh" || die - # Make symlinks untill binpath for amber will be fixed - dodir /usr/share/${PN}/bin - cd "${ED}/usr/bin" - for x in * - do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} - done - cd "${S}" -# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ -# -i "${ED}/usr/bin/xleap" \ -# -i "${ED}/usr/bin/tleap" || die - dodoc doc/AmberTools.pdf doc/leap_pg.pdf - dolib.a lib/* - insinto /usr/include/${PN} - doins include/* - insinto /usr/share/${PN} - doins -r dat - cd AmberTools - doins -r benchmarks - doins -r examples - doins -r test - cat >> "${T}"/99ambertools <<- EOF - AMBERHOME="${EPREFIX}/usr/share/ambertools" - EOF - doenvd "${T}"/99ambertools -} diff --git a/sci-chemistry/ambertools/ambertools-1.5.ebuild b/sci-chemistry/ambertools/ambertools-1.5.ebuild deleted file mode 100644 index 9ac9755e7..000000000 --- a/sci-chemistry/ambertools/ambertools-1.5.ebuild +++ /dev/null @@ -1,140 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" -HOMEPAGE="http://ambermd.org/#AmberTools" -SRC_URI=" - AmberTools-${PV}.tar.bz2 - mirror://gentoo/${P}-bugfix_1-3.patch.xz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="mpi openmp X" - -RESTRICT="fetch" - -RDEPEND=" - virtual/cblas - virtual/lapack - sci-libs/clapack - sci-libs/arpack - sci-libs/cifparse-obj - sci-chemistry/mopac7 - sci-libs/netcdf - sci-libs/fftw:2.1 - sci-chemistry/reduce - virtual/fortran" -DEPEND="${RDEPEND} - dev-util/byacc - dev-libs/libf2c - sys-devel/ucpp" -S="${WORKDIR}/amber11" - -pkg_nofetch() { - einfo "Go to ${HOMEPAGE} and get ${A}" - einfo "Place it in ${DISTDIR}" -} - -pkg_setup() { - fortran-2_pkg_setup - if use openmp; then - tc-has-openmp || \ - die "Please select an openmp capable compiler like gcc[openmp]" - fi - AMBERHOME="${S}" -} - -src_prepare() { - epatch \ - "${WORKDIR}/${P}-bugfix_1-3.patch" \ - "${FILESDIR}/${P}-gentoo.patch" - cd AmberTools/src - rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die -} - -src_configure() { - cd AmberTools/src - sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ - -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \ - -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ - -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ - -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ - -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \ - -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \ - -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \ - -e "s:fc=g77:fc=$(tc-getFC):g" \ - -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ - -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ - -e "s:-O3::g" \ - -i configure || die - sed -e "s:arsecond_:arscnd_:g" \ - -i sff/time.c \ - -i sff/sff.h \ - -i sff/sff.c || die - sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ - -i nss/Makefile || die - - local myconf - - use X || myconf="${myconf} -noX11" - - for x in mpi openmp; do - use ${x} && myconf="${myconf} -${x}" - done - - ./configure \ - ${myconf} \ - -nobintraj \ - -nomdgx \ - -nopython \ - -nomtkpp \ - gnu -# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') -} - -src_compile() { - cd AmberTools/src - emake || die -} - -src_install() { - rm -r bin/chemistry bin/MMPBSA_mods - rm bin/ante-MMPBSA.py bin/extractFrcmod.py - for x in bin/* - do dobin ${x} || die - done - rm "${ED}/usr/bin/yacc" - dobin AmberTools/src/antechamber/mopac.sh - sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ - -i "${ED}/usr/bin/mopac.sh" || die - # Make symlinks untill binpath for amber will be fixed - dodir /usr/share/${PN}/bin - cd "${ED}/usr/bin" - for x in * - do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} - done - cd "${S}" -# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ -# -i "${ED}/usr/bin/xleap" \ -# -i "${ED}/usr/bin/tleap" || die - dodoc doc/AmberTools.pdf doc/leap_pg.pdf - dolib.a lib/* - insinto /usr/include/${PN} - doins include/* - insinto /usr/share/${PN} - doins -r dat - cd AmberTools - doins -r benchmarks - doins -r examples - doins -r test - cat >> "${T}"/99ambertools <<- EOF - AMBERHOME="${EPREFIX}/usr/share/ambertools" - EOF - doenvd "${T}"/99ambertools -} diff --git a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch deleted file mode 100644 index c067928cb..000000000 --- a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch +++ /dev/null @@ -1,289 +0,0 @@ -diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure ---- amber11.orig/AmberTools/src/configure 2010-04-23 18:17:17.000000000 +0400 -+++ amber11/AmberTools/src/configure 2011-03-07 03:39:14.000000000 +0300 -@@ -288,11 +288,11 @@ - mpi_flag= - lex=flex - flibs_mkl= --lapack=install --blas=install -+lapack=skip -+blas=skip - f2c=skip --ucpp=install --cpp="\$(BINDIR)/ucpp -l" -+ucpp=skip -+cpp="\$(EPREFIX)/usr/bin/ucpp -l" - - #----------------------------------- - # skip building of sleap? -@@ -1241,24 +1241,24 @@ - #-------------------------------------------------------------------------- - # Configure fftw-3.2.2: - #-------------------------------------------------------------------------- -- if [ "$mdgx" = 'yes' ]; then -- mdgxflag="--prefix=$AMBERHOME --disable-fortran" -- echo -- echo "Configuring fftw-3.2.2; (may be time-consuming)" -- echo -- cd fftw-3.2.2 && \ -- env CC="$cc" CFLAGS="$cflags" ./configure $mdgxflag \ -- > ../fftw3_config.log 2>&1 -- ncerror=$? -- if [ $ncerror -gt 0 ]; then -- echo " Error: fftw configure returned $ncerror" -- echo " fftw configure failed! Check the fftw3_config.log file." -- exit 1 -- else -- echo " fftw-3.2.2 configure succeeded." -- fi -- cd .. -- fi -+ #if [ "$mdgx" = 'yes' ]; then -+ # mdgxflag="--prefix=$AMBERHOME --disable-fortran" -+ # echo -+ # echo "Configuring fftw-3.2.2; (may be time-consuming)" -+ # echo -+ # cd fftw-3.2.2 && \ -+ # env CC="$cc" CFLAGS="$cflags" ./configure $mdgxflag \ -+ # > ../fftw3_config.log 2>&1 -+ # ncerror=$? -+ # if [ $ncerror -gt 0 ]; then -+ # echo " Error: fftw configure returned $ncerror" -+ # echo " fftw configure failed! Check the fftw3_config.log file." -+ # exit 1 -+ # else -+ # echo " fftw-3.2.2 configure succeeded." -+ # fi -+ # cd .. -+ #fi - - #-------------------------------------------------------------------------- - # Set up MPI 3D-RISM in NAB and SANDER -@@ -1307,23 +1307,23 @@ - echo - echo "Configuring fftw-2.1.5; (may be time-consuming)" - echo -- cd fftw-2.1.5 -- if [ "$mpi" = 'yes' ]; then -- ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \ -- > ../fftw2_config.log 2>&1 -- else -- ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \ -- > ../fftw2_config.log 2>&1 -- fi -- ncerror=$? -- if [ $ncerror -gt 0 ]; then -- echo " Error: fftw configure returned $ncerror" -- echo " fftw configure failed! Check the fftw2_config.log file." -- exit 1 -- else -- echo " fftw-2.1.5 configure succeeded." -- fi -- cd .. -+ # cd fftw-2.1.5 -+ # if [ "$mpi" = 'yes' ]; then -+ # ./configure $rismflag --enable-mpi CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \ -+ # > ../fftw2_config.log 2>&1 -+ # else -+ # ./configure $rismflag CC="$cc" CFLAGS="$cflags" F77="$fc" FFLAGS="$fflags" \ -+ # > ../fftw2_config.log 2>&1 -+ # fi -+ # ncerror=$? -+ # if [ $ncerror -gt 0 ]; then -+ # echo " Error: fftw configure returned $ncerror" -+ # echo " fftw configure failed! Check the fftw2_config.log file." -+ # exit 1 -+ # else -+ # echo " fftw-2.1.5 configure succeeded." -+ # fi -+ # cd .. - flibs_fftw2="\$(LIBDIR)/libdrfftw.a \$(LIBDIR)/libdfftw.a" - if [ "$mpi" = 'yes' ]; then - flibs_fftw2="\$(LIBDIR)/libdrfftw_mpi.a \$(LIBDIR)/libdfftw_mpi.a $flibs_fftw2" -diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile ---- amber11.orig/AmberTools/src/Makefile 2010-04-14 17:36:31.000000000 +0400 -+++ amber11/AmberTools/src/Makefile 2011-03-07 03:39:38.000000000 +0300 -@@ -8,15 +8,15 @@ - - install: serial - --serial: configured_serial $(NETCDFLIB) -+serial: configured_serial - @echo "Starting installation of ${AMBERTOOLS} serial at `date`". - # utility routines and libraries: -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd byacc && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) -- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -+# (cd arpack && $(MAKE) install ); -+# (cd lapack && $(MAKE) $(LAPACK) ) -+# (cd blas && $(MAKE) $(BLAS) ) -+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) - (cd etc && $(MAKE) install ) - (cd chamber && $(MAKE) install ) - (cd pbsa && $(MAKE) install ) -@@ -30,14 +30,14 @@ - (cd ptraj && $(MAKE) install ) - - # miscellaneous: -- (cd reduce && $(MAKE) install ) -+# (cd reduce && $(MAKE) install ) - - # leap and gleap: - (cd leap && $(MAKE) install ) - (cd gleap && $(MAKE) install ) - - # nab: -- (cd cifparse && $(MAKE) install ) -+# (cd cifparse && $(MAKE) install ) - (cd nab && $(MAKE) install ) - (cd nss && $(MAKE) install ) - -@@ -50,15 +50,15 @@ - - nabonly: $(NETCDFLIB) - # utility routines and libraries: -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd byacc && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) -- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -+# (cd arpack && $(MAKE) install ); -+# (cd lapack && $(MAKE) $(LAPACK) ) -+# (cd blas && $(MAKE) $(BLAS) ) -+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) - - # nab: -- (cd cifparse && $(MAKE) install ) -+# (cd cifparse && $(MAKE) install ) - (cd nab && $(MAKE) install ) - (cd nss && $(MAKE) install ) - -diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile ---- amber11.orig/AmberTools/src/pbsa/Makefile 2010-04-14 17:26:17.000000000 +0400 -+++ amber11/AmberTools/src/pbsa/Makefile 2011-03-07 03:39:15.000000000 +0300 -@@ -47,10 +47,10 @@ - $(LIBDIR)/libpbsa.a $(LIBDIR)/libFpbsa.a - - #--------------------------------------------------------------------------- --pbsa$(SFX): $(OBJ) syslib netlib c9x-complex -+pbsa$(SFX): $(OBJ) syslib - $(FC) -o pbsa$(SFX) $(OBJ) ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS) - --simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex -+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib - $(FC) -o simplepbsa$(SFX) simplepbsa.o gopt.o libpbsa.a \ - $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS) - /bin/mv simplepbsa$(SFX) $(BINDIR) -@@ -76,15 +76,15 @@ - sfflib: - cd ../sff && $(MAKE) install - --netlib: -- cd ../lapack && $(MAKE) $(LAPACK) -- cd ../blas && $(MAKE) $(BLAS) -- cd ../arpack && $(MAKE) install -- --c9x-complex: -- @if test $(C9XCOMPLEX) != "skip"; then \ -- cd ../c9x-complex && $(MAKE) libmc.a; \ -- fi -+#netlib: -+# cd ../lapack && $(MAKE) $(LAPACK) -+# cd ../blas && $(MAKE) $(BLAS) -+# cd ../arpack && $(MAKE) install -+ -+#c9x-complex: -+# @if test $(C9XCOMPLEX) != "skip"; then \ -+# cd ../c9x-complex && $(MAKE) libmc.a; \ -+# fi - - %.LIBPBSA.o: %.f - $(FPP) -DLIBPBSA $< > _$< -diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile ---- amber11.orig/AmberTools/src/ptraj/Makefile 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/Makefile 2011-03-07 03:39:16.000000000 +0300 -@@ -60,20 +60,20 @@ - rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) - $(CC) $(LDFLAGS) -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) - --ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) -+ptraj$(SFX): libs $(NETCDFLIB) $(OBJECTS) - $(CC) $(LDFLAGS) -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) - --ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) -+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) - $(CC) $(LDFLAGS) -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM) - # - - libs: - cd pdb && $(MAKE) -- cd ../arpack && $(MAKE) -+# cd ../arpack && $(MAKE) - --netlib: -- cd ../lapack; $(MAKE) $(LAPACK) -- cd ../blas; $(MAKE) $(BLAS) -+#netlib: -+# cd ../lapack; $(MAKE) $(LAPACK) -+# cd ../blas; $(MAKE) $(BLAS) - - clean: - cd pdb; $(MAKE) clean -diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h ---- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-03-07 03:39:17.000000000 +0300 -@@ -4,7 +4,7 @@ - # include "../pnetcdf/include/pnetcdf.h" - # define nc_strerror ncmpi_strerror - # else --# include "../netcdf/include/netcdf.h" -+# include <netcdf.h> - # endif - #endif - -diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h ---- amber11.orig/AmberTools/src/ptraj/ptraj.h 2010-03-31 07:05:16.000000000 +0400 -+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-03-07 03:39:17.000000000 +0300 -@@ -94,7 +94,7 @@ - #define nc_strerror ncmpi_strerror - #include "../pnetcdf/include/pnetcdf.h" - #else --#include "../netcdf/include/netcdf.h" -+#include <netcdf.h> - #endif - #endif - -diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile ---- amber11.orig/AmberTools/src/sqm/Makefile 2010-04-14 16:13:28.000000000 +0400 -+++ amber11/AmberTools/src/sqm/Makefile 2011-03-07 03:39:17.000000000 +0300 -@@ -77,7 +77,7 @@ - install: sqm$(SFX) - mv sqm$(SFX) $(BINDIR) - --sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys -+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys - $(FC) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) $(FLIBSF) ../lib/sys.a $(LDFLAGS) - - #-----------LIBS -@@ -93,10 +93,10 @@ - sys: - cd ../lib; $(MAKE) sys.a - --netlib: -- cd ../lapack; $(MAKE) $(LAPACK) -- cd ../blas; $(MAKE) $(BLAS) -- cd ../arpack && $(MAKE) install -+#netlib: -+# cd ../lapack; $(MAKE) $(LAPACK) -+# cd ../blas; $(MAKE) $(BLAS) -+# cd ../arpack && $(MAKE) install - - clean: - /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch deleted file mode 100644 index 0e41d26d6..000000000 --- a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch +++ /dev/null @@ -1,386 +0,0 @@ -diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure ---- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 +0300 -+++ amber11/AmberTools/src/configure 2011-06-04 12:26:45.000000000 +0300 -@@ -293,7 +293,8 @@ - echo "Your AMBERHOME environment variable is not set! It should be set to" - echo "$ambhome NOT doing so may cause errors when you compile. Continue" - echo "anyway? (yes or no)" -- read answer -+ #read answer -+ answer='yes' - if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then - echo "" - echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily" -@@ -356,11 +357,11 @@ - mpi_flag= - lex=flex - flibs_mkl= --lapack=install --blas=install -+lapack=skip -+blas=skip - f2c=skip --ucpp=install --cpp="\$(BINDIR)/ucpp -l" -+ucpp=skip -+cpp="\$(EPREFIX)/usr/bin/ucpp -l" - - #----------------------------------- - # skip building of sleap? -@@ -1655,24 +1656,24 @@ - #-------------------------------------------------------------------------- - # Configure fftw-3.2.2: - #-------------------------------------------------------------------------- -- if [ "$mdgx" = 'yes' ]; then -- mdgxflag="--prefix=$AMBERHOME --disable-fortran" -- echo -- echo "Configuring fftw-3.2.2 (may be time-consuming)..." -- echo -- cd fftw-3.2.2 && \ -- env CC="$cc" CFLAGS="$cflags $cnooptflags" \ -- ./configure $mdgxflag > ../fftw3_config.log 2>&1 -- ncerror=$? -- if [ $ncerror -gt 0 ]; then -- echo " Error: FFTW configure returned $ncerror" -- echo " FFTW configure failed! Check the fftw3_config.log file." -- exit 1 -- else -- echo " fftw-3.2.2 configure succeeded." -- fi -- cd .. -- fi -+ #if [ "$mdgx" = 'yes' ]; then -+ # mdgxflag="--prefix=$AMBERHOME --disable-fortran" -+ # echo -+ # echo "Configuring fftw-3.2.2 (may be time-consuming)..." -+ # echo -+ # cd fftw-3.2.2 && \ -+ # env CC="$cc" CFLAGS="$cflags $cnooptflags" \ -+ # ./configure $mdgxflag > ../fftw3_config.log 2>&1 -+ # ncerror=$? -+ # if [ $ncerror -gt 0 ]; then -+ # echo " Error: FFTW configure returned $ncerror" -+ # echo " FFTW configure failed! Check the fftw3_config.log file." -+ # exit 1 -+ # else -+ # echo " fftw-3.2.2 configure succeeded." -+ # fi -+ # cd .. -+ #fi - - #-------------------------------------------------------------------------- - # Configure python -@@ -1792,27 +1793,27 @@ - echo - echo "Configuring fftw-2.1.5 (may be time-consuming)..." - echo -- cd fftw-2.1.5 -- if [ "$mpi" = 'yes' ]; then -- ./configure $rismflag --enable-mpi \ -- CC="$cc" CFLAGS="$cflags $coptflags" \ -- F77="$fc" FFLAGS="$fflags $foptflags" \ -- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 -- else -- ./configure $rismflag \ -- CC="$cc" CFLAGS="$cflags $coptflags" \ -- F77="$fc" FFLAGS="$fflags $foptflags" \ -- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 -- fi -- ncerror=$? -- if [ $ncerror -gt 0 ]; then -- echo " Error: fftw configure returned $ncerror" -- echo " fftw configure failed! Check the fftw2_config.log file." -- exit 1 -- else -- echo " fftw-2.1.5 configure succeeded." -- fi -- cd .. -+ # cd fftw-2.1.5 -+ # if [ "$mpi" = 'yes' ]; then -+ # ./configure $rismflag --enable-mpi \ -+ # CC="$cc" CFLAGS="$cflags $coptflags" \ -+ # F77="$fc" FFLAGS="$fflags $foptflags" \ -+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 -+ # else -+ # ./configure $rismflag \ -+ # CC="$cc" CFLAGS="$cflags $coptflags" \ -+ # F77="$fc" FFLAGS="$fflags $foptflags" \ -+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1 -+ # fi -+ # ncerror=$? -+ # if [ $ncerror -gt 0 ]; then -+ # echo " Error: fftw configure returned $ncerror" -+ # echo " fftw configure failed! Check the fftw2_config.log file." -+ # exit 1 -+ # else -+ # echo " fftw-2.1.5 configure succeeded." -+ # fi -+ # cd .. - flibs_fftw2="-ldrfftw -ldfftw" - if [ "$mpi" = 'yes' ]; then - flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2" -diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at ---- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300 -+++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-05-20 00:45:48.000000000 +0300 -@@ -65,8 +65,8 @@ - -/bin/rm FindDepend.o - -/bin/rm findDepend - --cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS) -- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -+cpptraj$(SFX): $(OBJECTS) -+ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp - - $(NETCDFLIB): ../../netcdf_config.log - cd ../../netcdf/src && $(MAKE) install -diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile ---- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 +0300 -+++ amber11/AmberTools/src/Makefile 2011-05-19 23:36:36.000000000 +0300 -@@ -8,15 +8,15 @@ - - install: $(INSTALLTYPE) - --serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP) -+serial: configured_serial - @echo "Starting installation of ${AMBERTOOLS} serial at `date`". - # utility routines and libraries: -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd byacc && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) -- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -+# (cd arpack && $(MAKE) install ); -+# (cd lapack && $(MAKE) $(LAPACK) ) -+# (cd blas && $(MAKE) $(BLAS) ) -+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) - (cd etc && $(MAKE) install ) - (cd chamber && $(MAKE) install ) - (cd pbsa && $(MAKE) install ) -@@ -32,7 +32,7 @@ - (cd cpptraj && $(MAKE) $(CPPTRAJ)) - - # miscellaneous: -- (cd reduce && $(MAKE) install ) -+# (cd reduce && $(MAKE) install ) - - # leap and gleap: - (cd leap && $(MAKE) install ) -@@ -42,7 +42,7 @@ - (cd rism && $(MAKE) install ) - - # nab: -- (cd cifparse && $(MAKE) install ) -+# (cd cifparse && $(MAKE) install ) - (cd sff && $(MAKE) install ) - (cd pbsa && $(MAKE) libinstall ) - (cd nab && $(MAKE) install ) -@@ -63,19 +63,19 @@ - @echo "Installation of ${AMBERTOOLS} serial is complete at `date`." - @echo "" - --nabonly: $(NETCDFLIB) -+nabonly: - # utility routines and libraries: -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd byacc && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) -- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -+# (cd arpack && $(MAKE) install ); -+# (cd lapack && $(MAKE) $(LAPACK) ) -+# (cd blas && $(MAKE) $(BLAS) ) -+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) - (cd pbsa && $(MAKE) libinstall ) - (cd rism && $(MAKE) install ) - - # nab: -- (cd cifparse && $(MAKE) install ) -+# (cd cifparse && $(MAKE) install ) - (cd sff && $(MAKE) install ) - (cd nab && $(MAKE) install ) - (cd nss && $(MAKE) install ) -diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile ---- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000000 +0300 -+++ amber11/AmberTools/src/mdgx/Makefile 2011-05-20 12:44:38.000000000 +0300 -@@ -109,7 +109,7 @@ - - FFTW_LIBS = $(LIBDIR)/libfftw3.a - --mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) -+mdgx$(SFX) : $(MDGX_OBJS) - $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ - -o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM) - -diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile ---- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000000 +0300 -+++ amber11/AmberTools/src/pbsa/Makefile 2011-05-19 22:27:40.000000000 +0300 -@@ -148,7 +148,7 @@ - ) - - #--------------------------------------------------------------------------- --pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial -+pbsa$(SFX): $(OBJ) syslib configured_serial - $(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \ - ../lib/nxtsec.o ../lib/random.o \ - $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) -@@ -158,7 +158,7 @@ - ../lib/nxtsec.o ../lib/random.o \ - $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) - --simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex -+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib - $(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \ - libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \ - $(LDFLAGS) $(AMBERLDFLAGS) -@@ -194,15 +194,15 @@ - sfflib: - cd ../sff && $(MAKE) install - --netlib: -- cd ../lapack && $(MAKE) $(LAPACK) -- cd ../blas && $(MAKE) $(BLAS) -- cd ../arpack && $(MAKE) install -- --c9x-complex: -- @if test $(C9XCOMPLEX) != "skip"; then \ -- cd ../c9x-complex && $(MAKE) libmc.a; \ -- fi -+#netlib: -+# cd ../lapack && $(MAKE) $(LAPACK) -+# cd ../blas && $(MAKE) $(BLAS) -+# cd ../arpack && $(MAKE) install -+ -+#c9x-complex: -+# @if test $(C9XCOMPLEX) != "skip"; then \ -+# cd ../c9x-complex && $(MAKE) libmc.a; \ -+# fi - - %.LIBPBSA.o: %.f - $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$< -diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile ---- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.000000000 +0300 -+++ amber11/AmberTools/src/ptraj/Makefile 2011-05-19 23:38:36.000000000 +0300 -@@ -57,25 +57,25 @@ - pubfft.o: pubfft.f - $(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $< - --rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) -+rdparm$(SFX): libs $(OBJECTS) - $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ - -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) - --ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) -+ptraj$(SFX): libs $(OBJECTS) - $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ - -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) - --ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) -+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) - $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ - -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM) - - libs: - cd pdb && $(MAKE) -- cd ../arpack && $(MAKE) -+# cd ../arpack && $(MAKE) - --netlib: -- cd ../lapack && $(MAKE) $(LAPACK) -- cd ../blas && $(MAKE) $(BLAS) -+#netlib: -+# cd ../lapack && $(MAKE) $(LAPACK) -+# cd ../blas && $(MAKE) $(BLAS) - - clean: - cd pdb && $(MAKE) clean -diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h ---- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19.000000000 +0300 -+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-05-19 22:30:43.000000000 +0300 -@@ -4,7 +4,7 @@ - # include "../../include/pnetcdf.h" - # define nc_strerror ncmpi_strerror - # else --# include "../../include/netcdf.h" -+# include <netcdf.h> - # endif - #endif - -diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h ---- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000000 +0300 -+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-06-04 13:25:01.000000000 +0300 -@@ -94,7 +94,7 @@ - #define nc_strerror ncmpi_strerror - #include "../../include/pnetcdf.h" - #else --#include "../../include/netcdf.h" -+#include <netcdf.h> - #endif - #endif - -diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile ---- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000000 +0300 -+++ amber11/AmberTools/src/rism/Makefile 2011-05-20 01:07:26.000000000 +0300 -@@ -49,7 +49,7 @@ - mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \ - fce_c.o erfcfun.o safemem.o blend.o timer_c.o - --librism: $(LIBOBJ) $(FLIBS_FFTW2) -+librism: $(LIBOBJ) - $(AR) $(LIBDIR)/$@.a $(LIBOBJ) - $(RANLIB) $(LIBDIR)/$@.a - -diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c ---- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.000000000 +0300 -+++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-05-20 10:49:06.000000000 +0300 -@@ -27,7 +27,7 @@ - #endif - - #ifdef BINTRAJ --#include "../../include/netcdf.h" -+#include <netcdf.h> - - #define NCFRAME "frame" - #define NCSPATIAL "spatial" -diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile ---- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.000000000 +0300 -+++ amber11/AmberTools/src/sff/Makefile 2011-05-20 09:53:27.000000000 +0300 -@@ -1,7 +1,7 @@ - include ../config.h - - .c.o: -- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $< -+ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $< - - OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \ - prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \ -diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile ---- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.000000000 +0300 -+++ amber11/AmberTools/src/sqm/Makefile 2011-05-19 22:31:49.000000000 +0300 -@@ -77,7 +77,7 @@ - install: sqm$(SFX) - mv sqm$(SFX) $(BINDIR) - --sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys -+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys - $(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \ - $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS) - -@@ -94,10 +94,10 @@ - sys: - cd ../lib; $(MAKE) sys.a - --netlib: -- cd ../lapack; $(MAKE) $(LAPACK) -- cd ../blas; $(MAKE) $(BLAS) -- cd ../arpack && $(MAKE) install -+#netlib: -+# cd ../lapack; $(MAKE) $(LAPACK) -+# cd ../blas; $(MAKE) $(BLAS) -+# cd ../arpack && $(MAKE) install - - clean: - /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) diff --git a/sci-libs/atlas/ChangeLog b/sci-libs/atlas/ChangeLog new file mode 100644 index 000000000..88c9d4caf --- /dev/null +++ b/sci-libs/atlas/ChangeLog @@ -0,0 +1,67 @@ +# ChangeLog for sci-libs/atlas +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*atlas-3.8.4 (06 Aug 2011) + + 06 Aug 2011; Andrea Arteaga <andyspiros@gmail.com> +atlas-3.8.4.ebuild: + Version 3.8.4 restored + +*atlas-3.9.47 (06 Aug 2011) + + 06 Aug 2011; Andrea Arteaga <andyspiros@gmail.com> atlas-3.9.47.ebuild: + Version bump + +*atlas-3.9.46 (03 Aug 2011) + + 03 Aug 2011; Andrea Arteaga <andyspiros@gmail.com> -atlas-3.8.4.ebuild, + -atlas-3.9.41.ebuild, +atlas-3.9.46.ebuild + Version bump and import from bicatali + +*atlas-3.8.4 (23 May 2011) + + 23 May 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.8.3.ebuild, + +atlas-3.8.4.ebuild: + Version bump of the stable branch + + 23 May 2011; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.9.41.ebuild: + Forces gcc whenever a version of gcc is used, avoiding upstream bug + +*atlas-3.9.41 (17 May 2011) + + 17 May 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.9.40-r1.ebuild, + +atlas-3.9.41.ebuild: + Version bump. Removed archdef 0 causing undefined symbols + +*atlas-3.9.40-r1 (29 Apr 2011) + + 29 Apr 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.9.40.ebuild, + +atlas-3.9.40-r1.ebuild: + Reworked entirely linking procedure: now explicitely treat each module blas, + cblas and lapack separately + +*atlas-3.9.40 (27 Apr 2011) + + 27 Apr 2011; Sébastien Fabbro <bicatali@gentoo.org> -atlas-3.9.39.ebuild, + +atlas-3.9.40.ebuild: + Bump + + 15 Apr 2011; Justin Lecher <jlec@gentoo.org> atlas-3.9.39.ebuild: + Correct syntax for cpufrq check being all CPUs under performance controll + +*atlas-3.9.39 (21 Mar 2011) + + 21 Mar 2011; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.9.39.ebuild: + Version bump. Seriously refactored the ebuild. Now choose posix threads over + openmp when the two are enabled + +*atlas-3.9.32 (05 Dec 2010) + + 05 Dec 2010; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.8.3.ebuild, + +atlas-3.9.32.ebuild: + Version bump. Still beta. + + 03 Dec 2010; Sébastien Fabbro <bicatali@gentoo.org> atlas-3.8.3.ebuild, + metadata.xml: + Initial import. Ebuilds merged from blas-atlas and lapack-atlas. + diff --git a/sci-libs/atlas/Manifest b/sci-libs/atlas/Manifest new file mode 100644 index 000000000..f17fdbf0f --- /dev/null +++ b/sci-libs/atlas/Manifest @@ -0,0 +1,10 @@ +AUX 3.9.39-bfr-overflow.patch 2755 RMD160 4f8204eee5b429e9d3db1c211af80396a575fc87 SHA1 9b59bd8a7bb55e7ed4138731262d17532949ece0 SHA256 19cdab39e50e06de0bdc2a080642388fec3a16c826657621f15fc294268d3438 +DIST atlas3.8.4.tar.bz2 2534071 RMD160 fa2828468459213fcf3f1ae4fd26671ba32f4776 SHA1 ef92bcbc4bec096b34ed7a0d29119d84c973df0c SHA256 0f7720fb16fa4b8b8a192ea791e57569546db6f5f016cf3caaee30a9d94583bf +DIST atlas3.9.46.tar.bz2 5572227 RMD160 1fbe0f403fc8a35b2b355edabc756c65c19befa2 SHA1 aef8b696bc1bc50b304db953e2f20a653b783317 SHA256 a6667438a04e8a640e5cad75addc7678b19ae7f188c1ae7eb41069f84d43cd1a +DIST atlas3.9.47.tar.bz2 5733559 RMD160 036dbe08784bbda33ce1fa94b20a1999b22772cd SHA1 a3a4797669decea28308bd7d3e0adcac44267471 SHA256 ff4d303c7e3e965cf53f6691e110c1dbff76419c292f56b1ba89e6e5c4174fa0 +DIST lapack-3.3.1.tgz 4945204 RMD160 5e9d90122110045e07351f3ab30dc4e2b43d52db SHA1 3ce437e05f0e9a3c8148ec41922f6efeef0ebdac SHA256 56821ab51c29369a34e5085728f92c549a9aa926f26acf7eeac87b61eed329e4 +EBUILD atlas-3.8.4.ebuild 7394 RMD160 4d60e4e8437f509e447988ee841da387d57f3b9e SHA1 bcf373b5fd94f2942e9eb1bd799ed782c21bc481 SHA256 48ce05edf409f60d8d1c9d404b021d0fc3d204194774ef097b838c6a7d0fa8ab +EBUILD atlas-3.9.46.ebuild 7396 RMD160 dd985c2b4d8b4fcdd2b41acb851600900b2da74a SHA1 58ffa873126c0cae86761139df14f4ff85c42a45 SHA256 03bb28d219c0dd759c5b68549beee6f6e1800869d1afef8dbe3eace47dce4e61 +EBUILD atlas-3.9.47.ebuild 7396 RMD160 dd985c2b4d8b4fcdd2b41acb851600900b2da74a SHA1 58ffa873126c0cae86761139df14f4ff85c42a45 SHA256 03bb28d219c0dd759c5b68549beee6f6e1800869d1afef8dbe3eace47dce4e61 +MISC ChangeLog 2120 RMD160 9cec6767d56d48f747d96ffe846f141db5c10db9 SHA1 b8d15d8423f24790a5af04629bd18857193cb447 SHA256 3431e99099f72e6bb3cb2248ae7ca206d7677b3deeaf7da494d8b8cf44b21bc3 +MISC metadata.xml 726 RMD160 e43f5ea9c594bbe2174f6640bbfdccd8b17d4a68 SHA1 0ab8c05e7925b4716d8c94acd952bf3ab85165cb SHA256 27ef4eee7e645ad923644830d057db45d32342ad250ad903ff10915a9ca068fd diff --git a/sci-libs/atlas/atlas-3.8.4.ebuild b/sci-libs/atlas/atlas-3.8.4.ebuild new file mode 100644 index 000000000..e0fc44deb --- /dev/null +++ b/sci-libs/atlas/atlas-3.8.4.ebuild @@ -0,0 +1,281 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 +inherit eutils toolchain-funcs versionator alternatives-2 + +LAPACKP=lapack-3.3.1 + +DESCRIPTION="Automatically Tuned Linear Algebra Software" +HOMEPAGE="http://math-atlas.sourceforge.net/" +SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2 + fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP}.tgz ) )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="fortran doc lapack static-libs threads" + +RDEPEND="fortran? ( virtual/fortran )" +DEPEND="${RDEPEND} + !prefix? ( sys-power/cpufrequtils )" + +S="${WORKDIR}/ATLAS" + +lapack_compile() { + cd "${WORKDIR}/${LAPACKP}" + local timer=INT_CPU_TIME + case $(tc-getFC) in + *gfortran|*g77) timer=INT_ETIME ;; + *ifort) timer=EXT_ETIME ;; + esac + cat > make.inc <<-EOF + FORTRAN = $(tc-getFC) + OPTS = ${FFLAGS} + NOOPT = -O0 + LOADER = $(tc-getFC) + LOADEROPTS = ${LDFLAGS} + ARCH = $(tc-getAR) + ARCHFLAGS = cr + RANLIB = $(tc-getRANLIB) + TIMER = ${timer} + EOF + if use static-libs; then + emake \ + LAPACKLIB=liblapack_nonpic.a \ + lapacklib || die "lapack static compilation failed" + emake clean + fi + emake \ + LAPACKLIB=liblapack_pic.a \ + OPTS="${FFLAGS} -fPIC" \ + NOOPT="-O0 -fPIC" \ + lapacklib || die "lapack pic compilation failed" +} + +atlas_configure() { + local mycc="$(tc-getCC)" + # http://sourceforge.net/tracker/?func=detail&aid=3301697&group_id=23725&atid=379483 + [[ ${mycc} == *gcc* ]] && mycc=gcc + local myconf=( + "--prefix=${ED}/usr" + "--libdir=${ED}/usr/$(get_libdir)" + "--incdir=${ED}/usr/include" + "--cc=${mycc}" + "-C ac ${mycc}" + "-D c -DWALL" + "-F ac '${CFLAGS}'" + "-Ss pmake '\$(MAKE) ${MAKEOPTS}'" + ) + + if use threads; then + myconf+=( "-t -1" ) + else + myconf+=( "-t 0" ) + fi + + if use amd64 || use ppc64 || use sparc; then + if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then + myconf+=( "-b 64" ) + elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then + myconf+=( "-b 32" ) + else + myconf+=( "-b 64" ) + fi + elif use ppc || use x86; then + myconf+=( "-b 32" ) + elif use ia64; then + myconf+=( "-b 64" ) + else #hppa alpha ... + myconf+=( "" ) + fi + if use fortran; then + myconf+=( + "-Si nof77 0" + "-C if $(tc-getFC)" + "-F if '${FFLAGS}'" + ) + use lapack && myconf+=( "--with-netlib-lapack=${LAPACKLIB}" ) + else + myconf+=( "-Si nof77 1" ) + fi + local confdir="${S}_${1}"; shift + myconf+=( $@ ) + mkdir "${confdir}" && cd "${confdir}" + "${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed" +} + +atlas_compile() { + pushd "${S}_${1}" > /dev/null + # atlas does its own parallel builds + emake -j1 build + cd lib + emake libclapack.a + popd > /dev/null +} + +# transform a static archive into a shared library and install them +# atlas_install_libs <mylib.a> [extra link flags] +atlas_install_libs() { + local libname=$(basename ${1%.*}) + einfo "Installing ${libname}" + local soname=${libname}.so.$(get_major_version) + shift + pushd "${S}_shared"/lib > /dev/null + ${LINK:-$(tc-getCC)} ${LDFLAGS} -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive \ + "$@" -o ${soname} || die "Creating ${soname} failed" + dolib.so ${soname} + ln -s ${soname} ${soname%.*} + dosym ${soname} /usr/$(get_libdir)/${soname%.*} + popd > /dev/null + use static-libs && dolib.a "${S}_static"/lib/${libname}.a +} + +# create and install a pkgconfig file +# atlas_install_pc <libname> <pkg name> [extra link flags] +atlas_install_pc() { + local libname=${1} ; shift + local pcname=${1} ; shift + cat <<-EOF > ${pcname}.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ${pcname} + Description: ${PN} ${pcname} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -l${libname} $@ + Cflags: -I\${includedir}/${PN} + ${PCREQ} + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ${pcname}.pc +} + +pkg_setup() { + if [[ -n $(type -P cpufreq-info) ]]; then + [[ -z $(cpufreq-info -d) ]] && return + local ncpu=$(LANG=C cpufreq-info | grep -c "analyzing CPU") + local cpu=0 + while [[ ${cpu} -lt ${ncpu} ]]; do + if ! $(LANG=C cpufreq-info -p -c ${cpu} | grep -q performance); then + ewarn "CPU $cpu is not set to performance" + ewarn "Run cpufreq-set -r -g performance as root" + fi + cpu=$(( cpu + 1 )) + done + else + ewarn "Please make sure to disable CPU throttling completely" + ewarn "during the compile of ${PN}. Otherwise, all ${PN}" + ewarn "generated timings will be completely random and the" + ewarn "performance of the resulting libraries will be degraded" + ewarn "considerably." + fi +} + +src_prepare() { + epatch "${FILESDIR}"/3.9.39-bfr-overflow.patch +} + +src_configure() { + if use fortran && use lapack; then + lapack_compile + LAPACKLIB="${WORKDIR}/${LAPACKP}/liblapack_pic.a" + fi + atlas_configure shared "-Fa alg -fPIC" + if use static-libs; then + use fortran && use lapack && \ + LAPACKLIB="${WORKDIR}/${LAPACKP}/liblapack_nonpic.a" + atlas_configure static + fi +} + +src_compile() { + atlas_compile shared + use static-libs && atlas_compile static +} + +src_test() { + cd "${S}_shared" + emake -j1 check + emake -j1 time +} + +src_install() { + cd "${S}_shared/lib" + # rename to avoid collision with other packages + local l + for l in {,c}{blas,lapack}; do + if [[ -e lib${l}.a ]]; then + mv lib{,atl}${l}.a + use static-libs && mv "${S}"_static/lib/lib{,atl}${l}.a + fi + done + + [[ -e libptcblas.a ]] && PTLIBS="-lpthread" + + # atlas + atlas_install_libs libatlas.a -lm ${PTLIBS} + + # cblas + atlas_install_libs libatlcblas.a -lm -L. -latlas + atlas_install_pc atlcblas atlas-cblas -lm -latlas + alternatives_for cblas atlas 0 \ + /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \ + /usr/include/cblas.h atlas/cblas.h + + # cblas threaded + if [[ -e libptcblas.a ]]; then + atlas_install_libs libptcblas.a -lm -L. -latlas ${PTLIBS} + atlas_install_pc ptcblas atlas-cblas-threads -lm -latlas ${PTLIBS} + alternatives_for cblas atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \ + /usr/include/cblas.h atlas/cblas.h + fi + + if use lapack; then + PCREQ="Requires: cblas" + # clapack + atlas_install_libs libatlclapack.a -lm -L. -latlas -latlcblas + atlas_install_pc atlclapack atlas-clapack -lm -latlas + fi + + if use fortran; then + LINK=$(tc-getF77) PCREQ= + # blas + atlas_install_libs libf77blas.a -lm -L. -latlas + atlas_install_pc f77blas atlas-blas -lm -latlas + alternatives_for blas atlas 0 \ + /usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc + + # blas threaded + if [[ -e libptf77blas.a ]]; then + atlas_install_libs libptf77blas.a -lm -L. -latlas ${PTLIBS} + atlas_install_pc ptf77blas atlas-blas-threads -lm -latlas ${PTLIBS} + alternatives_for blas atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc + fi + + if use lapack; then + PCREQ="Requires: blas cblas" + # lapack + atlas_install_libs libatllapack.a \ + -lm -L. -latlas -latlcblas -lf77blas + atlas_install_pc atllapack atlas-lapack -lm -latlas + alternatives_for lapack atlas 0 \ + /usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc + fi + fi + + cd "${S}" + insinto /usr/include/${PN} + doins include/*.h + + cd "${S}/doc" + dodoc INDEX.txt AtlasCredits.txt ChangeLog + use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf + use doc && use fortran && dodoc f77blas*pdf + use doc && use fortran && use lapack && dodoc lapack*pdf +} diff --git a/sci-libs/atlas/atlas-3.9.46.ebuild b/sci-libs/atlas/atlas-3.9.46.ebuild new file mode 100644 index 000000000..86157c94c --- /dev/null +++ b/sci-libs/atlas/atlas-3.9.46.ebuild @@ -0,0 +1,267 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 +inherit eutils toolchain-funcs versionator alternatives-2 + +LAPACKP=lapack-3.3.1 + +DESCRIPTION="Automatically Tuned Linear Algebra Software" +HOMEPAGE="http://math-atlas.sourceforge.net/" +SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2 + fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP}.tgz ) )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="fortran doc lapack static-libs threads" + +RDEPEND="fortran? ( virtual/fortran )" +DEPEND="${RDEPEND} + !prefix? ( sys-power/cpufrequtils )" + +S="${WORKDIR}/ATLAS" + +atlas_configure() { + local mycc="$(tc-getCC)" + # http://sourceforge.net/tracker/?func=detail&aid=3301697&group_id=23725&atid=379483 + [[ ${mycc} == *gcc* ]] && mycc=gcc + local myconf=( + "--prefix=${ED}/usr" + "--libdir=${ED}/usr/$(get_libdir)" + "--incdir=${ED}/usr/include" + "--cc=${mycc}" + "-C ac ${mycc}" + "-D c -DWALL" + "-F ac '${CFLAGS}'" + "-Ss pmake '\$(MAKE) ${MAKEOPTS}'" + ) + + # OpenMP shown to decreased performance over POSIX threads + # (at least in 3.9.39, see atlas-dev mailing list) + if use threads; then + myconf+=( "-t -1" "-Si omp 0" ) + else + myconf+=( "-t 0" "-Si omp 0" ) + fi + + if use amd64 || use ppc64 || use sparc; then + if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then + myconf+=( "-b 64" ) + elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then + myconf+=( "-b 32" ) + else + myconf+=( "-b 64" ) + fi + elif use ppc || use x86; then + myconf+=( "-b 32" ) + elif use ia64; then + myconf+=( "-b 64" ) + else #hppa alpha ... + myconf+=( "" ) + fi + if use fortran; then + myconf+=( + "-C if $(tc-getFC)" + "-F if '${FFLAGS}'" + ) + if use lapack; then + myconf+=( + "-Si latune 1" + "--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}.tgz" + ) + else + myconf+=( "-Si latune 0" ) + fi + else + myconf+=( "-Si latune 0" "--nof77" ) + fi + local confdir="${S}_${1}"; shift + myconf+=( $@ ) + mkdir "${confdir}" && cd "${confdir}" + "${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed" +} + +atlas_compile() { + pushd "${S}_${1}" > /dev/null + # atlas does its own parallel builds + emake -j1 build + cd lib + emake libclapack.a + [[ -e libptcblas.a ]] && emake libptclapack.a + popd > /dev/null +} + +# transform a static archive into a shared library and install them +# atlas_install_libs <mylib.a> [extra link flags] +atlas_install_libs() { + local libname=$(basename ${1%.*}) + einfo "Installing ${libname}" + local soname=${libname}.so.$(get_major_version) + shift + pushd "${S}_shared"/lib > /dev/null + ${LINK:-$(tc-getCC)} ${LDFLAGS} -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive \ + "$@" -o ${soname} || die "Creating ${soname} failed" + dolib.so ${soname} + ln -s ${soname} ${soname%.*} + dosym ${soname} /usr/$(get_libdir)/${soname%.*} + popd > /dev/null + use static-libs && dolib.a "${S}_static"/lib/${libname}.a +} + +# create and install a pkgconfig file +# atlas_install_pc <libname> <pkg name> [extra link flags] +atlas_install_pc() { + local libname=${1} ; shift + local pcname=${1} ; shift + cat <<-EOF > ${pcname}.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ${pcname} + Description: ${PN} ${pcname} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -l${libname} $@ + Cflags: -I\${includedir}/${PN} + ${PCREQ} + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ${pcname}.pc +} + +pkg_setup() { + if [[ -n $(type -P cpufreq-info) ]]; then + [[ -z $(cpufreq-info -d) ]] && return + local ncpu=$(LANG=C cpufreq-info | grep -c "analyzing CPU") + local cpu=0 + while [[ ${cpu} -lt ${ncpu} ]]; do + if ! $(LANG=C cpufreq-info -p -c ${cpu} | grep -q performance); then + ewarn "CPU $cpu is not set to performance" + ewarn "Run cpufreq-set -r -g performance as root" + die "${PN} needs all cpu set to performance" + fi + cpu=$(( cpu + 1 )) + done + else + ewarn "Please make sure to disable CPU throttling completely" + ewarn "during the compile of ${PN}. Otherwise, all ${PN}" + ewarn "generated timings will be completely random and the" + ewarn "performance of the resulting libraries will be degraded" + ewarn "considerably." + fi +} + +src_prepare() { + epatch "${FILESDIR}"/3.9.39-bfr-overflow.patch +} + +src_configure() { + atlas_configure shared "-Fa alg -fPIC" + use static-libs && atlas_configure static +} + +src_compile() { + atlas_compile shared + use static-libs && atlas_compile static +} + +src_test() { + cd "${S}_shared" + emake -j1 check + emake -j1 time +} + +src_install() { + cd "${S}_shared/lib" + # rename to avoid collision with other packages + local l + for l in {,c}{blas,lapack}; do + if [[ -e lib${l}.a ]]; then + mv lib{,atl}${l}.a + use static-libs && mv "${S}"_static/lib/lib{,atl}${l}.a + fi + done + + [[ -e libptcblas.a ]] && PTLIBS="-lpthread" + + # atlas + atlas_install_libs libatlas.a -lm ${PTLIBS} + + # cblas + atlas_install_libs libatlcblas.a -lm -L. -latlas + atlas_install_pc atlcblas atlas-cblas -lm -latlas + alternatives_for cblas atlas 0 \ + /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \ + /usr/include/cblas.h atlas/cblas.h + + # cblas threaded + if [[ -e libptcblas.a ]]; then + atlas_install_libs libptcblas.a -lm -L. -latlas ${PTLIBS} + atlas_install_pc ptcblas atlas-cblas-threads -lm -latlas ${PTLIBS} + alternatives_for cblas atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \ + /usr/include/cblas.h atlas/cblas.h + fi + + if use lapack; then + PCREQ="Requires: cblas" + # clapack + atlas_install_libs libatlclapack.a -lm -L. -latlas -latlcblas + atlas_install_pc atlclapack atlas-clapack -lm -latlas + + # clapack threaded + if [[ -e libptclapack.a ]]; then + atlas_install_libs libptclapack.a -lm -L. -latlas -lptcblas ${PTLIBS} + atlas_install_pc ptclapack atlas-clapack-threads -lm -latlas ${PTLIBS} + fi + fi + + if use fortran; then + LINK=$(tc-getF77) PCREQ= + # blas + atlas_install_libs libf77blas.a -lm -L. -latlas + atlas_install_pc f77blas atlas-blas -lm -latlas + alternatives_for blas atlas 0 \ + /usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc + + # blas threaded + if [[ -e libptf77blas.a ]]; then + atlas_install_libs libptf77blas.a -lm -L. -latlas ${PTLIBS} + atlas_install_pc ptf77blas atlas-blas-threads -lm -latlas ${PTLIBS} + alternatives_for blas atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc + fi + + if use lapack; then + PCREQ="Requires: blas cblas" + # lapack + atlas_install_libs libatllapack.a \ + -lm -L. -latlas -latlcblas -lf77blas + atlas_install_pc atllapack atlas-lapack -lm -latlas + alternatives_for lapack atlas 0 \ + /usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc + # lapack threaded + if [[ -e libptlapack.a ]]; then + atlas_install_libs libptlapack.a \ + -lm -L. -latlas -lptcblas -lptf77blas ${PTLIBS} + atlas_install_pc ptlapack atlas-lapack-threads \ + -lm -latlas ${PTLIBS} + alternatives_for lapack atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack-threads.pc + fi + fi + fi + + cd "${S}" + insinto /usr/include/${PN} + doins include/*.h + + cd "${S}/doc" + dodoc INDEX.txt AtlasCredits.txt ChangeLog + use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf + use doc && use fortran && dodoc f77blas*pdf + use doc && use fortran && use lapack && dodoc lapack*pdf +} diff --git a/sci-libs/atlas/atlas-3.9.47.ebuild b/sci-libs/atlas/atlas-3.9.47.ebuild new file mode 100644 index 000000000..86157c94c --- /dev/null +++ b/sci-libs/atlas/atlas-3.9.47.ebuild @@ -0,0 +1,267 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 +inherit eutils toolchain-funcs versionator alternatives-2 + +LAPACKP=lapack-3.3.1 + +DESCRIPTION="Automatically Tuned Linear Algebra Software" +HOMEPAGE="http://math-atlas.sourceforge.net/" +SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2 + fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP}.tgz ) )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="fortran doc lapack static-libs threads" + +RDEPEND="fortran? ( virtual/fortran )" +DEPEND="${RDEPEND} + !prefix? ( sys-power/cpufrequtils )" + +S="${WORKDIR}/ATLAS" + +atlas_configure() { + local mycc="$(tc-getCC)" + # http://sourceforge.net/tracker/?func=detail&aid=3301697&group_id=23725&atid=379483 + [[ ${mycc} == *gcc* ]] && mycc=gcc + local myconf=( + "--prefix=${ED}/usr" + "--libdir=${ED}/usr/$(get_libdir)" + "--incdir=${ED}/usr/include" + "--cc=${mycc}" + "-C ac ${mycc}" + "-D c -DWALL" + "-F ac '${CFLAGS}'" + "-Ss pmake '\$(MAKE) ${MAKEOPTS}'" + ) + + # OpenMP shown to decreased performance over POSIX threads + # (at least in 3.9.39, see atlas-dev mailing list) + if use threads; then + myconf+=( "-t -1" "-Si omp 0" ) + else + myconf+=( "-t 0" "-Si omp 0" ) + fi + + if use amd64 || use ppc64 || use sparc; then + if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then + myconf+=( "-b 64" ) + elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then + myconf+=( "-b 32" ) + else + myconf+=( "-b 64" ) + fi + elif use ppc || use x86; then + myconf+=( "-b 32" ) + elif use ia64; then + myconf+=( "-b 64" ) + else #hppa alpha ... + myconf+=( "" ) + fi + if use fortran; then + myconf+=( + "-C if $(tc-getFC)" + "-F if '${FFLAGS}'" + ) + if use lapack; then + myconf+=( + "-Si latune 1" + "--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}.tgz" + ) + else + myconf+=( "-Si latune 0" ) + fi + else + myconf+=( "-Si latune 0" "--nof77" ) + fi + local confdir="${S}_${1}"; shift + myconf+=( $@ ) + mkdir "${confdir}" && cd "${confdir}" + "${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed" +} + +atlas_compile() { + pushd "${S}_${1}" > /dev/null + # atlas does its own parallel builds + emake -j1 build + cd lib + emake libclapack.a + [[ -e libptcblas.a ]] && emake libptclapack.a + popd > /dev/null +} + +# transform a static archive into a shared library and install them +# atlas_install_libs <mylib.a> [extra link flags] +atlas_install_libs() { + local libname=$(basename ${1%.*}) + einfo "Installing ${libname}" + local soname=${libname}.so.$(get_major_version) + shift + pushd "${S}_shared"/lib > /dev/null + ${LINK:-$(tc-getCC)} ${LDFLAGS} -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive \ + "$@" -o ${soname} || die "Creating ${soname} failed" + dolib.so ${soname} + ln -s ${soname} ${soname%.*} + dosym ${soname} /usr/$(get_libdir)/${soname%.*} + popd > /dev/null + use static-libs && dolib.a "${S}_static"/lib/${libname}.a +} + +# create and install a pkgconfig file +# atlas_install_pc <libname> <pkg name> [extra link flags] +atlas_install_pc() { + local libname=${1} ; shift + local pcname=${1} ; shift + cat <<-EOF > ${pcname}.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ${pcname} + Description: ${PN} ${pcname} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -l${libname} $@ + Cflags: -I\${includedir}/${PN} + ${PCREQ} + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ${pcname}.pc +} + +pkg_setup() { + if [[ -n $(type -P cpufreq-info) ]]; then + [[ -z $(cpufreq-info -d) ]] && return + local ncpu=$(LANG=C cpufreq-info | grep -c "analyzing CPU") + local cpu=0 + while [[ ${cpu} -lt ${ncpu} ]]; do + if ! $(LANG=C cpufreq-info -p -c ${cpu} | grep -q performance); then + ewarn "CPU $cpu is not set to performance" + ewarn "Run cpufreq-set -r -g performance as root" + die "${PN} needs all cpu set to performance" + fi + cpu=$(( cpu + 1 )) + done + else + ewarn "Please make sure to disable CPU throttling completely" + ewarn "during the compile of ${PN}. Otherwise, all ${PN}" + ewarn "generated timings will be completely random and the" + ewarn "performance of the resulting libraries will be degraded" + ewarn "considerably." + fi +} + +src_prepare() { + epatch "${FILESDIR}"/3.9.39-bfr-overflow.patch +} + +src_configure() { + atlas_configure shared "-Fa alg -fPIC" + use static-libs && atlas_configure static +} + +src_compile() { + atlas_compile shared + use static-libs && atlas_compile static +} + +src_test() { + cd "${S}_shared" + emake -j1 check + emake -j1 time +} + +src_install() { + cd "${S}_shared/lib" + # rename to avoid collision with other packages + local l + for l in {,c}{blas,lapack}; do + if [[ -e lib${l}.a ]]; then + mv lib{,atl}${l}.a + use static-libs && mv "${S}"_static/lib/lib{,atl}${l}.a + fi + done + + [[ -e libptcblas.a ]] && PTLIBS="-lpthread" + + # atlas + atlas_install_libs libatlas.a -lm ${PTLIBS} + + # cblas + atlas_install_libs libatlcblas.a -lm -L. -latlas + atlas_install_pc atlcblas atlas-cblas -lm -latlas + alternatives_for cblas atlas 0 \ + /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \ + /usr/include/cblas.h atlas/cblas.h + + # cblas threaded + if [[ -e libptcblas.a ]]; then + atlas_install_libs libptcblas.a -lm -L. -latlas ${PTLIBS} + atlas_install_pc ptcblas atlas-cblas-threads -lm -latlas ${PTLIBS} + alternatives_for cblas atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas-threads.pc \ + /usr/include/cblas.h atlas/cblas.h + fi + + if use lapack; then + PCREQ="Requires: cblas" + # clapack + atlas_install_libs libatlclapack.a -lm -L. -latlas -latlcblas + atlas_install_pc atlclapack atlas-clapack -lm -latlas + + # clapack threaded + if [[ -e libptclapack.a ]]; then + atlas_install_libs libptclapack.a -lm -L. -latlas -lptcblas ${PTLIBS} + atlas_install_pc ptclapack atlas-clapack-threads -lm -latlas ${PTLIBS} + fi + fi + + if use fortran; then + LINK=$(tc-getF77) PCREQ= + # blas + atlas_install_libs libf77blas.a -lm -L. -latlas + atlas_install_pc f77blas atlas-blas -lm -latlas + alternatives_for blas atlas 0 \ + /usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas.pc + + # blas threaded + if [[ -e libptf77blas.a ]]; then + atlas_install_libs libptf77blas.a -lm -L. -latlas ${PTLIBS} + atlas_install_pc ptf77blas atlas-blas-threads -lm -latlas ${PTLIBS} + alternatives_for blas atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/blas.pc atlas-blas-threads.pc + fi + + if use lapack; then + PCREQ="Requires: blas cblas" + # lapack + atlas_install_libs libatllapack.a \ + -lm -L. -latlas -latlcblas -lf77blas + atlas_install_pc atllapack atlas-lapack -lm -latlas + alternatives_for lapack atlas 0 \ + /usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack.pc + # lapack threaded + if [[ -e libptlapack.a ]]; then + atlas_install_libs libptlapack.a \ + -lm -L. -latlas -lptcblas -lptf77blas ${PTLIBS} + atlas_install_pc ptlapack atlas-lapack-threads \ + -lm -latlas ${PTLIBS} + alternatives_for lapack atlas-threads 0 \ + /usr/$(get_libdir)/pkgconfig/lapack.pc atlas-lapack-threads.pc + fi + fi + fi + + cd "${S}" + insinto /usr/include/${PN} + doins include/*.h + + cd "${S}/doc" + dodoc INDEX.txt AtlasCredits.txt ChangeLog + use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf + use doc && use fortran && dodoc f77blas*pdf + use doc && use fortran && use lapack && dodoc lapack*pdf +} diff --git a/sci-libs/atlas/files/3.9.39-bfr-overflow.patch b/sci-libs/atlas/files/3.9.39-bfr-overflow.patch new file mode 100644 index 000000000..a4ae52a1b --- /dev/null +++ b/sci-libs/atlas/files/3.9.39-bfr-overflow.patch @@ -0,0 +1,72 @@ + ATLAS/tune/blas/level1/axpysrch.c | 2 +- + ATLAS/tune/blas/level1/copysrch.c | 2 +- + ATLAS/tune/blas/level1/iamaxsrch.c | 2 +- + ATLAS/tune/blas/level1/scalsrch.c | 2 +- + ATLAS/tune/blas/level1/swapsrch.c | 2 +- + 5 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/ATLAS/tune/blas/level1/axpysrch.c b/ATLAS/tune/blas/level1/axpysrch.c +index 48bd756..f7f7845 100644 +--- a/ATLAS/tune/blas/level1/axpysrch.c ++++ b/ATLAS/tune/blas/level1/axpysrch.c +@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre) + { + FILE *fpin; + FILENODE *fbase, *fn, *fp=NULL; +- char ln[512], rout[256], auth[256], cc[256], ccflags[256]; ++ char ln[512], rout[256], auth[256], cc[256], ccflags[512]; + char *pcc, *pccflags; + int i, n, ID, alpha, beta, incX, incY; + +diff --git a/ATLAS/tune/blas/level1/copysrch.c b/ATLAS/tune/blas/level1/copysrch.c +index 3a9fcfc..736f501 100644 +--- a/ATLAS/tune/blas/level1/copysrch.c ++++ b/ATLAS/tune/blas/level1/copysrch.c +@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre) + { + FILE *fpin; + FILENODE *fbase, *fn, *fp=NULL; +- char ln[512], rout[256], auth[256], cc[256], ccflags[256]; ++ char ln[512], rout[256], auth[256], cc[256], ccflags[512]; + char *pcc, *pccflags; + int i, n, ID, alpha, beta, incX, incY; + +diff --git a/ATLAS/tune/blas/level1/iamaxsrch.c b/ATLAS/tune/blas/level1/iamaxsrch.c +index e9e766a..91b3acd 100644 +--- a/ATLAS/tune/blas/level1/iamaxsrch.c ++++ b/ATLAS/tune/blas/level1/iamaxsrch.c +@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre) + { + FILE *fpin; + FILENODE *fbase, *fn, *fp=NULL; +- char ln[512], rout[256], auth[256], cc[256], ccflags[256]; ++ char ln[512], rout[256], auth[256], cc[256], ccflags[512]; + char *pcc, *pccflags; + int i, n, ID, alpha, beta, incX, incY; + +diff --git a/ATLAS/tune/blas/level1/scalsrch.c b/ATLAS/tune/blas/level1/scalsrch.c +index 48be97e..35d724d 100644 +--- a/ATLAS/tune/blas/level1/scalsrch.c ++++ b/ATLAS/tune/blas/level1/scalsrch.c +@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre) + { + FILE *fpin; + FILENODE *fbase, *fn, *fp=NULL; +- char ln[512], rout[256], auth[256], cc[256], ccflags[256]; ++ char ln[512], rout[256], auth[256], cc[256], ccflags[512]; + char *pcc, *pccflags; + int i, n, ID, alpha, beta, incX, incY; + +diff --git a/ATLAS/tune/blas/level1/swapsrch.c b/ATLAS/tune/blas/level1/swapsrch.c +index 776d2d7..5281ae5 100644 +--- a/ATLAS/tune/blas/level1/swapsrch.c ++++ b/ATLAS/tune/blas/level1/swapsrch.c +@@ -159,7 +159,7 @@ FILENODE *ReadFile(char pre) + { + FILE *fpin; + FILENODE *fbase, *fn, *fp=NULL; +- char ln[512], rout[256], auth[256], cc[256], ccflags[256]; ++ char ln[512], rout[256], auth[256], cc[256], ccflags[512]; + char *pcc, *pccflags; + int i, n, ID, alpha, beta, incX, incY; + diff --git a/sci-libs/atlas/metadata.xml b/sci-libs/atlas/metadata.xml new file mode 100644 index 000000000..93eedfbca --- /dev/null +++ b/sci-libs/atlas/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<longdescription lang='en'> + ATLAS is an approach for the automatic generation and optimization of + numerical software. Currently ATLAS supplies optimized versions for the + complete set of linear algebra kernels known as the Basic Linear Algebra + Subroutines (BLAS) for both c and F77 interfaces. It can also build + a subset of the linear algebra routine LAPACK library or the full + LAPACK using the reference LAPACK from Netlib. +</longdescription> +<use> + <flag name='xblas'>Build LAPACK with extra precision (needs <pkg>sci-libs/xblas</pkg>)</flag> +</use> +</pkgmetadata> diff --git a/sci-libs/libspatialindex/ChangeLog b/sci-libs/libspatialindex/ChangeLog new file mode 100644 index 000000000..3264865b2 --- /dev/null +++ b/sci-libs/libspatialindex/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-libs/libspatialindex +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*libspatialindex-1.6.1 (01 Aug 2011) + + 01 Aug 2011; Andrey Kislyuk <weaver@gentoo.org> + +libspatialindex-1.6.1.ebuild, +metadata.xml: + New package, ebuild written by me + diff --git a/sci-libs/libspatialindex/Manifest b/sci-libs/libspatialindex/Manifest new file mode 100644 index 000000000..7b52d262f --- /dev/null +++ b/sci-libs/libspatialindex/Manifest @@ -0,0 +1,4 @@ +DIST spatialindex-src-1.6.1.tar.bz2 346819 RMD160 19d22e77305364d5e5d23ffe67fd5c9cf5e8e72c SHA1 b2044558c7af036b14f155f9228ad5eac7e20943 SHA256 42dc4149c04f7436632b3e15d5470fe80172e91f16a16665ffc5587b8c576fe4 +EBUILD libspatialindex-1.6.1.ebuild 548 RMD160 53bfd1216b24a257a64aa82c376d1dbb3d66363e SHA1 be114c019d5648e1151af4958b824f24b25191ac SHA256 7ee05e5efacb20dc89801742257eff2fc95aee68626e7bae09123b2b9569a876 +MISC ChangeLog 298 RMD160 8e48e08c243eb1c5f4768f86664f0eea987a126e SHA1 7d83c5f45daddd24415f82fbf73e551461ab696a SHA256 6128a205c3290c58521d69caa89cfe6a1a849876054bc11868c7142ef12f0786 +MISC metadata.xml 169 RMD160 e1db75ae5d177dffc400468c7d76a7e1fe41876d SHA1 0c953712f9b97d5ab3f95ae71997ffbc96c4007d SHA256 36837b011d26f0b83477c7a8632cb0099aedbcba5a3e45c61f20292e079f6180 diff --git a/sci-libs/libspatialindex/libspatialindex-1.6.1.ebuild b/sci-libs/libspatialindex/libspatialindex-1.6.1.ebuild new file mode 100644 index 000000000..9286f0250 --- /dev/null +++ b/sci-libs/libspatialindex/libspatialindex-1.6.1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header$ + +EAPI=4 + +MY_PN="spatialindex-src" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="General framework for developing spatial indices" +HOMEPAGE="http://trac.gispython.org/spatialindex/wiki" +SRC_URI="http://download.osgeo.org/libspatialindex/${MY_P}.tar.bz2" +LICENSE="GPL-2" + +KEYWORDS="~x86 ~amd64" +SLOT="0" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_install() { + emake DESTDIR="${D}" install || die "einstall failed" +} diff --git a/sci-libs/libspatialindex/metadata.xml b/sci-libs/libspatialindex/metadata.xml new file mode 100644 index 000000000..3190fbf9c --- /dev/null +++ b/sci-libs/libspatialindex/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-geosciences</herd> +</pkgmetadata> diff --git a/sci-libs/msms/Manifest b/sci-libs/msms/Manifest index 15ebe54a0..be39111dd 100644 --- a/sci-libs/msms/Manifest +++ b/sci-libs/msms/Manifest @@ -1,14 +1,5 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - +AUX build-with-linux-3.0.patch 363 RMD160 bfae4530988139c11162a713d04853420af7b1e8 SHA1 4436f3e5142c4b9ab05ff4d1dac19c781becf2b4 SHA256 ba8c0e7e3a3852364f94a3d0d57ca93cfe6ae1fb7b062bc97cdffae56303bbb4 DIST mgltools_source_1.5.4.tar.gz 25503517 RMD160 250e3d8fc9db2703c3f4ac1842286e272fd31bb8 SHA1 b88c40175c8299d1d4d264c2c6659fbb6ab8d581 SHA256 1ea3da342b4d49d7a92dcb5d6da1d805e71652fd70ba7a5653335990629c80f0 -EBUILD msms-1.5.4-r1.ebuild 927 RMD160 e7a4cdb4fa6cd26d678e69c7e4425752ebd1e7c1 SHA1 30603d8e3d151bf2de0b648a416b69f2763e98b7 SHA256 349fe5e884360475192a8740be55a19fa6ffd07b01104b3fc7a4695dcaf42232 +EBUILD msms-1.5.4-r1.ebuild 1131 RMD160 f901fd72b8a769f0c6700e462058627a96661e5b SHA1 29680ccccb70ab9a63675e3e652a0471ae01a158 SHA256 98ff384376c5e65a41dae3b55dce49de12a0f94fd27ab6804f19c4bb5c785379 MISC ChangeLog 604 RMD160 12730f455f6f15a5109ea4855ea37ae67f1ff13c SHA1 6d5f258da4c6c33610d21ce56f2804c851dbe6ba SHA256 2d39b0aaa94f45ebdccfe7f689d1dfeef3bce6186d5461d7c72442008cb98bf3 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk2kfZYACgkQgAnW8HDreRbkFgCgtuksFeAd1vce7bV/IBWUrDzc -cJMAoIwUuDhBJtlq55/LD5oZZSGh0fyg -=sDvJ ------END PGP SIGNATURE----- diff --git a/sci-libs/msms/files/build-with-linux-3.0.patch b/sci-libs/msms/files/build-with-linux-3.0.patch new file mode 100644 index 000000000..849f80a9e --- /dev/null +++ b/sci-libs/msms/files/build-with-linux-3.0.patch @@ -0,0 +1,11 @@ +--- mslib-1.5.4.orig/setup.py 2011-07-30 07:46:02.628300605 -0500 ++++ mslib-1.5.4/setup.py 2011-07-30 07:46:30.628188677 -0500 +@@ -18,7 +18,7 @@ + platform = sys.platform + + # amd64 +-if (platform == "linux2"): ++if platform in ["linux2", "linux3"]: + lUname = os.uname() + if lUname[-1] == 'x86_64': + platform = lUname[-1] + lUname[0] + lUname[2][0] diff --git a/sci-libs/msms/msms-1.5.4-r1.ebuild b/sci-libs/msms/msms-1.5.4-r1.ebuild index cc934ded8..4b551c2c6 100644 --- a/sci-libs/msms/msms-1.5.4-r1.ebuild +++ b/sci-libs/msms/msms-1.5.4-r1.ebuild @@ -6,7 +6,7 @@ EAPI="3" PYTHON_DEPEND="2" SUPPORT_PYTHON_ABIS="1" -inherit distutils +inherit distutils eutils MY_PN="mslib" MY_P="${MY_PN}-${PV}" @@ -33,6 +33,16 @@ src_unpack() { tar xzpf mgltools_source_${PV}/MGLPACKS/${MY_P}.tar.gz } +src_prepare() { + epatch "${FILESDIR}"/build-with-linux-3.0.patch + pushd "${S}"/lib >/dev/null + # Set up symlinks for 3.x kernels + for x in *inux2; do + ln -s ${x} ${x%2}3 + done + popd >/dev/null +} + pkg_postinst() { python_mod_optimize ${MY_PN} } diff --git a/sci-libs/ni-visa/Manifest b/sci-libs/ni-visa/Manifest index b1c63e34b..1f731472a 100644 --- a/sci-libs/ni-visa/Manifest +++ b/sci-libs/ni-visa/Manifest @@ -1,4 +1,5 @@ AUX 70nivisa 73 RMD160 e1dcc750f9b87b3a334a6e0a84636a312274a275 SHA1 2441b85cd506555ff2fb2a8d10533fbad310adbb SHA256 d510cc282cc2d6e6dc988105953486e6c242f00e91dae52ce3cdeed5621ae93c DIST NI-VISA-0.0.1.iso 1 RMD160 c0da025038ed83c687ddc430da9846ecb97f3998 SHA1 adc83b19e793491b1c6ea0fd8b46cd9f32e592fc SHA256 01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b EBUILD ni-visa-0.0.1.ebuild 1069 RMD160 bae5ac6cb5d994f7be68d4298abf71ae58689f82 SHA1 181b6e7bcedf01338cc3dc6af319462482df20bf SHA256 bb66b971dc0954f8cf514315194a8b70cb122b9a46a626105981c0a246cf527d +MISC ChangeLog 327 RMD160 1a42b53a27acef6c47eb070af84118ce3a9c6ea0 SHA1 1085bd819f72708f4d581cc6b6f7182d07d95750 SHA256 d4560b2e24c7281e9a1ed0cfbe3040ccb8f57f396fb38f145859b89a189ef91c MISC metadata.xml 225 RMD160 aa7d7690bc9d41aa160500739ec29a5aecb24958 SHA1 a7fa143a3c80636c1f82827063de2327d4380d57 SHA256 3b760abcba804d12e90e8101abef730ff1be333e8c01f273f7a05e68f5f1df88 diff --git a/sci-libs/openblas/ChangeLog b/sci-libs/openblas/ChangeLog new file mode 100644 index 000000000..d04e0a991 --- /dev/null +++ b/sci-libs/openblas/ChangeLog @@ -0,0 +1,27 @@ +# ChangeLog for sci-libs/openblas +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*openblas-0.1_alpha2 (03 Aug 2011) + + 03 Aug 2011 Andrea Arteaga <andyspiros@gmail.com> openblas-0.1_alpha2.ebuild + Import from bicatali overlay. Added alpha version. + + 20 Jun 2011; Sébastien Fabbro <bicatali@gentoo.org> openblas-9999.ebuild: + Added more include files, thanks François Bissey for his note + + 31 May 2011; Sébastien Fabbro <bicatali@gentoo.org> openblas-9999.ebuild, + +files/openblas-aliasing.patch: + Fixed shared libs. Make ebuild easier to debug with a generated rule Makefile + instead of dynamic. Added a aliasing patch. Switched to EAPI4. + + 23 Feb 2011; Sébastien Fabbro <bicatali@gentoo.org> openblas-9999.ebuild, + files/openblas-sharedlibs.patch: + fixed ldflags propagation + +*openblas-9999 (23 Feb 2011) + + 23 Feb 2011; Sébastien Fabbro <bicatali@gentoo.org> +openblas-9999.ebuild, + +files/openblas-sharedlibs.patch, +metadata.xml: + Initial import + diff --git a/sci-libs/openblas/Manifest b/sci-libs/openblas/Manifest new file mode 100644 index 000000000..09773e7de --- /dev/null +++ b/sci-libs/openblas/Manifest @@ -0,0 +1,6 @@ +AUX openblas-aliasing.patch 421 RMD160 1c4b38a0145f937f4c35afa03ec54196646ff311 SHA1 08a33e39d9e0a753e82b9298da73094d79311cbd SHA256 8d7c2fff88c9a51b3bc419897194bbf513fa96b9dbb6b9063c9a8e9e0d3c7773 +AUX openblas-sharedlibs.patch 1929 RMD160 87db891bb2e0b538da7a4f21c10c65b78149a26c SHA1 031912957004745f5e68c2cdf3899f0e80118377 SHA256 fc5f014d6b81a481a9c9c29d82de07f5a5182d9355f90071ba89b680f7e09c1b +EBUILD openblas-0.1_alpha2.ebuild 3097 RMD160 d2623429b5413918af2b7c512fda6d7e0b893fee SHA1 35b2fe1f3aa4f2bcdb740f13abf762a9f1017b6d SHA256 78c93659310ad188049d24ff6efba367af61129da34cadfe63952c410d1efde1 +EBUILD openblas-9999.ebuild 2920 RMD160 f89a457ee107ba206f3096109beed45f254a6e59 SHA1 8996ac70e009300e376b5e812f011565d260168e SHA256 a670c80e9234c1166dd4f3c655ab67f3766bc12305f95a671fc4aedad5cee22a +MISC ChangeLog 1005 RMD160 7a86f0865e676e102bc9ddaef65a1dba5ad7db31 SHA1 243b375c60cc511f5e78af51f87e6c93f5e5312c SHA256 2b4b80e94bf335082b9ced2e1cd0ed9de61d94e5be9279efe03fc85e69408305 +MISC metadata.xml 569 RMD160 4405ffe0e8941f0806ce0b7f984052be2ee4ed8b SHA1 ae10082e791ba7635e3c5986b0842fd74ff9ef38 SHA256 ddd3fa2f35204325b559955bc761c1c837265b9fc3ecc31dac760bc30fa082d2 diff --git a/sci-libs/openblas/files/openblas-aliasing.patch b/sci-libs/openblas/files/openblas-aliasing.patch new file mode 100644 index 000000000..8c59b1c63 --- /dev/null +++ b/sci-libs/openblas/files/openblas-aliasing.patch @@ -0,0 +1,11 @@ +--- driver/others/init.c.orig 2011-05-31 18:59:24.000000000 +0100 ++++ driver/others/init.c 2011-05-31 20:18:51.000000000 +0100 +@@ -261,7 +261,7 @@ + for (node = 0; node < MAX_NODES; node ++) common -> node_info[node] = 0; + + while ((dir = readdir(dp)) != NULL) { +- if (*(unsigned int *) dir -> d_name == 0x065646f6eU) { ++ if (*(char *) dir -> d_name == 0x065646f6eU) { + + node = atoi(&dir -> d_name[4]); + diff --git a/sci-libs/openblas/files/openblas-sharedlibs.patch b/sci-libs/openblas/files/openblas-sharedlibs.patch new file mode 100644 index 000000000..3ebe3076a --- /dev/null +++ b/sci-libs/openblas/files/openblas-sharedlibs.patch @@ -0,0 +1,45 @@ +--- exports/Makefile.orig 2010-11-12 05:30:06.000000000 +0000 ++++ exports/Makefile 2010-11-12 06:33:41.000000000 +0000 +@@ -97,10 +97,10 @@ + so : ../$(LIBSONAME) + + ../$(LIBSONAME) : ../$(LIBNAME) linux.def linktest.c +- $(CC) $(CFLAGS) -shared -o ../$(LIBSONAME) \ +- -Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive \ +- -Wl,--retain-symbols-file=linux.def $(EXTRALIB) +- $(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK. ++ $(CC) $(LDFLAGS) -shared \ ++ -Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive -Wl,--soname=$(LIBSONAME) \ ++ -Wl,--retain-symbols-file=linux.def $(EXTRALIB) -o ../$(LIBSONAME) ++ $(CC) $(CFLAGS) -w linktest.c ../$(LIBSONAME) $(FEXTRALIB) -o linktest && echo OK. + rm -f linktest + + endif +@@ -110,10 +110,10 @@ + so : ../$(LIBSONAME) + + ../$(LIBSONAME) : ../$(LIBNAME) linux.def linktest.c +- $(CC) $(CFLAGS) -shared -o ../$(LIBSONAME) \ +- -Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive \ +- -Wl,--retain-symbols-file=linux.def $(EXTRALIB) +- $(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK. ++ $(CC) $(LDFLAGS) -shared \ ++ -Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive -Wl,--soname=$(LIBSONAME) \ ++ -Wl,--retain-symbols-file=linux.def $(EXTRALIB) -o ../$(LIBSONAME) ++ $(CC) $(CFLAGS) -w linktest.c ../$(LIBSONAME) $(FEXTRALIB) -o linktest && echo OK. + rm -f linktest + + endif +@@ -129,9 +129,9 @@ + ifeq ($(OSNAME), SunOS) + + so : ../$(LIBSONAME) +- $(CC) $(CFLAGS) -shared -o ../$(LIBSONAME) \ +- -Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive $(EXTRALIB) +- $(CC) $(CFLAGS) -w -o linktest linktest.c ../$(LIBSONAME) $(FEXTRALIB) && echo OK. ++ $(CC) $(LDFLAGS) -shared -Wl,--soname=$(LIBSONAME) \ ++ -Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive $(EXTRALIB) -o ../$(LIBSONAME) ++ $(CC) $(CFLAGS) -w linktest.c ../$(LIBSONAME) $(FEXTRALIB) -o linktest && echo OK. + rm -f linktest + + endif diff --git a/sci-libs/openblas/metadata.xml b/sci-libs/openblas/metadata.xml new file mode 100644 index 000000000..fd35350ed --- /dev/null +++ b/sci-libs/openblas/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci</herd> +<longdescription lang="en"> + OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD + version. See <pkg>sci-libs/gotoblas2</pkg> for more on GotoBLAS2. +</longdescription> +<use> + <flag name='int64'>Build the 64 bits integer library</flag> + <flag name='incblas'>Build the CBLAS interface</flag> + <flag name='dynamic'>Build dynamic architecture detection at run time (for multi targets)</flag> +</use> +</pkgmetadata> diff --git a/sci-libs/openblas/openblas-0.1_alpha2.ebuild b/sci-libs/openblas/openblas-0.1_alpha2.ebuild new file mode 100644 index 000000000..ef417e657 --- /dev/null +++ b/sci-libs/openblas/openblas-0.1_alpha2.ebuild @@ -0,0 +1,116 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs alternatives-2 git-2 + +DESCRIPTION="Optimized BLAS library based on GotoBLAS2" +HOMEPAGE="http://xianyi.github.com/OpenBLAS/" +EGIT_REPO_URI="git://github.com/xianyi/OpenBLAS.git" +EGIT_COMMIT="v0.1alpha2.2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +IUSE="+incblas int64 dynamic openmp static-libs threads" + +RDEPEND="virtual/fortran" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}" + +pkg_setup() { + ewarn "If the compilation fails, try setting the TARGET environment variable" + ewarn "to your CPU's codename and run emerge again." +} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-{sharedlibs,aliasing}.patch + # respect LDFLAGS + sed -i -e '/^LDFLAGS\s*=/d' Makefile.* || die + # respect CFLAGS only if dynamic flag not enabled + if ! use dynamic; then + sed -i \ + -e "/^COMMON_OPT/s/-O2/${CFLAGS}/" \ + Makefile.rule || die + fi + # fix executable stacks + local i + for i in $(find . -name \*.S); do + cat >> ${i} <<-EOF + #if defined(__ELF__) + .section .note.GNU-stack,"",%progbits + #endif + EOF + done +} + +src_configure() { + local use_openmp=$(use openmp && echo 1) + use threads && use openmp && use_openmp="" && \ + einfo "openmp and threads enabled: using threads" + sed -i \ + -e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \ + -e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC):" \ + -e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC):" \ + -e "s:^#\s*\(USE_THREAD\)\s*=.*:\1=$(use threads && echo 1 || echo 0):" \ + -e "s:^#\s*\(USE_OPENMP\)\s*=.*:\1=${use_openmp}:" \ + -e "s:^#\s*\(DYNAMIC_ARCH\)\s*=.*:\1=$(use dynamic && echo 1):" \ + -e "s:^#\s*\(INTERFACE64\)\s*=.*:\1=$(use int64 && echo 1):" \ + -e "s:^#\s*\(NO_CBLAS\)\s*=.*:\1=$(use incblas || echo 1):" \ + Makefile.rule || die +} + +src_compile() { + mkdir solibs + emake libs shared && mv *.so solibs/ + use static-libs && emake clean && emake libs NEED_PIC= +} + +src_test() { + emake tests +} + +src_install() { + local profname=${PN} threads + use int64 && profname=${profname}-int64 + if use threads; then + threads="-pthread" + profname=${profname}-threads + elif use openmp; then + profname=${profname}-openmp + fi + + dolib.so solibs/lib*.so + use static-libs && dolib.a lib*.a + + # create pkg-config file and associated eselect file + cat <<-EOF > ${profname}.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ${PN} + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lopenblas -lm ${threads} + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ${profname}.pc + + alternatives_for blas ${profname} 0 \ + "/usr/$(get_libdir)/pkgconfig/blas.pc" "${profname}.pc" + + if use incblas; then + insinto /usr/include/${PN} + doins cblas.h common*.h config.h param.h + echo >> ${profname}.pc "Cflags: -I\${includedir}/${PN}" + alternatives_for cblas ${profname} 0 \ + "/usr/$(get_libdir)/pkgconfig/cblas.pc" "${profname}.pc" \ + "/usr/include/cblas.h" "${PN}/cblas.h" + fi + dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt +} diff --git a/sci-libs/openblas/openblas-9999.ebuild b/sci-libs/openblas/openblas-9999.ebuild new file mode 100644 index 000000000..143c24eda --- /dev/null +++ b/sci-libs/openblas/openblas-9999.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit eutils toolchain-funcs alternatives-2 git-2 + +DESCRIPTION="Optimized BLAS library based on GotoBLAS2" +HOMEPAGE="http://xianyi.github.com/OpenBLAS/" +EGIT_REPO_URI="git://github.com/xianyi/OpenBLAS.git" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +IUSE="+incblas int64 dynamic openmp static-libs threads" + +RDEPEND="virtual/fortran" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-{sharedlibs,aliasing}.patch + # respect LDFLAGS + sed -i -e '/^LDFLAGS\s*=/d' Makefile.* || die + # respect CFLAGS only if dynamic flag not enabled + if ! use dynamic; then + sed -i \ + -e "/^COMMON_OPT/s/-O2/${CFLAGS}/" \ + Makefile.rule || die + fi + # fix executable stacks + local i + for i in $(find . -name \*.S); do + cat >> ${i} <<-EOF + #if defined(__ELF__) + .section .note.GNU-stack,"",%progbits + #endif + EOF + done +} + +src_configure() { + local use_openmp=$(use openmp && echo 1) + use threads && use openmp && use_openmp="" && \ + einfo "openmp and threads enabled: using threads" + sed -i \ + -e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \ + -e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC):" \ + -e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC):" \ + -e "s:^#\s*\(USE_THREAD\)\s*=.*:\1=$(use threads && echo 1 || echo 0):" \ + -e "s:^#\s*\(USE_OPENMP\)\s*=.*:\1=${use_openmp}:" \ + -e "s:^#\s*\(DYNAMIC_ARCH\)\s*=.*:\1=$(use dynamic && echo 1):" \ + -e "s:^#\s*\(INTERFACE64\)\s*=.*:\1=$(use int64 && echo 1):" \ + -e "s:^#\s*\(NO_CBLAS\)\s*=.*:\1=$(use incblas || echo 1):" \ + Makefile.rule || die +} + +src_compile() { + mkdir solibs + emake libs shared && mv *.so solibs/ + use static-libs && emake clean && emake libs NEED_PIC= +} + +src_test() { + emake tests +} + +src_install() { + local profname=${PN} threads + use int64 && profname=${profname}-int64 + if use threads; then + threads="-pthread" + profname=${profname}-threads + elif use openmp; then + profname=${profname}-openmp + fi + + dolib.so solibs/lib*.so + use static-libs && dolib.a lib*.a + + # create pkg-config file and associated eselect file + cat <<-EOF > ${profname}.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ${PN} + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lopenblas -lm ${threads} + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ${profname}.pc + + alternatives_for blas ${profname} 0 \ + "/usr/$(get_libdir)/pkgconfig/blas.pc" "${profname}.pc" + + if use incblas; then + insinto /usr/include/${PN} + doins cblas.h common*.h config.h param.h + echo >> ${profname}.pc "Cflags: -I\${includedir}/${PN}" + alternatives_for cblas ${profname} 0 \ + "/usr/$(get_libdir)/pkgconfig/cblas.pc" "${profname}.pc" \ + "/usr/include/cblas.h" "${PN}/cblas.h" + fi + dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt +} diff --git a/sci-mathematics/Macaulay2/ChangeLog b/sci-mathematics/Macaulay2/ChangeLog index 80813e5bf..e3e7937dc 100644 --- a/sci-mathematics/Macaulay2/ChangeLog +++ b/sci-mathematics/Macaulay2/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 09 Aug 2011; Thomas Kahle <tomka@gentoo.org> Macaulay2-9999.ebuild: + adjusting boehm-gc source file + 08 Jul 2011; Thomas Kahle <tomka@gentoo.org> -files/1.4-paths-of-external-programs.patch, -Macaulay2-1.3.1-r4.ebuild, Macaulay2-9999.ebuild, -files/respect-CFLAGS.patch: diff --git a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild b/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild index 67c914a54..1ea1cde3d 100644 --- a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild +++ b/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild @@ -15,7 +15,7 @@ HOMEPAGE="http://www.math.uiuc.edu/Macaulay2/" SRC_BASE="http://www.math.uiuc.edu/${PN}/Downloads/" SRC_URI="${SRC_BASE}/OtherSourceCode/1.3/factory-3-1-1.tar.gz ${SRC_BASE}/OtherSourceCode/1.3/libfac-3-1-1.tar.gz - http://www.math.uiuc.edu/Macaulay2/Extra/gc-7.2alpha5-2010-09-03.tar.gz" + http://www.math.uiuc.edu/Macaulay2/Extra/gc-7.2alpha7-2011-07-25.tar.gz" SLOT="0" LICENSE="GPL-2" @@ -71,10 +71,10 @@ src_prepare() { || die "copy failed" cp "${DISTDIR}/libfac-3-1-1.tar.gz" "${S}/BUILD/tarfiles/" \ || die "copy failed" - # Macaulay 2 in this version insists on a snapshot of boehm-gc that is not available elsewhere - # We will let it build its internal version until >=boehm-gc-7.2_alpha5 is in in tree. Note: + # Macaulay 2 insists on a snapshot of boehm-gc that is not available elsewhere + # We will let it build its internal version for now. Note: # The resulting QA warning is known. - cp "${DISTDIR}/gc-7.2alpha5-2010-09-03.tar.gz" "${S}/BUILD/tarfiles/" \ + cp "${DISTDIR}/gc-7.2alpha7-2011-07-25.tar.gz" "${S}/BUILD/tarfiles/" \ || die "copy failed" eautoreconf diff --git a/sci-mathematics/Macaulay2/Manifest b/sci-mathematics/Macaulay2/Manifest index eb19de9b5..31da42797 100644 --- a/sci-mathematics/Macaulay2/Manifest +++ b/sci-mathematics/Macaulay2/Manifest @@ -1,21 +1,9 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA256 - AUX 70Macaulay2-gentoo.el 597 RMD160 bdf3a30bb4d15a77e0dff86c866134d06c443fa0 SHA1 d4a4036042ab13bc20d8be90b559e9168bfc0ef5 SHA256 e5583d11e6ab662261abb32e90fcf31ccf6bd56f2b23b691b9255d1b8d8acb2f AUX 9999-paths-of-external-programs.patch 3175 RMD160 ad0f634b52b3fe883e49a53815481ca5b73d93c3 SHA1 4644c4b8c64678ca8205515436666651f467ee58 SHA256 162823069e075d7b7712db841d8c7bb8e1f03f2c33d4ade18e0b7a20543f5230 AUX paths-of-dependencies.patch 2437 RMD160 9b63baeee97428406bed8bfbf67cf6fead95974a SHA1 cf245ad8bcdbe119e127242119b2b96342100035 SHA256 bffbaaf077f99f1e135fe0eff61be702c6eb138f4b4ae715cec8c5be62ee8046 DIST factory-3-1-1.tar.gz 540431 RMD160 63b5d71c93b1c0f628d758959822f61b0a9c702c SHA1 2b0e087de5ff4d4b63c003e1b6f9926577f17264 SHA256 1f86833248ef2bb5fd7820201d08df864bda2d8be58bc69255ecdca6fdf12c1b -DIST gc-7.2alpha5-2010-09-03.tar.gz 1257818 RMD160 58954216c702add21e24eecb2225274e760faf49 SHA1 1686ccc823376e7e693cae3b3c387c2aa052154b SHA256 adba7f6663d911d4031a1a6a87de6f75d5d8f7870ad362e16f5395449911c1fa +DIST gc-7.2alpha7-2011-07-25.tar.gz 1318092 RMD160 dfbf3c54ec301c02831029bd7fb8c2d7a4abcec5 SHA1 cd4fc4731fe1ad09574185c13bee17f240b35e8c SHA256 2578feb8d0cba997794277c7da0a8898838b34bf313d16e95a302eae16d1ec29 DIST libfac-3-1-1.tar.gz 90104 RMD160 8ca086ad2dc1dfbf3d8824e244f0b1af087eef62 SHA1 3753363a6f56cfeb0d0be3bdf471d6bd55c14ede SHA256 4c463af2d22375aa62be4fb1f9a32cada6723ca5e3ddbd8a4f5cab72b675e33a -EBUILD Macaulay2-9999.ebuild 3762 RMD160 87098eaed32eeeb5b75cd11bc7ef5668038e07c7 SHA1 15ca80b1a7942b6588f1264293f73cca7b4786d9 SHA256 5c7d3ceb12da58d7d37a98e0dc9452c9b4929ff635e1b540e1b6fd6301f39913 -MISC ChangeLog 4380 RMD160 ff5c441eb702a8b05f85b3489d925815d737a756 SHA1 2d05dd08c80f902f713262792e581548a512fd5e SHA256 8ec0b885c26c7c213ed25cbb7af479884bfd02f20db7b739f8ebccbd9b4e083f +EBUILD Macaulay2-9999.ebuild 3712 RMD160 3200c5bb3234285f0d5c1aea31c26aec80083b97 SHA1 2131ea2af59c472b4cd0b990ea1025a4a0e7a295 SHA256 c88d90668a8cc1e5ccba7a045ebf9016af10c8e84687af98ee971f97ad6c5ce7 +MISC ChangeLog 4484 RMD160 9ed1c1c0d4d07624df625cc56ff17fbd02ab603a SHA1 060a6455b1536ef49224cf7e3155371e6311bd03 SHA256 67b99d2bfd949a2f643a05a94719330adb318bd595f8f9cca779aa86d8a158d2 MISC metadata.xml 486 RMD160 0e913360cd4f3dd6b814bf44341c83005739a22b SHA1 83fb4a5ca743b184562281c8f1a5b8f722528514 SHA256 5937610a5ea0ddb9d15953121aa4f512f6ba8c2bcd35882a2dfe401f1dbddaa7 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iJwEAQEIAAYFAk4W5zgACgkQQYXt1pFHaaGodwP/ayJiZ3bkjDNWIHI25i32q3ch -NjolUy16AKwAeiNP6VsN8DjMyNar8N+oqOUnVBnC2qt/IQyUfSffUdQo+Jc+KY/z -P9SkJC6fHBbm9yHMLKiq3VADYq9at8JBCWNJ7MKdYrXbEO/Jrli26oDhp/iwMMwO -GRO+weeXKeDgn8pDQY0= -=rmQB ------END PGP SIGNATURE----- diff --git a/sci-physics/elk/Manifest b/sci-physics/elk/Manifest index 3be1566ef..1848bf6b3 100644 --- a/sci-physics/elk/Manifest +++ b/sci-physics/elk/Manifest @@ -1,3 +1,4 @@ DIST elk-1.3.15.tgz 1834503 RMD160 584eab8a026abad3b669cafee75103d6089025c2 SHA1 e4cc2e696f90c96b3a07f5b9a12de50c0123e9a0 SHA256 6e35d1c3830aeea0fe8016e25efa9debddf0e4bd90fe910520a35608a2f81fcf EBUILD elk-1.3.15.ebuild 2594 RMD160 5d503607169fc24119f0b216ab03d9b38ffa6a56 SHA1 5bc242e79c188d9b778b59f80986152487ddc194 SHA256 4b9b74082e74ab914cc1b07946614e6f401eda4d26f380be1d440d2edfa97c51 MISC ChangeLog 468 RMD160 ff92023da29bafb7b4e86f8e78566a3ad70ee4a3 SHA1 c9258e2ebfc0c91b7b3a010c1c76885f03b3035d SHA256 10c4b0f20ed89a213df9ee0cdcae62424f461f7e68fe7a8ea1c272bb00658eb9 +MISC metadata.xml 780 RMD160 c0bf373f142e8afc4acec0be314a34d778c073ba SHA1 0644ef0e7870199edd3178eff84da941e9c6b9b9 SHA256 0fe5272ad6b71bb76063a646fa9ad691b9c0860819941f465fe100473aed313b diff --git a/sci-physics/fastjet/ChangeLog b/sci-physics/fastjet/ChangeLog new file mode 100644 index 000000000..5950d5bc4 --- /dev/null +++ b/sci-physics/fastjet/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-physics/fastjet +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 30 Jul 2011; Kacper Kowalik <xarthisius@gentoo.org> fastjet-2.4.4.ebuild: + Remove unused eutils.eclass, shorten DESC, add missing license, sort + KEYWORDS, add static-libs, docs IUSE, add dependency on doxygen for [doc], + build only shared libs by default, install documentation + diff --git a/sci-physics/fastjet/Manifest b/sci-physics/fastjet/Manifest new file mode 100644 index 000000000..9799ea001 --- /dev/null +++ b/sci-physics/fastjet/Manifest @@ -0,0 +1,4 @@ +DIST fastjet-2.4.4.tar.gz 1849383 RMD160 f732143605c27ddd06ef3b3c740408f132acffdd SHA1 d4a255086aa2944eb17f437934c8407483d9dc87 SHA256 4d97a8494e9aae7e5738e97d224f5aafb44ae8c5d5021f836d5c8c20fc5030fc +EBUILD fastjet-2.4.4.ebuild 1658 RMD160 70d58483f5dfbfe9be3800daa820d32d29ae1afc SHA1 7c0eb4d6ce17c8669b0be39aefab801608269010 SHA256 ca626b13a0fd7105b5d70f8330c0609a13313f63c04b6fa8fdda1addee0c42d5 +MISC ChangeLog 404 RMD160 661f67e9437b3bc019eeb32afcb390bc60d4147d SHA1 b22b0ac54d5a97ab74ab8d4c2d02c0d517e5be46 SHA256 fc04dd5ce97b47231f17f7d112edf2d2619058c215013730a4c382ffe966b278 +MISC metadata.xml 952 RMD160 c12a86ae6429b7e145fac282fc3267e84c208992 SHA1 c787bac70e44abe374bb1a9a1b88032bcc9ae3da SHA256 420feae21bdeda91fb6b9b07adf9fae13626ff63811cde894fe5b66f9cca8795 diff --git a/sci-physics/fastjet/fastjet-2.4.4.ebuild b/sci-physics/fastjet/fastjet-2.4.4.ebuild new file mode 100644 index 000000000..73991c782 --- /dev/null +++ b/sci-physics/fastjet/fastjet-2.4.4.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +DESCRIPTION="Fast implementation of several recombination jet algorithms" +HOMEPAGE="http://www.lpthe.jussieu.fr/~salam/fastjet/" +SRC_URI="http://www.lpthe.jussieu.fr/~salam/fastjet/repo/${PF}.tar.gz" + +LICENSE="GPL-2 QPL" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+allplugins +allcxxplugins cgal doc static-libs" + +RDEPEND="cgal? ( sci-mathematics/cgal )" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +pkg_setup() { + if use allplugins || use allcxxplugins; then + echo + elog "Will build all plugins since you have one of allplugins or allcxxplugins set." + elog "The following plugins are available:" + elog " - siscone" + elog " - cdfcones" + elog " - pxcone" + elog " - d0runiicone" + elog " - nesteddefs" + elog " - trackjet" + elog " - atlascone" + elog " - cmsiterativecone" + elog " - eecambridge" + elog " - jade" + echo + fi +} + +src_configure() { + econf \ + $(use_enable allplugins) \ + $(use_enable allcxxplugins) \ + $(use_enable cgal) \ + $(use_enable static-libs static) +# --enable-siscone \ +# --enable-cdfcones \ +# --enable-pxcone \ +# --enable-d0runiicone \ +# --enable-nesteddefs \ +# --enable-trackjet \ +# --enable-atlascone \ +# --enable-cmsiterativecone \ +# --enable-eecambridge \ +# --enable-jade +} + +src_compile() { + default_src_compile + if use doc; then + $(type -p doxygen) Doxyfile || die + fi +} + +src_install() { + default_src_install + nonfatal dodoc AUTHORS BUGS ChangeLog NEWS README + if use doc; then + dohtml html/* + fi + if ! use static-libs; then + find "${D}" -name '*.la' -exec rm -f {} + fi +} diff --git a/sci-physics/fastjet/metadata.xml b/sci-physics/fastjet/metadata.xml new file mode 100644 index 000000000..4f1287dda --- /dev/null +++ b/sci-physics/fastjet/metadata.xml @@ -0,0 +1,28 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-physics</herd> + <maintainer> + <email>bbannier+gentoo_bugs@gmail.com</email> + <description>please assign bugs</description> + </maintainer> + <longdescription lang="en"> + The FastJet package provides a fast implementation of the longitudinally + invariant kt longitudinally invariant inclusive Cambridge/Aachen and + anti-kt jet finders and a uniform interface to external jet finders + (notably SISCone) via a plugin mechanism. It also includes tools for + calculating jet areas and performing background (pileup/UE) subtraction. + </longdescription> + <use> + <flag name='allplugins'> + Build all standard plugins. + </flag> + <flag name='allcxxplugins'> + Build all C++ plugins. + </flag> + <flag name='cgal'> + Use <pkg>sci-mathematics/cgal</pkg> instead of bundled algorithms. + </flag> + </use> +</pkgmetadata> + diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog new file mode 100644 index 000000000..91b9580c0 --- /dev/null +++ b/sci-physics/root/ChangeLog @@ -0,0 +1,28 @@ +# ChangeLog for sci-physics/root +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 02 Aug 2011; Andrew Savchenko <bircoph@gmail.com> root-5.30.00.ebuild: + Enable rpath if prefix is used, see bug 346933. + +*root-5.30.00 (02 Aug 2011) + + 02 Aug 2011; Andrew Savchenko <bircoph@gmail.com> + +files/root-5.28.00b-asneeded.patch, +files/root-5.28.00b-glibc212.patch, + +files/root-5.28.00b-prop-ldflags.patch, +files/root-5.28.00b-unuran.patch, + +root-5.30.00.ebuild, +files/root-5.30.00-lzma.patch, + +files/root-5.30.00-nobyte-compile.patch, + +files/root-5.30.00-xrootd-prop-flags.patch, +files/olbd.confd, + +files/olbd.initd, +files/proofd.confd, +files/proofd.initd, + +files/rootd.confd, +files/rootd.initd, +files/xrootd.confd, + +files/xrootd.initd, +metadata.xml: + Version bump. This are changes from bug 374709 including: + - upatchset update; + - lzma support (for root file data compression); + - X support is now optional (but enabled by default, of course), + this is extremely useful on X-less computating stations; + - fix tmva and roofit documentation installation (pdfs were missed due to + ebuild typo; + - some missed deps. + - libXft dep is controlled by xft flag. + diff --git a/sci-physics/root/Manifest b/sci-physics/root/Manifest new file mode 100644 index 000000000..3ea74a2ad --- /dev/null +++ b/sci-physics/root/Manifest @@ -0,0 +1,22 @@ +AUX olbd.confd 197 RMD160 798de1808502f3e4ecfc5f024b56a419d9824057 SHA1 f2a4385fdf9849eafb1d5457727f6fbe80af1da3 SHA256 5a34da76bbe56cd3b8128f05c0d9900f9d7f7ffdcffc5deeb816c78ea46679ba +AUX olbd.initd 714 RMD160 77189b1808d0ef1947652f3aa22852001b57c4af SHA1 be3cc5c39c15707f1e9113ca8c70bed601074f8b SHA256 1c4bde12002e9535d298b653c7f74ff6bab305cde70676f574450c843ef52489 +AUX proofd.confd 415 RMD160 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b/sci-physics/root/files/olbd.confd new file mode 100644 index 000000000..848f4d7ba --- /dev/null +++ b/sci-physics/root/files/olbd.confd @@ -0,0 +1,9 @@ +# conf.d file for olbd daemon + +# User to run as (default is `xrootd') +OLBD_USER="root" + +# +# Please refer to the olbd(1) man(1) page for more +# information on command line parameters. +OLBD_OPTS="" diff --git a/sci-physics/root/files/olbd.initd b/sci-physics/root/files/olbd.initd new file mode 100644 index 000000000..95b7bc56e --- /dev/null +++ b/sci-physics/root/files/olbd.initd @@ -0,0 +1,26 @@ +#!/sbin/runscript +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/files/olbd.initd,v 1.1 2008/12/18 18:10:18 bicatali Exp $ + +depend() { + need net + use dns logger + provide root-file-server +} + +start() { + ebegin "Starting ROOT open load balancer server" + start-stop-daemon --start --quiet --user=${OLBD_USER} \ + --make-pidfile --pidfile=/var/run/olbd.pid \ + --exec /usr/bin/olbd --background -- ${OLBD_OPTS} + eend $? +} + +stop() { + ebegin "Stopping ROOT open load balancer server" + start-stop-daemon --stop --quiet \ + --pidfile=/var/run/olbd.pid \ + --exec /usr/bin/olbd + eend $? +} diff --git a/sci-physics/root/files/proofd.confd b/sci-physics/root/files/proofd.confd new file mode 100644 index 000000000..81720a7eb --- /dev/null +++ b/sci-physics/root/files/proofd.confd @@ -0,0 +1,12 @@ +# conf.d file for proof daemon +# +# Please refer to the proofd(1) man(1) page for more information on +# command line parameters. +# +PROOFD_OPTS= + +# Specify your base of your PROOF directory here. If left blank, it +# will use the system default (e.g., /usr/share/root/proof). +# Note, however, that ROOT recommends that this directory is shared (via +# NFS or similar) among all the nodes of the cluster. +PROOF_DIR= diff --git a/sci-physics/root/files/proofd.initd b/sci-physics/root/files/proofd.initd new file mode 100644 index 000000000..3fac75c4d --- /dev/null +++ b/sci-physics/root/files/proofd.initd @@ -0,0 +1,26 @@ +#!/sbin/runscript +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/files/proofd.initd,v 1.2 2009/01/20 18:04:09 bicatali Exp $ + +depend() { + need root-file-server + use logger +} + +start() { + ebegin "Starting parallel ROOT facility server" + start-stop-daemon --start --quiet \ + --pidfile /var/run/proofd.pid \ + --exec /usr/bin/proofd -- ${PROOFD_OPTS} ${PROOF_DIR} + pidof /usr/bin/proofd > /var/run/proofd.pid + eend $? +} + +stop() { + ebegin "Stopping parallel ROOT facility server" + start-stop-daemon --stop --quiet \ + --pidfile /var/run/proofd.pid \ + --exec /usr/bin/proofd + eend $? +} diff --git a/sci-physics/root/files/root-5.28.00b-asneeded.patch b/sci-physics/root/files/root-5.28.00b-asneeded.patch new file mode 100644 index 000000000..b845247e1 --- /dev/null +++ b/sci-physics/root/files/root-5.28.00b-asneeded.patch @@ -0,0 +1,20 @@ +--- root.orig/configure 2010-12-20 07:17:54.000000000 +0000 ++++ root/configure 2010-12-20 07:16:05.000000000 +0000 +@@ -709,7 +709,7 @@ + cat <<EOF > conftest.mk + include ${ac_srcdir}/config/Makefile.${arch} + conftest: conftest.c +- \$(CC) \$(CFLAGS) \$(LDFLAGS) $linkdir $linklib \$< -o \$@ ++ \$(CC) \$(CFLAGS) \$(LDFLAGS) \$< $linkdir $linklib -o \$@ + + conftest.c: + echo "int main() { return 0; }" > \$@ +@@ -723,7 +723,7 @@ + cat <<EOF > conftest.mk + include ${ac_srcdir}/config/Makefile.${arch} + conftest:conftest.c +- \$(CC) \$(CFLAGS) \$(LDFLAGS) $linkdir $linklib \$< -o \$@ ++ \$(CC) \$(CFLAGS) \$(LDFLAGS) \$< $linkdir $linklib -o \$@ + + conftest.c: + echo "extern int $linksymbol (); " > \$@ diff --git a/sci-physics/root/files/root-5.28.00b-glibc212.patch b/sci-physics/root/files/root-5.28.00b-glibc212.patch new file mode 100644 index 000000000..a36543139 --- /dev/null +++ b/sci-physics/root/files/root-5.28.00b-glibc212.patch @@ -0,0 +1,11 @@ +--- root.orig/net/auth/src/TAFS.cxx 2010-09-14 03:22:22.647915854 +0400 ++++ root/net/auth/src/TAFS.cxx 2010-09-14 03:22:39.034599899 +0400 +@@ -11,6 +11,7 @@ + + #ifndef WIN32 + # include <unistd.h> ++# include <sys/stat.h> + #else + # define ssize_t int + # include <io.h> + diff --git a/sci-physics/root/files/root-5.28.00b-prop-ldflags.patch b/sci-physics/root/files/root-5.28.00b-prop-ldflags.patch new file mode 100644 index 000000000..732431943 --- /dev/null +++ b/sci-physics/root/files/root-5.28.00b-prop-ldflags.patch @@ -0,0 +1,13 @@ +diff -Naur root.orig/config/Makefile.in root/config/Makefile.in +--- root.orig/config/Makefile.in 2010-12-14 17:20:26.000000000 +0300 ++++ root/config/Makefile.in 2010-12-17 22:33:34.902161458 +0300 +@@ -27,7 +27,7 @@ + + EXTRA_CFLAGS := -Iinclude @cflags@ + EXTRA_CXXFLAGS := -Iinclude @cflags@ +-EXTRA_LDFLAGS := @ldflags@ ++EXTRA_LDFLAGS := @ldflags@ $(LDFLAGS) + WINRTDEBUG := @winrtdebug@ + + GLBPATCHFLAGS := @glbpatchcflags@ + diff --git a/sci-physics/root/files/root-5.28.00b-unuran.patch b/sci-physics/root/files/root-5.28.00b-unuran.patch new file mode 100644 index 000000000..76422daed --- /dev/null +++ b/sci-physics/root/files/root-5.28.00b-unuran.patch @@ -0,0 +1,39 @@ +diff -ur root-trunk.orig/math/unuran/Module.mk root-trunk/math/unuran/Module.mk +--- root.orig/math/unuran/Module.mk 2010-11-25 20:41:32.000000000 +0100 ++++ root/math/unuran/Module.mk 2010-11-25 20:51:47.190704977 +0100 +@@ -20,7 +20,7 @@ + UNURANETAG := $(call stripsrc,$(UNURANDIRS)/headers.d) + UNRCFG := $(call stripsrc,$(UNURANDIRS)/$(UNRVERS)/config.h) + +-UNRTARCONTENT:=$(subst $(UNRVERS),$(UNRDIRS),$(shell mkdir -p $(UNRDIR); cd $(UNRDIR); gunzip -c $(UNRSRCS) | tar tf -)) ++UNRTARCONTENT:= + UNRS := $(filter %.c, \ + $(filter $(UNRDIRS)/src/utils/%,$(UNRTARCONTENT)) \ + $(filter $(UNRDIRS)/src/methods/%,$(UNRTARCONTENT)) \ +@@ -69,10 +69,9 @@ + ##### local rules ##### + .PHONY: all-$(MODNAME) clean-$(MODNAME) distclean-$(MODNAME) + +-include/%.h: $(UNURANDIRI)/%.h $(UNURANETAG) ++include/%.h: $(UNURANDIRI)/%.h + cp $< $@ + +-$(UNURANDEP): $(UNRCFG) + $(UNRS): $(UNURANETAG) + + $(UNURANETAG): $(UNRSRCS) +@@ -125,12 +124,12 @@ + GNUMAKE=$(MAKE) ./configure CC="$$ACC" \ + CFLAGS="$$ACFLAGS"); + +-$(UNURANLIB): $(UNRCFG) $(UNRO) $(UNURANO) $(UNURANDO) $(ORDER_) \ ++$(UNURANLIB): $(UNURANO) $(UNURANDO) $(ORDER_) \ + $(MAINLIBS) $(UNURANLIBDEP) + @$(MAKELIB) $(PLATFORM) $(LD) "$(LDFLAGS)" \ + "$(SOFLAGS)" libUnuran.$(SOEXT) $@ \ + "$(UNURANO) $(UNURANDO)" \ +- "$(UNURANLIBEXTRA) $(UNRO)" ++ "$(UNURANLIBEXTRA) -lunuran" + + $(UNURANDS): $(UNRINIT) $(UNURANDH1) $(UNURANL) $(ROOTCINTTMPDEP) + $(MAKEDIR) diff --git a/sci-physics/root/files/root-5.30.00-lzma.patch b/sci-physics/root/files/root-5.30.00-lzma.patch new file mode 100644 index 000000000..b35f7fddd --- /dev/null +++ b/sci-physics/root/files/root-5.30.00-lzma.patch @@ -0,0 +1,13 @@ +--- root/configure.orig 2011-07-10 11:51:42.000000000 +0400 ++++ root/configure 2011-07-10 11:54:40.053175390 +0400 +@@ -2430,8 +2430,8 @@ + check_header "lzma.h" "" \ + $LZMA ${LZMA:+$LZMA/include} \ + ${finkdir:+$finkdir/include} \ +- /usr/local/include /usr/include/lzma /usr/local/include/lzma \ +- /opt/lzma/include /usr/include ++ /usr/local/include /usr/include /usr/local/include \ ++ /opt/lzma/include + if test "x$found_dir" = "x" ; then + enable_builtin_lzma=yes + else diff --git a/sci-physics/root/files/root-5.30.00-nobyte-compile.patch b/sci-physics/root/files/root-5.30.00-nobyte-compile.patch new file mode 100644 index 000000000..179e5790c --- /dev/null +++ b/sci-physics/root/files/root-5.30.00-nobyte-compile.patch @@ -0,0 +1,137 @@ +diff -Naur root.as-needed/Makefile root/Makefile +--- root.as-needed/Makefile 2011-07-10 10:42:49.758191296 +0400 ++++ root/Makefile 2011-07-10 10:43:21.493339703 +0400 +@@ -1167,10 +1167,7 @@ + if test "x$(RFLX_GRFLXPY)" != "x"; then \ + rm -f $(DESTDIR)$(LIBDIR)/$(RFLX_GRFLXPY); \ + fi; \ +- if test "x$(RFLX_GRFLXPYC)" != "x"; then \ +- rm -f $(DESTDIR)$(LIBDIR)/$(RFLX_GRFLXPYC); \ +- fi; \ +- if test "x$(RFLX_GRFLXPY)$(RFLX_GRFLXPYC)" != "x"; then \ ++ if test "x$(RFLX_GRFLXPY)" != "x"; then \ + dir=$(RFLX_GRFLXDD:lib/=); \ + while test "x$${dir}" != "x" && \ + test -d $(DESTDIR)$(LIBDIR)/$${dir} && \ +diff -Naur root.as-needed/bindings/pyroot/Module.mk root/bindings/pyroot/Module.mk +--- root.as-needed/bindings/pyroot/Module.mk 2011-07-10 10:42:48.991561304 +0400 ++++ root/bindings/pyroot/Module.mk 2011-07-10 10:43:21.493339703 +0400 +@@ -48,8 +48,6 @@ + ROOTPY := $(subst $(MODDIR),$(LPATH),$(ROOTPYS)) + $(LPATH)/%.py: $(MODDIR)/%.py; cp $< $@ + endif +-ROOTPYC := $(ROOTPY:.py=.pyc) +-ROOTPYO := $(ROOTPY:.py=.pyo) + + # used in the main Makefile + ALLHDRS += $(patsubst $(MODDIRI)/%.h,include/%.h,$(PYROOTH)) +@@ -68,10 +66,8 @@ + include/%.h: $(PYROOTDIRI)/%.h + cp $< $@ + +-%.pyc: %.py; python -c 'import py_compile; py_compile.compile( "$<" )' +-%.pyo: %.py; python -O -c 'import py_compile; py_compile.compile( "$<" )' + +-$(PYROOTLIB): $(PYROOTO) $(PYROOTDO) $(ROOTPY) $(ROOTPYC) $(ROOTPYO) \ ++$(PYROOTLIB): $(PYROOTO) $(PYROOTDO) $(ROOTPY) \ + $(ROOTLIBSDEP) $(PYTHONLIBDEP) + @$(MAKELIB) $(PLATFORM) $(LD) "$(LDFLAGS)" \ + "$(SOFLAGS)" libPyROOT.$(SOEXT) $@ \ +@@ -113,7 +109,7 @@ + + distclean-$(MODNAME): clean-$(MODNAME) + @rm -f $(PYROOTDEP) $(PYROOTDS) $(PYROOTDH) $(PYROOTLIB) \ +- $(ROOTPY) $(ROOTPYC) $(ROOTPYO) $(PYROOTMAP) \ ++ $(ROOTPY) $(PYROOTMAP) \ + $(PYROOTPYD) $(PYTHON64DEP) $(PYTHON64) + + distclean:: distclean-$(MODNAME) +diff -Naur root.as-needed/build/package/debian/rules root/build/package/debian/rules +--- root.as-needed/build/package/debian/rules 2011-07-10 10:42:49.241549346 +0400 ++++ root/build/package/debian/rules 2011-07-10 10:48:06.989670589 +0400 +@@ -691,10 +691,6 @@ + -X$(SYSCONFDIR)/root/system.rootauthrc \ + -X$(SYSCONFDIR)/root/system.rootdaemonrc \ + -X$(PREFIX)/lib/root/$(SOVERS)/libAfterImage.a \ +- -X$(PREFIX)/lib/root/$(SOVERS)/PyCintex.pyc \ +- -X$(PREFIX)/lib/root/$(SOVERS)/PyCintex.pyo \ +- -X$(PREFIX)/lib/root/$(SOVERS)/ROOT.pyc \ +- -X$(PREFIX)/lib/root/$(SOVERS)/ROOT.pyo \ + -X$(PREFIX)/lib/root/$(SOVERS)/cint7 \ + -X$(PREFIX)/include/root/Minuit2 + # $(foreach i, \ +diff -Naur root.as-needed/cint/cintex/Module.mk root/cint/cintex/Module.mk +--- root.as-needed/cint/cintex/Module.mk 2011-07-10 10:42:49.104889217 +0400 ++++ root/cint/cintex/Module.mk 2011-07-10 10:43:21.496672876 +0400 +@@ -31,10 +31,6 @@ + CINTEXPY := $(subst $(MODDIR)/python,$(LPATH),$(CINTEXPYS)) + $(LPATH)/%.py: $(MODDIR)/python/%.py; cp $< $@ + endif +-ifneq ($(BUILDPYTHON),no) +-CINTEXPYC := $(CINTEXPY:.py=.pyc) +-CINTEXPYO := $(CINTEXPY:.py=.pyo) +-endif + + # used in the main Makefile + ALLHDRS += $(patsubst $(MODDIRI)/Cintex/%.h,include/Cintex/%.h,$(CINTEXH)) +@@ -86,8 +82,6 @@ + fi) + cp $< $@ + +-%.pyc: %.py; python -c 'import py_compile; py_compile.compile( "$<" )' +-%.pyo: %.py; python -O -c 'import py_compile; py_compile.compile( "$<" )' + + $(CINTEXLIB): $(CINTEXO) $(CINTEXPY) $(CINTEXPYC) $(CINTEXPYO) \ + $(ORDER_) $(subst $(CINTEXLIB),,$(MAINLIBS)) $(CINTEXLIBDEP) +diff -Naur root.as-needed/cint/reflex/Module.mk root/cint/reflex/Module.mk +--- root.as-needed/cint/reflex/Module.mk 2011-07-10 10:42:49.074890651 +0400 ++++ root/cint/reflex/Module.mk 2011-07-10 10:43:21.496672876 +0400 +@@ -48,9 +48,6 @@ + RFLX_GRFLXS := $(wildcard $(RFLX_GRFLXSD)/*.py) + RFLX_GRFLXPY := $(patsubst $(RFLX_GRFLXSD)/%.py,$(RFLX_GRFLXDD)/%.py,$(RFLX_GRFLXS)) + RFLX_GRFLXPY += $(RFLX_GCCXMLPATHPY) +-ifneq ($(BUILDPYTHON),no) +-RFLX_GRFLXPYC := $(subst .py,.pyc,$(RFLX_GRFLXPY)) +-endif + + RFLX_LIBDIR = $(LIBDIR) + +@@ -92,7 +89,7 @@ + + ALLEXECS += $(RFLX_GENMAPX) + +-POSTBIN += $(RFLX_GRFLXPYC) $(RFLX_GRFLXPY) ++POSTBIN += $(RFLX_GRFLXPY) + + ##### local rules ##### + .PHONY: all-$(MODNAME) clean-$(MODNAME) distclean-$(MODNAME) \ +@@ -122,8 +119,6 @@ + mkdir -p lib/python/genreflex; fi ) + cp $< $@ + +-$(RFLX_GRFLXDD)/%.pyc: $(RFLX_GRFLXDD)/%.py +- @python -c 'import py_compile; py_compile.compile( "$<" )' + + $(RFLX_GENMAPO) : CXXFLAGS += -I$(REFLEXDIRS)/genmap + +@@ -149,7 +144,7 @@ + $(RLIBMAP) -o $@ -l $(REFLEXDICTLIB) \ + -d $(REFLEXDICTLIBDEPM) -c $(REFLEXL) + +-all-$(MODNAME): $(REFLEXLIB) $(REFLEXDICTLIB) $(REFLEXDICTMAP) $(RFLX_GRFLXPYC) $(RFLX_GRFLXPY) ++all-$(MODNAME): $(REFLEXLIB) $(REFLEXDICTLIB) $(REFLEXDICTMAP) $(RFLX_GRFLXPY) + + clean-genreflex: + @rm -rf lib/python/genreflex +diff -Naur root.as-needed/cint/reflex/python/CMakeLists.txt root/cint/reflex/python/CMakeLists.txt +--- root.as-needed/cint/reflex/python/CMakeLists.txt 2011-07-10 10:42:49.074890651 +0400 ++++ root/cint/reflex/python/CMakeLists.txt 2011-07-10 10:43:21.496672876 +0400 +@@ -15,7 +15,7 @@ + ##################### sources #################### + + FILE(GLOB_RECURSE GENREFLEX_SRCS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} genreflex/*.py) +-SET(GENREFLEX_SCRIPT ${CMAKE_CURRENT_BINARY_DIR}/genreflex/genreflex.pyc PARENT_SCOPE) ++SET(GENREFLEX_SCRIPT PARENT_SCOPE) + + ##################### gccxmlpath #################### + diff --git a/sci-physics/root/files/root-5.30.00-xrootd-prop-flags.patch b/sci-physics/root/files/root-5.30.00-xrootd-prop-flags.patch new file mode 100644 index 000000000..671cfe3df --- /dev/null +++ b/sci-physics/root/files/root-5.30.00-xrootd-prop-flags.patch @@ -0,0 +1,623 @@ +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.env.in root/net/xrootd/src/xrootd/config/GNUmake.env.in +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.env.in 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.env.in 2011-07-10 10:27:45.001375019 +0400 +@@ -47,6 +47,7 @@ + CFHASXRDCRYPTO = @hasxrdcrypto@ + + CFLAGS += $(CFSTRLCPY) $(CFHASOLDHDRS) $(CFFSTATAT) $(CFHASLIBZ) $(CFATOMICS) ++CFLAGS += $(CXXFLAGS) + + # AFS relevant variables + @incafs@ +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.options.in root/net/xrootd/src/xrootd/config/GNUmake.options.in +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.options.in 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.options.in 2011-07-10 10:24:16.131357441 +0400 +@@ -16,7 +16,7 @@ + CF32="$(TYPECF32)" \ + CFOP="$(@buildopt@)" \ + LD="$(TYPELD)" \ +-LDOP="$(@buildopt@)" \ ++LDOP="$(LDFLAGS)" \ + LDSO="$(TYPELDSO)" \ + LIBS=" @ldsyslibs@ $(TYPELIBS)" \ + TYPE="$(TYPE)" +@@ -33,7 +33,7 @@ + CF32="$(TYPECF32)" \ + CFOP="$(@buildopt@)" \ + LD="$(TYPELD)" \ +-LDOP="$(@buildopt@)" \ ++LDOP="$(LDFLAGS)" \ + LDSO="$(TYPELDSO)" \ + LIBS=" @ldsyslibs@ $(TYPELIBS)" \ + TYPE="$(TYPE)" +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.fbsd root/net/xrootd/src/xrootd/config/GNUmake.rules.fbsd +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.fbsd 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.fbsd 2011-07-10 10:24:16.131357441 +0400 +@@ -11,7 +11,7 @@ + -Wall -Wno-deprecated $(CFTRACE) + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + TYPELDSO = -shared + TYPESHLIB = so +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.gcc root/net/xrootd/src/xrootd/config/GNUmake.rules.gcc +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.gcc 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.gcc 2011-07-10 10:24:16.131357441 +0400 +@@ -11,7 +11,7 @@ + -Wall -Wno-deprecated -D__linux__ $(CFTRACE) + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + TYPELDSO = -shared + TYPESHLIB = so +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.gccia64 root/net/xrootd/src/xrootd/config/GNUmake.rules.gccia64 +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.gccia64 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.gccia64 2011-07-10 10:24:16.131357441 +0400 +@@ -11,7 +11,7 @@ + -Wall -Wno-deprecated -D__linux__ $(CFTRACE) + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + TYPELDSO = -shared + TYPESHLIB = so +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.gccx8664 root/net/xrootd/src/xrootd/config/GNUmake.rules.gccx8664 +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.gccx8664 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.gccx8664 2011-07-10 10:24:16.131357441 +0400 +@@ -11,7 +11,7 @@ + -Wall -Wno-deprecated -D__linux__ $(CFTRACE) + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + TYPELDSO = -m64 -shared + TYPESHLIB = so +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.icc root/net/xrootd/src/xrootd/config/GNUmake.rules.icc +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.icc 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.icc 2011-07-10 10:24:16.131357441 +0400 +@@ -13,7 +13,7 @@ + -ansi -D__linux__ -D__ICC__ -wd1476 -wd191 -wd468 -wd858 -wd1224 -wd584 $(CFTRACE) + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + TYPELDSO = -m32 -shared + TYPESHLIB = so +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.iccx8664 root/net/xrootd/src/xrootd/config/GNUmake.rules.iccx8664 +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.iccx8664 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.iccx8664 2011-07-10 10:24:16.131357441 +0400 +@@ -14,7 +14,7 @@ + -wd1572 -wd584 -i-dynamic $(CFTRACE) + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + TYPELDSO = -m64 -shared + TYPESHLIB = so +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.macos root/net/xrootd/src/xrootd/config/GNUmake.rules.macos +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.macos 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.macos 2011-07-10 10:24:16.131357441 +0400 +@@ -18,7 +18,7 @@ + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 + TYPELINK = -undefined dynamic_lookup -multiply_defined suppress +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + ifeq ($(subst $(MACOSX_MINOR),,1234),1234) + TYPELDSO = $(TYPELINK) -dynamiclib -single_module -m32 +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.macos64 root/net/xrootd/src/xrootd/config/GNUmake.rules.macos64 +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.macos64 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.macos64 2011-07-10 10:24:16.131357441 +0400 +@@ -15,7 +15,7 @@ + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 + TYPELINK = -undefined dynamic_lookup -multiply_defined suppress +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + ifeq ($(subst $(MACOSX_MINOR),,1234),1234) + TYPELDSO = $(TYPELINK) -dynamiclib -single_module -m64 +diff -Naur root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.sungcc root/net/xrootd/src/xrootd/config/GNUmake.rules.sungcc +--- root.orig/net/xrootd/src/xrootd/config/GNUmake.rules.sungcc 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/config/GNUmake.rules.sungcc 2011-07-10 10:24:16.131357441 +0400 +@@ -11,7 +11,7 @@ + -Wall -Wno-deprecated -DSUNGCC $(CFTRACE) + TYPECF32 = + TYPECF64 = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 +-TYPEOPT = $(TYPEMISC) -O2 ++TYPEOPT = $(TYPEMISC) $(CXXFLAGS) + TYPEDBG = $(TYPEMISC) -g + TYPELDSO = -shared + TYPESHLIB = so +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdAcc/GNUmakefile root/net/xrootd/src/xrootd/src/XrdAcc/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdAcc/GNUmakefile 2011-06-28 13:49:42.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdAcc/GNUmakefile 2011-07-10 10:24:16.131357441 +0400 +@@ -71,7 +71,7 @@ + + $(TESTBIN): $(OBJECTB) $(LIBDEPS) + @echo Creating executable $(TESTBIN) +- $(ECHO)$(LD) $(CFLAGS) $(LDOP) $(OBJECTB) $(BINLIBS) $(LIBS) -o $(TESTBIN) ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(OBJECTB) $(BINLIBS) $(LIBS) -o $(TESTBIN) + + $(OBJDIR)/XrdAccAccess.o: XrdAccAccess.cc XrdAccAccess.hh \ + XrdAccCapability.hh XrdAccConfig.hh XrdAccGroups.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdApps/GNUmakefile root/net/xrootd/src/xrootd/src/XrdApps/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdApps/GNUmakefile 2011-06-28 13:49:42.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdApps/GNUmakefile 2011-07-10 10:24:16.131357441 +0400 +@@ -59,7 +59,7 @@ + + $(XRDADLER32): $(XRDADLER32_OBJ) $(XRDADLERDEPT) + @echo Creating executable $(XRDADLER32) +- $(ECHO)$(LD) $(LDOP) $(XRDADLER32_OBJ) $(XRDADLERDEPS) $(XRDADLERLIBS) -o $(XRDADLER32) ++ $(ECHO) $(LD) $(LDFLAGS) $(XRDADLER32_OBJ) $(XRDADLERDEPS) $(XRDADLERLIBS) -o $(XRDADLER32) + + $(XRDADLER32_OBJ): Xrdadler32.cc \ + XrdPosixExtern.hh XrdPosixXrootd.hh \ +@@ -90,7 +90,7 @@ + + $(XRDMPXBIN): $(XRDMPXOBJ) $(XrdMPXDEPS) + @echo Creating executable $(XRDMPXBIN) +- $(ECHO)$(LD) $(LDOP) $(XRDMPXOBJ) $(XRDMPXLIBS) $(LIBS) -o $(XRDMPXBIN) ++ $(ECHO)$(CC) $(CXXFLAGS) $(LDFLAGS) $(XRDMPXOBJ) $(XRDMPXLIBS) $(LIBS) -o $(XRDMPXBIN) + + $(XRDMPXOBJ): XrdMpxStats.cc \ + XrdNetDNS.hh XrdNetSocket.hh XrdNetOpts.hh \ +@@ -106,7 +106,7 @@ + + $(XRDW41): $(XRDW41_OBJ) $(XRDW41_DEPS) + @echo Creating executable $(XRDW41) +- $(ECHO)$(LD) $(LDOP) $(XRDW41_OBJ) $(XRDW41LIBS) -o $(XRDW41) ++ $(ECHO)$(CC) $(CXXFLAGS) $(LDFLAGS) $(XRDW41_OBJ) $(XRDW41LIBS) -o $(XRDW41) + + $(XRDW41_OBJ): XrdWait41.cc \ + XrdOucTList.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdBwm/GNUmakefile root/net/xrootd/src/xrootd/src/XrdBwm/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdBwm/GNUmakefile 2011-06-28 13:49:43.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdBwm/GNUmakefile 2011-07-10 10:24:16.131357441 +0400 +@@ -67,7 +67,7 @@ + $(ECHO)ranlib $(LIBARCH) + + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(CFLAGS) $(OBJECTS) $(OBJFS) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY) ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(OBJECTS) $(OBJFS) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY) + + $(OBJDIR)/XrdBwm.o: XrdBwm.cc XrdBwm.hh \ + XrdAccAuthorize.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdClient/GNUmakefile root/net/xrootd/src/xrootd/src/XrdClient/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdClient/GNUmakefile 2011-06-28 13:49:41.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdClient/GNUmakefile 2011-07-10 10:24:16.131357441 +0400 +@@ -160,17 +160,17 @@ + $(LIBSHARED): $(OBJECTS) $(LIBDEP) + @echo Creating shared library $(LIBSHARED) + $(ECHO)rm -f $(LIBSHARED) +- $(ECHO)$(CC) $(CFLAGS) $(OBJECTS) $(LDSO) $(LIBLIBS) $(LIBS) -o $(LIBSHARED) ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(OBJECTS) $(LDSO) $(LIBLIBS) $(LIBS) -o $(LIBSHARED) + ifneq ($(subst $(MACOSX_MINOR),,1234),1234) + $(ECHO)if [ "x$(TYPE)" = "xDarwin" ]; then \ +- $(CC) $(CFLAGS) $(OBJECTS) $(TYPELDDY) $(LIBLIBS) $(LIBS) -o $(LIBDIR)/libXrdClient.$(TYPEDYLIB); \ ++ $(CC) $(CFLAGS) $(LDFLAGS) $(OBJECTS) $(TYPELDDY) $(LIBLIBS) $(LIBS) -o $(LIBDIR)/libXrdClient.$(TYPEDYLIB); \ + fi + endif + + $(LIBRARY_JNI): $(OBJECT_JNI) + @echo Creating shared library $(LIBRARY_JNI) + $(ECHO)rm -f $(LIBRARY_JNI); +- $(ECHO)$(CC) $(CFLAGS) $(OBJECT_JNI) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY_JNI) ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(OBJECT_JNI) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY_JNI) + + $(CLASS_JNI_TARGET): $(CLASS_JNI).java + @echo Creating JNI class file $(CLASS_JNI_TARGET) +@@ -178,27 +178,27 @@ + + $(BINDIR)/TestXrdClient_read: $(OBJECTS) $(OBJECTD) $(LIBDEPS) + @echo Creating executable $(BINDIR)/TestXrdClient_read +- $(ECHO)$(LD) $(LDOP) $(OBJECTD) $(BINLIBS) $(LIBS) -o $(BINDIR)/TestXrdClient_read ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTD) $(BINLIBS) $(LIBS) -o $(BINDIR)/TestXrdClient_read + + $(BINDIR)/TestXrdClient: $(OBJECTS) $(OBJECTB) $(LIBDEPS) + @echo Creating executable $(BINDIR)/TestXrdClient +- $(ECHO)$(LD) $(LDOP) $(OBJECTB) $(BINLIBS) $(LIBS) -o $(BINDIR)/TestXrdClient ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTB) $(BINLIBS) $(LIBS) -o $(BINDIR)/TestXrdClient + + $(XRDCP): $(OBJECTS) $(OBJECTC) $(LIBDEPS) + @echo Creating executable $(XRDCP) +- $(ECHO)$(LD) $(LDOP) $(OBJECTC) $(BINLIBS) $(LIBS) $(LIBZ) -o $(XRDCP) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTC) $(BINLIBS) $(LIBS) $(LIBZ) -o $(XRDCP) + + $(XRDPREPTOOL): $(OBJECTS) $(OBJECT_PREPTOOL) $(LIBDEPS) + @echo Creating executable $(XRDPREPTOOL) +- $(ECHO)$(LD) $(LDOP) $(OBJECT_PREPTOOL) $(BINLIBS) $(LIBS) -o $(XRDPREPTOOL) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECT_PREPTOOL) $(BINLIBS) $(LIBS) -o $(XRDPREPTOOL) + + $(XRDSTAGETOOL): $(OBJECTS) $(OBJECT_STAGETOOL) $(LIBDEPS) + @echo Creating executable $(XRDSTAGETOOL) +- $(ECHO)$(LD) $(LDOP) $(OBJECT_STAGETOOL) $(BINLIBS) $(LIBS) -o $(XRDSTAGETOOL) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECT_STAGETOOL) $(BINLIBS) $(LIBS) -o $(XRDSTAGETOOL) + + $(XRDCLI): $(OBJECTS) $(OBJECT_CLI) $(LIBDEPS) + @echo Creating executable $(XRDCLI) +- $(ECHO)$(LD) $(LDOP) $(OBJECT_CLI) $(BINLIBS) $(LIBS) $(LIBREADLINE) -o $(XRDCLI) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECT_CLI) $(BINLIBS) $(LIBS) $(LIBREADLINE) -o $(XRDCLI) + + $(XRDADMIN): $(PERLMOD) + $(ECHO)if [ "$(PERLBIN)" != "" ]; then \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdCms/GNUmakefile root/net/xrootd/src/xrootd/src/XrdCms/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdCms/GNUmakefile 2011-06-28 13:49:43.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdCms/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -136,7 +136,7 @@ + + $(BINARY): $(OBJSRVR) $(OBJBOTH) $(LIBDEPS) + @echo Creating executable $(BINARY) +- $(ECHO)$(LD) $(LDOP) $(OBJSRVR) $(OBJBOTH) $(BINLIBS) $(LIBS) $(TYPELIBMT) -o $(BINARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJSRVR) $(OBJBOTH) $(BINLIBS) $(LIBS) $(TYPELIBMT) -o $(BINARY) + + + $(LIBRARY): $(OBJCLNT) $(OBJBOTH) +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdCns/GNUmakefile root/net/xrootd/src/xrootd/src/XrdCns/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdCns/GNUmakefile 2011-06-28 13:49:41.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdCns/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -90,11 +90,11 @@ + + $(TARGCNSD): $(OBJCNSD) $(OBJCOM) $(LIBDEP) + @echo Creating executable $(BINDIR)/XrdCnsd +- $(ECHO)$(LD) $(LDOP) $(CFLAGS) $(OBJCNSD) $(OBJCOM) $(LIBDEP) $(MORELIBS) $(LIBS) -o $(BINDIR)/XrdCnsd ++ $(ECHO)$(CC) $(LDFLAGS) $(CFLAGS) $(OBJCNSD) $(OBJCOM) $(LIBDEP) $(MORELIBS) $(LIBS) -o $(BINDIR)/XrdCnsd + + $(TARGSSI): $(OBJSSI) $(OBJCOM) $(LIBDEP) + @echo Creating executable $(BINDIR)/cns_ssi +- $(ECHO)$(LD) $(LDOP) $(CFLAGS) $(OBJSSI) $(OBJCOM) $(LIBDEP) $(MORELIBS) $(LIBS) -o $(BINDIR)/cns_ssi ++ $(ECHO)$(CC) $(LDFLAGS) $(CFLAGS) $(OBJSSI) $(OBJCOM) $(LIBDEP) $(MORELIBS) $(LIBS) -o $(BINDIR)/cns_ssi + + $(OBJDIR)/XrdCnsConfig.o: XrdCnsConfig.hh XrdCnsConfig.cc \ + XrdCnsDaemon.hh XrdCnsLogRec.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdCrypto/GNUmakefile root/net/xrootd/src/xrootd/src/XrdCrypto/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdCrypto/GNUmakefile 2011-06-28 13:49:42.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdCrypto/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -139,7 +139,7 @@ + + $(LIBRARY): $(OBJECTS) $(LIBUTIL) + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(OBJECTS) $(LDSO) $(LIBUTIL) -o $(LIBRARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LDSO) $(LIBUTIL) -o $(LIBRARY) + + $(LIBASSL): $(OBJCSSL) + @echo Creating archive $(LIBASSL) +@@ -149,11 +149,11 @@ + + $(LIBCSSL): $(OBJCSSL) $(LIBARCH) $(LIBUTIL) + @echo Creating shared library $(LIBCSSL) +- $(ECHO)$(LD) $(OBJCSSL) $(LDSO) $(LIBSSL) $(LIBARCH) $(LIBUTIL) -o $(LIBCSSL) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJCSSL) $(LDSO) $(LIBSSL) $(LIBARCH) $(LIBUTIL) -o $(LIBCSSL) + + $(CRYPTOTEST): $(OBJECTA) $(LIBARCH) $(LIBDEPS) + @echo Creating executable $(CRYPTOTEST) +- $(ECHO)$(LD) $(OBJECTA) $(LIBARCH) $(BINLIBS) $(LIBS) -o $(CRYPTOTEST) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTA) $(LIBARCH) $(BINLIBS) $(LIBS) -o $(CRYPTOTEST) + + $(OBJDIR)/XrdCryptotest.o: XrdCryptotest.cc XrdSutAux.hh XProtocol.hh XrdSutBucket.hh \ + XrdCryptoAux.hh XrdCryptoFactory.hh XrdCryptoCipher.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdFfs/GNUmakefile root/net/xrootd/src/xrootd/src/XrdFfs/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdFfs/GNUmakefile 2011-06-28 13:49:41.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdFfs/GNUmakefile 2011-07-10 10:37:08.791154841 +0400 +@@ -82,7 +82,7 @@ + + $(BINARY): $(OBJECTS) $(OBJBIN) $(BINDEPS) + @echo Creating executable $(BINARY) +- $(ECHO)$(LD) $(LDOP) $(OBJBIN) $(BINDEPS) $(BINLIBS) $(LIBS) $(TYPELIBMT) -o $(BINARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJBIN) $(BINDEPS) $(BINLIBS) $(LIBS) $(TYPELIBMT) -o $(BINARY) + + $(OBJDIR)/XrdFfsDent.o: XrdFfsDent.cc XrdFfsDent.hh + @echo Compiling XrdFfsDent.cc +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdFrm/GNUmakefile root/net/xrootd/src/xrootd/src/XrdFrm/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdFrm/GNUmakefile 2011-06-28 13:49:42.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdFrm/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -134,15 +134,15 @@ + + $(BINADMIN): $(OBJLIB) $(OBJADMIN) $(OBJDEPS) + @echo Creating executable $(BINADMIN) +- $(ECHO)$(LD) $(LDOP) $(OBJADMIN) $(OBJADDS) $(LIBREADLINE) $(LIBS) $(BINLIBS) $(TYPELIBMT) -o $(BINADMIN) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJADMIN) $(OBJADDS) $(LIBREADLINE) $(BINLIBS) $(LIBS) $(TYPELIBMT) -o $(BINADMIN) + + $(BINPURGD): $(OBJLIB) $(OBJPURG) $(OBJADDS) $(OBJDEPS) + @echo Creating executable $(BINPURGD) +- $(ECHO)$(LD) $(LDOP) $(OBJPURG) $(OBJADDS) $(LIBS) $(BINLIBS) $(TYPELIBMT) -o $(BINPURGD) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJPURG) $(OBJADDS) $(BINLIBS) $(LIBS) $(TYPELIBMT) -o $(BINPURGD) + + $(BINXFRD): $(OBJLIB) $(OBJXFR) $(OBJADDS) $(OBJDEPS) + @echo Creating executables $(BINXFRD) +- $(ECHO)$(LD) $(LDOP) $(OBJXFR) $(OBJADDS) $(LIBS) $(BINLIBS) $(TYPELIBMT) -o $(BINXFRD) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJXFR) $(OBJADDS) $(BINLIBS) $(LIBS) $(TYPELIBMT) -o $(BINXFRD) + + $(BINAGNT): $(BINXFRD) + @echo Creating executables $(BINAGNT) +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdMon/GNUmakefile root/net/xrootd/src/xrootd/src/XrdMon/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdMon/GNUmakefile 2011-06-28 13:49:43.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdMon/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -141,45 +141,45 @@ + + $(ADMIN): $(OBJECTS_BIN_ADM) $(LIBRARY_SND) $(LIBRARY_OUC) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -lresolv -o $@ $^ -L$(LIBDIR) -lXrdSys ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -lresolv -o $@ $^ -L$(LIBDIR) -lXrdSys + + $(COLLECTOR): $(OBJECTS_BIN_CTR) $(LIBRARY_CTR) \ + $(LIBRARY_DEC) $(LIBRARY_OUC) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -o $@ $^ -L$(LIBDIR) -lXrdSys ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -o $@ $^ -L$(LIBDIR) -lXrdSys + + $(CONVTIME): $(OBJECTS_BIN_CTM) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -o $@ $^ ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -o $@ $^ + + $(COUT2FILE): $(OBJECTS_BIN_C2F) $(LIBRARY_DEC) $(LIBRARY_OUC) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -lresolv -o $@ $^ ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -lresolv -o $@ $^ + + $(DEBUGPACKET): $(OBJECTS_BIN_DBP) $(LIBRARY_DEC) $(LIBRARY_OUC) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -o $@ $^ ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -o $@ $^ + + $(DECODER): $(OBJECTS_BIN_DEC) $(LIBRARY_DEC) $(LIBRARY_OUC) \ + $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -o $@ $^ ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -o $@ $^ + + $(DUMPPACKETS): $(OBJECTS_BIN_DMP) $(LIBRARY_DEC) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -o $@ $^ ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -o $@ $^ + + $(FSENDER): $(OBJECTS_BIN_FSD) $(LIBRARY_SND) $(LIBRARY_OUC) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -lresolv -o $@ $^ ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -lresolv -o $@ $^ + + $(SENDER): $(OBJECTS_BIN_SND) $(LIBRARY_SND) $(LIBRARY_OUC) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -lresolv -o $@ $^ -L$(LIBDIR) -lXrdSys ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -lresolv -o $@ $^ -L$(LIBDIR) -lXrdSys + + $(TESTPARSER): $(OBJECTS_BIN_TPR) $(LIBRARY_COMMON) + @echo Creating executable $(@F) +- $(ECHO)$(CC) $(CFLAGS) $(LDOP) $(LIBS) -lresolv -o $@ $^ ++ $(ECHO)$(CC) $(CFLAGS) $(LDFLAGS) $(LIBS) -lresolv -o $@ $^ + + $(OBJDIR)/%.o : %.cc + @echo Compiling $(<F) +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdPosix/GNUmakefile root/net/xrootd/src/xrootd/src/XrdPosix/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdPosix/GNUmakefile 2011-06-28 13:49:40.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdPosix/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -76,14 +76,14 @@ + + $(LIBPLDR): $(OBJECTP) $(OBJECTS) $(OBJECTT) $(LIBDEP) + @echo Creating shared library $(LIBPLDR) +- $(ECHO)$(CC) $(CFLAGS) $(OBJECTS) $(OBJECTT) $(OBJECTU) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBPLDR) ++ $(ECHO)$(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTS) $(OBJECTT) $(OBJECTU) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBPLDR) + + $(LIBRARY): $(OBJECTP) $(OBJECTS) $(OBJECTT) $(LIBDEP) + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(CFLAGS) $(OBJECTS) $(OBJECTU) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTS) $(OBJECTU) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY) + ifneq ($(subst $(MACOSX_MINOR),,1234),1234) + $(ECHO)if [ "x$(TYPE)" = "xDarwin" ]; then \ +- $(CC) $(CFLAGS) $(OBJECTS) $(TYPELDDY) $(MORELIBS) $(LIBS) -o $(LIBDIR)/libXrdPosix.$(TYPEDYLIB); \ ++ $(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTS) $(TYPELDDY) $(MORELIBS) $(LIBS) -o $(LIBDIR)/libXrdPosix.$(TYPEDYLIB); \ + fi + endif + # MacOS X does not support linking against shared libraries so include +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdPss/GNUmakefile root/net/xrootd/src/xrootd/src/XrdPss/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdPss/GNUmakefile 2011-06-28 13:49:40.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdPss/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -70,7 +70,7 @@ + + $(TARGETS): $(OBJECTS) $(OBJECTT) $(LIBDEP) + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(CFLAGS) $(OBJECTT) $(OBJECTS) $(OBJECTU) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTT) $(OBJECTS) $(OBJECTU) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY) + + $(OBJDIR)/XrdPss.o: XrdPss.cc XrdPss.hh \ + XrdFfsPosix.hh XrdPosixXrootd.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdRootd/GNUmakefile root/net/xrootd/src/xrootd/src/XrdRootd/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdRootd/GNUmakefile 2011-06-28 13:49:42.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdRootd/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -6,7 +6,7 @@ + + include ../GNUmake.env + +-LFLAGS = -L$(LIBDIR) -lXrdOuc $(LDSO) ++LFLAGS = $(LDSO) -L$(LIBDIR) -lXrdOuc + + LIBDEPS = $(LIBDIR)/libXrdOuc.a + +@@ -48,7 +48,7 @@ + + $(TARGETS): $(OBJECTS) $(LIBDEPS) + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(OBJECTS) $(LFLAGS) -o $(LIBRARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LFLAGS) -o $(LIBRARY) + + $(OBJDIR)/XrdRootdProtocol.o: XrdRootdProtocol.hh XrdLink.hh \ + XrdScheduler.hh XrdTrace.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSec/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSec/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSec/GNUmakefile 2011-06-28 13:49:42.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSec/GNUmakefile 2011-07-10 10:24:16.138023789 +0400 +@@ -78,15 +78,15 @@ + + $(LIBRARY): $(OBJSLIB) $(LIBDEPS) + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(OBJSLIB) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY); ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJSLIB) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY); + + $(TSTBINA): $(OBJECTA) $(LIBDEPS) + @echo Creating executable $(TSTBINA) +- $(ECHO)$(LD) $(LDOP) $(OBJECTA) $(LIBS) $(BINLIBS) -o $(TSTBINA) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTA) $(LIBS) $(BINLIBS) -o $(TSTBINA) + + $(TSTBINB): $(OBJECTB) $(LIBDEPS) + @echo Creating executable $(TSTBINB) +- $(ECHO)$(LD) $(LDOP) $(OBJECTB) $(LIBS) $(BINLIBS) -o $(TSTBINB) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTB) $(LIBS) $(BINLIBS) -o $(TSTBINB) + + $(OBJDIR)/XrdSecClient.o: XrdSysPthread.hh XrdSecPManager.hh XrdSecInterface.hh \ + XrdOucErrInfo.hh XrdSecClient.cc XrdSecEntity.hh +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSecgsi/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSecgsi/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSecgsi/GNUmakefile 2011-06-28 13:49:42.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSecgsi/GNUmakefile 2011-07-10 10:31:48.396441015 +0400 +@@ -115,23 +115,23 @@ + + $(LIBRARY): $(OBJECTS) $(LIBDEPS) + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(LD) $(OBJECTS) $(LDSO) $(LIBLIBS) $(LIBS) -o $(LIBRARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LDSO) $(LIBLIBS) $(LIBS) -o $(LIBRARY) + + $(LIBGMLDAP): $(OBJECTC) + @echo Creating shared library $(LIBGMLDAP) +- $(ECHO)$(LD) $(OBJECTC) $(LDSO) $(LIBS) -o $(LIBGMLDAP) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTC) $(LDSO) $(LIBS) -o $(LIBGMLDAP) + + $(LIBGMDN): $(OBJECTD) + @echo Creating shared library $(LIBGMDN) +- $(ECHO)$(LD) $(OBJECTD) $(LDSO) $(LIBDIR)/libXrdOuc.a $(LIBS) -o $(LIBGMDN) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTD) $(LDSO) $(LIBDIR)/libXrdOuc.a $(LIBS) -o $(LIBGMDN) + + $(SECGSITEST): $(OBJECTA) $(LIBDEPS) + @echo Creating executable $(SECGSITEST) +- $(ECHO)$(LD) $(LDOP) $(OBJECTA) $(BINLIBS) $(LIBS) -o $(SECGSITEST) ++ $(ECHO)$(CC) $(LDFLAGS) $(LDOP) $(OBJECTA) $(BINLIBS) $(LIBS) -o $(SECGSITEST) + + $(SECGSIPROXY): $(OBJECTB) $(LIBDEPS) + @echo Creating executable $(SECGSIPROXY) +- $(ECHO)$(LD) $(LDOP) $(OBJECTB) $(BINLIBS) $(LIBS) -o $(SECGSIPROXY) ++ $(ECHO)$(CC) $(LDFLAGS) $(LDOP) $(OBJECTB) $(BINLIBS) $(LIBS) -o $(SECGSIPROXY) + + $(OBJDIR)/XrdSecgsitest.o: XrdSecgsitest.cc XrdOucString.hh \ + XrdSysError.hh XrdSutAux.hh XProtocol.hh XPtypes.hh XrdCryptoAux.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSeckrb4/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSeckrb4/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSeckrb4/GNUmakefile 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSeckrb4/GNUmakefile 2011-07-10 10:24:16.141356963 +0400 +@@ -45,7 +45,7 @@ + + $(TARGETS): $(OBJECTS) $(LIBDEPS) + @echo Creating shared library $(TARGETS) +- $(ECHO)$(CC) $(OBJECTS) $(LDSO) $(MORELIBS) $(LIBS) -o $(TARGETS); ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LDSO) $(MORELIBS) $(LIBS) -o $(TARGETS); + + $(OBJDIR)/XrdSecProtocolkrb4.o: XrdSecProtocolkrb4.cc XrdSecInterface.hh \ + XrdSysPthread.hh XrdOucTokenizer.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSeckrb5/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSeckrb5/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSeckrb5/GNUmakefile 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSeckrb5/GNUmakefile 2011-07-10 10:24:16.141356963 +0400 +@@ -49,7 +49,7 @@ + + $(TARGETS): $(OBJECTS) $(LIBDEPS) + @echo Creating shared library $(TARGETS) +- $(ECHO)$(CC) $(OBJECTS) $(LDSO) $(MORELIBS) $(LIBS) -o $(TARGETS); ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LDSO) $(MORELIBS) $(LIBS) -o $(TARGETS); + + $(OBJDIR)/XrdSecProtocolkrb5.o: XrdSecProtocolkrb5.cc XrdSecInterface.hh \ + XrdSysPthread.hh XrdOucTokenizer.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSecpwd/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSecpwd/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSecpwd/GNUmakefile 2011-06-28 13:49:43.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSecpwd/GNUmakefile 2011-07-10 10:24:16.141356963 +0400 +@@ -65,11 +65,11 @@ + + $(LIBRARY): $(OBJECTS) $(LIBDEPS) + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(OBJECTS) $(LDSO) $(BINLIBS) $(LIBS) $(RESOLVLIB) -o $(LIBRARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LDSO) $(BINLIBS) $(LIBS) $(RESOLVLIB) -o $(LIBRARY) + + $(SRVADMIN): $(OBJECTA) $(LIBDEPS) + @echo Creating executable $(SRVADMIN) +- $(ECHO)$(LD) $(LDOP) $(OBJECTA) $(BINLIBS) $(LIBS) $(RESOLVLIB) -o $(SRVADMIN) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTA) $(BINLIBS) $(LIBS) $(RESOLVLIB) -o $(SRVADMIN) + + $(OBJDIR)/XrdSecpwdSrvAdmin.o: XrdSecpwdSrvAdmin.cc \ + XrdOucString.hh XrdSutAux.hh XProtocol.hh XPtypes.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSecssl/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSecssl/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSecssl/GNUmakefile 2011-06-28 13:49:44.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSecssl/GNUmakefile 2011-07-10 10:24:16.141356963 +0400 +@@ -85,7 +85,7 @@ + + $(LIBRARY): $(OBJECTS) $(LIBDEPS) + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(OBJECTS) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY); ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LDSO) $(MORELIBS) $(LIBS) -o $(LIBRARY); + + $(LIBGRST): $(OBJGRST) + @echo Creating archive $(LIBGRST) +@@ -95,7 +95,7 @@ + + $(SECSSLTEST): $(OBJECTA) $(LIBDEPS) + @echo Creating executable $(SECSSLTEST) +- $(ECHO)$(LD) $(LDOP) $(OBJECTA) -L$(LIBDIR) -lXrdSecssl $(MORELIBS) $(LIBS) -o $(SECSSLTEST) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTA) -L$(LIBDIR) -lXrdSecssl $(MORELIBS) $(LIBS) -o $(SECSSLTEST) + + $(OBJDIR)/XrdSecProtocolsslProc.o: XrdSecProtocolsslProc.cc XrdSecProtocolsslProc.hh \ + XrdOucString.hh XrdOucHash.hh +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSecsss/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSecsss/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSecsss/GNUmakefile 2011-06-28 13:49:40.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSecsss/GNUmakefile 2011-07-10 10:24:16.141356963 +0400 +@@ -77,11 +77,11 @@ + + $(TARGLSO): $(OBJSLIB) $(LIBDEPS) + @echo Creating shared library $(TARGLSO) +- $(ECHO)$(CC) $(OBJSLIB) $(LDSO) $(MORELIBS) $(LIBSSL) $(LIBS) -o $(TARGLSO); ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJSLIB) $(LDSO) $(MORELIBS) $(LIBSSL) $(LIBS) -o $(TARGLSO); + + $(TARGBIN): $(OBJSBIN) + @echo Creating executable $(TARGBIN) +- $(ECHO)$(LD) $(LDOP) $(OBJSBIN) $(MORELIBS) $(LIBS) -o $(TARGBIN); ++ $(ECHO) $(LD) $(LDFLAGS) $(OBJSBIN) $(MORELIBS) $(LIBS) -o $(TARGBIN); + + $(OBJDIR)/XrdSecProtocolsss.o: XrdSecProtocolsss.cc XrdSecProtocolsss.hh \ + XrdNetDNS.hh XrdOucErrInfo.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSecunix/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSecunix/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSecunix/GNUmakefile 2011-06-28 13:49:42.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSecunix/GNUmakefile 2011-07-10 10:24:16.141356963 +0400 +@@ -45,7 +45,7 @@ + + $(TARGETS): $(OBJECTS) $(LIBDEPS) + @echo Creating shared library $(TARGETS) +- $(ECHO)$(CC) $(OBJECTS) $(LDSO) $(MORELIBS) $(LIBS) -o $(TARGETS); ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LDSO) $(MORELIBS) $(LIBS) -o $(TARGETS); + + $(OBJDIR)/XrdSecProtocolunix.o: XrdSecProtocolunix.cc XrdSecInterface.hh \ + XrdSysHeaders.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdSut/GNUmakefile root/net/xrootd/src/xrootd/src/XrdSut/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdSut/GNUmakefile 2011-06-28 13:49:40.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdSut/GNUmakefile 2011-07-10 10:24:16.141356963 +0400 +@@ -67,7 +67,7 @@ + + $(LIBRARY): $(OBJECTS) $(LIBDIR)/libXrdOuc.a + @echo Creating shared library $(LIBRARY) +- $(ECHO)$(CC) $(OBJECTS) $(LIBDIR)/libXrdOuc.a $(LDSO) -o $(LIBRARY) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(LIBDIR)/libXrdOuc.a $(LDSO) -o $(LIBRARY) + + $(OBJDIR)/XrdSutPFAdmin.o: XrdSutPFAdmin.cc XrdOucString.hh \ + XrdSutAux.hh XProtocol.hh XPtypes.hh \ +diff -Naur root.orig/net/xrootd/src/xrootd/src/XrdXrootd/GNUmakefile root/net/xrootd/src/xrootd/src/XrdXrootd/GNUmakefile +--- root.orig/net/xrootd/src/xrootd/src/XrdXrootd/GNUmakefile 2011-06-28 13:49:41.000000000 +0400 ++++ root/net/xrootd/src/xrootd/src/XrdXrootd/GNUmakefile 2011-07-10 10:24:16.141356963 +0400 +@@ -95,7 +95,7 @@ + + $(TARGETS): $(OBJECTS) $(OBJDEPS) + @echo Creating executable $(TARGETS) +- $(ECHO)$(LD) $(LDOP) $(OBJECTS) $(OBJFS) $(LIBS) $(BINLIBS) $(TYPELIBMT) -o $(TARGETS) ++ $(ECHO)$(CC) $(LDFLAGS) $(OBJECTS) $(OBJFS) $(LIBS) $(BINLIBS) $(TYPELIBMT) -o $(TARGETS) + + $(OBJDIR)/XrdXrootdAdmin.o: XrdXrootdAdmin.hh XrdXrootdAdmin.cc \ + XrdXrootdTrace.hh XrdXrootdProtocol.hh \ diff --git a/sci-physics/root/files/rootd.confd b/sci-physics/root/files/rootd.confd new file mode 100644 index 000000000..7516b8c9b --- /dev/null +++ b/sci-physics/root/files/rootd.confd @@ -0,0 +1,8 @@ +# conf.d file for root daemon + +# User to run as (default is `rootd') +ROOTD_USER="rootd" + +# Please refer to the rootd(1) man(1) page for more information on +# command line parameters. +ROOTD_OPTS="" diff --git a/sci-physics/root/files/rootd.initd b/sci-physics/root/files/rootd.initd new file mode 100644 index 000000000..de42e93dd --- /dev/null +++ b/sci-physics/root/files/rootd.initd @@ -0,0 +1,28 @@ +#!/sbin/runscript +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/files/rootd.initd,v 1.2 2009/01/20 18:04:09 bicatali Exp $ + +depend() { + need net + use logger + provide root-file-server +} + +start() { + ebegin "Starting ROOT file server" + pid=$(start-stop-daemon --start --quiet --user ${ROOTD_USER} \ + --pidfile /var/run/rootd.pid \ + --exec /usr/bin/rootd -- ${ROOTD_OPTS}) + retval=$? + echo ${ROOTD_PID} > /var/run/rootd.pid + eend ${retval} +} + +stop() { + ebegin "Stopping ROOT file server" + start-stop-daemon --stop --quiet \ + --pidfile /var/run/rootd.pid \ + --exec /usr/bin/rootd + eend $? +} diff --git a/sci-physics/root/files/xrootd.confd b/sci-physics/root/files/xrootd.confd new file mode 100644 index 000000000..e725cd1e7 --- /dev/null +++ b/sci-physics/root/files/xrootd.confd @@ -0,0 +1,8 @@ +# conf.d file for xroot daemon + +# User to run as (default is `root') +XROOTD_USER="root" + +# Please refer to the xrootd(1) man(1) page for more +# information on command line parameters. +XROOTD_OPTS="" diff --git a/sci-physics/root/files/xrootd.initd b/sci-physics/root/files/xrootd.initd new file mode 100644 index 000000000..27e0001a9 --- /dev/null +++ b/sci-physics/root/files/xrootd.initd @@ -0,0 +1,26 @@ +#!/sbin/runscript +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/files/xrootd.initd,v 1.2 2009/01/20 18:04:09 bicatali Exp $ + +depend() { + need net + use logger dns + provide root-file-server +} + +start() { + ebegin "Starting extended ROOTD file server" + start-stop-daemon --start --quiet --user ${XROOTD_USER} \ + --make-pidfile --pidfile /var/run/xrootd.pid \ + --exec /usr/bin/xrootd --background -- ${XROOTD_OPTS} + eend $? +} + +stop() { + ebegin "Stopping extended ROOTD file server" + start-stop-daemon --stop --quiet \ + --pidfile /var/run/xrootd.pid \ + --exec /usr/bin/xrootd + eend $? +} diff --git a/sci-physics/root/metadata.xml b/sci-physics/root/metadata.xml new file mode 100644 index 000000000..ba7366814 --- /dev/null +++ b/sci-physics/root/metadata.xml @@ -0,0 +1,31 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-physics</herd> +<longdescription lang="en"> + ROOT Object Oriented Technologies is an object oriented data + analysis framework written in C++ by the CERN. Widely used in + high energy physics, but also in other data analysis applications. It + contains the CINT C/C++ interpreter and many classes such as + statistics, serialization, optimization, linear algebra, graphics, + GUI toolkit, and a complete visualization framework. +</longdescription> +<use> + <flag name="clarens"> + Buld the Clarens and PEAC plug-ins, to use in a GRID enabled + analysis.</flag> + <flag name="fits">Support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag> + <flag name="llvm">Build the new cling interactive interpreter based on <pkg>sys-devel/llvm</pkg></flag> + <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag> + <flag name="pythia6"> + Builds the interface to Pythia-6 (<pkg>sci-physics/pythia</pkg>) + high energy physics generation events library + </flag> + <flag name="pythia8"> + Builds the interface to Pythia-8 (<pkg>sci-physics/pythia</pkg>) + high energy physics generation events library + </flag> + <flag name="reflex">Builds the reflection database for the C++ interpretor </flag> + <flag name="xrootd">Build the xrootd low latency file server</flag> +</use> +</pkgmetadata> diff --git a/sci-physics/root/root-5.30.00.ebuild b/sci-physics/root/root-5.30.00.ebuild new file mode 100644 index 000000000..f802d1338 --- /dev/null +++ b/sci-physics/root/root-5.30.00.ebuild @@ -0,0 +1,339 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.28.00d.ebuild,v 1.3 2011/06/21 14:31:50 jlec Exp $ + +EAPI=3 +PYTHON_DEPEND="python? 2" +inherit versionator eutils fortran-2 elisp-common fdo-mime python toolchain-funcs flag-o-matic + +#DOC_PV=$(get_major_version)_$(get_version_component_range 2) +DOC_PV=5_26 +ROOFIT_DOC_PV=2.91-33 +TMVA_DOC_PV=4.03 +PATCH_PV=5.28.00b + +DESCRIPTION="C++ data analysis framework and interpreter from CERN" +HOMEPAGE="http://root.cern.ch/" +SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz + doc? ( ftp://root.cern.ch/${PN}/doc/Users_Guide_${DOC_PV}.pdf + math? ( + ftp://root.cern.ch/${PN}/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf + http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf ) )" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="+X afs avahi clarens doc emacs examples fits fftw graphviz kerberos ldap + llvm +math mpi mysql ncurses odbc +opengl openmp oracle postgres prefix + pythia6 pythia8 python +reflex ruby qt4 ssl xft xml xinetd xrootd" + +CDEPEND="app-arch/xz-utils + >=dev-lang/cfortran-4.4-r2 + dev-libs/libpcre + media-libs/freetype + media-libs/giflib + media-libs/libpng + media-libs/tiff + sys-apps/shadow + sys-libs/zlib + virtual/jpeg + X? ( + media-libs/ftgl + media-libs/glew + x11-libs/libX11 + x11-libs/libXext + x11-libs/libXpm + || ( >=media-libs/libafterimage-1.20 >=x11-wm/afterstep-2.2.11 ) + opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps ) + qt4? ( x11-libs/qt-gui:4 + x11-libs/qt-opengl:4 + x11-libs/qt-qt3support:4 + x11-libs/qt-svg:4 + x11-libs/qt-webkit:4 + x11-libs/qt-xmlpatterns:4 ) + xft? ( x11-libs/libXft ) ) + afs? ( net-fs/openafs ) + avahi? ( net-dns/avahi ) + clarens? ( dev-libs/xmlrpc-c ) + emacs? ( virtual/emacs ) + fits? ( sci-libs/cfitsio ) + fftw? ( sci-libs/fftw:3.0 ) + graphviz? ( media-gfx/graphviz ) + kerberos? ( virtual/krb5 ) + ldap? ( net-nds/openldap ) + llvm? ( sys-devel/llvm ) + math? ( sci-libs/gsl sci-mathematics/unuran mpi? ( virtual/mpi ) ) + mysql? ( virtual/mysql ) + ncurses? ( sys-libs/ncurses ) + odbc? ( || ( dev-db/libiodbc dev-db/unixODBC ) ) + oracle? ( dev-db/oracle-instantclient-basic ) + postgres? ( dev-db/postgresql-base ) + pythia6? ( sci-physics/pythia:6 ) + pythia8? ( sci-physics/pythia:8 ) + ruby? ( dev-lang/ruby + dev-ruby/rubygems ) + ssl? ( dev-libs/openssl ) + xml? ( dev-libs/libxml2 )" + +DEPEND="${CDEPEND} + dev-util/pkgconfig" + +RDEPEND=" + virtual/fortran +${CDEPEND} + reflex? ( dev-cpp/gccxml ) + xinetd? ( sys-apps/xinetd )" + +S="${WORKDIR}/${PN}" + +pkg_setup() { + fortran-2_pkg_setup + elog + elog "There are extra options on packages not yet in Gentoo:" + elog "AliEn, castor, Chirp, dCache, gfal, gLite, Globus," + elog "HDFS, Monalisa, MaxDB/SapDB, SRP." + elog "You can use the env variable EXTRA_ECONF variable for this." + elog "For example, for SRP, you would set: " + elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=/usr/$(get_libdir)\"" + elog + enewgroup rootd + enewuser rootd -1 -1 /var/spool/rootd rootd + + if use math; then + if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then + ewarn "You are using gcc and OpenMP is available with gcc >= 4.2" + ewarn "If you want to build this package with OpenMP, abort now," + ewarn "and set CC to an OpenMP capable compiler" + elif use openmp; then + export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1 + elif use mpi; then + export USE_MPI=1 USE_PARALLEL_MINUIT2=1 + fi + fi +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-xrootd-prop-flags.patch \ + "${FILESDIR}"/${PN}-${PATCH_PV}-prop-ldflags.patch \ + "${FILESDIR}"/${PN}-${PATCH_PV}-asneeded.patch \ + "${FILESDIR}"/${P}-nobyte-compile.patch \ + "${FILESDIR}"/${PN}-${PATCH_PV}-glibc212.patch \ + "${FILESDIR}"/${PN}-${PATCH_PV}-unuran.patch \ + "${FILESDIR}"/${P}-lzma.patch + + # make sure we use system libs and headers + rm montecarlo/eg/inc/cfortran.h README/cfortran.doc + rm -rf graf2d/asimage/src/libAfterImage + rm -rf graf3d/ftgl/{inc,src} + rm -rf graf2d/freetype/src + rm -rf graf3d/glew/{inc,src} + rm -rf core/pcre/src + rm -rf math/unuran/src/unuran-*.tar.gz + find core/zip -type f -name "[a-z]*" | xargs rm + rm -rf core/lzma/src/*.tar.gz + rm graf3d/gl/{inc,src}/gl2ps.* + sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' graf3d/gl/Module.mk + + # TODO: unbundle xrootd as a new package + #rm -rf net/xrootd/src + #sed -i \ + # -e 's:-lXrdOuc:-lXrd &:' \ + # -e 's:$(XROOTDDIRL)/lib\(Xrd\w*\).a:-l\1:g' \ + # proof/proofd/Module.mk || die + + # In Gentoo, libPythia6 is called libpythia6 + # libungif is called libgif, + # iodbc is in /usr/include/iodbc + # pg_config.h is checked instead of libpq-fe.h + sed -i \ + -e 's:libPythia6:libpythia6:g' \ + -e 's:ungif:gif:g' \ + -e 's:$ODBCINC:$ODBCINC /usr/include/iodbc:' \ + -e 's:libpq-fe.h:pg_config.h:' \ + configure || die "adjusting configure for Gentoo failed" + + # prefixify the configure script + sed -i \ + -e 's:/usr:${EPREFIX}/usr:g' \ + configure || die "prefixify configure failed" + + # QTDIR only used for qt3 in gentoo, and configure looks for it. + unset QTDIR +} + +src_configure() { + # the configure script is not the standard autotools + ./configure \ + --prefix="${EPREFIX}"/usr \ + --etcdir="${EPREFIX}"/etc/root \ + --libdir="${EPREFIX}"/usr/$(get_libdir)/${PN} \ + --docdir="${EPREFIX}"/usr/share/doc/${PF} \ + --tutdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tutorials \ + --testdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tests \ + --with-cc=$(tc-getCC) \ + --with-cxx=$(tc-getCXX) \ + --with-f77=$(tc-getFC) \ + --with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps \ + --disable-builtin-afterimage \ + --disable-builtin-freetype \ + --disable-builtin-ftgl \ + --disable-builtin-glew \ + --disable-builtin-pcre \ + --disable-builtin-zlib \ + --disable-builtin-lzma \ + --enable-astiff \ + --enable-exceptions \ + --enable-explicitlink \ + --enable-gdml \ + --enable-memstat \ + --enable-shadowpw \ + --enable-shared \ + --enable-soversion \ + --enable-table \ + --fail-on-missing \ + --with-afs-shared=yes \ + $(use_enable X x11) \ + $(use_enable X asimage) \ + $(use_enable afs) \ + $(use_enable avahi bonjour) \ + $(use_enable clarens) \ + $(use_enable clarens peac) \ + $(use_enable ncurses editline) \ + $(use_enable fits fitsio) \ + $(use_enable fftw fftw3) \ + $(use_enable graphviz gviz) \ + $(use_enable kerberos krb5) \ + $(use_enable ldap) \ + $(use_enable llvm cling) \ + $(use_enable math gsl-shared) \ + $(use_enable math genvector) \ + $(use_enable math mathmore) \ + $(use_enable math minuit2) \ + $(use_enable math roofit) \ + $(use_enable math tmva) \ + $(use_enable math unuran) \ + $(use_enable mysql) \ + $(use_enable odbc) \ + $(use_enable opengl) \ + $(use_enable postgres pgsql) \ + $(use_enable prefix rpath) \ + $(use_enable pythia6) \ + $(use_enable pythia8) \ + $(use_enable python) \ + $(use_enable qt4 qt) \ + $(use_enable qt4 qtgsi) \ + $(use_enable reflex cintex) \ + $(use_enable reflex) \ + $(use_enable ruby) \ + $(use_enable ssl) \ + $(use_enable xft) \ + $(use_enable xml) \ + $(use_enable xrootd) \ + ${EXTRA_ECONF} \ + || die "configure failed" +} + +src_compile() { + emake OPT="${CFLAGS}" F77OPT="${FFLAGS}" || die "emake failed" + if use emacs; then + elisp-compile build/misc/*.el || die "elisp-compile failed" + fi +} + +doc_install() { + cd "${S}" + if use doc; then + einfo "Installing user's guides" + dodoc "${DISTDIR}"/Users_Guide_${DOC_PV}.pdf + use math && dodoc \ + "${DISTDIR}"/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf \ + "${DISTDIR}"/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf + fi + + if use examples; then + # these should really be taken care of by the root make install + insinto /usr/share/doc/${PF}/examples/tutorials/tmva + doins -r tmva/test + else + rm -rf "${ED}"/usr/share/doc/${PF}/examples + fi +} + +daemon_install() { + cd "${S}" + local daemons="rootd proofd" + dodir /var/spool/rootd + fowners rootd:rootd /var/spool/rootd + dodir /var/spool/rootd/{pub,tmp} + fperms 1777 /var/spool/rootd/{pub,tmp} + + use xrootd && daemons="${daemons} xrootd olbd" + for i in ${daemons}; do + newinitd "${FILESDIR}"/${i}.initd ${i} + newconfd "${FILESDIR}"/${i}.confd ${i} + done + if use xinetd; then + insinto /etc/xinetd + doins etc/daemons/{rootd,proofd}.xinetd + fi +} + +desktop_install() { + cd "${S}" + sed -e 's,@prefix@,/usr,' \ + build/package/debian/root-system-bin.desktop.in > root.desktop + domenu root.desktop + doicon "${S}"/build/package/debian/root-system-bin.png + + insinto /usr/share/icons/hicolor/48x48/mimetypes + doins build/package/debian/application-x-root.png + + insinto /usr/share/icons/hicolor/48x48/apps + doicon build/package/debian/root-system-bin.xpm +} + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" + + echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/root" > 99root + use pythia8 && echo "PYTHIA8=${EPREFIX}/usr" >> 99root + use python && echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/root" >> 99root + use ruby && echo "RUBYLIB=${EPREFIX}/usr/$(get_libdir)/root" >> 99root + doenvd 99root || die "doenvd failed" + + # The build system installs Emacs support unconditionally and in the wrong + # directory. Remove it and call elisp-install in case of USE=emacs. + rm -rf "${ED}"/usr/share/emacs + if use emacs; then + elisp-install ${PN} build/misc/*.{el,elc} || die "elisp-install failed" + fi + + doc_install + daemon_install + desktop_install + + # Cleanup of files either already distributed or unused on Gentoo + rm "${ED}"usr/share/doc/${PF}/{INSTALL,LICENSE,COPYING.CINT} + rm "${ED}"usr/share/root/fonts/LICENSE + pushd "${ED}"usr/$(get_libdir)/root/cint/cint/lib > /dev/null + rm -f posix/mktypes dll_stl/setup \ + G__* dll_stl/G__* dll_stl/rootcint_* posix/exten.o + rm -f "${ED}"usr/$(get_libdir)/root/cint/cint/include/makehpib + rm -f "${ED}"/etc/root/proof/*.sample + rm -rf "${ED}"/etc/root/daemons + popd > /dev/null + # these should be in PATH + mv "${ED}"usr/share/root/proof/utils/pq2/pq2* \ + "${ED}"usr/bin +} + +pkg_postinst() { + fdo-mime_desktop_database_update + use python && python_mod_optimize /usr/$(get_libdir)/root +} + +pkg_postrm() { + fdo-mime_desktop_database_update + use python && python_mod_cleanup /usr/$(get_libdir)/root +} diff --git a/sci-visualization/gri/ChangeLog b/sci-visualization/gri/ChangeLog deleted file mode 100644 index c1976851b..000000000 --- a/sci-visualization/gri/ChangeLog +++ /dev/null @@ -1,191 +0,0 @@ -# ChangeLog for sci-visualization/gri -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-visualization/gri/ChangeLog,v 1.5 2010/11/29 21:29:18 fauli Exp $ - - 8 Apr 2011; Dongxu Li <dongxuli2011@gmail.com> gri-2.12.22.ebuild: - version bump; dependency of sci-libs/netcdf updated to the current stable in tree - - 29 Nov 2010; Christian Faulhammer <fauli@gentoo.org> metadata.xml: - Drop from emacs herd - - 26 Dec 2009; Peter Volkov <pva@gentoo.org> gri-2.12.19.ebuild: - virtual/ghostscript->app-text/ghostscript-gpl: ghostscript-gpl is the only - implementation left in the tree. - - 20 Nov 2009; Christian Faulhammer <fauli@gentoo.org> - -gri-2.12.16-r1.ebuild, -gri-2.12.18.ebuild: - clean up - - 20 Nov 2009; Markus Meier <maekke@gentoo.org> gri-2.12.19.ebuild: - amd64/x86 stable, bug #293708 - - 21 Jul 2009; Christian Faulhammer <fauli@gentoo.org> - +files/50gri-gentoo.el, +gri-2.12.16-r1.ebuild, +gri-2.12.18.ebuild, - +files/gri-2.12.18-postscript.patch, +gri-2.12.19.ebuild, +metadata.xml: - move from sci-misc category, as suggested in bug 161787 - -*gri-2.12.19 (21 Jul 2009) - - 21 Jul 2009; Christian Faulhammer <fauli@gentoo.org> +gri-2.12.19.ebuild: - version bump - - 13 Feb 2009; Patrick Kursawe <phosphan@gentoo.org> gri-2.12.16-r1.ebuild, - gri-2.12.18.ebuild: - Setting VARTEXFONTS (see bug #223077) - - 13 Feb 2009; Patrick Kursawe <phosphan@gentoo.org> -gri-2.12.17.ebuild: - Removed unneeded version. - - 01 Nov 2008; Markus Dittrich <markusle@gentoo.org> - +files/gri-2.12.18-postscript.patch, gri-2.12.18.ebuild: - Added patch to support proper postscript output (see bug #158828). - Thanks much to Sebastiaan for his patch. - -*gri-2.12.18 (27 Sep 2008) - - 27 Sep 2008; Markus Dittrich <markusle@gentoo.org> +gri-2.12.18.ebuild: - Version bump. - - 24 Aug 2008; Ulrich Mueller <ulm@gentoo.org> -gri-2.12.14.ebuild, - gri-2.12.16-r1.ebuild, gri-2.12.17.ebuild: - Fix Emacs support, bug 235602. Remove old. - -*gri-2.12.17 (09 Jun 2008) - - 09 Jun 2008; Markus Dittrich <markusle@gentoo.org> gri-2.12.14.ebuild, - gri-2.12.16-r1.ebuild, +gri-2.12.17.ebuild: - Version bump. Also switched virtual/tetex -> virtual/latex-base - (see bug #222501). - - 02 Nov 2007; Steve Dibb <beandog@gentoo.org> gri-2.12.16-r1.ebuild: - amd64 stable, bug 196887 - - 24 Oct 2007; Christian Faulhammer <opfer@gentoo.org> - gri-2.12.16-r1.ebuild: - stable x86, bug 196887 - - 01 Oct 2007; Christian Faulhammer <opfer@gentoo.org> -gri-2.12.9.ebuild: - clean up - - 29 Sep 2007; Wulf C. Krueger <philantrop@gentoo.org> gri-2.12.14.ebuild: - Marked stable on amd64 as per bug 193684. - - 25 Sep 2007; Christian Faulhammer <opfer@gentoo.org> -gri-2.12.7.ebuild, - -gri-2.12.11.ebuild, -gri-2.12.13.ebuild, -gri-2.12.16.ebuild: - clean up - -*gri-2.12.16-r1 (25 Sep 2007) - - 25 Sep 2007; Christian Faulhammer <opfer@gentoo.org> - +gri-2.12.16-r1.ebuild: - introduce doc and examples USE flag, handling emacs USE flag correctly by - preventing a file to be installed if it is not set - - 25 Sep 2007; Christian Faulhammer <opfer@gentoo.org> gri-2.12.16.ebuild: - correct the sed macro so it actually replaces the correct line - - 24 Sep 2007; Christian Faulhammer <opfer@gentoo.org> gri-2.12.14.ebuild: - stable x86, bug 193684 - - 24 Sep 2007; Christian Faulhammer <opfer@gentoo.org> ChangeLog: - fix ChangeLog - -*gri-2.12.16 (24 Sep 2007) - - 24 Sep 2007; Christian Faulhammer <opfer@gentoo.org> gri-2.12.14.ebuild, - +gri-2.12.16.ebuild: - version bump plus some QA fixes; RESTRICT test as they won't succeed - - 22 Feb 2007; Markus Ullmann <jokey@gentoo.org> ChangeLog: - Redigest for Manifest2 - -*gri-2.12.14 (18 Jan 2007) - - 18 Jan 2007; Christian Faulhammer <opfer@gentoo.org> - -files/info-install.patch, +gri-2.12.14.ebuild: - version bump; adjusted ghostscript dependency to virtual/ghostscript, as the - problem is resolved, reported by James Cloos <cloos@jhcloos.com> in bug - 162630; added some quotes; removed stray patch - -*gri-2.12.13 (07 Dec 2006) - - 07 Dec 2006; Christian Faulhammer <opfer@gentoo.org> +gri-2.12.13.ebuild: - version bump - - 23 Nov 2006; Christian Faulhammer <opfer@gentoo.org> gri-2.12.7.ebuild, - gri-2.12.9.ebuild, gri-2.12.11.ebuild: - Added comment, why app-text/ghostscript-esp is used as a dependency and not - virtual/ghostscript - - 22 Nov 2006; Christian Faulhammer <opfer@gentoo.org> gri-2.12.7.ebuild, - gri-2.12.9.ebuild, gri-2.12.11.ebuild: - hard dependency on app-text/ghostscript-esp, as that is the only version - working from virtual/ghostscript, fixex bug #155236 reported by Patrick - Lauer <bugs@dev.gentooexperimental.org> - -*gri-2.12.11 (19 May 2006) - - 19 May 2006; Matthew Kennedy <mkennedy@gentoo.org> +files/50gri-gentoo.el, - metadata.xml, +gri-2.12.11.ebuild: - New upstream version; Resolves Bug #117312; Added Emacs Herd to metadata.xml - for Emacs portion maintainership; Added missing virtual/ghostscript - depdendency; Resolves Bug #133397. - - 15 Jan 2006; Marcus D. Hanwell <cryos@gentoo.org> gri-2.12.7.ebuild, - gri-2.12.9.ebuild: - Added media-gfx/imagemagick to DEPEND, closes bug 111087. Also marked stable - on amd64. - -*gri-2.12.9 (10 Mar 2005) - - 10 Mar 2005; Patrick Kursawe <phosphan@gentoo.org> -gri-2.12.5.ebuild, - gri-2.12.7.ebuild, +gri-2.12.9.ebuild: - Bug #82456, version bump and cleanup. - -*gri-2.12.5 (27 Dec 2004) - - 27 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +files/info-install.patch, +gri-2.12.5.ebuild, +gri-2.12.7.ebuild: - Moved from app-sci/gri to sci-misc/gri. - - 06 Jun 2004; Danny van Dyk <kugelfang@gentoo.org> gri-2.12.7.ebuild: - Marked stable on amd64. - - 22 Apr 2004; David Holm <dholm@gentoo.org> gri-2.12.7.ebuild: - Added to ~ppc. - - 22 Apr 2004; Danny van Dyk <kugelfang@gentoo.org> gri-2.12.7.ebuild: - marked ~amd64 - -*gri-2.12.7 (22 Apr 2004) - - 22 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> gri-2.12.4.ebuild, - gri-2.12.5.ebuild, gri-2.12.7.ebuild: - Version bump - - 18 Nov 2003; Patrick Kursawe <phosphan@gentoo.org> gri-2.12.5.ebuild, - files/info-install.patch: - Fixing bug 33396, no revision bump. - -*gri-2.12.5 (30 Jun 2003) - - 30 Jun 2003; Daniel Ahlberg <aliz@gentoo.org> gri-2.12.5.ebuild : - Version bump. - -*gri-2.12.4 (16 May 2003) - - 16 May 2003; George Shapovalov <george@gentoo.org> gri-2.12.4.ebuild : - new version - -*gri-2.12.1 (06 Dec 2002) - - 07 Jan 2003; George Shapovalov <george@gentoo.org> gri-2.12.1.ebuild : - - incorporated changes suggested by Jose "to fix the path of the documentation in the startup msg" - added IUSE - - 06 Dec 2002; George Shapovalov <george@gentoo.org> ChangeLog, gri-2.12.1.ebuild, files/digest-gri-2.12.1 : - initial release (#10695) - Gri is a language for scientific graphics programming. - ebuild submitted by Jose Fonseca <j_r_fonseca@yahoo.co.uk> - diff --git a/sci-visualization/gri/Manifest b/sci-visualization/gri/Manifest deleted file mode 100644 index 6471a8b3f..000000000 --- a/sci-visualization/gri/Manifest +++ /dev/null @@ -1,16 +0,0 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - -AUX 50gri-gentoo.el 147 RMD160 2e69a5f9034ef82901a6c004a3f9e167e1e426e4 SHA1 530c8bf902635e5baa3215084b9fa454dcb1c31e SHA256 d3f04f7eb861ed663013e74d99981ea7c08ebf199de67c0ddd255eabc10ea09d -AUX gri-2.12.18-postscript.patch 3997 RMD160 4b390be9c915573812ba2e3d2289b2d9037e85ad SHA1 c2993812fc3fbbbbb21bd0516c43e094d6a78090 SHA256 2d3c2d44f39507270581744de930fb92bdcab6c5e3d846653e08ccfec07375b9 -DIST gri-2.12.22.tar.gz 1669555 RMD160 d1301823bb3510022f4146f23c42f059e0f4d2fc SHA1 e9778d9e01dd500dd13cc9c995691207cabd9a45 SHA256 01b5dfdb79125d87a17250c1e0aa0b1a894e5dc095473ae209f3a3fadebdba0e -EBUILD gri-2.12.22.ebuild 2002 RMD160 e34e62cac74abee2e10014bd05f798be8a2f80fb SHA1 2a4df4436d80a131cb83d128af126200ed6ce60a SHA256 776b37070852aff7e0afbed71daf78f65c07fde11120814d84e2d7e5f90ea7d0 -MISC ChangeLog 6769 RMD160 84bcfc795cc6c21cb98ab6811e29f83366c841d3 SHA1 f0153b5a4bc61de72a042f9e019aaec3de6afae4 SHA256 dd527c5a26d05787fa521815a4750b38812de75a48b5a08a31453652af9a101b -MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4EsDQACgkQgAnW8HDreRZaggCfZL0evOrTydXYTIYSrAgS9Rji -UdoAnjUtsyOmGa8HPkOmd2BVwNXOeang -=vV+k ------END PGP SIGNATURE----- diff --git a/sci-visualization/gri/files/50gri-gentoo.el b/sci-visualization/gri/files/50gri-gentoo.el deleted file mode 100644 index e07d47c85..000000000 --- a/sci-visualization/gri/files/50gri-gentoo.el +++ /dev/null @@ -1,3 +0,0 @@ -(add-to-list 'load-path "@SITELISP@") -(autoload 'gri-mode "gri-mode" "Enter Gri-mode." t) -(add-to-list 'auto-mode-alist '("\\.gri\\'" . gri-mode)) diff --git a/sci-visualization/gri/files/gri-2.12.18-postscript.patch b/sci-visualization/gri/files/gri-2.12.18-postscript.patch deleted file mode 100644 index b3f3b7301..000000000 --- a/sci-visualization/gri/files/gri-2.12.18-postscript.patch +++ /dev/null @@ -1,97 +0,0 @@ -diff -Naur gri-2.12.18/src/extern.hh gri-2.12.18.new/src/extern.hh ---- gri-2.12.18/src/extern.hh 2003-06-07 13:37:55.000000000 -0400 -+++ gri-2.12.18.new/src/extern.hh 2008-11-01 10:46:40.000000000 -0400 -@@ -137,6 +137,7 @@ - - extern int _arrow_type; - extern bool _warn_offpage; -+extern bool _export_postscript; - - extern std::vector<double> _dash; - -diff -Naur gri-2.12.18/src/gr.cc gri-2.12.18.new/src/gr.cc ---- gri-2.12.18/src/gr.cc 2008-09-04 13:32:21.000000000 -0400 -+++ gri-2.12.18.new/src/gr.cc 2008-11-01 10:52:24.000000000 -0400 -@@ -397,7 +397,16 @@ - /* - * write conforming postscript prolog - */ -- fprintf(fp, "%%!PS-Adobe-2.0 EPSF-1.2\n"); -+ //fprintf(fp, "%%!PS-Adobe-2.0 EPSF-1.2\n"); -+ extern bool _export_postscript; -+ if (_export_postscript) -+ { -+ fprintf(fp, "%%!PS-Adobe-2.0\n"); -+ } -+ else -+ { -+ fprintf(fp, "%%!PS-Adobe-2.0 EPSF-1.2\n"); -+ } - if (privacy) - fprintf(fp, "%%%%Creator: %s\n", ""); - else -diff -Naur gri-2.12.18/src/gri.cc gri-2.12.18.new/src/gri.cc ---- gri-2.12.18/src/gri.cc 2006-06-16 19:18:40.000000000 -0400 -+++ gri-2.12.18.new/src/gri.cc 2008-11-01 10:46:40.000000000 -0400 -@@ -35,6 +35,7 @@ - // Globals used elsewhere (variables begin with _). - int _arrow_type; - bool _warn_offpage; -+bool _export_postscript; - std::vector<double> _dash; - std::vector<DataFile> _dataFILE; - std::vector<CmdFile> _cmdFILE; -diff -Naur gri-2.12.18/src/startup.cc gri-2.12.18.new/src/startup.cc ---- gri-2.12.18/src/startup.cc 2008-06-12 08:57:26.000000000 -0400 -+++ gri-2.12.18.new/src/startup.cc 2008-11-01 10:57:26.000000000 -0400 -@@ -188,6 +188,7 @@ - _axes_offset = 0.0; - _use_default_for_query = false; - _warn_offpage = true; -+ _export_postscript = false; - PUT_VAR("..use_default_for_query..", 0.0); - PUT_VAR("..words_in_dataline..", 0.0); // just in case tested - PUT_VAR("..batch..", 0.0); -@@ -681,6 +682,7 @@ - #define FLAG_PUBLICATION 1009 - #define FLAG_SUPERUSER 1010 - #define FLAG_WARN_OFFPAGE 1011 -+#define FLAG_POSTSCRIPT 1012 - // I use the 'FLAG_...' numbers for options that lack single-character abbreviations. - static struct poptOption optionsTable[] = { - { "batch", 'b', POPT_ARG_NONE | POPT_ARGFLAG_ONEDASH, NULL, 'b' }, -@@ -703,6 +705,7 @@ - { "version", 'v', POPT_ARG_NONE | POPT_ARGFLAG_ONEDASH, NULL, 'v' }, - { "warn_offpage", '\0', POPT_ARG_NONE | POPT_ARGFLAG_ONEDASH, NULL, FLAG_WARN_OFFPAGE }, - { "yes", 'y', POPT_ARG_NONE | POPT_ARGFLAG_ONEDASH, NULL, 'y' }, -+ { "postscript", '\0', POPT_ARG_NONE | POPT_ARGFLAG_ONEDASH, NULL, FLAG_POSTSCRIPT }, - { 0, 0, 0, 0, 0 } - }; - const poptContext optCon = -@@ -872,6 +875,8 @@ - printf("Gri cannot read in '%s'\n",optArg); - } - break; -+ case FLAG_POSTSCRIPT -+ _export_postscript = true; - default: - printf("Unknown option\n"); - break; -@@ -1058,6 +1063,8 @@ - } else if (!strcmp(argv[i], "-y") || !strcmp(argv[i], "-yes")) { - _use_default_for_query = true; - PUT_VAR("..use_default_for_query..", 1.0); -+ } else if (!strcmp(argv[i], "-postscript")){ -+ _export_postscript = true; - #if 0 - } else if (!strcmp(argv[i], "-e")) { - // User wants to do cmd in argv[i+1] -@@ -1190,6 +1197,8 @@ - gr_textput(" Makes Gri print out command lines as they are executed.\n"); - gr_textput(" -true or -y\n"); - gr_textput(" Makes Gri think the answer to all `query's is RETURN.\n"); -+ gr_textput(" -postscript\n"); -+ gr_textput(" Export a PostScript file instead of an EPS file.\n"); - #if 0 - gr_textput(" -e cmd\n"); - gr_textput(" BUG: NOT IMPLEMENTED YET!\n"); diff --git a/sci-visualization/gri/gri-2.12.22.ebuild b/sci-visualization/gri/gri-2.12.22.ebuild deleted file mode 100644 index e05011e87..000000000 --- a/sci-visualization/gri/gri-2.12.22.ebuild +++ /dev/null @@ -1,84 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-visualization/gri/gri-2.12.19.ebuild,v 1.3 2009/12/26 17:46:54 pva Exp $ - -EAPI=2 - -inherit elisp-common eutils - -DESCRIPTION="language for scientific graphics programming" -HOMEPAGE="http://gri.sourceforge.net/" -SRC_URI="mirror://sourceforge/gri/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 ~ppc x86" -IUSE="doc emacs examples" -RESTRICT="test" - -DEPEND=">=sci-libs/netcdf-4.1.0 - virtual/latex-base - media-gfx/imagemagick - app-text/ghostscript-gpl - emacs? ( virtual/emacs )" - -RDEPEND="${DEPEND}" - -SITEFILE="50gri-gentoo.el" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-2.12.18-postscript.patch -} - -src_compile() { - VARTEXFONTS="${T}/fonts" emake || die - if use emacs; then - elisp-compile src/*.el || die - fi -} - -src_install() { - # Replace PREFIX now and correct paths in the startup message. - sed -e s,PREFIX/share/gri/doc/,/usr/share/doc/${P}/, -i "${S}/src/startup.msg" - - einstall || die - - # license text not necessary - rm "${D}"/usr/share/gri/doc/license.txt - - # install target installs it always and in the wrong location - # remove it here and call elisp-install in case of USE=emacs below - rm -rf "${D}"/usr/share/emacs - - if ! use doc; then - sed -e "s/Manual at.*//" -i "${D}"/usr/share/gri/startup.msg - rm "${D}"/usr/share/gri/doc/cmdrefcard.ps - rm "${D}"/usr/share/gri/doc/refcard.ps - rm -rf "${D}"/usr/share/gri/doc/html - fi - if ! use examples; then - sed -e "s/Examples at.*//" -i "${D}"/usr/share/gri/startup.msg - rm -rf "${D}"/usr/share/gri/doc/examples - fi - - dodoc README - - #move docs to the proper place - mv "${D}"/usr/share/gri/doc/* "${D}/usr/share/doc/${PF}" - rmdir "${D}/usr/share/gri/doc/" - - if use emacs; then - cd src - elisp-install ${PN} *.{el,elc} || die - elisp-site-file-install "${FILESDIR}/${SITEFILE}" \ - || die - fi -} - -pkg_postinst() { - use emacs && elisp-site-regen -} - -pkg_postrm() { - use emacs && elisp-site-regen -} diff --git a/scripts/make_path64_snapshot.sh b/scripts/make_path64_snapshot.sh new file mode 100644 index 000000000..35924953a --- /dev/null +++ b/scripts/make_path64_snapshot.sh @@ -0,0 +1,37 @@ +#!/bin/bash + +clean_git() { + for f in $(find ./"$1" -name ".git"); do rm -rf $f; done +} + +TEMP=/dev/shm/path64 +TODAY=$(date -u +%Y%m%d) + +[[ -d ${TEMP} ]] && rm -rf ${TEMP} +mkdir "${TEMP}" && cd "${TEMP}" + +git clone git://github.com/pathscale/path64-suite.git path64 +clean_git path64 +ver=$(grep 'SET(PSC_FULL_VERSION' path64/CMakeLists.txt | cut -d'"' -f2) +tar cjf path64-suite-${ver}_pre${TODAY}.tbz2 path64 + +[[ -d ${TEMP}/path64/compiler ]] || mkdir -p ${TEMP}/path64/compiler +cd ${TEMP}/path64/compiler + +for f in compiler assembler ; do + git clone git://github.com/path64/$f.git +done +git clone git://github.com/path64/debugger.git pathdb +for f in compiler-rt libcxxrt libdwarf-bsd libunwind stdcxx ; do + git clone git://github.com/pathscale/$f.git +done + +clean_git +cd "${TEMP}" +tar cjf path64-compiler-${ver}_pre${TODAY}.tbz2 \ + path64/compiler/{compiler,compiler-rt,libcxxrt,libdwarf-bsd,libunwind,stdcxx} +tar cjf path64-debugger-${ver}_pre${TODAY}.tbz2 \ + path64/compiler/pathdb +tar cjf path64-assembler-${ver}_pre${TODAY}.tbz2 \ + path64/compiler/assembler + diff --git a/skel.ChangeLog b/skel.ChangeLog index c3d77a853..6eff27d09 100644 --- a/skel.ChangeLog +++ b/skel.ChangeLog @@ -1,5 +1,5 @@ # ChangeLog for <CATEGORY>/<PACKAGE_NAME> -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ *<PACKAGE_NAME>-<PACKAGE_VERSION>-<PACKAGE_RELEASE> (DD MMM YYYY) diff --git a/skel.ebuild b/skel.ebuild index f7a353613..7c3273ced 100644 --- a/skel.ebuild +++ b/skel.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -12,23 +12,22 @@ # generated to contain the correct data. # The EAPI variable tells the ebuild format in use. -# Defaults to 0 if not specified. The current PMS draft contains details on -# a proposed EAPI=0 definition but is not finalized yet. -# Eclasses will test for this variable if they need to use EAPI > 0 features. -# Ebuilds should not define EAPI > 0 unless they absolutely need to use -# features added in that version. -#EAPI=0 +# Defaults to 0 if not specified. +# It is suggested that you the latest EAPI approved by the Council. +# The PMS contains specifications for all EAPIs. Eclasses will test for this +# variable if they need to use EAPI > 0 features. +EAPI=4 # inherit lists eclasses to inherit functions from. Almost all ebuilds should # inherit eutils, as a large amount of important functionality has been -# moved there. For example, the $(get_libdir) mentioned below wont work +# moved there. For example, the epatch call mentioned below wont work # without the following line: inherit eutils # A well-used example of an eclass function that needs eutils is epatch. If # your source needs patches applied, it's suggested to put your patch in the # 'files' directory and use: # -# epatch ${FILESDIR}/patch-name-here +# epatch "${FILESDIR}"/patch-name-here # # eclasses tend to list descriptions of how to use their functions properly. # take a look at /usr/portage/eclasses/ for more examples. @@ -43,6 +42,7 @@ HOMEPAGE="http://foo.bar.com/" # Portage. SRC_URI="ftp://foo.bar.com/${P}.tar.gz" + # License of the package. This must match the name of file(s) in # /usr/portage/licenses/. For complex license combination see the developer # docs on gentoo.org for details. @@ -65,7 +65,7 @@ SLOT="0" # instead of relying on an external package.mask file. Right now, you should # set the KEYWORDS variable for every ebuild so that it contains the names of # all the architectures with which the ebuild works. All of the official -# architectures can be found in the keywords.desc file which is in +# architectures can be found in the arch.list file which is in # /usr/portage/profiles/. Usually you should just set this to "~x86". The ~ # in front of the architecture indicates that the package is new and should be # considered unstable until testing proves its stability. So, if you've @@ -89,6 +89,7 @@ IUSE="gnome X" # for details. Usually not needed. #RESTRICT="strip" + # Build-time dependencies, such as # ssl? ( >=dev-libs/openssl-0.9.6b ) # >=dev-lang/perl-5.6.1-r1 @@ -96,7 +97,7 @@ IUSE="gnome X" # had installed on your system when you tested the package. Then # other users hopefully won't be caught without the right version of # a dependency. -DEPEND="" +#DEPEND="" # Run-time dependencies. Must be defined to whatever this depends on to run. # The below is valid if the same run-time depends are required to compile. @@ -108,10 +109,14 @@ RDEPEND="${DEPEND}" # to keep it tidy. #S="${WORKDIR}/${P}" -src_compile() { + +# The following src_configure function is implemented as default by portage, so +# you only need to call it if you need a different behaviour. +# This function is available only in EAPI 2 and later. +#src_configure() { # Most open-source packages use GNU autoconf for configuration. - # The quickest (and preferred) way of running configure is: - econf || die "econf failed" + # The default, quickest (and preferred) way of running configure is: + #econf # # You could use something similar to the following lines to # configure your package before compilation. The "|| die" portion @@ -123,11 +128,18 @@ src_compile() { # --host=${CHOST} \ # --prefix=/usr \ # --infodir=/usr/share/info \ - # --mandir=/usr/share/man || die "./configure failed" + # --mandir=/usr/share/man || die # Note the use of --infodir and --mandir, above. This is to make # this package FHS 2.2-compliant. For more information, see # http://www.pathname.com/fhs/ - +#} + +# The following src_compile function is implemented as default by portage, so +# you only need to call it, if you need different behaviour. +# For EAPI < 2 src_compile runs also commands currently present in +# src_configure. Thus, if you're using an older EAPI, you need to copy them +# to your src_compile and drop the src_configure function. +#src_compile() { # emake (previously known as pmake) is a script that calls the # standard GNU make with parallel building options for speedier # builds (especially on SMP systems). Try emake first. It might @@ -135,15 +147,20 @@ src_compile() { # related to parallelism, in these cases, use emake -j1 to limit # make to a single process. The -j1 is a visual clue to others # that the makefiles have bugs that have been worked around. - emake || die "emake failed" -} -src_install() { + #emake || die +#} + +# The following src_install function is implemented as default by portage, so +# you only need to call it, if you need different behaviour. +# For EAPI < 4 src_install is just returing true, so you need to always specify +# this function in older EAPIs. +#src_install() { # You must *personally verify* that this trick doesn't install # anything outside of DESTDIR; do this by reading and # understanding the install part of the Makefiles. # This is the preferred way to install. - emake DESTDIR="${D}" install || die "emake install failed" + #emake DESTDIR="${D}" install || die # When you hit a failure with emake, do not just use make. It is # better to fix the Makefiles to allow proper parallelization. @@ -159,11 +176,11 @@ src_install() { # mandir="${D}"/usr/share/man \ # infodir="${D}"/usr/share/info \ # libdir="${D}"/usr/$(get_libdir) \ - # install || die "emake install failed" + # install || die # Again, verify the Makefiles! We don't want anything falling # outside of ${D}. # The portage shortcut to the above command is simply: # - #einstall || die "einstall failed" -} + #einstall || die +#} diff --git a/skel.metadata.xml b/skel.metadata.xml index d747d72a2..d31449d1d 100644 --- a/skel.metadata.xml +++ b/skel.metadata.xml @@ -1,8 +1,34 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!-- +This is the example metadata file. +The root element of this file is <pkgmetadata>. Within this element a +number of subelements are allowed: herd, maintainer, and +longdescription. herd is a required subelement. + +For a full description look at: +http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4 + + +Before committing, please remove the comments from this file. They are +not relevant for general metadata.xml files. +--> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> +<maintainer> + <email>@gentoo.org</email> +<!-- <description>Description of the maintainership</description> --> +</maintainer> +<longdescription> + Long description of the package +</longdescription> +<!-- +<use> + <flag name='flag'>Description of how USE='flag' affects this package</flag> + <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this + package</flag> + <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking. + Requires an installed dictionary from <cat>app-dicts</cat></flag> +</use> +--> </pkgmetadata> diff --git a/sys-cluster/open-mx/Manifest b/sys-cluster/open-mx/Manifest index 9ae9d8967..0bc0fa667 100644 --- a/sys-cluster/open-mx/Manifest +++ b/sys-cluster/open-mx/Manifest @@ -3,23 +3,25 @@ Hash: SHA256 AUX omxoed.initd 924 RMD160 20e120177652eb1df67e6b2e47b22fe4939f731a SHA1 7155b34d333f5632d5970f6b609798f7d9592c95 SHA256 2ea867e4dbf1a0609ffcdce06e68c81c04150667a6baa4d00af40cd085370701 AUX open-mx-1.4.0-driver.patch 284 RMD160 d97cb11234a48b37748fa101b12d8ccc628f333c SHA1 cc8b123dd3d9b3a479ace1d12bc790e2de7a0ffb SHA256 cf6b97ecdd350e531c40154ca5efe6e134cec25f60b34d5cebd9f7d5ae3814c8 -DIST open-mx-1.4.0.tar.gz 1028002 RMD160 131a6a0c8512e7852887a87c774200be693a219f SHA1 344b4eed70ddc575fd49b97d4148220e2d028748 SHA256 708046da0a6bb72ba022ac34640caaee8a544a4b26b5fe56420942d5ba26259e -EBUILD open-mx-1.4.0.ebuild 1702 RMD160 ad493629d2f8a5f1ac1c661e6a9e882e1d4f6af4 SHA1 5513f8b37c76735451aa0a1b8b4970847eb5ef2a SHA256 93bf0756ed95742ea6d0a26543a02bbe0e4fe9e99bf47b561d442e985bb716b4 +DIST open-mx-1.4.0.tar.gz 1028002 RMD160 9c1185a5c5e9fc54612808977ee8f548b2258d31 SHA1 da39a3ee5e6b4b0d3255bfef95601890afd80709 SHA256 e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 +DIST open-mx-1.5.0.tar.gz 1073137 RMD160 432a302de247490c90f4cf82b204ab28a3e837e2 SHA1 77d8e42fb7f1855a8c7f5595e77ad7faec4e0ae2 SHA256 96a89c630e61e61288a644c09944b3bb729f087013a66535d9d244f936abec17 +EBUILD open-mx-1.4.0.ebuild 1696 RMD160 c61916437bba2c15ebed7034982e45a09bebdbb3 SHA1 46e6e37c58a148f2467d6411db6d5c05230d67ff SHA256 abbc8a17d08af4522cfe2bf35395d70fbefa745e698515c2bb279cdc37ce0d5d +EBUILD open-mx-1.5.0.ebuild 1839 RMD160 a706cf7e349f6b2eb5f2d32c4d72fd508984f0ec SHA1 7514ff66abb40e2e2b98e9a067bfe1466cf8cfc7 SHA256 6a3416d12765b196fd524267d18f8a8046bb1677577853f4269ca615746d9392 MISC metadata.xml 256 RMD160 297cebf084cdeb7898dc63f961ebecc0d2b1eb41 SHA1 6ed907e703b338a26cd2652a1f63c2dbb11b85d4 SHA256 c2578751d289276468e4ab84773d4bb935f059a2e0e6a3416e3d3ef311d206e6 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) +Version: GnuPG v2.0.18 (GNU/Linux) -iQIcBAEBCAAGBQJOH3zPAAoJEOf+E+/4L5LmpfYP/2WG6XER9Q30Ppe8RHz4Sk3a -/fbe2Dg/JqHpnol5am+rSq0VSvefxRQ7KrWaVidpZNvLsA8I/Z8/2ugYdHFzPmV8 -3meX7qn8hqRWir5X6uBkcF37Lo55udk4rw7KLg7688UGHzH0QWd1L+LYd86Jwns9 -pl4ehblc5JXNeN8XMqoRkny4Nz+aAh3vDuEWCICZm8T9yD13kYsGuUlhveqq3uLP -H1TfqWp/CAJ1Sa2vkd7LFkjFL+oz6PvgCmCSJwgFA2xkUZQXllH6LKxzoHsNqV1g -SA+mstxEGcP5xziU+YurFUkkRZvKAp5DpaC7myDLn9cxItz7t3neQ77tc2dDaxxc -vDm8HXLqms1DN/XR7w4ncbMg5Ec0xX3b1puzP962l1ArJoIRt/i/Iv/kJABCAWWq -Vynf6TLBR5vUgsARl3Z1xRPDwK/WphzrIkM/yQ8fXuXEStdCiwFT69PgXS0MWGuM -I0vI+4uXSv8HeHy0gAJbKmpCiZmtLRNlH8zD900GDglSXlw3xqt49tuwb+pM50v7 -1FknqBVg1iGJc/VCGEPVzwbTlIMAZ79jOtZncKkzVkbMo1YOXesjVHz3jQo6/64j -SubUU0TWdfLTM7+NvAIQ4HiSZQnx0kKcUz8gjsgoyqp61bBm0Ta7SHZ/sDERatJe -N/RS4jNMlnKbp9efzYPz -=EMUN +iQIcBAEBCAAGBQJORU0vAAoJEOf+E+/4L5Lm6goP/jRTrVY87hpwR4wlVWDiNLG3 +aMrKXBBl396PDeYv3nwIzh+w8NBw5kc2EZk9/cCNAPprJQPUq3U++TOwxCPpl4Mc +zyiAQGysughcopFwGDyMnGvvwx0k5bs1llrzrsKOAajc4dIE+0VaS+Qqf9HaQnq1 +Hyu/h3Nqps9nY7wZcczX4jPLUAnSRpjTCXCt+P7VzxT8gldwJ37YwTRxhGKZCmDY +dQLRSfsdSRm9uIKftoMGWS/aRDpeNZE/8UjOmljtYpSz3nAFMSrgNo+sBJTqi5Ks +6HxSABGsbUGkCNwTxR1YfwFpppCE03SMg3Dtc68w7y2tZgRHIhGao9FBPdEkfbtk +4QU9wHe8qnsSi7by+iobPqIAGted9Kq29aPqJ86SaJ2oLtTx3z+LoOr3jVIG6yte +NtdjA5loQLLy6ZTVnaZJhczBqvI211JKq/8C2r8f1Q1KFv2j2dNkAK0QCkmjr6OA +ctrjXm18hhCMbURDfY/SUcka8C5eRaF+BfOeWE9yeTkwTVUF8R7Fr5klGkJLy7oj +A1uMXd4RhoN4bpxnMou/HBpqI8HIjqZPumeM/42JVX1ZqMa9copNlC4uVFlOn8RB +8uLIBLnDDVf0R4spgzL111Bp7DGDgfTx9pQfS2+ZQ2eI9h3r7u/4pgEUBAxvXb1+ +etQAY2aX69huE6OSlXZQ +=pdph -----END PGP SIGNATURE----- diff --git a/sys-cluster/open-mx/open-mx-1.4.0.ebuild b/sys-cluster/open-mx/open-mx-1.4.0.ebuild index 669e7bd67..e640ef8f7 100644 --- a/sys-cluster/open-mx/open-mx-1.4.0.ebuild +++ b/sys-cluster/open-mx/open-mx-1.4.0.ebuild @@ -17,7 +17,7 @@ IUSE="debug modules static-libs" DEPEND=" sys-apps/hwloc - >=virtual/linux-sources-2.6" + virtual/linux-sources" RDEPEND=" sys-apps/hwloc sys-apps/module-init-tools" diff --git a/sys-cluster/open-mx/open-mx-1.5.0.ebuild b/sys-cluster/open-mx/open-mx-1.5.0.ebuild new file mode 100644 index 000000000..46addf1da --- /dev/null +++ b/sys-cluster/open-mx/open-mx-1.5.0.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +inherit autotools linux-mod multilib + +DESCRIPTION="Open-MX - Myrinet Express over Generic Ethernet Hardware" +HOMEPAGE="http://open-mx.gforge.inria.fr/" +SRC_URI="http://gforge.inria.fr/frs/download.php/28871/${P}.tar.gz" + +LICENSE="GPL-2 LGPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug modules static-libs" + +DEPEND=" + sys-apps/hwloc + virtual/linux-sources" +RDEPEND=" + sys-apps/hwloc + sys-apps/module-init-tools" + +MODULE_NAMES="open-mx(misc:${S}/driver/linux)" +BUILD_TARGETS="all" +BUILD_PARAMS="KDIR=${KERNEL_DIR}" + +pkg_setup() { + einfo "You can set desired mtu by setting OPEN_MX_MTU in make.conf" + linux-mod_pkg_setup +} + +src_prepare() { + # We still want to configure driver but dont want to build it at all + epatch "${FILESDIR}/open-mx-1.4.0-driver.patch" + # We dont want tests + sed -e 's:tests/mx::g' \ + -e 's:tests::g' \ + -i Makefile.am || die "sed failed" + eautoreconf +} + +src_configure() { + econf \ + --with-mtu=${OPEN_MX_MTU:-9000} \ + $(use_enable static-libs static) \ + $(use_enable debug) +} + +src_compile() { + default + if use modules; then + cd "${S}/driver/linux" + linux-mod_src_compile || die "failed to build driver" + fi +} + +src_install() { + default + use static-libs || find "${ED}" -name '*.*a' -exec rm {} + + # Drop init scripts + rm -rf "${ED}/usr/sbin" || die + rm "${ED}/usr/bin/omx_check" + # install udev rules + insinto /etc/udev/rules.d + doins "${ED}/etc/open-mx/10-open-mx.rules" + dodoc "${ED}/usr/share/open-mx/FAQ.html" + # Drop misc stuff + rm "${ED}/etc/open-mx/10-open-mx.rules" || die + rm -rf "${ED}/usr/share/open-mx" || die + newinitd "${FILESDIR}/omxoed.initd" omxoed + if use modules; then + cd "${S}/driver/linux" + linux-mod_src_install || die "failed to install driver" + fi +} diff --git a/sys-devel/ucpp/ChangeLog b/sys-devel/ucpp/ChangeLog deleted file mode 100644 index 810d0c643..000000000 --- a/sys-devel/ucpp/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sys-devel/ucpp -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 07 Jan 2011; Justin Lecher <jlec@gentoo.org> ucpp-1.3.ebuild: - Some QA on ebuild style - -*ucpp-1.3 (22 Mar 2009) - - 22 Mar 2009; justin Lecher (jlec) <jlec@j-schmitz.net> - +files/tune.h.patch, +metadata.xml, +ucpp-1.3.ebuild: - initial checkin - diff --git a/sys-devel/ucpp/Manifest b/sys-devel/ucpp/Manifest deleted file mode 100644 index f58fc295d..000000000 --- a/sys-devel/ucpp/Manifest +++ /dev/null @@ -1,15 +0,0 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - -AUX tune.h.patch 723 RMD160 411f358400f0c0a8f813e25f580f69b22bf759d3 SHA1 022f30c77266c9b4c0773e9bdf54296503570971 SHA256 27bdbc0e81ba1c60b4f069b6a05eedb44445d4768b2a5808e53117a7ed7e7871 -DIST ucpp-1.3.tar.bz2 73958 RMD160 08f9ef1ada15c7451b7966733fb0a63bbe6b179a SHA1 12caf535986e3919d58c47ca35ae9ed4efaa1cf0 SHA256 d0a51c20040385b143f15fc08eefec6119773fb07232a14c08bbb49cb1c5f1fa -EBUILD ucpp-1.3.ebuild 679 RMD160 532b7c5e391823e31fed386986ec226d597a432d SHA1 5d4ed0b064db619a2513175ff603bf7bde0d5ad1 SHA256 60bc54eb43a28f1ae834ba8c71f9a4266a18ee36c3099b5e09d82c2f2f2104a1 -MISC ChangeLog 363 RMD160 eb1cf5a5381c54b50ff78ba4ebd6a3235d84a1cf SHA1 87b9ff7b57ce16e2d368306d007137bd135ff459 SHA256 58f1024b6da9925a18fd2c6421cd9190e4eec9bd65c085b2f4e24e9a56936bca -MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c ------BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) - -iEYEARECAAYFAk4Euc4ACgkQgAnW8HDreRaqgACeK3Uyu4nfGXY95Lx+qGtHXZ1L -hecAoM0d7n6fOQ2uryyNfdHxEj76Dpv8 -=t9dK ------END PGP SIGNATURE----- diff --git a/sys-devel/ucpp/files/tune.h.patch b/sys-devel/ucpp/files/tune.h.patch deleted file mode 100644 index 7455dd242..000000000 --- a/sys-devel/ucpp/files/tune.h.patch +++ /dev/null @@ -1,28 +0,0 @@ ---- tune.h 2008-10-01 19:15:41.000000000 +0200 -+++ tune.h.new 2009-03-22 11:59:42.000000000 +0100 -@@ -281,10 +281,10 @@ - * - * If you want no standard assertion, define STD_ASSERT to 0. - */ --/* -+ - #define STD_ASSERT "cpu(i386)", "machine(i386)", "system(unix)", \ - "system(freebsd)" --*/ -+ - - /* ====================================================================== */ - /* -@@ -293,10 +293,10 @@ - * Each string must be either "name" or "name=token-list". If you want - * no predefined macro, define STD_MACROS to 0. - */ --/* -+ - #define STD_MACROS "__FreeBSD=4", "__unix", "__i386", \ - "__FreeBSD__=4", "__unix__", "__i386__" --*/ -+ - - /* ====================================================================== */ - /* diff --git a/sys-devel/ucpp/ucpp-1.3.ebuild b/sys-devel/ucpp/ucpp-1.3.ebuild deleted file mode 100644 index 93085f9c4..000000000 --- a/sys-devel/ucpp/ucpp-1.3.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit eutils toolchain-funcs - -DESCRIPTION="A quick and light preprocessor, but anyway fully compliant to C99" -HOMEPAGE="http://code.google.com/p/ucpp/" -SRC_URI="http://ucpp.googlecode.com/files/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -src_prepare() { - epatch "${FILESDIR}"/tune.h.patch -} - -src_compile() { - emake \ - FLAGS="${CFLAGS} -DSTAND_ALONE" \ - CC=$(tc-getCC) \ - STAND_ALONE="-DSTAND_ALONE" || die -} - -src_install() { - dolib.a lib${PN}.a || die - doman ${PN}.1 || die - dobin ${PN} || die - dodoc README || die -} |