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authorAndreas Schäfer <gentryx@gmx.de>2013-05-15 09:04:28 +0200
committerAndreas Schäfer <gentryx@gmx.de>2013-05-15 09:04:28 +0200
commitdbf1d3a5ed02ce670672682a4bdc6fec652edd92 (patch)
treed8449f0f083a639b9676c2b88788e64a8c74dd28
parentadding ebuild for AMD APP (diff)
parentselectively call cuda.eclass, depending on use flag (diff)
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-rw-r--r--sci-visualization/ferret-bin/Manifest10
-rw-r--r--sci-visualization/ferret-bin/ferret-bin-6.6.4.ebuild52
-rw-r--r--sci-visualization/ferret-bin/metadata.xml12
-rw-r--r--sci-visualization/gnuplot/ChangeLog18
-rw-r--r--sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild213
-rw-r--r--sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild202
-rw-r--r--sci-visualization/gnuplot/metadata.xml26
-rw-r--r--sci-visualization/paraview/ChangeLog6
-rw-r--r--sci-visualization/paraview/metadata.xml36
-rw-r--r--sci-visualization/paraview/paraview-3.10.1.ebuild28
-rw-r--r--sci-visualization/paraview/paraview-3.12.0.ebuild26
-rw-r--r--sci-visualization/paraview/paraview-3.14.1-r4.ebuild16
-rw-r--r--sci-visualization/v_sim/ChangeLog6
-rw-r--r--sci-visualization/v_sim/Manifest4
-rw-r--r--sci-visualization/v_sim/metadata.xml26
-rw-r--r--sci-visualization/v_sim/v_sim-3.5.1.ebuild80
-rw-r--r--sci-visualization/v_sim/v_sim-3.5.2.ebuild87
-rw-r--r--sci-visualization/v_sim/v_sim-3.6.0.ebuild4
-rw-r--r--sci-visualization/yt/yt-9999.ebuild3
-rw-r--r--skel.ChangeLog2
-rw-r--r--skel.ebuild2
-rw-r--r--skel.metadata.xml38
-rw-r--r--sys-apps/likwid/metadata.xml2
-rw-r--r--sys-cluster/blcr/ChangeLog5
-rw-r--r--sys-cluster/blcr/blcr-0.8.4.ebuild3
-rw-r--r--sys-cluster/blcr/metadata.xml4
-rw-r--r--sys-cluster/empi/ChangeLog10
-rw-r--r--sys-cluster/empi/empi-0.8.ebuild (renamed from sys-cluster/empi/empi-0.7.ebuild)2
-rw-r--r--sys-cluster/empi/files/ChangeLog-0.7164
-rw-r--r--sys-cluster/empi/files/ChangeLog-0.868
-rwxr-xr-xsys-cluster/empi/files/empi-0.7408
-rwxr-xr-xsys-cluster/empi/files/empi-0.8492
-rw-r--r--sys-cluster/empi/files/eselect.mpi-0.8 (renamed from sys-cluster/empi/files/eselect.mpi-0.7)2
-rw-r--r--sys-cluster/hpl/ChangeLog9
-rw-r--r--sys-cluster/hpl/Manifest2
-rw-r--r--sys-cluster/hpl/hpl-2.0-r1.ebuild20
-rw-r--r--sys-cluster/hpl/metadata.xml12
-rw-r--r--sys-cluster/lustre/ChangeLog333
-rw-r--r--sys-cluster/lustre/files/0001-LU-2982-build-make-AC-check-for-linux-arch-sandbox-f.patch95
-rw-r--r--sys-cluster/lustre/files/0002-LU-1812-kernel-3.0-SuSE-and-3.6-FC18-server-patches.patch21302
-rw-r--r--sys-cluster/lustre/files/0003-LU-2686-kernel-sock_map_fd-replaced-by-sock_alloc_fi.patch137
-rw-r--r--sys-cluster/lustre/files/0004-LU-2686-kernel-Kernel-update-for-3.7.2-201.fc18.patch184
-rw-r--r--sys-cluster/lustre/files/0005-LU-2850-compat-posix_acl_-to-from-_xattr-take-user_n.patch159
-rw-r--r--sys-cluster/lustre/files/0006-LU-2800-llite-introduce-local-getname.patch91
-rw-r--r--sys-cluster/lustre/files/0007-LU-2987-llite-rcu-free-inode.patch89
-rw-r--r--sys-cluster/lustre/files/0008-LU-2850-kernel-3.8-upstream-removes-vmtruncate.patch83
-rw-r--r--sys-cluster/lustre/files/0009-LU-2850-kernel-3.8-upstream-kills-daemonize.patch2966
-rw-r--r--sys-cluster/lustre/files/0010-LU-3079-kernel-3.9-hlist_for_each_entry-uses-3-args.patch115
-rw-r--r--sys-cluster/lustre/files/0011-LU-3079-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch82
-rw-r--r--sys-cluster/lustre/files/0012-LU-3179-fids-fix-compilation-error-with-gcc-4.7.2.patch29
-rw-r--r--sys-cluster/lustre/files/0013-LU-3117-build-zfs-0.6.1-kmod-dkms-compatibility.patch1038
-rw-r--r--sys-cluster/lustre/lustre-9999.ebuild94
-rw-r--r--sys-cluster/lustre/metadata.xml3
-rw-r--r--sys-cluster/mvapich2/ChangeLog7
-rw-r--r--sys-cluster/mvapich2/Manifest2
-rw-r--r--sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild4
-rw-r--r--sys-cluster/openmpi/ChangeLog6
-rw-r--r--sys-cluster/openmpi/Manifest2
-rw-r--r--sys-cluster/openmpi/openmpi-1.6.4.ebuild (renamed from sys-cluster/openmpi/openmpi-1.6.3.ebuild)7
-rw-r--r--sys-cluster/ovis/ChangeLog5
-rw-r--r--sys-cluster/ovis/metadata.xml10
-rw-r--r--sys-cluster/ovis/ovis-3.0.1.ebuild6
-rw-r--r--virtual/blas/ChangeLog2
-rw-r--r--virtual/lapack/ChangeLog8
-rw-r--r--virtual/lapack/lapack-3.3.ebuild23
-rw-r--r--virtual/lapack/lapack-3.4.ebuild23
-rw-r--r--virtual/lapack/metadata.xml3
-rw-r--r--virtual/scalapack/ChangeLog9
-rw-r--r--virtual/scalapack/metadata.xml4
-rw-r--r--virtual/scalapack/scalapack-2.0.ebuild (renamed from virtual/scalapack/scalapack-1.8.ebuild)6
-rw-r--r--x11-libs/xview-bin/ChangeLog9
-rw-r--r--x11-libs/xview-bin/Manifest2
-rw-r--r--x11-libs/xview-bin/metadata.xml10
-rw-r--r--x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild6
-rw-r--r--x11-libs/xview/ChangeLog12
-rw-r--r--x11-libs/xview/Manifest1
-rw-r--r--x11-libs/xview/metadata.xml10
-rw-r--r--x11-libs/xview/xview-3.2-r6.ebuild4
-rw-r--r--x11-libs/xview/xview-3.2-r7.ebuild4
-rw-r--r--x11-libs/xview/xview-3.2-r8.ebuild108
920 files changed, 36397 insertions, 9390 deletions
diff --git a/README.md b/README.md
index a4fa9e856..d4dc43f76 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,12 @@
-Gentoo Science Overlay
-===
-
-Please fork! We will merge! \ No newline at end of file
+Gentoo Science Overlay
+======================
+
+An overlay for Gentoo, geared towards scientific packages.
+
+Please fork! We will merge!
+
+Ask for help in #gentoo-science in irc freenode.
+
+Report issues on the github site:
+
+https://github.com/gentoo-science/sci/issues
diff --git a/app-doc/root-docs/ChangeLog b/app-doc/root-docs/ChangeLog
index ebc679f65..3ddaf4a61 100644
--- a/app-doc/root-docs/ChangeLog
+++ b/app-doc/root-docs/ChangeLog
@@ -1,7 +1,14 @@
# ChangeLog for app-doc/root-docs
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*root-docs-5.34.05 (23 Feb 2013)
+
+ 23 Feb 2013; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.32.04.ebuild,
+ -root-docs-5.34.03.ebuild, +root-docs-5.34.05.ebuild, root-docs-9999.ebuild:
+ Version bump. Remove old. Do not compress files (mostly headers) as
+ this renders them unusable from html pages.
+
*root-docs-5.34.03 (25 Oct 2012)
25 Oct 2012; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.34.02.ebuild,
diff --git a/app-doc/root-docs/Manifest b/app-doc/root-docs/Manifest
index 7711ba20f..f8e3e5537 100644
--- a/app-doc/root-docs/Manifest
+++ b/app-doc/root-docs/Manifest
@@ -1,2 +1 @@
-DIST root_v5.32.04.source.tar.gz 55526502 SHA256 0c0130ba3d74b86caee3071deeceb46545cfde34def8ad2107601e133506acf2 SHA512 796d7f6fe92700232da3fcaac042438e13c13e504179a7375105b2ff06e1fac571ef4d59f270d73844b2a481b0762a873985d22eee2b1a0b156071b777d4417a WHIRLPOOL c5ce0f81331e08b3f79e97c894bff60185bba562388e789d3d1716d3523045a55c24e1cebded4ad19a09023c4b5275fd7d44acb726a1f248a9616ed95addd609
-DIST root_v5.34.03.source.tar.gz 56290003 SHA256 4ce18154f507fcdd8d580b776568d4b87004756d7d17f86796fcba0b2499a1a1 SHA512 522dbcb0ddcc3030f440939e8e5849e0b33ae4e4f7a0de3dd213404e8a9801954ef40a06ef9c206b62be8997d7eec2da72e1b0f1bbfd9fa99683961b99540e4b WHIRLPOOL 5f1bb9900b4a6238e51bc67be935f8a4cfa4455a0b4ef601e11f9235a17f918aa350169ae2eecbdb4f74af6badcd61a5bc3a4d16dce913e32277a458e55cc7ae
+DIST root_v5.34.05.source.tar.gz 64021235 SHA256 448e180a5ed6f53b5ee49ead014a98e742e97198a4ca760f086467db5d230c9d SHA512 37d26849114c7764b8cb877e29f5e3b24603680b317ceab52d784ca2c17d66f38e99dfa1b369e587517ea5ffd4a11cefe51eb84db47d767ad16aee12b7ce79bf WHIRLPOOL 195f32c1251088ff55a5c7834bc3db3d07a4fbcfff018f329e6c39c6618aa98b7f3c2f6a0f7aba883367a016ca260c0c061c7641caa75c8c6e077cad0bb43516
diff --git a/app-doc/root-docs/root-docs-5.32.04.ebuild b/app-doc/root-docs/root-docs-5.32.04.ebuild
deleted file mode 100644
index 65095a299..000000000
--- a/app-doc/root-docs/root-docs-5.32.04.ebuild
+++ /dev/null
@@ -1,96 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.32.03.ebuild,v 1.4 2012/07/14 18:45:53 jdhore Exp $
-
-EAPI=4
-
-ROOT_PN="root"
-PATCH_PV="5.32"
-
-if [[ ${PV} == "9999" ]] ; then
- _SVN_DEP="dev-vcs/subversion"
- SRC_URI=""
- KEYWORDS=""
-else
- SRC_URI="ftp://root.cern.ch/${ROOT_PN}/${ROOT_PN}_v${PV}.source.tar.gz"
- KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-fi
-
-inherit eutils multilib toolchain-funcs virtualx
-
-DESCRIPTION="API documentation for ROOT (An Object-Oriented Data Analysis Framework)"
-HOMEPAGE="http://root.cern.ch/"
-
-SLOT="0"
-LICENSE="LGPL-2.1"
-IUSE=""
-
-S="${WORKDIR}/${ROOT_PN}"
-VIRTUALX_REQUIRED="always"
-
-DEPEND="
- ~sci-physics/root-${PV}[X,doc,graphviz,htmldoc,opengl]
- virtual/pkgconfig
- ${_SVN_DEP}"
-RDEPEND=""
-
-pkg_setup() {
- # sandboxed user can't access video hardware, so xorg-x11 implementation
- # should be used
- GL_IMPLEM=$(eselect opengl show)
- eselect opengl set xorg-x11
-}
-
-src_unpack() {
- # can't use subversion eclass functions,
- # we need to svn export the same root tree:
- # 1) svn revisions for root and root-docs must be the same;
- # 2) no need to abuse server twice.
- if [[ ${PV} == "9999" ]] ; then
- addpredict "${PORTAGE_ACTUAL_DISTDIR:-${DISTDIR}}/svn-src/${ROOT_PN}/trunk/.svn"
- svn export "${PORTAGE_ACTUAL_DISTDIR:-${DISTDIR}}/svn-src/${ROOT_PN}/trunk" \
- "${S}" || die "svn export failed"
- else
- default
- fi
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/${PN}-${PATCH_PV}-makehtml.patch
-}
-
-src_configure() {
- # we need only to setup paths here, html docs doesn't depend on USE flags
- ./configure \
- --prefix="${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=$(tc-getFC) \
- --with-ld=$(tc-getCXX) \
- --with-afs-shared=yes \
- --with-llvm-config="${EPREFIX}"/usr/bin/llvm-config \
- --with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps
-}
-
-src_compile() {
- ROOTSYS="${S}" Xemake html
- # if root.exe crashes, return code will be 0 due to gdb attach,
- # so we need to check if last html file was generated;
- # this check is volatile and can't catch crash on the last file.
- [[ -f htmldoc/timespec.html ]] || die "looks like html doc generation crashed"
-}
-
-src_install() {
- dodir /usr/share/doc/${PF}
- # too large data to copy
- mv htmldoc/* "${ED}usr/share/doc/${PF}/"
-}
-
-pkg_postinst() {
- eselect opengl set ${GL_IMPLEM}
-}
diff --git a/app-doc/root-docs/root-docs-5.34.03.ebuild b/app-doc/root-docs/root-docs-5.34.05.ebuild
index f873d30b2..3bab6fafe 100644
--- a/app-doc/root-docs/root-docs-5.34.03.ebuild
+++ b/app-doc/root-docs/root-docs-5.34.05.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.01.ebuild,v 1.1 2012/07/22 20:34:45 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.03.ebuild,v 1.1 2012/10/26 15:39:53 bicatali Exp $
EAPI=4
@@ -89,6 +89,7 @@ src_install() {
dodir /usr/share/doc/${PF}
# too large data to copy
mv htmldoc/* "${ED}usr/share/doc/${PF}/"
+ docompress -x "${EPREFIX}/usr/share/doc/${PF}/"
}
pkg_postinst() {
diff --git a/app-doc/root-docs/root-docs-9999.ebuild b/app-doc/root-docs/root-docs-9999.ebuild
index 27260c209..4763153c4 100644
--- a/app-doc/root-docs/root-docs-9999.ebuild
+++ b/app-doc/root-docs/root-docs-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.00.ebuild,v 1.2 2012/06/27 17:31:12 bicatali Exp $
@@ -89,6 +89,7 @@ src_install() {
dodir /usr/share/doc/${PF}
# too large data to copy
mv htmldoc/* "${ED}usr/share/doc/${PF}/"
+ docompress -x "${EPREFIX}/usr/share/doc/${PF}/"
}
pkg_postinst() {
diff --git a/app-doc/scalapack-docs/ChangeLog b/app-doc/scalapack-docs/ChangeLog
index 8cddf15fb..bab4c5a37 100644
--- a/app-doc/scalapack-docs/ChangeLog
+++ b/app-doc/scalapack-docs/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for app-doc/scalapack-docs
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 Feb 2013; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml,
+ scalapack-docs-2.0.ebuild:
+ app-doc/scalapack-docs: Cleaning and keywording for prefix
+
*scalapack-docs-2.0 (23 Feb 2012)
23 Feb 2012; Sébastien Fabbro <bicatali@gentoo.org>
@@ -13,4 +17,3 @@
13 Dec 2010; Sébastien Fabbro <bicatali@gentoo.org>
+scalapack-docs-1.8.ebuild, +metadata.xml:
Initial import
-
diff --git a/app-doc/scalapack-docs/metadata.xml b/app-doc/scalapack-docs/metadata.xml
index bdb160f44..6f1066877 100644
--- a/app-doc/scalapack-docs/metadata.xml
+++ b/app-doc/scalapack-docs/metadata.xml
@@ -9,6 +9,7 @@
style using explicit message passing for interprocessor
communication. It assumes matrices are laid out in a two-dimensional
block cyclic decomposition.
- This package contains manual pages for the routines, and quick reference guides.
+ This package contains manual pages for the routines, and quick
+ reference guides.
</longdescription>
</pkgmetadata>
diff --git a/app-doc/scalapack-docs/scalapack-docs-2.0.ebuild b/app-doc/scalapack-docs/scalapack-docs-2.0.ebuild
index c66bc5af5..a8027218e 100644
--- a/app-doc/scalapack-docs/scalapack-docs-2.0.ebuild
+++ b/app-doc/scalapack-docs/scalapack-docs-2.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
DESCRIPTION="Documentation reference and man pages for ScaLAPACK implementations"
HOMEPAGE="http://www.netlib.org/scalapack/"
@@ -10,7 +10,7 @@ SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"
LICENSE="BSD"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
S="${WORKDIR}"
diff --git a/app-forensics/vine/ChangeLog b/app-forensics/vine/ChangeLog
new file mode 100644
index 000000000..1cb3961e3
--- /dev/null
+++ b/app-forensics/vine/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for app-forensics/vine
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*vine-1.0 (16 Mar 2013)
+
+ 16 Mar 2013; Christoph Junghans <ottxor@gentoo.org>
+ +files/vine-1.0-binutils.patch, +files/vine-1.0-gcc46.patch,
+ +files/vine-1.0-install.patch, +files/vine-1.0-ocamlgraph182.patch,
+ +metadata.xml, +vine-1.0.ebuild:
+ initial commit
diff --git a/app-forensics/vine/Manifest b/app-forensics/vine/Manifest
new file mode 100644
index 000000000..91dd64f8c
--- /dev/null
+++ b/app-forensics/vine/Manifest
@@ -0,0 +1 @@
+DIST vine-1.0.tar.gz 3401264 SHA256 d31b13ef6d5bcdd8f4183f94c561971e3770e4682b088b3b48ae32b34ab14329 SHA512 9e204fe1954331bc2cfc5f1c648f828e9441adc8ba2e7cdec5f09f805ecc89c97a7995d9bf8a78574b9b37e53cac7b433b3f9b22d7148add2931fbbb8821cf70 WHIRLPOOL e1926ec7a09c91cff3b3c9daac2fd15811b1e842c5d4cf1daab6e1e3304ce9801efe6547650b5707594c472b84e7909ffa66f0dec4a6bdedbe8af3a4495adff8
diff --git a/app-forensics/vine/files/vine-1.0-binutils.patch b/app-forensics/vine/files/vine-1.0-binutils.patch
new file mode 100644
index 000000000..b9d55daa0
--- /dev/null
+++ b/app-forensics/vine/files/vine-1.0-binutils.patch
@@ -0,0 +1,16 @@
+https://groups.google.com/d/msg/bitblaze-users/Zpg7Ddzngns/o7LNnR0qqxwJ
+
+Index: libasmir/src/disasm/asm_program.cpp
+===================================================================
+--- libasmir/src/disasm/asm_program.cpp (older version)
++++ libasmir/src/disasm/asm_program.cpp (fixed version)
+@@ -7,6 +7,11 @@
+ #include "debug.h"
+ #include "asm_program.h"
+ #include "objdump.h"
++/* Some versions of glibc and the binutils libiberty library give
++ conflicting prototypes for basename(). We don't use that function
++ anyway, but to work around the problem, make libliberty.h think
++ that it has already been declared. */
++#define HAVE_DECL_BASENAME 1
+ #include "libiberty.h"
diff --git a/app-forensics/vine/files/vine-1.0-gcc46.patch b/app-forensics/vine/files/vine-1.0-gcc46.patch
new file mode 100644
index 000000000..89a52290b
--- /dev/null
+++ b/app-forensics/vine/files/vine-1.0-gcc46.patch
@@ -0,0 +1,37 @@
+https://groups.google.com/d/msg/bitblaze-users/sTTPlFEzWo0/0ZjPL0QYC8IJ
+
+Index: libasmir/src/vex/irtoir-i386.cpp
+===================================================================
+--- libasmir/src/vex/irtoir-i386.cpp (old revision)
++++ libasmir/src/vex/irtoir-i386.cpp (new revision)
+@@ -9,6 +9,13 @@
+ web site at: http://bitblaze.cs.berkeley.edu/
+ */
+
++/* Because we use offsetof() for values that go in switch statement
++ cases, we need a definition in terms of __builtin_offsetof so that
++ GCC >= 4.6 can accept the results of offsetof() as a constant
++ expression. They've stopped supporting the traditional definition
++ as a macro &((type*)0)->memb, which appears in VEX's headers. */
++#include <stddef.h>
++
+ #include <string>
+ #include <vector>
+ #include <iostream>
+Index: libasmir/src/vex/irtoir-arm.cpp
+===================================================================
+--- libasmir/src/vex/irtoir-arm.cpp (old revision)
++++ libasmir/src/vex/irtoir-arm.cpp (new revision)
+@@ -9,6 +9,12 @@
+ web site at: http://bitblaze.cs.berkeley.edu/
+ */
+
++/* Because we use offsetof() for values that go in switch statement
++ cases, we need a definition in terms of __builtin_offsetof so that
++ GCC >= 4.6 can accept the results of offsetof() as a constant
++ expression. They've stopped supporting the traditional definition
++ as a macro &((type*)0)->memb, which appears in VEX's headers. */
++#include <stddef.h>
+
+ #include "irtoir-internal.h"
+ #include "libvex_guest_arm.h"
diff --git a/app-forensics/vine/files/vine-1.0-install.patch b/app-forensics/vine/files/vine-1.0-install.patch
new file mode 100644
index 000000000..62a84bca1
--- /dev/null
+++ b/app-forensics/vine/files/vine-1.0-install.patch
@@ -0,0 +1,89 @@
+--- vine-1.0.orig/stp/ocaml/Makefile 2009-09-24 15:45:57.000000000 -0600
++++ vine-1.0/stp/ocaml/Makefile 2013-03-14 20:22:49.993194747 -0600
+@@ -14,3 +14,6 @@
+ Makefile
+
+ include $(OCAMLMAKEFILE)
++
++install: rawinstall
++
+--- vine-1.0.orig/stp/ocaml/OCamlMakefile 2009-09-24 15:45:57.000000000 -0600
++++ vine-1.0/stp/ocaml/OCamlMakefile 2013-03-14 20:20:23.012069386 -0600
+@@ -1126,10 +1126,10 @@
+ .PHONY: rawinstall
+ rawinstall: all
+ $(QUIET)printf "\nInstalling library to: $(OCAML_LIB_INSTALL)\n"
+- -install -d $(OCAML_LIB_INSTALL)
++ -install -d $(DESTDIR)$(OCAML_LIB_INSTALL)
+ for i in $(LIBINSTALL_FILES); do \
+ if [ -f $$i ]; then \
+- install -c -m 0644 $$i $(OCAML_LIB_INSTALL); \
++ install -c -m 0644 $$i $(DESTDIR)$(OCAML_LIB_INSTALL); \
+ fi; \
+ done
+ $(QUIET)printf "\nInstallation successful.\n"
+
+--- vine-1.0.orig/ocaml/Makefile 2009-09-24 15:45:57.000000000 -0600
++++ vine-1.0/ocaml/Makefile 2013-03-14 20:22:49.993194747 -0600
+@@ -14,3 +14,6 @@
+
+
+ include $(OCAMLMAKEFILE)
++
++install: rawinstall
++
+--- vine-1.0.orig/ocaml/OCamlMakefile 2009-09-24 15:45:57.000000000 -0600
++++ vine-1.0/ocaml/OCamlMakefile 2013-03-14 20:20:23.012069386 -0600
+@@ -1126,10 +1126,10 @@
+ .PHONY: rawinstall
+ rawinstall: all
+ $(QUIET)printf "\nInstalling library to: $(OCAML_LIB_INSTALL)\n"
+- -install -d $(OCAML_LIB_INSTALL)
++ -install -d $(DESTDIR)$(OCAML_LIB_INSTALL)
+ for i in $(LIBINSTALL_FILES); do \
+ if [ -f $$i ]; then \
+- install -c -m 0644 $$i $(OCAML_LIB_INSTALL); \
++ install -c -m 0644 $$i $(DESTDIR)$(OCAML_LIB_INSTALL); \
+ fi; \
+ done
+ $(QUIET)printf "\nInstallation successful.\n"
+--- vine-1.0.orig/trace/Makefile 2009-09-24 15:45:57.000000000 -0600
++++ vine-1.0/trace/Makefile 2013-03-14 20:22:49.993194747 -0600
+@@ -14,3 +14,6 @@
+
+
+ include $(OCAMLMAKEFILE)
++
++install: rawinstall
++
+--- vine-1.0.orig/trace_utils/Makefile 2009-09-24 15:45:57.000000000 -0600
++++ vine-1.0/trace_utils/Makefile 2013-03-16 14:31:46.375690732 -0600
+@@ -88,6 +88,8 @@
+ # * subprjs
+
+
++install:
++
+
+ %:
+ make -f $(OCAMLMAKEFILE) subprojs SUBTARGET=$@
+--- vine-1.0.orig/utils/Makefile 2009-09-24 15:45:57.000000000 -0600
++++ vine-1.0/utils/Makefile 2013-03-16 14:31:46.375690732 -0600
+@@ -88,6 +88,8 @@
+ # * subprjs
+
+
++install:
++
+
+ %:
+ make -f $(OCAMLMAKEFILE) subprojs SUBTARGET=$@
+--- vine-1.0.orig/doc/Makefile 2009-09-24 15:45:57.000000000 -0600
++++ vine-1.0/doc/Makefile 2013-03-16 14:41:59.182926821 -0600
+@@ -17,3 +17,6 @@
+
+ clean:
+ (cd howto && $(MAKE) clean)
++
++install:
++
diff --git a/app-forensics/vine/files/vine-1.0-ocamlgraph182.patch b/app-forensics/vine/files/vine-1.0-ocamlgraph182.patch
new file mode 100644
index 000000000..5cb79f224
--- /dev/null
+++ b/app-forensics/vine/files/vine-1.0-ocamlgraph182.patch
@@ -0,0 +1,68 @@
+Index: ocaml/vine_cfg.mli
+===================================================================
+--- ocaml/vine_cfg.mli (old version)
++++ ocaml/vine_cfg.mli (new version)
+@@ -86,6 +86,11 @@
+ (** [cfg#iter_edges f] calls [f a b] forall [(a,b)] where there is an edge
+ vine-1.0-from [a] to [b] in the CFG. *)
+
++ method fold_edges : 'b. ('a bb -> 'a bb -> 'b -> 'b) -> 'b -> 'b
++ (** [cfg#fold_edges f init] computes [f uN uN (... (f u1 v1
++init)...)] where [(u1, v1) ... (uN, vN)] is an enumeration of all
++the edges in the graph, in an unspecified order. *)
++
+ method get_info : 'a bb -> 'a
+ (** Returns the info associated with the given bb. *)
+
+@@ -225,6 +230,7 @@
+ val iter_vertex : (bbid -> unit) -> t -> unit
+ val fold_vertex : (vertex -> 'a -> 'a) -> t -> 'a -> 'a
+ val iter_edges_e : (E.t -> unit) -> t -> unit
++ val fold_edges_e : (E.t -> 'a -> 'a) -> t -> 'a -> 'a
+ val iter_succ : (vertex -> unit) -> t -> vertex -> unit
+ val iter_pred : (vertex -> unit) -> t -> vertex -> unit
+ val in_degree : t -> vertex -> int
+Index: ocaml/vine_cfg.ml
+===================================================================
+--- ocaml/vine_cfg.ml (old version)
++++ ocaml/vine_cfg.ml (new version)
+@@ -115,6 +115,7 @@
+ method iter_bb : ('a bb -> unit) -> unit
+ method fold_bb : 'b. ('a bb -> 'b -> 'b) -> 'b -> 'b
+ method iter_edges : ('a bb -> 'a bb -> unit) -> unit
++ method fold_edges : 'b. ('a bb -> 'a bb -> 'b -> 'b) -> 'b -> 'b
+ method get_info : 'a bb -> 'a
+ method set_info : 'a bb -> 'a -> unit
+ method get_id : 'a bb -> bbid
+@@ -306,6 +307,14 @@
+ self#iter_bb (fun b -> List.iter (f b) (self#succ b));
+ self#check_graph;
+
++ method fold_edges f a =
++ self#check_graph;
++ let res = self#fold_bb
++ (fun b a2 -> List.fold_left (fun a3 b2 -> f b b2 a3) a2 (self#succ b)) a
++ in
++ self#check_graph;
++ res
++
+ method length = Hashtbl.length blktbl
+
+ method get_info b =
+@@ -1122,6 +1131,7 @@
+ val iter_vertex : (bbid -> unit) -> t -> unit
+ val fold_vertex : (bbid -> 'a -> 'a) -> t -> 'a -> 'a
+ val iter_edges_e : (E.t -> unit) -> t -> unit
++ val fold_edges_e : (E.t -> 'a -> 'a) -> t -> 'a -> 'a
+ val iter_succ : (vertex -> unit) -> t -> vertex -> unit
+ val iter_pred : (vertex -> unit) -> t -> vertex -> unit
+ val in_degree : t -> vertex -> int
+@@ -1170,6 +1180,8 @@
+ let fold_vertex f (g:t) a = g#fold_bb (fun b -> f b.id) a
+ let iter_edges_e f (g:t) =
+ g#iter_edges (fun x y -> f (g#get_id x, g#get_id y))
++ let fold_edges_e f (g:t) a =
++ g#fold_edges (fun x y a -> f (g#get_id x, g#get_id y) a) a
+ let iter_succ f g v = List.iter f (bb_succ g v)
+ let iter_pred f g v = List.iter f (bb_pred g v)
+ let in_degree g v = List.length (bb_pred g v)
diff --git a/app-forensics/vine/metadata.xml b/app-forensics/vine/metadata.xml
new file mode 100644
index 000000000..745b9e1ce
--- /dev/null
+++ b/app-forensics/vine/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>ottxor@gentoo.org</email>
+ <name>Christoph Junghans</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/app-forensics/vine/vine-1.0.ebuild b/app-forensics/vine/vine-1.0.ebuild
new file mode 100644
index 000000000..522599029
--- /dev/null
+++ b/app-forensics/vine/vine-1.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-libs/gmetadom/gmetadom-0.2.6.ebuild,v 1.9 2012/05/04 18:35:48 jdhore Exp $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="The BitBlaze Static Analysis Component"
+HOMEPAGE="http://bitblaze.cs.berkeley.edu/vine.html"
+SRC_URI="http://bitblaze.cs.berkeley.edu/release/${P}/${P}.tar.gz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+ dev-lang/ocaml
+ dev-ml/findlib
+ dev-ml/camlidl
+ >=dev-libs/gmetadom-0.2.6-r1[ocaml]
+ dev-ml/extlib
+ sys-devel/binutils
+ dev-ml/ocamlgraph"
+RDEPEND="${DEPEND}"
+
+MAKEOPTS="${MAKEOPTS} -j1"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-binutils.patch \
+ "${FILESDIR}"/${P}-gcc46.patch \
+ "${FILESDIR}"/${P}-install.patch \
+ "${FILESDIR}"/${P}-ocamlgraph182.patch
+}
+
+src_compile() {
+ emake CC=$(tc-getCC) CCFLAGS="${CFLAGS} -fpic"
+}
diff --git a/app-portage/g-octave/ChangeLog b/app-portage/g-octave/ChangeLog
index 27a8cc36f..94d0a710e 100644
--- a/app-portage/g-octave/ChangeLog
+++ b/app-portage/g-octave/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for app-portage/g-octave
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> g-octave-9999.ebuild,
+ metadata.xml:
+ Migrate to new python eclasses, git2 eclass and EAPI=5
+
25 Oct 2011; Justin Lecher <jlec@gentoo.org> metadata.xml:
Removed no-herd from herd tag in metadata.xml
diff --git a/app-portage/g-octave/g-octave-9999.ebuild b/app-portage/g-octave/g-octave-9999.ebuild
index 7bec90ae5..2e05b3fc4 100644
--- a/app-portage/g-octave/g-octave-9999.ebuild
+++ b/app-portage/g-octave/g-octave-9999.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="2"
+EAPI=5
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_DEPEND="*:2.6"
+PYTHON_COMPAT=( python{2_5,2_6,2_7,3_1,3_2} pypy{1_9,2_0} )
-inherit distutils git
+inherit distutils-r1 git-2
DESCRIPTION="A tool that generates and installs ebuilds for Octave-Forge"
HOMEPAGE="http://www.g-octave.org/"
@@ -18,35 +17,24 @@ SLOT="0"
KEYWORDS=""
IUSE="doc test"
-DEPEND=">=dev-python/docutils-0.6
- doc? ( >=dev-python/sphinx-1.0 )"
+DEPEND="
+ dev-python/docutils[${PYTHON_USEDEP}]
+ doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )"
RDEPEND="sys-apps/portage"
S="${WORKDIR}/${PN}"
-PYTHON_MODNAME="g_octave"
-
-src_compile() {
- distutils_src_compile
- if use doc; then
- emake -C docs html
- fi
+python_compile_all() {
+ use doc && emake -C docs html
}
-src_install() {
- distutils_src_install
- dohtml ${PN}.html
- doman ${PN}.1
- if use doc; then
- mv docs/_build/{html,sphinx}
- dohtml -r docs/_build/sphinx
- fi
+python_test() {
+ ${PYTHON} scripts/run_tests.py || die
}
-src_test() {
- testing() {
- PYTHONPATH="build-${PYTHON_ABI}/lib" "$(PYTHON)" \
- scripts/run_tests.py || die 'test failed.'
- }
- python_execute_function testing
+python_install_all() {
+ doman ${PN}.1
+ use doc && HTML_DOCS=( docs/_build/html/. )
+ HTML_DOCS+=( ${PN}.html )
+ distutils-r1_python_install_all
}
diff --git a/app-portage/g-octave/metadata.xml b/app-portage/g-octave/metadata.xml
index 772748d54..33a64d286 100644
--- a/app-portage/g-octave/metadata.xml
+++ b/app-portage/g-octave/metadata.xml
@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>rafael@rafaelmartins.eng.br</email>
- <name>Rafael Goncalves Martins</name>
- </maintainer>
- <longdescription lang="en">
+ <maintainer>
+ <email>rafael@rafaelmartins.eng.br</email>
+ <name>Rafael Goncalves Martins</name>
+ </maintainer>
+ <longdescription lang="en">
g-octave is a tool that generates and installs ebuilds for Octave-Forge
packages "on-the-fly" to Gentoo Linux, using Portage. It's capable to
generate ebuilds and Manifest files for the packages, and to install
diff --git a/app-text/jabref/ChangeLog b/app-text/jabref/ChangeLog
index 61fae0608..220d66d29 100644
--- a/app-text/jabref/ChangeLog
+++ b/app-text/jabref/ChangeLog
@@ -2,6 +2,18 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 08 Apr 2013; Nicolas Bock <nicolasbock@gmail.com> jabref-2.10b.ebuild:
+ Jabref-2.10b does not build anymore with Java 6. Bumping java requirement to
+ java 7.
+
+*jabref-2.10b (05 Apr 2013)
+
+ 05 Apr 2013; Nicolas Bock <nicolasbock@gmail.com> +jabref-2.10b.ebuild:
+ Adding jabref-2.10b (beta) ebuild.
+
+ 20 Feb 2013; Sébastien Fabbro <bicatali@gentoo.org> jabref-2.9.2-r1.ebuild:
+ app-text/jabref: Fixed doc generation, keyword amd64-linux and x86-linux
+
*jabref-2.9.2-r1 (15 Feb 2013)
15 Feb 2013; Nicolas Bock <nicolasbock@gmail.com> +jabref-2.9.2-r1.ebuild,
diff --git a/app-text/jabref/Manifest b/app-text/jabref/Manifest
index 04872ddea..d677c9d40 100644
--- a/app-text/jabref/Manifest
+++ b/app-text/jabref/Manifest
@@ -1 +1,2 @@
+DIST JabRef-2.10b-src.tar.bz2 16785780 SHA256 d44848d75072f54bb1db2352f43714fe951c8f967bd44a4ff1f6ce981dc94b10 SHA512 35cfb46c3e31f1e7a058e0d63bc041e7b3a416a1b56cac98bd96dec8073e56416e561865dc92cf5918b6a6f2b5ff022c01463ed56ce6d84b63901e2a48c8956f WHIRLPOOL bdeb845e6ed026ce7a6f11495f1791380aeb7a2bb26557242e349c6669aa8833fc358ca500c9f8c2989ff360fd096db07287806eba9679d4e6dfe6326ee25d4f
DIST JabRef-2.9.2-src.tar.bz2 16664284 SHA256 12bc7e489709bc6f57327bf8e15c6bc9ceaa600369dca6452b7c13d792215e83 SHA512 40eb5d3f3528e92c4d5c62abce12d87ea63b84a58778a32151cd1af2a0198c49aa354ee295f8b3c9449d5b078f7119163babd3c29f358b0d56b3776980292463 WHIRLPOOL d2115e497066f31a3772085510f6820e46a55fbe36778471e6c81a4973f45607761cca80655cfefffb1308f65315ef72fb17791fe964d004826f345322ca0dcf
diff --git a/app-text/jabref/jabref-2.10b.ebuild b/app-text/jabref/jabref-2.10b.ebuild
new file mode 100644
index 000000000..3c60f1b5e
--- /dev/null
+++ b/app-text/jabref/jabref-2.10b.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+EANT_DOC_TARGET=javadocs
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java GUI for managing BibTeX and other bibliographies"
+HOMEPAGE="http://jabref.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/JabRef-${PV}-src.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc"
+
+EANT_BUILD_TARGET="jars"
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
+
+src_install() {
+ java-pkg_newjar build/lib/JabRef-${PV}.jar
+ use doc && java-pkg_dojavadoc build/docs/API
+ dodoc src/txt/README
+ java-pkg_dolauncher ${PN} --main net.sf.jabref.JabRef
+ newicon src/images/JabRef-icon-48.png JabRef-icon.png
+ make_desktop_entry ${PN} JabRef JabRef-icon Office
+}
diff --git a/app-text/jabref/jabref-2.9.2-r1.ebuild b/app-text/jabref/jabref-2.9.2-r1.ebuild
index 4de57b8f3..8b116f2c2 100644
--- a/app-text/jabref/jabref-2.9.2-r1.ebuild
+++ b/app-text/jabref/jabref-2.9.2-r1.ebuild
@@ -4,15 +4,16 @@
EAPI=5
+EANT_DOC_TARGET=javadocs
inherit java-pkg-2 java-ant-2
-DESCRIPTION="Java GUI frontend for managing BibTeX and other bibliographies."
+DESCRIPTION="Java GUI for managing BibTeX and other bibliographies"
HOMEPAGE="http://jabref.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/JabRef-${PV}-src.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~x86 ~amd64"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="doc"
EANT_BUILD_TARGET="jars"
@@ -22,9 +23,9 @@ RDEPEND=">=virtual/jre-1.6"
src_install() {
java-pkg_newjar build/lib/JabRef-${PV}.jar
- use doc && java-pkg_dojavadoc build/docs/api
+ use doc && java-pkg_dojavadoc build/docs/API
dodoc src/txt/README
java-pkg_dolauncher ${PN} --main net.sf.jabref.JabRef
- newicon src/images/JabRef-icon-48.png JabRef-icon.png || die "failed to create icon"
+ newicon src/images/JabRef-icon-48.png JabRef-icon.png
make_desktop_entry ${PN} JabRef JabRef-icon Office
}
diff --git a/dev-cpp/eigen/ChangeLog b/dev-cpp/eigen/ChangeLog
index ca03e5194..0a1984ddf 100644
--- a/dev-cpp/eigen/ChangeLog
+++ b/dev-cpp/eigen/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for dev-cpp/eigen
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/dev-cpp/eigen/ChangeLog,v 1.44 2011/03/25 16:01:28 jlec Exp $
+*eigen-3.1.3-r1 (29 Apr 2013)
+
+ 29 Apr 2013; Sébastien Fabbro <bicatali@gentoo.org> +eigen-3.1.3-r1.ebuild,
+ -eigen-3.1.2.ebuild, eigen-9999.ebuild:
+ dev-cpp/eigen: Version bump
+
12 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> -eigen-3.1.1-r1.ebuild:
dev-cpp/eigen: Removed old
diff --git a/dev-cpp/eigen/Manifest b/dev-cpp/eigen/Manifest
index 152f1a5ad..27328215a 100644
--- a/dev-cpp/eigen/Manifest
+++ b/dev-cpp/eigen/Manifest
@@ -1 +1 @@
-DIST eigen-3.1.2.tar.bz2 1052120 SHA256 5efddc5b11f651bc531b46e4a00b805b16f8bb356db361a533c92145ecdadcc3 SHA512 7f7cbada67fc4c63fd60ebfefaa2492432546e91e014a32103f958cd1f9644dff424a2e1046d8de51982dc9072873a96dfbe75e95a1529fd47880069989ae837 WHIRLPOOL f1809ae4157f7ef86737fa5283bff17fc8e902fbf31bbc8be02c67143e9ab7cb43e72a3a51e444d753b4bc2054ca6d1bdc16aa68998f9fc6962978ca1c29f0d8
+DIST eigen-3.1.3.tar.bz2 1052724 SHA256 1a443145f321dd47a5ca11f176e7319056198a6124a7577723d92e3c3cd59ece SHA512 7b6b816416570c9592ed9ca09e61970346f02bed492df7073fed3e657ded0c2bb736fb024554f92064ee783cbf1180952ccb87ed724899fa353f34c6a49210a4 WHIRLPOOL 53c667def19d882bff0e6a7b8476028a211ca2b4617d579b8555738c726ed1d4f3d4aed0e87b39c00a941484505f2a54fb82dba19444cc04f7f438fa1fc22c45
diff --git a/dev-cpp/eigen/eigen-3.1.2.ebuild b/dev-cpp/eigen/eigen-3.1.3-r1.ebuild
index eafd77401..eafd77401 120000
--- a/dev-cpp/eigen/eigen-3.1.2.ebuild
+++ b/dev-cpp/eigen/eigen-3.1.3-r1.ebuild
diff --git a/dev-cpp/eigen/eigen-9999.ebuild b/dev-cpp/eigen/eigen-9999.ebuild
index 9d52cff4f..199918a89 100644
--- a/dev-cpp/eigen/eigen-9999.ebuild
+++ b/dev-cpp/eigen/eigen-9999.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
FORTRAN_NEEDED=fortran
@@ -35,9 +35,7 @@ CDEPEND="
dev-cpp/sparsehash
sci-libs/cholmod[metis]
sci-libs/superlu
- sci-libs/umfpack
- )"
-
+ sci-libs/umfpack )"
DEPEND="
doc? ( app-doc/doxygen[dot,latex] )
test? ( ${CDEPEND} )"
@@ -49,7 +47,7 @@ RDEPEND="
src_configure() {
# TOFIX: static-libs for blas are always built with PIC
# TOFIX: is it worth fixing all the automagic given no library is built?
- mycmakeargs=(
+ local mycmakeargs=(
-DEIGEN_BUILD_BTL=OFF
-DEIGEN_TEST_NO_OPENGL=ON
$(cmake-utils_use test EIGEN_BUILD_TESTS)
diff --git a/dev-db/cppdb/ChangeLog b/dev-db/cppdb/ChangeLog
new file mode 100644
index 000000000..8017ba41e
--- /dev/null
+++ b/dev-db/cppdb/ChangeLog
@@ -0,0 +1,26 @@
+# ChangeLog for dev-db/cppdb
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 18 Mar 2013; Justin Lecher <jlec@gentoo.org> +cppdb-0.3.1-r1.ebuild,
+ +metadata.xml:
+ Import from sunrise
+
+*cppdb-0.3.1-r1 (08 Mar 2013)
+
+ 08 Mar 2013; Patrick Lauer <patrick@gentoo.org> -cppdb-0.3.1.ebuild,
+ +cppdb-0.3.1-r1.ebuild:
+ Add ~amd64 keyword, EAPI bump
+
+*cppdb-0.3.1 (28 Jun 2012)
+
+ 28 Jun 2012; Jauhien Piatlicki (jauhien) piatlicki@gmail.com
+ -cppdb-0.3.0.ebuild, +cppdb-0.3.1.ebuild:
+ Version bump: dev-db/cppdb-0.3.1
+
+*cppdb-0.3.0 (03 Apr 2012)
+
+ 03 Apr 2012; Jauhien Piatlicki (jauhien) piatlicki@gmail.com
+ +cppdb-0.3.0.ebuild, +metadata.xml:
+ New ebuild for bug #410713 thanks to people from #gentoo-sunrise
+
diff --git a/dev-db/cppdb/Manifest b/dev-db/cppdb/Manifest
new file mode 100644
index 000000000..20de58c2f
--- /dev/null
+++ b/dev-db/cppdb/Manifest
@@ -0,0 +1 @@
+DIST cppdb-0.3.1.tar.bz2 251449 SHA256 d60eef5a732d8f84ef5e4a2845a8cefc543a6c75bf3782589c2cf6aa150b992e SHA512 19e60becbffef7a252eda5fdd5821b44c2eeb5d69e84cf46e89ed6af3cea315f3cfe7b2cc4f62fbe154be8abdad3363761dd0252f94671421010273eeae65678 WHIRLPOOL 71ab865ef7ffeae43ec8c7278553225ab0b6ccddc8355213a60ab77c835af569d157c77ff417e651754c3f34187b516f6e16fb982321de8701fa60619e19b77d
diff --git a/dev-db/cppdb/cppdb-0.3.1-r1.ebuild b/dev-db/cppdb/cppdb-0.3.1-r1.ebuild
new file mode 100644
index 000000000..8bf4320ff
--- /dev/null
+++ b/dev-db/cppdb/cppdb-0.3.1-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils multilib
+
+DESCRIPTION="An SQL connectivity library for platform and database independent connectivity"
+HOMEPAGE="http://cppcms.com/sql/cppdb/"
+SRC_URI="mirror://sourceforge/cppcms/${P}.tar.bz2"
+
+LICENSE="|| ( Boost-1.0 MIT )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples mysql mysql_internal odbc odbc_internal postgres postgres_internal sqlite sqlite_internal"
+
+DEPEND="
+ mysql? ( virtual/mysql )
+ odbc? ( dev-db/unixODBC )
+ postgres? ( dev-db/postgresql-base )
+ sqlite? ( dev-db/sqlite:3 )"
+RDEPEND="${DEPEND}"
+
+src_configure() {
+ local mycmakeargs="
+ $(cmake-utils_use_disable mysql MYSQL)
+ $(cmake-utils_use mysql_internal MYSQL_BACKEND_INTERNAL)
+ $(cmake-utils_use_disable odbc ODBC)
+ $(cmake-utils_use odbc_internal ODBC_BACKEND_INTERNAL)
+ $(cmake-utils_use_disable postgres PQ)
+ $(cmake-utils_use postgres_internal PQ_BACKEND_INTERNAL)
+ $(cmake-utils_use_disable sqlite SQLITE)
+ $(cmake-utils_use sqlite_internal SQLITE_BACKEND_INTERNAL)
+ -DLIBDIR=$(get_libdir)"
+ cmake-utils_src_configure
+}
+
+src_install() {
+ cmake-utils_src_install
+ if use doc; then
+ rm docs/build.txt || die
+ dodoc -r docs/*
+ dohtml -r html/*
+ fi
+ if use examples; then
+ insinto /usr/share/doc/${PF}
+ doins -r examples
+ fi
+}
diff --git a/dev-db/cppdb/metadata.xml b/dev-db/cppdb/metadata.xml
new file mode 100644
index 000000000..247592e77
--- /dev/null
+++ b/dev-db/cppdb/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>maintainer-wanted@gentoo.org</email>
+ </maintainer>
+ <use>
+ <flag name="mysql_internal">Don't build a separate mysql loadable module but rather build it into the cppdb library itself</flag>
+ <flag name="odbc_internal">Don't build a separate postgresql loadable module but rather build it into the cppdb library itself</flag>
+ <flag name="postgres_internal">Don't build a separate odbc loadable module but rather build it into the cppdb library itself</flag>
+ <flag name="sqlite_internal">Don't build a separate sqlite3 loadable module but rather build it into the cppdb library itself</flag>
+ </use>
+</pkgmetadata>
diff --git a/dev-java/flexdock/Manifest b/dev-java/flexdock/Manifest
index d13a831e4..b1fe81744 100644
--- a/dev-java/flexdock/Manifest
+++ b/dev-java/flexdock/Manifest
@@ -1,2 +1,2 @@
DIST flexdock-1.1.1-src.zip 6163036 SHA256 e0bed4b633dd09da20651d495eb87b985150938564dd124083483c98bda09cf3 SHA512 104398a573b2aade0ed6b848920f8a3903964feabd755c653d8e62ea986251d9c31a07e88308c9cffe7e696c99109a3dfca249f0ca0357e88a896fc5769170f4 WHIRLPOOL 3265875a173911f5635d76824c1c98bc5f0fef3761abc7f5efc3ddc3582f354562391982f6c6f0f286ac2677bafc94237ce09e63ae877da79cad7dfcd50855b9
-DIST flexdock-1.2.2.tar.gz 5976519 SHA256 d3f47568de768c2591df9786a5ac8465f20bce49575171f2c34506146d76b25a SHA512 0caa2917c793669b8ef391e1fe71b6947e6c6f2d48dd982ff6ef54ebb74f3794c58acdb625e57deda4c5394b62b1789be5822ccbf2f19ee22365eb4960a52655 WHIRLPOOL bc3cb09245d5f29bc9beb24b649f38cdf9768fb27dbc6086cd88adb20e728335580b559cfec3105b4ba80ce39753464e2407335c293b524aba36a0c7fd47a0d7
+DIST flexdock-1.2.3.tar.gz 5976737 SHA256 4f895f9cdc181c60923c138f96f9b805a59e7d78bba08006de2e5c344e57aacb SHA512 7e7b49f36e19a130b6e36598c20215ada0a567591e52c240154dc6ebea2b3216a7b405f1f4b0fca1c4b6117099d024b4fc52625b608f0d17827beef80ab44c7b WHIRLPOOL 926d7cae181dc5932d42d478bc5ca0ebe6f72dacd28a2dc2e1d07bcde7642fe3884f322522d004188e81762434491a138a54aa1fac96dd890cdc46b97d3920c6
diff --git a/dev-java/flexdock/files/flexdock-1.2.2-nodemo.patch b/dev-java/flexdock/files/flexdock-1.2.3-nodemo.patch
index 415301d20..415301d20 100644
--- a/dev-java/flexdock/files/flexdock-1.2.2-nodemo.patch
+++ b/dev-java/flexdock/files/flexdock-1.2.3-nodemo.patch
diff --git a/dev-java/flexdock/flexdock-1.2.2.ebuild b/dev-java/flexdock/flexdock-1.2.3.ebuild
index 75c36ee36..c13ee05ce 100644
--- a/dev-java/flexdock/flexdock-1.2.2.ebuild
+++ b/dev-java/flexdock/flexdock-1.2.3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="2"
+EAPI=5
JAVA_PKG_IUSE="doc source"
inherit java-pkg-2 java-ant-2
@@ -17,8 +17,8 @@ KEYWORDS="~x86 ~amd64"
IUSE=""
-RDEPEND=">=virtual/jre-1.4"
-DEPEND=">=virtual/jdk-1.4
+RDEPEND=">=virtual/jre-1.5"
+DEPEND=">=virtual/jdk-1.5
app-arch/unzip
dev-java/skinlf"
diff --git a/dev-java/gluegen/ChangeLog b/dev-java/gluegen/ChangeLog
index 13587c9e2..8b5ba2af2 100644
--- a/dev-java/gluegen/ChangeLog
+++ b/dev-java/gluegen/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> gluegen-2.0_rc8.ebuild,
+ metadata.xml:
+ Keyworded for ~x86
+
*gluegen-2.0_rc8 (03 Feb 2013)
03 Feb 2013; Guillaume Horel <guillaume.horel@gmail.com>
diff --git a/dev-java/gluegen/gluegen-2.0_rc8.ebuild b/dev-java/gluegen/gluegen-2.0_rc8.ebuild
index 4dd5ee36c..4ce9ace78 100644
--- a/dev-java/gluegen/gluegen-2.0_rc8.ebuild
+++ b/dev-java/gluegen/gluegen-2.0_rc8.ebuild
@@ -22,7 +22,7 @@ SRC_URI="http://jogamp.org/deployment/${MY_PV}/archive/Sources/${MY_P}.tar.7z"
LICENSE="BSD"
SLOT="2"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
COMMON_DEP="
diff --git a/dev-java/gluegen/metadata.xml b/dev-java/gluegen/metadata.xml
index c4f41a72e..981cb4c21 100644
--- a/dev-java/gluegen/metadata.xml
+++ b/dev-java/gluegen/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>java</herd>
- <longdescription lang="en">
+ <herd>java</herd>
+ <longdescription lang="en">
GlueGen is a tool which automatically generates the Java and JNI code necessary
to call C libraries. It reads as input ANSI C header files and separate
configuration files which provide control over many aspects of the glue code
diff --git a/dev-java/jcip-annotations/ChangeLog b/dev-java/jcip-annotations/ChangeLog
index abeec0e60..477afa165 100644
--- a/dev-java/jcip-annotations/ChangeLog
+++ b/dev-java/jcip-annotations/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-java/jcip-annotations
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> jcip-annotations-1.0-r1.ebuild,
+ metadata.xml:
+ Correct license name
+
*jcip-annotations-1.0-r1 (14 May 2012)
14 May 2012; Sébastien Fabbro <bicatali@gentoo.org>
diff --git a/dev-java/jcip-annotations/Manifest b/dev-java/jcip-annotations/Manifest
index 5d5a730b5..fc63ac630 100644
--- a/dev-java/jcip-annotations/Manifest
+++ b/dev-java/jcip-annotations/Manifest
@@ -1 +1 @@
-DIST jcip-annotations-src.jar 4998 RMD160 a4b9a825fb0b2c313ebf5d11f246a654e30109b3 SHA1 c685e640967c817cc66d9df598772e68721161f8 SHA256 221f5cbe0b00a4c5f3c8870639de3573223fb9aa2636c631f901302fd4339efc
+DIST jcip-annotations-src.jar 4998 SHA256 221f5cbe0b00a4c5f3c8870639de3573223fb9aa2636c631f901302fd4339efc
diff --git a/dev-java/jcip-annotations/jcip-annotations-1.0-r1.ebuild b/dev-java/jcip-annotations/jcip-annotations-1.0-r1.ebuild
index 1ee0f8510..dd2acb9b3 100644
--- a/dev-java/jcip-annotations/jcip-annotations-1.0-r1.ebuild
+++ b/dev-java/jcip-annotations/jcip-annotations-1.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -13,7 +13,7 @@ DESCRIPTION="Annotations for Concurrency"
HOMEPAGE="http://www.jcip.net/"
SRC_URI="http://www.jcip.net/${PN}-src.jar"
-LICENSE="CCPL-Attribution-ShareAlike-2.5"
+LICENSE="CC-BY-SA-2.5"
#Confirm license before entering tree.
SLOT="0"
KEYWORDS="~amd64 ~x86"
@@ -21,7 +21,8 @@ KEYWORDS="~amd64 ~x86"
IUSE=""
RDEPEND=">=virtual/jre-1.5"
-DEPEND=">=virtual/jdk-1.5
+DEPEND="
+ >=virtual/jdk-1.5
app-arch/unzip"
S="${WORKDIR}"
diff --git a/dev-java/jcip-annotations/metadata.xml b/dev-java/jcip-annotations/metadata.xml
index ba0008fb8..b39c888fa 100644
--- a/dev-java/jcip-annotations/metadata.xml
+++ b/dev-java/jcip-annotations/metadata.xml
@@ -1,14 +1,13 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>java</herd>
- <maintainer>
- <email>ali_bush@gentoo.org</email>
- <name>Alistair Bush</name>
- </maintainer>
- <longdescription lang="en">
+ <herd>java</herd>
+ <maintainer>
+ <email>ali_bush@gentoo.org</email>
+ <name>Alistair Bush</name>
+ </maintainer>
+ <longdescription lang="en">
Annotations used within the Java Concurrency in Practice book by
Brain Goetz.
</longdescription>
</pkgmetadata>
-
diff --git a/dev-java/jlatexmath-fop/Manifest b/dev-java/jlatexmath-fop/Manifest
index b3a18c0c6..9b17143a6 100644
--- a/dev-java/jlatexmath-fop/Manifest
+++ b/dev-java/jlatexmath-fop/Manifest
@@ -1,2 +1 @@
-DIST jlatexmath-src-all-0.9.7.zip 1177126 SHA256 f27772c54e438034ea5cd70fc53b5cef8775578b50b41597bf23e2960c98d4f6 SHA512 1d2f1e66ec55f90e81bf7c4ffe1719589de2527f40fb7872e6e653ca2deb31f5fe6da6f3a90a608e3df02be4b625485403cc1d1d4a2b4738ecf5f2f35604c816 WHIRLPOOL 408f19aca68d494a75b452efdec8d2be1a295e04dafff934715a7af934068edb176b101ef8bd56f07a89a8bf8bb6040a646f83429c8ce706991bb39271c70dd1
-DIST jlatexmath-src-all-1.0.0.zip 1177772 SHA256 0e21fa493d30e878ee533f372ffd4d51cc85084a83c7fc79bf4f89a9d9b7268e SHA512 0d5dcb3d2b02c98be6cf17fa9fe313c4694bc353755b958bdfd3e1da83a99d5447fcb742c7e7bd0cc97a0face0b89dc7f8668abb7f7eb8f7753868986cca1b0f WHIRLPOOL e723c2a86aafcb84e6dec4199ed5df58478e0800a3039f777b89c372c87229c429af936cf0b134fc8f43e8b3f23684606500fa6f81b308132296bdc74d18482a
+DIST jlatexmath-fop-src-1.0.2.zip 114459 SHA256 40becda795ee73a6a80805d614c5e30a763da333c2c568465234e7548f260fdf SHA512 4154c38e4c9a66a7e260d471710810331b04bf651df120d3e24f49335799bdf0f5000f0b0c01c4aea24d753a36a05c76c97405fa22c1059aa8944e8995757f81 WHIRLPOOL b98cdac4aab40a8ff147930b045e31756f639bdff5c0ce8628ca6620370c756f0e6eb47143fa1f403f2daffaa83b45aa41467571b59bade5cfbf1812f451eb67
diff --git a/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.2-fixpaths.patch b/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.2-fixpaths.patch
new file mode 100644
index 000000000..a03051c36
--- /dev/null
+++ b/dev-java/jlatexmath-fop/files/jlatexmath-fop-1.0.2-fixpaths.patch
@@ -0,0 +1,13 @@
+diff -urN work-orig/build.xml work/build.xml
+--- work-orig/build.xml 2013-04-23 20:42:19.776644942 -0400
++++ work/build.xml 2013-04-23 20:42:36.821646638 -0400
+@@ -1,7 +1,7 @@
+ <?xml version="1.0" encoding="ISO-8859-1"?>
+ <project name="jlatexmath-fop" basedir="." default="buildJar">
+- <import file="${basedir}/../../version.xml"/>
+- <property file="../../fop.properties"/>
++ <import file="${basedir}/version.xml"/>
++ <property file="fop.properties"/>
+
+ <path id="libs-build-classpath">
+ <pathelement location="${fop.jar}"/>
diff --git a/dev-java/jlatexmath-fop/files/version.xml b/dev-java/jlatexmath-fop/files/version.xml
new file mode 100644
index 000000000..7f1d9c225
--- /dev/null
+++ b/dev-java/jlatexmath-fop/files/version.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project name="version_jlm">
+ <property name="version" value="1.0.2" />
+ <property name="java_version" value="5" />
+</project>
diff --git a/dev-java/jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild b/dev-java/jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild
deleted file mode 100644
index 0641c214c..000000000
--- a/dev-java/jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-JAVA_PKG_IUSE="examples source"
-
-inherit java-pkg-2 java-ant-2
-
-MY_PN="${PN/-fop/}"
-MY_P="${P/-fop/}"
-
-DESCRIPTION="jlatexmath plugin for dev-java/fop"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${MY_PN}-src-all-${PV}.zip"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-
-IUSE=""
-CDEPEND="dev-java/jlatexmath
- dev-java/avalon-framework
- dev-java/fop"
-REPEND=">=virtual/jdk-1.5
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.5
- ${CDEPEND}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-EANT_BUILD_TARGET="buildJar"
-
-S="${WORKDIR}/${MY_P}/plugin/fop"
-
-src_prepare() {
- cd "${WORKDIR}/${MY_P}"
- sed -i \
- -e "s:/usr/share/java/fop.jar:$(java-pkg_getjar fop fop.jar):g" \
- -e "s:/usr/share/java/xmlgraphics-commons.jar:$(java-pkg_getjar xmlgraphics-commons-1.3 xmlgraphics-commons.jar):g" \
- -e "s:/usr/share/java/batik.jar:$(java-pkg_getjar batik-1.7 batik-all.jar):g" \
- -e "s:/usr/share/java/avalon-framework.jar:$(java-pkg_getjar avalon-framework-4.2 avalon-framework.jar):g" \
- -e "s:/usr/share/java/commons-io.jar:$(java-pkg_getjar commons-io-1 commons-io.jar):g" \
- -e "s:/usr/share/java/commons-logging.jar:$(java-pkg_getjar commons-logging commons-logging.jar):g" \
- -e "s:/usr/share/java/xml-apis-ext.jar:$(java-pkg_getjar xml-commons-external-1.3 xml-apis-ext.jar):g" \
- fop.properties || die
-}
-
-src_install() {
- java-pkg_newjar dist/${P}.jar ${PN}.jar
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild b/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild
deleted file mode 100644
index 465f6f5bf..000000000
--- a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-JAVA_PKG_IUSE="examples source"
-
-inherit java-pkg-2 java-ant-2
-
-MY_PN="${PN/-fop/}"
-MY_P="${P/-fop/}"
-
-DESCRIPTION="jlatexmath plugin for dev-java/fop"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${MY_PN}-src-all-${PV}.zip"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-
-IUSE=""
-CDEPEND="dev-java/jlatexmath:1
- dev-java/avalon-framework
- dev-java/fop"
-REPEND=">=virtual/jdk-1.5
- ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.5
- ${CDEPEND}"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-EANT_BUILD_TARGET="buildJar"
-
-S="${WORKDIR}/${MY_P}/plugin/fop"
-
-src_prepare() {
- cd "${WORKDIR}/${MY_P}"
- sed -i \
- -e "s:/usr/share/java/fop.jar:$(java-pkg_getjar fop fop.jar):g" \
- -e "s:/usr/share/java/xmlgraphics-commons.jar:$(java-pkg_getjar xmlgraphics-commons-1.3 xmlgraphics-commons.jar):g" \
- -e "s:/usr/share/java/batik.jar:$(java-pkg_getjar batik-1.7 batik-all.jar):g" \
- -e "s:/usr/share/java/avalon-framework.jar:$(java-pkg_getjar avalon-framework-4.2 avalon-framework.jar):g" \
- -e "s:/usr/share/java/commons-io.jar:$(java-pkg_getjar commons-io-1 commons-io.jar):g" \
- -e "s:/usr/share/java/commons-logging.jar:$(java-pkg_getjar commons-logging commons-logging.jar):g" \
- -e "s:/usr/share/java/xml-apis-ext.jar:$(java-pkg_getjar xml-commons-external-1.3 xml-apis-ext.jar):g" \
- fop.properties || die
-}
-
-src_install() {
- java-pkg_newjar dist/${P}.jar ${PN}.jar
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild b/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild
new file mode 100644
index 000000000..759e03791
--- /dev/null
+++ b/dev-java/jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+JAVA_PKG_IUSE="examples source"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="jlatexmath plugin for dev-java/fop"
+HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
+SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
+
+LICENSE="GPL-2"
+SLOT="1"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+CDEPEND="dev-java/jlatexmath:1
+ dev-java/xmlgraphics-commons:1.5
+ >=dev-java/fop-0.9.5:0"
+DEPEND=">=virtual/jdk-1.5
+ ${CDEPEND}"
+RDEPEND=">=virtual/jre-1.5
+ ${CDEPEND}"
+
+EANT_BUILD_TARGET="buildJar"
+
+S="${WORKDIR}"
+
+src_prepare() {
+ epatch "${FILESDIR}/${P}-fixpaths.patch"
+ cp "${FILESDIR}/version.xml" "${S}" || die
+ echo "fop.jar=$(java-pkg_getjar fop fop.jar)
+xmlgraphics-commons.jar=$(java-pkg_getjar xmlgraphics-commons-1.5 xmlgraphics-commons.jar)
+jlatexmath.jar=$(java-pkg_getjar jlatexmath-1 jlatexmath.jar)" \
+ >>fop.properties || die
+}
+
+src_install() {
+ java-pkg_newjar dist/${P}.jar ${PN}.jar
+ use source && java-pkg_dosrc src/org
+ use examples && java-pkg_doexamples examples
+}
diff --git a/dev-java/jlatexmath/Manifest b/dev-java/jlatexmath/Manifest
index 22218fa56..6e3878792 100644
--- a/dev-java/jlatexmath/Manifest
+++ b/dev-java/jlatexmath/Manifest
@@ -1,2 +1 @@
-DIST jlatexmath-src-0.9.7.zip 1060786 SHA256 d348ab583359e81390627c8fa2d8d08c1d4ff33fb009c47d8314ea0cfebfe1ea SHA512 dc9a244fd8733a3b3c5dcd1f88a3c8e36ee8a46114d03b02508c3fb728878b03a8040c9dcf468a4ce297c792954b99f25db83e4dc7d4ede101ab09cb2af37eab WHIRLPOOL 8370e07d8013f1ab626c081615f0dcce7766fcfe7219403c88152d366ca6e9bb3c4ebc1afb17cc90ce77f1abd773051e9d8fc3a33232adc3b25310f14ded81e8
-DIST jlatexmath-src-1.0.0.zip 1061432 SHA256 bc8630c8506c333d4bb1e55c0724f0811d18d55664dc4dc1952211fd5560feea SHA512 022f8f05b7dc0906091cb2473aecaad70880a4cf8b18f61929b2714f0dafee1064c26186e576fb94eb3db01d8bfa7bcaa0a4dd185fcedb0913da5ee976615c5d WHIRLPOOL 3242d45c41e575996ff6c4208ebfd5f41eb58df21416384adad4e2b817c06a886d5fec182e41b41282616a4bcc4a698582a20c52409680beed7fa8b1c2f059c7
+DIST jlatexmath-src-1.0.2.zip 1074659 SHA256 470345426179197134aa7e61ee0251a1a87c06393482474c53893de2aa595cf4 SHA512 c91af6dd37c5b62058fda35c41b1d34bb8a0f4eea9b5e9a5b76054b8f72c09f049a08de9aa761208fe18a66ee77ff0812d267f7137d015a63e200cac28a32c48 WHIRLPOOL fc3c2b91d96fd707874481d871d020ebf1f65c4cdb1dea368067e3d94e6a49a94e7c1a2a26b1f94bdaea7b8c372e5564357df98310e643c202ea21dd48bcad00
diff --git a/dev-java/jlatexmath/jlatexmath-1.0.0.ebuild b/dev-java/jlatexmath/jlatexmath-1.0.0.ebuild
deleted file mode 100644
index 80245c71b..000000000
--- a/dev-java/jlatexmath/jlatexmath-1.0.0.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="A Java API to render LaTeX"
-SRC_URI="http://forge.scilab.org/index.php/p/${PN}/downloads/get/${PN}-src-${PV}.zip"
-HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-
-IUSE="doc examples source"
-DEPEND=">=virtual/jdk-1.5
- app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
-
-LICENSE="GPL-2"
-SLOT="1"
-KEYWORDS="~amd64 ~x86"
-
-EANT_BUILD_TARGET="buildJar"
-EANT_DOC_TARGET="doc"
-
-src_install() {
- java-pkg_newjar dist/${P}.jar ${PN}.jar
- use doc && java-pkg_dojavadoc doc
- use source && java-pkg_dosrc src/org
- use examples && java-pkg_doexamples examples
-}
diff --git a/dev-java/jlatexmath/jlatexmath-0.9.7.ebuild b/dev-java/jlatexmath/jlatexmath-1.0.2.ebuild
index ff19bded1..b6b597952 100644
--- a/dev-java/jlatexmath/jlatexmath-0.9.7.ebuild
+++ b/dev-java/jlatexmath/jlatexmath-1.0.2.ebuild
@@ -1,31 +1,31 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
-JAVA_PKG_IUSE="doc source"
+JAVA_PKG_IUSE="doc examples source"
inherit java-pkg-2 java-ant-2
DESCRIPTION="A Java API to render LaTeX"
-SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
HOMEPAGE="http://forge.scilab.org/index.php/p/jlatexmath"
-
-IUSE="doc examples source"
-DEPEND=">=virtual/jdk-1.5
- app-arch/unzip"
-RDEPEND=">=virtual/jre-1.5"
+SRC_URI="http://forge.scilab.org/upload/jlatexmath/files/${PN}-src-${PV}.zip"
LICENSE="GPL-2"
-SLOT="0"
+SLOT="1"
KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.5
+ app-arch/unzip"
+RDEPEND=">=virtual/jre-1.5"
EANT_BUILD_TARGET="buildJar"
EANT_DOC_TARGET="doc"
src_install() {
- java-pkg_newjar dist/${P}.jar ${PN}.jar
+ java-pkg_newjar dist/"${P}.jar" "${PN}.jar"
use doc && java-pkg_dojavadoc doc
use source && java-pkg_dosrc src/org
use examples && java-pkg_doexamples examples
diff --git a/dev-java/jogl/ChangeLog b/dev-java/jogl/ChangeLog
index 23d373902..cb34d4a31 100644
--- a/dev-java/jogl/ChangeLog
+++ b/dev-java/jogl/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> jogl-2.0_rc8-r1.ebuild,
+ metadata.xml:
+ Keyworded for ~x86
+
*jogl-2.0_rc8-r1 (03 Feb 2013)
03 Feb 2013; Guillaume Horel <guillaume.horel@gmail.com>
diff --git a/dev-java/jogl/jogl-2.0_rc8-r1.ebuild b/dev-java/jogl/jogl-2.0_rc8-r1.ebuild
index fb6d64e3a..2a98c2a8a 100644
--- a/dev-java/jogl/jogl-2.0_rc8-r1.ebuild
+++ b/dev-java/jogl/jogl-2.0_rc8-r1.ebuild
@@ -21,7 +21,7 @@ SRC_URI="http://jogamp.org/deployment/${MY_PV}/archive/Sources/${MY_P}.tar.7z"
LICENSE="BSD"
SLOT="2"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE="cg"
COMMON_DEP="
diff --git a/dev-java/jogl/metadata.xml b/dev-java/jogl/metadata.xml
index 248b6b7b7..d0ca5182c 100644
--- a/dev-java/jogl/metadata.xml
+++ b/dev-java/jogl/metadata.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>java</herd>
- <longdescription lang="en">
+ <herd>java</herd>
+ <longdescription lang="en">
JOGL provides Java with a Binding for the OpenGL® API (JSR-231), and is designed
to provide hardware-supported 3D graphics to applications written in Java.
</longdescription>
- <use>
- <flag name="cg">Enable NVidia Cg binding.</flag>
- </use>
+ <use>
+ <flag name="cg">Enable NVidia Cg binding.</flag>
+ </use>
</pkgmetadata>
diff --git a/dev-java/netcdf/Manifest b/dev-java/netcdf/Manifest
index 31af092c4..5133fdc93 100644
--- a/dev-java/netcdf/Manifest
+++ b/dev-java/netcdf/Manifest
@@ -1 +1 @@
-DIST ncSrc-4.2.zip 59857406 SHA256 1160c8e59efb9341e6b3ffa0988df45bd5df86de69a28821afe7a70c5be318f2 SHA512 9d6d165e0db784196238b4e599805c17618d02e952a4cf12e5f692de6ec135161367083d336e688a5f269af5f592103bd812a50fe617a5f722ed7cd6ec2f8097 WHIRLPOOL 067192ac3f435591b8d6f2d30ad6133f540656b6dae6e096c617c7134ca24186648848e57190210cdfac5f218a3aa3f05eb09086050986992c7bc3b6deb7bbc1
+DIST ncSrc-4.2.zip 59888846 SHA256 4440d82ea4c740b9f3df834c3cf22b62784ab2301a0db74729e50e877d8c7c76 SHA512 1cf22c55a43f53bbb573c6bcbc9e40b0020ed9d576c68a0d54639ca9892393735b25bfa0078fcb763c71d5d875fb1f315c6d580d6a859434d362693f6500d652 WHIRLPOOL 9d6717d58e54cbe4ffcefb529dd2023037f462c2ffef0880077f567a9e5ec6f171dd718e91f5e0b4b4f5ac95c709b5ec8ab27fda12fcf9f4cc7ca728353d9f7c
diff --git a/dev-java/scirenderer/Manifest b/dev-java/scirenderer/Manifest
index 832d2b4a8..6b5509527 100644
--- a/dev-java/scirenderer/Manifest
+++ b/dev-java/scirenderer/Manifest
@@ -1 +1 @@
-DIST scirenderer-1.0.5.tar.gz 111907 SHA256 237ddc9b3968a935d61114e830ea1ccfe09124e66f3292b65ff70ab7d257fc3d SHA512 bd18ff4f32123dfa002caef9b6326260dbe66885e4b94d9f20c6c021dda78407898c17dee16a5917b7a93f20044b0eeac1de7a52a945e269c72d5f64ddbc9458 WHIRLPOOL c4994a72b1a4792fdb9e39ed8c2d7e3a48719d1ad22825720ad2678127a8414842369cc0381fa4d019e4abfb755d38f27b2f62df35cd681538a68a7d24451d54
+DIST scirenderer-1.1.0.tar.gz 113929 SHA256 fb467bc1a887c6db324e02a8bb6a2379a845206b5e966793d440734a5ba4609c SHA512 b2f636b65517fd1c472d2eef4bf141f93b7782b1bcf7961f3b18994659ee9e4a4466ca1c63e8c782acdd7250b2f9a20d0140375a4e2e2108a98af1f696894b95 WHIRLPOOL 1a3f296821aba5d61404218ba249d878e45fe99cce605efc694e941a06a54043b40ba767837964d8b3668c7fac2d88c4c6fb66f5228788bc8a6b2613bc7d4fdf
diff --git a/dev-java/scirenderer/scirenderer-1.0.5.ebuild b/dev-java/scirenderer/scirenderer-1.1.0.ebuild
index cdc3a6e3d..c4d81942e 100644
--- a/dev-java/scirenderer/scirenderer-1.0.5.ebuild
+++ b/dev-java/scirenderer/scirenderer-1.1.0.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
JAVA_PKG_IUSE="doc source"
diff --git a/dev-java/xmlgraphics-commons/Manifest b/dev-java/xmlgraphics-commons/Manifest
new file mode 100644
index 000000000..0f77c12b4
--- /dev/null
+++ b/dev-java/xmlgraphics-commons/Manifest
@@ -0,0 +1 @@
+DIST xmlgraphics-commons-1.5-src.tar.gz 2597097 SHA256 f73322f1fafdcf5391d0411a377ac6c566e17536daf64b29f1370d6e718d0867 SHA512 af120dab18972f32e1b23f8bed1a9c519d7e2bcebd9c32fa77db61394f31a5821d909ddfe0e9a27cda7fcdf44966cf2576a94fc7c9af047f66c4081b8c35f398 WHIRLPOOL 043d57d08945713e3a14c28274551ac8cd76890f09b52ff1774f6201619792dddbcd827e55680a72b8bb711060ee6d6d270056846f53e35aaee2506052a52eb4
diff --git a/dev-java/xmlgraphics-commons/files/disable-iccprofile-test.patch b/dev-java/xmlgraphics-commons/files/disable-iccprofile-test.patch
new file mode 100644
index 000000000..6d226e6e1
--- /dev/null
+++ b/dev-java/xmlgraphics-commons/files/disable-iccprofile-test.patch
@@ -0,0 +1,38 @@
+Description: This test fails with openjdk-7 (and oracle java 7).
+ Skip for the time being until upstream resolve - see Bug.
+Author: James Page <james.page@ubuntu.com>
+Bug: https://issues.apache.org/bugzilla/show_bug.cgi?id=53328
+
+Index: xmlgraphics-commons/test/java/org/apache/xmlgraphics/image/loader/ImageLoaderTestCase.java
+===================================================================
+--- xmlgraphics-commons.orig/test/java/org/apache/xmlgraphics/image/loader/ImageLoaderTestCase.java 2012-05-30 17:12:37.000324000 +0100
++++ xmlgraphics-commons/test/java/org/apache/xmlgraphics/image/loader/ImageLoaderTestCase.java 2012-05-30 17:13:03.184417043 +0100
+@@ -159,28 +159,6 @@
+ sessionContext.checkAllStreamsClosed();
+ }
+
+- public void testICCProfiles() throws Exception {
+- MyImageSessionContext sessionContext = createImageSessionContext();
+- List/* <ICC_Profile> */profiles = new ArrayList();
+-
+- runReaders(profiles, sessionContext, "iccTest.png", "image/png",
+- ImageFlavor.RAW_PNG);
+- runReaders(profiles, sessionContext, "iccTest.jpg", "image/jpeg",
+- ImageFlavor.RAW_JPEG);
+-
+- ICC_Profile first = (ICC_Profile) profiles.get(0);
+- byte[] firstData = first.getData();
+- for (int i = 1; i < profiles.size(); i++) {
+- ICC_Profile icc = (ICC_Profile) profiles.get(i);
+- byte[] data = icc.getData();
+- assertEquals("Embedded ICC Profiles are not the same size!",
+- firstData.length, data.length);
+- for (int j = 0; j < firstData.length; j++) {
+- assertEquals("Embedded ICC Profiles differ at index " + j,
+- firstData[j], data[j]);
+- }
+- }
+- }
+
+ private void runReaders(List profiles, ImageSessionContext isc, String uri,
+ String mime, ImageFlavor rawFlavor) throws Exception {
diff --git a/sci-libs/csrosetta-pdbh/metadata.xml b/dev-java/xmlgraphics-commons/metadata.xml
index efb490d78..838c00a4a 100644
--- a/sci-libs/csrosetta-pdbh/metadata.xml
+++ b/dev-java/xmlgraphics-commons/metadata.xml
@@ -1,8 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
+<herd>java</herd>
</pkgmetadata>
diff --git a/dev-java/xmlgraphics-commons/xmlgraphics-commons-1.5.ebuild b/dev-java/xmlgraphics-commons/xmlgraphics-commons-1.5.ebuild
new file mode 100644
index 000000000..700233e7b
--- /dev/null
+++ b/dev-java/xmlgraphics-commons/xmlgraphics-commons-1.5.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-java/xmlgraphics-commons/xmlgraphics-commons-1.3.1.ebuild,v 1.7 2011/12/31 16:46:14 sera Exp $
+
+EAPI=4
+JAVA_PKG_IUSE="doc examples source test"
+VIRTUALX_REQUIRED="manual"
+VIRTUALX_COMMAND="eant"
+
+inherit java-pkg-2 java-ant-2 virtualx
+
+DESCRIPTION="A library of several reusable components used by Apache Batik and Apache FOP."
+HOMEPAGE="http://xmlgraphics.apache.org/commons/index.html"
+SRC_URI="mirror://apache/xmlgraphics/commons/source/${P}-src.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="1.5"
+KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos ~sparc-solaris ~x86-solaris"
+IUSE=""
+
+CDEPEND="dev-java/commons-io:1
+ >=dev-java/commons-logging-1:0"
+DEPEND=">=virtual/jdk-1.5
+ test? ( dev-java/ant-junit4 )
+ ${CDEPEND}"
+
+RDEPEND=">=virtual/jre-1.5
+ ${CDEPEND}"
+
+# TODO investigate producing .net libraries
+# strategies for non sun jdk's/jre's
+
+JAVA_ANT_IGNORE_SYSTEM_CLASSES="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+java_prepare() {
+ #see https://issues.apache.org/bugzilla/show_bug.cgi?id=53328
+ epatch "${FILESDIR}"/disable-iccprofile-test.patch
+ find "${S}" -name '*.jar' -print -delete || die
+ rm -v test/java/org/apache/xmlgraphics/java2d/ps/PSGraphics2DTestCase.java \
+ || die
+}
+
+EANT_GENTOO_CLASSPATH="commons-io-1,commons-logging"
+EANT_EXTRA_ARGS="-Djdk15.present=true"
+EANT_BUILD_TARGET="jar-main"
+EANT_DOC_TARGET="javadocs"
+
+src_test() {
+ java-pkg_jarfrom --into lib junit-4,commons-io-1
+ ANT_TASKS="ant-junit4" virtualmake -Djdk15.present=true junit
+}
+
+src_install(){
+ java-pkg_newjar build/"${P}".jar
+ use source && java-pkg_dosrc src/java/org
+ use doc && java-pkg_dojavadoc build/javadocs
+}
diff --git a/dev-lang/berkeley_upc/ChangeLog b/dev-lang/berkeley_upc/ChangeLog
new file mode 100644
index 000000000..cb902f129
--- /dev/null
+++ b/dev-lang/berkeley_upc/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for dev-lang/berkeley_upc
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*berkeley_upc-2.16.0 (17 Mar 2013)
+
+ 17 Mar 2013; Jauhien Piatlicki (jauhien) <piatlicki@gmail.com>
+ +berkeley_upc-2.16.0.ebuild, +metadata.xml:
+ ebuild for bug#462026
+
diff --git a/dev-lang/berkeley_upc/Manifest b/dev-lang/berkeley_upc/Manifest
new file mode 100644
index 000000000..31d78a44b
--- /dev/null
+++ b/dev-lang/berkeley_upc/Manifest
@@ -0,0 +1 @@
+DIST berkeley_upc-2.16.0.tar.gz 6459848 SHA256 0435bcfe82441dc8879b4d256f654525412eecb9e353b677a3e06e9318ed357e SHA512 e1df721ab8b63e998eaba1ce1d763a78a8c1b290b05e0d8f8168cc5bb99f98c6bdf6847a22cdbad31b3a204d5e699dbdc5add7c73cb0c51a812ee776cb1a085f WHIRLPOOL 928cb36ea094f417d1ed547a3d12eadc420abed23f2d883b7e8f42109b978a0e097adac11c6f6a0ba55ecddf52fc9d5c37ebb0c61ef190d7687d4ab76059a360
diff --git a/dev-lang/berkeley_upc/berkeley_upc-2.16.0.ebuild b/dev-lang/berkeley_upc/berkeley_upc-2.16.0.ebuild
new file mode 100644
index 000000000..19e12d340
--- /dev/null
+++ b/dev-lang/berkeley_upc/berkeley_upc-2.16.0.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="The Berkeley UPC Runtime/driver"
+HOMEPAGE="http://upc.lbl.gov/"
+SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
+LICENSE="BSD-4"
+
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="mpi mpi-compat pshm +segment-fast segment-large +single +sptr-packed
+ sptr-struct sptr-symmetric threads +udp"
+
+REQUIRED_USE="
+ ^^ ( segment-fast segment-large )
+ ^^ ( sptr-packed sptr-struct sptr-symmetric )"
+
+pkg_setup() {
+ elog "There is a lot of options for this package,"
+ elog "especially network conduits settings."
+ elog "You can set them using EXTRA_ECONF variable."
+ elog "To see full list of options visit ${HOMEPAGE}download/dist/INSTALL.TXT"
+}
+
+src_configure() {
+ ./configure \
+ --prefix="${EPREFIX}"/usr/libexec/${P} \
+ --mandir="${EPREFIX}"/usr/share/man/ \
+ --disable-aligned-segments \
+ --disable-auto-conduit-detect \
+ $(use_enable mpi) \
+ $(use_enable mpi-compat) \
+ $(use_enable pshm) \
+ $(use_enable segment-fast) \
+ $(use_enable segment-large) \
+ $(use_enable single smp) \
+ $(use_enable sptr-packed) \
+ $(use_enable sptr-struct) \
+ $(use_enable sptr-symmetric) \
+ $(use_enable threads par) \
+ $(use_enable udp) \
+ ${EXTRA_ECONF} || die
+}
+
+src_install() {
+ default
+ dodir /usr/bin
+ dosym ../libexec/${P}/bin/upc_trace /usr/bin/upc_trace
+ dosym ../libexec/${P}/bin/upcc /usr/bin/upcc
+ dosym ../libexec/${P}/bin/upcdecl /usr/bin/upcdecl
+ dosym ../libexec/${P}/bin/upcrun /usr/bin/upcrun
+}
diff --git a/dev-lang/berkeley_upc/metadata.xml b/dev-lang/berkeley_upc/metadata.xml
new file mode 100644
index 000000000..7da2d6d71
--- /dev/null
+++ b/dev-lang/berkeley_upc/metadata.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+
+<pkgmetadata>
+ <maintainer>
+ <email>piatlicki@gmail.com</email>
+ </maintainer>
+ <use>
+ <flag name="mpi-compat">Enable interoperability with MPI</flag>
+ <flag name="pshm">Build UPC Runtime/GASNet with Process-SHared Memory enabled</flag>
+ <flag name="segment-fast">
+ Select GASNet's FAST segments (default), for the fastest remote access with a possible
+ cost in max shared memory size
+ </flag>
+ <flag name="segment-large">
+ Select GASNet's LARGE segments, for the largest possible shared memory size, at a
+ possible cost in remote access time
+ </flag>
+ <flag name="single">Support running over smp loopback (no network)</flag>
+ <flag name="sptr-packed">Use the more efficient 'packed' shared pointer representation</flag>
+ <flag name="sptr-struct">Use the 'struct' shared pointer representation</flag>
+ <flag name="sptr-symmetric">Enable 'symmetric' pointer variant where available (64-bit smp and shmem)</flag>
+ <flag name="udp">Support running over UDP</flag>
+ </use>
+</pkgmetadata>
diff --git a/dev-lang/berkeley_upc_translator/ChangeLog b/dev-lang/berkeley_upc_translator/ChangeLog
new file mode 100644
index 000000000..b7e769de8
--- /dev/null
+++ b/dev-lang/berkeley_upc_translator/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for dev-lang/berkeley_upc_translator
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*berkeley_upc_translator-2.16.0 (19 Mar 2013)
+
+ 19 Mar 2013; Jauhien Piatlicki (jauhien) <piatlicki@gmail.com>
+ +berkeley_upc_translator-2.16.0.ebuild,
+ +files/berkeley_upc_translator-2.16.0-stackoverflow.patch, +metadata.xml:
+ ebuild for bug#462296, thanks to Paul H. Hargrove
+
diff --git a/dev-lang/berkeley_upc_translator/Manifest b/dev-lang/berkeley_upc_translator/Manifest
new file mode 100644
index 000000000..627b1f5c0
--- /dev/null
+++ b/dev-lang/berkeley_upc_translator/Manifest
@@ -0,0 +1 @@
+DIST berkeley_upc_translator-2.16.0.tar.gz 7255911 SHA256 72cc1933e481f6603cb74c7df3a4dfd09d89aaec61e3c93c8f3404e33c458149 SHA512 6ede727f6df661d844a6b71c41923edb4ba3db18a5fe4a67d42f6293d94ddcd3cac96af2c9cee7016a34dc126024921bfe1ba11b13766d2ccdb8935a4e3a8bc5 WHIRLPOOL 9694542b303eba32687839694d9fc16795276907ef45cf4e88ca6ae2cc76e7dd9d83e14bb9cfca866c035158abf5741b1e114dfb16cab3db0b727b0e23baebf3
diff --git a/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.16.0.ebuild b/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.16.0.ebuild
new file mode 100644
index 000000000..9112d6658
--- /dev/null
+++ b/dev-lang/berkeley_upc_translator/berkeley_upc_translator-2.16.0.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="The Berkeley UPC-to-C translator"
+HOMEPAGE="http://upc.lbl.gov/"
+SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz"
+LICENSE="BSD-4"
+
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+DEPEND="app-shells/tcsh"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-stackoverflow.patch
+}
+
+src_compile() {
+ emake -j1
+}
+
+src_install() {
+ emake install PREFIX="${D}/usr/libexec/${P}"
+}
diff --git a/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.16.0-stackoverflow.patch b/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.16.0-stackoverflow.patch
new file mode 100644
index 000000000..44c6a8e78
--- /dev/null
+++ b/dev-lang/berkeley_upc_translator/files/berkeley_upc_translator-2.16.0-stackoverflow.patch
@@ -0,0 +1,18 @@
+Author: Paul H. Hargrove
+See https://upc-bugs.lbl.gov/bugzilla/show_bug.cgi?id=3141
+--- open64/osprey1.0/gccfe/tree_symtab.h
++++ open64/osprey1.0/gccfe/tree_symtab.h
+@@ -45,7 +45,12 @@
+ #include <set>
+ #include <upc_symtab_utils.h>
+
+-#define MAX_PATH 500
++#include <limits>
++#ifdef PATH_MAX
++ #define MAX_PATH PATH_MAX
++#else
++ #define MAX_PATH 4096
++#endif
+
+ extern int Scope_level;
+ extern int For_scope;
diff --git a/sci-libs/libcmatrix/metadata.xml b/dev-lang/berkeley_upc_translator/metadata.xml
index 5ef07a39e..94a760560 100644
--- a/sci-libs/libcmatrix/metadata.xml
+++ b/dev-lang/berkeley_upc_translator/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+
<pkgmetadata>
- <herd>sci</herd>
<maintainer>
- <email>jlec@gentoo.org</email>
+ <email>piatlicki@gmail.com</email>
</maintainer>
</pkgmetadata>
diff --git a/dev-lang/julia/files/julia-nopatchelf.patch b/dev-lang/julia/files/julia-nopatchelf.patch
new file mode 100644
index 000000000..2ac5a80d4
--- /dev/null
+++ b/dev-lang/julia/files/julia-nopatchelf.patch
@@ -0,0 +1,14 @@
+diff -urN julia-9999-orig/deps/Makefile julia-9999/deps/Makefile
+--- julia-9999-orig/deps/Makefile 2013-04-01 19:43:13.868529747 -0400
++++ julia-9999/deps/Makefile 2013-04-01 19:45:35.261543816 -0400
+@@ -37,10 +37,6 @@
+ endif
+ endif
+
+-ifeq ($(OS), Linux)
+-STAGE1_DEPS += patchelf
+-endif
+-
+ WGET = $(abspath .)/jldownload
+ WGET_DASH_O = $(WGET)
+
diff --git a/dev-lang/julia/julia-9999.ebuild b/dev-lang/julia/julia-9999.ebuild
index c6f774e60..c0668705b 100644
--- a/dev-lang/julia/julia-9999.ebuild
+++ b/dev-lang/julia/julia-9999.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
EGIT_REPO_URI="git://github.com/JuliaLang/julia.git"
@@ -15,7 +15,7 @@ SRC_URI=""
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="doc emacs notebook"
+IUSE="doc emacs"
RDEPEND=">=sys-devel/llvm-3.0
sys-libs/readline
@@ -24,18 +24,19 @@ RDEPEND=">=sys-devel/llvm-3.0
sci-libs/arpack
sci-libs/fftw
dev-libs/gmp
+ >=dev-libs/double-conversion-1.1.1
>=sys-libs/libunwind-1.1
dev-libs/libpcre
sci-mathematics/glpk
sys-libs/zlib
virtual/blas
- virtual/lapack
- notebook? ( www-servers/lighttpd )"
+ virtual/lapack"
DEPEND="${RDEPEND}
virtual/pkgconfig"
src_prepare() {
+ epatch "${FILESDIR}/julia-nopatchelf.patch"
# Folder /usr/include/suitesparse does not exists, everything should be in /usr/include
sed -e "s|SUITESPARSE_INC = -I /usr/include/suitesparse|SUITESPARSE_INC = |g" \
-i deps/Makefile
@@ -57,32 +58,23 @@ src_prepare() {
}
src_compile() {
- emake -j1
+ emake
use doc && emake -C doc html
- if use notebook; then
- emake -C ui/webserver
- sed -e "s|etc|/share/julia/etc|" \
- -i usr/bin/launch-julia-webserver ||die
- fi
use emacs && elisp-compile contrib/julia-mode.el
}
src_install() {
- emake -j1 install PREFIX="${D}/usr"
+ emake install PREFIX="${D}/usr"
cat > 99julia <<-EOF
LDPATH=/usr/$(get_libdir)/julia
EOF
doenvd 99julia
- if use notebook; then
- cp -R ui/website "${D}/usr/share/julia"
- insinto /usr/share/julia/etc
- doins deps/lighttpd.conf
- fi
+
if use emacs; then
elisp-install "${PN}" contrib/julia-mode.el
elisp-site-file-install "${FILESDIR}"/63julia-gentoo.el
fi
- use doc && dodoc -r doc/_build/html
+ use doc && dohtml -r doc/_build/html/
dodoc README.md
}
diff --git a/dev-lang/julia/metadata.xml b/dev-lang/julia/metadata.xml
index 03a860095..afa3d5374 100644
--- a/dev-lang/julia/metadata.xml
+++ b/dev-lang/julia/metadata.xml
@@ -1,10 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>guillaume.horel@gmail.com</email>
- <name>Guillaume Horel</name>
- </maintainer>
+ <herd>python</herd>
<longdescription>
Julia is a high-level, high-performance dynamic programming language for
technical computing, with syntax that is familiar to users of other
@@ -17,7 +14,4 @@
around defining functions, and overloading them for different combinations
of argument types (which can also be user-defined).
</longdescription>
-<use>
- <flag name="notebook">Install requirements for the web notebook based on <pkg>www-servers/lighttpd</pkg></flag>
-</use>
</pkgmetadata>
diff --git a/dev-lang/vtune/ChangeLog b/dev-lang/vtune/ChangeLog
index 11717bf9c..6a45d9737 100644
--- a/dev-lang/vtune/ChangeLog
+++ b/dev-lang/vtune/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for dev-lang/vtune
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*vtune-13.1.4.270817 (03 Mar 2013)
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> -vtune-11.0.7.221625.ebuild,
+ +vtune-13.1.4.270817.ebuild, metadata.xml:
+ Version Bump; move to parallel studio tarball; add missing multilib.eclass
+
12 May 2012; Alexey Shvetsov <alexxy@gentoo.org> +metadata.xml,
vtune-11.0.7.221625.ebuild:
[dev-lang/vtune] Fix ebuild eapi parsing and other minor issues
diff --git a/dev-lang/vtune/Manifest b/dev-lang/vtune/Manifest
index beb7fa30d..07814eda6 100644
--- a/dev-lang/vtune/Manifest
+++ b/dev-lang/vtune/Manifest
@@ -1 +1,3 @@
-DIST vtune_amplifier_xe_2011_update8.tar.gz 189819836 SHA256 bd4ed8d3e074c83026ec6fae0f251c3138c9d6c30a83f800f46ed5fc1e68443f SHA512 4719496b985273d3863d8249e599eff66949578a2e14adbb255aa23475004699e9f44560a110f8e36ccb5a70149e33ff720c6e0e3c8b8b8b2bea58ff74876c21 WHIRLPOOL 345dd2f28985770041f417a584da2f2bf322ad33e2d2d487122a9e4c9cd8442cdef0a87a6e4c3e9c22809be125eef2fee124cbb2deb231ad74486084c9f13c78
+DIST parallel_studio_xe_2013_update2.tgz 2152945149 SHA256 e8ddf6141f7d84c1f242891fabe0882c40269c358c0b946fee22ee6caa37121c SHA512 633370f58bd9fc14140912d5b3dd251ca4819a926b004a8053f92c83de6f9fdfdad192b425c5224d8b5aee47042a1a99d49628e6e2bb53e623ae429eefcfaac4 WHIRLPOOL 5b4a7c0c9cab758885ccffab25f1aaf64a6f5576d02df81a4797a2b9ae2151efb5e564e43397a2b61040d4af66024107a5a9c537982d3e17723655414dcba166
+DIST parallel_studio_xe_2013_update2_ia32.tgz 1190613262 SHA256 13063ea9c47c781ea8f368566d328434351002e7321b2021b5f04ff741a5d55f SHA512 1488a1b8c9b84881041ccf42d9f856d44aa0654ce3171b0f92114a3408d8cb1f1a18a6d488db6bbfd7322d5a230748612b53378b6ac01b8b7b3e66b3b8f94333 WHIRLPOOL f7d2b307d2f4e226004ddfcf073db087fff6d68e94f849e85350dc18894db884b62362bb3929076fdd531e29f5c49e2cd94eba8685b13fc52e293226516d909d
+DIST parallel_studio_xe_2013_update2_intel64.tgz 1488277925 SHA256 6136774de466de19f4024eeb5a8176ffbf559143b048fecc83848c27008361d6 SHA512 8260ab223d9a959089ae66c8948d90ce119cceeb719ef18c1a9d258ccd77e9b6a67af1a3e203d96a1c3c774def9a6fc302c126001072b7c5aa2bb3cdc68bc4dd WHIRLPOOL 006dc0e925c8265abf174682cd54f2c2fc4c4f1e059e045407d523b3e3b659cadc47da005126236a8b01b882fd0b4dfa7dadce0c52f640d5c0ada8122a9d6d08
diff --git a/dev-lang/vtune/metadata.xml b/dev-lang/vtune/metadata.xml
index 61737103f..118746197 100644
--- a/dev-lang/vtune/metadata.xml
+++ b/dev-lang/vtune/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>nbigaouette@gmail.com</email>
- <name>Nicolas Bigaouette</name>
- </maintainer>
+ <maintainer>
+ <email>nbigaouette@gmail.com</email>
+ <name>Nicolas Bigaouette</name>
+ </maintainer>
</pkgmetadata>
diff --git a/dev-lang/vtune/vtune-11.0.7.221625.ebuild b/dev-lang/vtune/vtune-11.0.7.221625.ebuild
deleted file mode 100644
index 594a1f4cf..000000000
--- a/dev-lang/vtune/vtune-11.0.7.221625.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-RESTRICT="primaryuri"
-
-INTEL_DPN=vtune_amplifier_xe
-INTEL_DID=2526
-INTEL_DPV=2011_update8
-INTEL_SUBDIR=vtune_amplifier_xe
-
-inherit intel-sdp
-
-DESCRIPTION="Intel VTune Amplifier XE"
-HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
-SRC_URI="http://registrationcenter-download.intel.com/akdlm/irc_nas/${INTEL_DID}/${INTEL_DPN}_${INTEL_DPV}.tar.gz"
-
-IUSE=""
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-QA_PREBUILT="
- ${INTEL_SDP_DIR}/bin32/*
- ${INTEL_SDP_DIR}/bin64/*
- ${INTEL_SDP_DIR}/lib32/*
- ${INTEL_SDP_DIR}/lib64/*"
-QA_PRESTRIPPED="
- ${INTEL_SDP_DIR}/bin32/*
- ${INTEL_SDP_DIR}/bin64/*
- ${INTEL_SDP_DIR}/lib32/*
- ${INTEL_SDP_DIR}/lib64/*"
-
-INTEL_BIN_RPMS="vtune-amplifier-xe-cli vtune-amplifier-xe-gui"
-INTEL_DAT_RPMS="vtune-amplifier-xe-sep vtune-amplifier-xe-pwr vtune-amplifier-xe-cli-common vtune-amplifier-xe-common vtune-amplifier-xe-doc vtune-amplifier-xe-gui-common"
-INTEL_RPMS_DIRS="rpm CLI_install/rpm"
-
-create_bin_symlink() {
- _libdir=$(get_libdir)
- _arch=${_libdir/lib/}
- dosym /${INTEL_SDP_DIR}/bin${_arch}/${1} /usr/bin/
-}
-
-src_install() {
- intel-sdp_src_install
-
- # Create symbolic links
- create_bin_symlink amplxe-gui
- create_bin_symlink amplxe-cl
- create_bin_symlink amplxe-configurator
- create_bin_symlink amplxe-feedback
- create_bin_symlink amplxe-runsa
- create_bin_symlink amplxe-runss
-
- # Create desktop file
- insinto /usr/share/pixmaps/
- newins "${D}/${INTEL_SDP_DIR}/documentation/en/help/GUID-A894E299-C7E2-4635-AD52-D98A09736EC8-low.jpg" vtune.jpg
- dodir /usr/share/applications
- echo "[Desktop Entry]
-Encoding=UTF-8
-Name=VTune Amplifier XE
-GenericName=VTune Amplifier XE
-Comment=VTune Amplifier XE
-Type=Application
-Exec=amplxe-gui
-Icon=vtune
-Categories=Development;Debugger;" > ${D}/usr/share/applications/vtune.desktop || die "Can't create desktop file!"
-}
diff --git a/dev-lang/vtune/vtune-13.1.4.270817.ebuild b/dev-lang/vtune/vtune-13.1.4.270817.ebuild
new file mode 100644
index 000000000..4a1e08952
--- /dev/null
+++ b/dev-lang/vtune/vtune-13.1.4.270817.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+INTEL_DPN=parallel_studio_xe
+INTEL_DID=2987
+INTEL_DPV=2013_update2
+INTEL_SUBDIR=vtune_amplifier_xe
+
+inherit intel-sdp multilib
+
+DESCRIPTION="Intel VTune Amplifier XE"
+HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/"
+
+IUSE=""
+KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+INTEL_BIN_RPMS="vtune-amplifier-xe-gui"
+INTEL_DAT_RPMS="vtune-amplifier-xe-gui-common"
+#INTEL_RPMS_DIRS="rpm CLI_install/rpm"
+
+create_bin_symlink() {
+ _libdir=$(get_libdir)
+ _arch=${_libdir/lib/}
+ dosym /${INTEL_SDP_DIR}/bin${_arch}/${1} /opt/bin/${1}
+}
+
+src_install() {
+ intel-sdp_src_install
+
+ # Create symbolic links
+ create_bin_symlink amplxe-gui
+ create_bin_symlink amplxe-configurator
+
+ make_desktop_entry amplxe-gui "VTune Amplifier XE" "" "Development;Debugger"
+}
diff --git a/dev-libs/double-conversion/ChangeLog b/dev-libs/double-conversion/ChangeLog
index f18cefbf7..72834ac59 100644
--- a/dev-libs/double-conversion/ChangeLog
+++ b/dev-libs/double-conversion/ChangeLog
@@ -1,7 +1,15 @@
# ChangeLog for dev-libs/double-conversion
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*double-conversion-1.1.1 (02 Apr 2013)
+
+ 02 Apr 2013; Guillaume Horel <guillaume.horel@gmail.com>
+ -double-conversion-1.1.ebuild, +double-conversion-1.1.1.ebuild,
+ +files/double-conversion-1.1.1-scons.patch,
+ -files/double-conversion-1.1-scons.patch:
+ Version bump and move header files into subdirectory
+
*double-conversion-1.1 (11 Jul 2012)
11 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org>
diff --git a/dev-libs/double-conversion/Manifest b/dev-libs/double-conversion/Manifest
index 187ca624c..26009ce29 100644
--- a/dev-libs/double-conversion/Manifest
+++ b/dev-libs/double-conversion/Manifest
@@ -1 +1 @@
-DIST double-conversion-1.1.tar.gz 7009789 SHA256 addee31d11350e4dde2b19c749eda648cb0ab38a68b0dd0d0a45dc49c7346fe7 SHA512 78d66fe6f1b31bccbfda916af3ab4cf292a7b4ed4ff40a83de600df1860fceb0f20cf340a964f61e57ecf03e350defa7023febbbc27ae29b49ed7b4988011304 WHIRLPOOL f4c1de563056f4c4b3b3abeceb79a42a16d2dbb05afe22c15243207b8d6ad0af10a01507c762365e518cc7119d7b203d45384fd99b216d804965de1e8ae842d3
+DIST double-conversion-1.1.1.tar.gz 7012946 SHA256 e1cabb73fd69e74f145aea91100cde483aef8b79dc730fcda0a34466730d4d1d SHA512 e116196eb60077565050995b060049747a3c72e743eea21c6c9fb68414adc533d456d19e1ca241f08895cca97a38511477bdc7d2e0cae38d149c83cb9d6896ad WHIRLPOOL d69604fbb6e1b5cac8d4dd0f8cf0af4621e32548e9e5061dcb843067a3f821c6f52e918e3e367988076b9ccf0be0ab68107cc6a21b02f4de424a1d98b399fc33
diff --git a/dev-libs/double-conversion/double-conversion-1.1.ebuild b/dev-libs/double-conversion/double-conversion-1.1.1.ebuild
index 7649df227..870187fa7 100644
--- a/dev-libs/double-conversion/double-conversion-1.1.ebuild
+++ b/dev-libs/double-conversion/double-conversion-1.1.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
inherit scons-utils eutils
@@ -40,7 +40,7 @@ src_test() {
src_install() {
dolib.so ${LIBNAME}.so
use static-libs && dolib.a ${LIBNAME}.a
- insinto /usr/include
- doins src/double-conversion*h
+ insinto /usr/include/double-conversion
+ doins src/double-conversion.h src/utils.h
dodoc README Changelog AUTHORS
}
diff --git a/dev-libs/double-conversion/files/double-conversion-1.1-scons.patch b/dev-libs/double-conversion/files/double-conversion-1.1.1-scons.patch
index eea519f5f..eea519f5f 100644
--- a/dev-libs/double-conversion/files/double-conversion-1.1-scons.patch
+++ b/dev-libs/double-conversion/files/double-conversion-1.1.1-scons.patch
diff --git a/dev-libs/fortrancl/ChangeLog b/dev-libs/fortrancl/ChangeLog
new file mode 100644
index 000000000..1fe7bbc2b
--- /dev/null
+++ b/dev-libs/fortrancl/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for dev-libs/fortrancl
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> fortrancl-0.1_alpha3.ebuild,
+ metadata.xml:
+ Clean whitespace errors
+
diff --git a/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild b/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild
index 09ebd9338..06a80b920 100644
--- a/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild
+++ b/dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild
@@ -1,8 +1,9 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=4
+
AUTOTOOLS_AUTORECONF=1
inherit autotools-utils fortran-2
@@ -28,7 +29,7 @@ DOCS=( AUTHORS ChangeLog README )
PATCHES=( "${FILESDIR}"/${P}-gentoo.patch )
src_install() {
- autotools-utils_src_install
+ autotools-utils_src_install
if use examples ; then
insinto /usr/share/doc/${PF}/examples
doins examples/*.{f90,cl}
diff --git a/dev-libs/fortrancl/metadata.xml b/dev-libs/fortrancl/metadata.xml
index 626f07372..399d32c0c 100644
--- a/dev-libs/fortrancl/metadata.xml
+++ b/dev-libs/fortrancl/metadata.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci</herd>
- <maintainer>
- <email>xarthisius@gentoo.org</email>
- <name>Kacper Kowalik</name>
- </maintainer>
- <longdescription>
+ <herd>sci</herd>
+ <maintainer>
+ <email>xarthisius@gentoo.org</email>
+ <name>Kacper Kowalik</name>
+ </maintainer>
+ <longdescription>
FortranCL is an OpenCL interface for Fortran 90. It allows programmers to call
the OpenCL parallel programming framework directly from Fortran, so developers
can accelerate their Fortran code using graphical processing units (GPU) and
diff --git a/dev-libs/libpfm/ChangeLog b/dev-libs/libpfm/ChangeLog
new file mode 100644
index 000000000..eab15dd01
--- /dev/null
+++ b/dev-libs/libpfm/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for dev-libs/libpfm
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 28 Feb 2013; Alexey Shvetsov <alexxy@gentoo.org> libpfm-4.3.0.ebuild:
+ Add ~x86
+
+*libpfm-4.3.0 (28 Feb 2013)
+
+ 28 Feb 2013; Alexey Shvetsov <alexxy@gentoo.org> +libpfm-4.3.0.ebuild,
+ +metadata.xml:
+ Initial import
diff --git a/dev-libs/libpfm/Manifest b/dev-libs/libpfm/Manifest
new file mode 100644
index 000000000..d84d1e79c
--- /dev/null
+++ b/dev-libs/libpfm/Manifest
@@ -0,0 +1 @@
+DIST libpfm-4.3.0.tar.gz 581976 SHA256 a23eb9affbff279e13563a39317c0ad71c4de28908d4243c8bc109138430cc3b SHA512 556bc1e4e2bcd5672dbf083f2d726c3f94a2434791a8085da28137d763aa3c1fdd45e947b11d467ca6dc131c7f7141eaf3ca5397d8fd260f0c8c81359adf97c8 WHIRLPOOL 5cd0dd88f8068617025fa408798b9fe7db6cc0a2e5d2b5b0522839f7579b7304a93af1c7a24971f848e330e1ff216c7f9568275203156c262ab06b2191b878c2
diff --git a/dev-libs/libpfm/libpfm-4.3.0.ebuild b/dev-libs/libpfm/libpfm-4.3.0.ebuild
new file mode 100644
index 000000000..7e02cc7b3
--- /dev/null
+++ b/dev-libs/libpfm/libpfm-4.3.0.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit multilib toolchain-funcs
+
+DESCRIPTION="Hardware-based performance monitoring interface for Linux"
+HOMEPAGE="http://perfmon2.sourceforge.net"
+SRC_URI="mirror://sourceforge/perfmon2/${PN}4/${P}.tar.gz"
+
+LICENSE="GPL-2 MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ sed -e "s:SLDFLAGS=:SLDFLAGS=\$(LDFLAGS) :g" \
+ -i lib/Makefile || die
+ sed -e "s:LIBDIR=\$(PREFIX)/lib:LIBDIR=\$(PREFIX)/$(get_libdir):g" \
+ -i config.mk || die
+}
+
+src_compile() {
+ emake CC=$(tc-getCC)
+}
+
+src_install() {
+ emake DESTDIR="${D}" LDCONFIG=true PREFIX="${EPREFIX}/usr" install
+ use static-libs || find "${ED}" -name '*.a' -exec rm -f '{}' +
+}
diff --git a/dev-libs/libpfm/metadata.xml b/dev-libs/libpfm/metadata.xml
new file mode 100644
index 000000000..fe317282e
--- /dev/null
+++ b/dev-libs/libpfm/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</herd>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-libs/mathjax/ChangeLog b/dev-libs/mathjax/ChangeLog
deleted file mode 100644
index ca20ec9ab..000000000
--- a/dev-libs/mathjax/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# ChangeLog for dev-libs/mathjax
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*mathjax-2.0 (29 Jun 2012)
-
- 29 Jun 2012; Sebastien Fabbro <fabbros@gentoo.org> +mathjax-2.0.ebuild,
- +metadata.xml:
- dev-libs/mathjax: Initial import
-
diff --git a/dev-libs/mathjax/Manifest b/dev-libs/mathjax/Manifest
deleted file mode 100644
index f05d81e8b..000000000
--- a/dev-libs/mathjax/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mathjax-2.0.tar.gz 9456567 RMD160 ef3c40c5a11211488d7c93f4d258b7e07e418ac4 SHA1 d64e377da82c00c7bb4ee5be152875f4c1f0d9c9 SHA256 7cab646dfb9a60970a3b16809b5532cae5cc3155b504e52bbd8870d2dabfac87 SHA512 b74213eb9e84a970a4c7d90921a3eade259c3dcd7392e4bd2cfa95951c82c4c9a51ad629492ea5db1c7fbc7adb4065ff51d5fa3294ec8411b68eeff0a13da8cf WHIRLPOOL c21be9cb8556fffd327ea78e9018c7326f0fe13f74994a15fd3f51213199a879459f6a02ac8d4c668d441abc63c8c5902835cce2f0d0d5b6d6cc71abad100ee9
diff --git a/dev-libs/mathjax/mathjax-2.0.ebuild b/dev-libs/mathjax/mathjax-2.0.ebuild
deleted file mode 100644
index 14e5e5afd..000000000
--- a/dev-libs/mathjax/mathjax-2.0.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-DESCRIPTION="JavaScript display engine for LaTeX, MathML and AsciiMath"
-HOMEPAGE="http://www.mathjax.org/"
-SRC_URI="https://github.com/mathjax/MathJax/tarball/v${PV} -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-
-DEPEND=""
-RDEPEND=""
-
-src_unpack() {
- unpack ${A} && mv ${PN}-MathJax-* ${P}
-}
-
-src_install() {
- find . -name .gitignore -delete
- dodoc README*
- use doc && dohtml -r docs/html/*
- if use examples; then
- insinto /usr/share/doc/${PF}/examples
- doins -r test/*
- fi
- rm -rf test docs LICENSE README*
- #local installdir=/var/www/${PN}
- local installdir=/usr/share/${PN}
- insinto ${installdir}
- doins -r *
- # web server config file - should we really do this?
- cat > MathJax.conf <<-EOF
- Alias /MathJax/ ${EPREFIX}${installdir}/
- Alias /mathjax/ ${EPREFIX}${installdir}/
-
- <Directory ${EPREFIX}${installdir}>
- Options None
- AllowOverride None
- Order allow,deny
- Allow from all
- </Directory>
- EOF
- insinto /etc/httpd/conf.d
- doins MathJax.conf
-}
diff --git a/dev-libs/mathjax/metadata.xml b/dev-libs/mathjax/metadata.xml
deleted file mode 100644
index 0544fc366..000000000
--- a/dev-libs/mathjax/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<longdescription lang='en'>
- MathJax is an open-source JavaScript display engine for LaTeX and
- MathML that works in all modern browsers. It was designed with the
- goal of consolidating the recent advances in web technologies into a
- single, definitive, math-on-the-web platform supporting the major
- browsers and operating systems. It requires no setup on the part of
- the user (no plugins to downlaod or software to install), so the
- page author can write web documents that include mathematics and be
- confident that users will be able to view it naturally and
- easily. One simply includes MathJax and some mathematics in a web
- page, and MathJax does the rest.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-libs/papi/ChangeLog b/dev-libs/papi/ChangeLog
new file mode 100644
index 000000000..4ea86d2ce
--- /dev/null
+++ b/dev-libs/papi/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for dev-libs/papi
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*papi-5.1.0.2 (28 Feb 2013)
+
+ 28 Feb 2013; Alexey Shvetsov <alexxy@gentoo.org> +metadata.xml,
+ +papi-5.1.0.2.ebuild:
+ Initial import
diff --git a/dev-libs/papi/Manifest b/dev-libs/papi/Manifest
new file mode 100644
index 000000000..2c2064a83
--- /dev/null
+++ b/dev-libs/papi/Manifest
@@ -0,0 +1 @@
+DIST papi-5.1.0.2.tar.gz 3781062 SHA256 141fd3dbeb32120ba8ca5f6a64250c22167b5224457f8ea1c3f28c8774468a1c SHA512 c52a762ba5492c25fde284f86999fdbe38007da73ee09949d15c392935bd03004304a1194e331032961d370247c3b6c49c62504b0fce42985fd8fcf6cc97702f WHIRLPOOL 58642c1f49f5f554553245cca38d6f034dbe4981efffecf32fadff468e07670b98618c1a793980dfa6194a55dc7d9668efd9c0eb4bfed899504cadaa64968aad
diff --git a/dev-libs/papi/metadata.xml b/dev-libs/papi/metadata.xml
new file mode 100644
index 000000000..fe317282e
--- /dev/null
+++ b/dev-libs/papi/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</herd>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-libs/papi/papi-5.1.0.2.ebuild b/dev-libs/papi/papi-5.1.0.2.ebuild
new file mode 100644
index 000000000..56fab5adf
--- /dev/null
+++ b/dev-libs/papi/papi-5.1.0.2.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit versionator
+
+DESCRIPTION="Performance Application Programming Interface"
+HOMEPAGE="http://icl.cs.utk.edu/papi/index.html"
+SRC_URI="http://icl.cs.utk.edu/projects/papi/downloads/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+ dev-libs/libpfm[static-libs]
+ "
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}-$(get_version_component_range 1-3)/src"
+
+src_configure() {
+ econf \
+ --with-perf-events \
+ --with-pfm-prefix="${EPREFIX}/usr" \
+ $(use_with static-libs)
+}
diff --git a/dev-ml/lacaml/ChangeLog b/dev-ml/lacaml/ChangeLog
index d9eb022ae..d66dc0b54 100644
--- a/dev-ml/lacaml/ChangeLog
+++ b/dev-ml/lacaml/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-ml/lacaml
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 22 Feb 2013; Justin Lecher <jlec@gentoo.org> lacaml-7.0.3.ebuild,
+ metadata.xml:
+ Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
+
*lacaml-7.0.3 (28 Jul 2012)
28 Jul 2012; Guillaume Horel <guillaume.horel@gmail.com>
diff --git a/dev-ml/lacaml/lacaml-7.0.3.ebuild b/dev-ml/lacaml/lacaml-7.0.3.ebuild
index ad9fbd152..1b6d6f541 100644
--- a/dev-ml/lacaml/lacaml-7.0.3.ebuild
+++ b/dev-ml/lacaml/lacaml-7.0.3.ebuild
@@ -1,11 +1,12 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=4
OASIS_BUILD_DOCS=1
-inherit oasis
+
+inherit oasis toolchain-funcs
DESCRIPTION="BLAS/LAPACK interface for OCaml"
HOMEPAGE="http://forge.ocamlcore.org/projects/lacaml"
@@ -16,7 +17,8 @@ SLOT="0"
KEYWORDS="~x86"
IUSE=""
-RDEPEND="virtual/blas
+RDEPEND="
+ virtual/blas
virtual/lapack"
DEPEND="${DEPEND}
virtual/pkgconfig"
@@ -27,10 +29,10 @@ src_prepare() {
if use doc; then
cp "${FILESDIR}/API.odocl" . || die
fi
- cclib="$(pkg-config --libs blas lapack)"
+ cclib="$($(tc-getPKG_CONFIG) --libs blas lapack)"
cclib="[$(echo $cclib|sed -e 's/\(-[a-z0-9]*\) /\"\1\"\;/g' -e \
's/\(-[a-z0-9]*\)$/\"\1\"/')]"
sed -i "s/cclib = \[\]/cclib = ${cclib}/" setup.conf
#would like to do the below, but doesn't work from ebuild
- #oasis_configure_opts="--override conf_cclib $(pkg-config --libs blas lapack)"
+ #oasis_configure_opts="--override conf_cclib $($(tc-getPKG_CONFIG) --libs blas lapack)"
}
diff --git a/dev-ml/lacaml/metadata.xml b/dev-ml/lacaml/metadata.xml
index 8925df672..e0b7a097d 100644
--- a/dev-ml/lacaml/metadata.xml
+++ b/dev-ml/lacaml/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci</herd>
-<longdescription lang='en'>
+ <herd>sci</herd>
+ <longdescription lang="en">
BLAS/LAPACK-interface for OCaml
</longdescription>
</pkgmetadata>
diff --git a/dev-ml/zarith/ChangeLog b/dev-ml/zarith/ChangeLog
index 51d9f4486..aab4931c7 100644
--- a/dev-ml/zarith/ChangeLog
+++ b/dev-ml/zarith/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> zarith-1.1.ebuild, metadata.xml:
+ Clean wrong space and blank lines; move EAPI=5
+
14 Jan 2013; J.-C. Demay <jcdemay@gmail.com>
+zarith-1.1.ebuild:
initial commit
diff --git a/dev-ml/zarith/Manifest b/dev-ml/zarith/Manifest
index 2e431650c..5ba03d9d8 100644
--- a/dev-ml/zarith/Manifest
+++ b/dev-ml/zarith/Manifest
@@ -1,4 +1 @@
DIST zarith-1.1.tgz 68383 SHA256 a0ba322c8d4f5bffa43f1c571e839baa0c7b155b67630bbd8481df21eb636b6e SHA512 60f36282eb5721df164437a0b24f36b601639914b4369ed0b9ca089fda1e75191163c1c57a3890f6f9c92c64eb99f9092f045822223c448298eccf9baed535e5 WHIRLPOOL 5671caa5f942084215d52f691257fb40229607f6394ad1a1e4c932df3cf3c0bcf598caf72dc16a23c849e2bba4e9caaad659a186475ea0173b78fad6799bd859
-EBUILD zarith-1.1.ebuild 996 SHA256 8870a7c4d815a475711cbd0e7ab752a707cab028642c20fa1f56296db60d84f9 SHA512 71c6b10abf237818acbb87b379496d6da96247b11717f57a8a8f0b9a174d4f943469e7972b8cfec0e0014897fe54aea2422ba29886fa6ec53e16a1a4d79c9ede WHIRLPOOL dfb796f709914ad9b9f7dc24ee438f30b9dd8fff610010351d41f3d4c95ad67d725741011c98240ca30232a97064dae313761a16887f2d77b1b691285bea4508
-MISC ChangeLog 201 SHA256 9f3fca09e091ca62ee913a3a31991b1619e6cd359be9b8fec854c789a662b2bc SHA512 860a0454dd8b97d9cf700bfd287f9708c4b8451dc4f5f09b8fc39cb6576e4129efdde0d6a9ef3695409b980e30e55c668cb07273336682d72e996f17bba22d6b WHIRLPOOL cceda1002b2bc2fcf458fe0c5f3f27eb8c184bc718fcfa3b6c7244d0691d92d5ebe306f7dfe9f19385a2ee08e6c56d79dc17396727ab2cd1528307e9412edbca
-MISC metadata.xml 576 SHA256 f2e3b72798b53b5cc8de7f84bb15a4f936b202798dff0924a8dc3153fc02eba3 SHA512 fabad704c895e72ced7561f1e5db01869f3b5b7ecca6d96d3a1474e7febad1170a8ad9087346aa8caf8741a5cd719290567581297ef452cb1eb94f706cb14e6e WHIRLPOOL 15466f22d6b3f39bc2c294a642dccc215a34c84325443b385a9e4aeccef0e8a178b389ce76380769edd55992d6e665b8f440236a132141b85a8885d26d2de108
diff --git a/dev-ml/zarith/metadata.xml b/dev-ml/zarith/metadata.xml
index d2e969145..e75004328 100644
--- a/dev-ml/zarith/metadata.xml
+++ b/dev-ml/zarith/metadata.xml
@@ -1,17 +1,17 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci</herd>
- <longdescription>
+ <herd>sci</herd>
+ <longdescription>
The Zarith library implements arithmetic and logical operations over
arbitrary-precision integers. It uses GMP to efficiently implement
arithmetic over big integers. Small integers are represented as Caml
unboxed integers, for speed and space economy.
</longdescription>
- <maintainer>
- <email>sci@gentoo.org</email>
- </maintainer>
- <use>
- <flag name="ocamlopt">?ocamlopt?</flag>
- </use>
+ <maintainer>
+ <email>sci@gentoo.org</email>
+ </maintainer>
+ <use>
+ <flag name="ocamlopt">?ocamlopt?</flag>
+ </use>
</pkgmetadata>
diff --git a/dev-ml/zarith/zarith-1.1.ebuild b/dev-ml/zarith/zarith-1.1.ebuild
index 795378fb7..61220fefe 100644
--- a/dev-ml/zarith/zarith-1.1.ebuild
+++ b/dev-ml/zarith/zarith-1.1.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
DESCRIPTION="The Zarith library implements arithmetic and logical operations over arbitrary-precision integers"
HOMEPAGE="http://forge.ocamlcore.org/projects/zarith"
@@ -13,28 +13,29 @@ SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86"
IUSE="+ocamlopt"
-OCAMLDIR=`ocamlc -where`
-
-DEPEND=">=dev-lang/ocaml-3.10.2[ocamlopt?]
- dev-libs/gmp"
+DEPEND="
+ >=dev-lang/ocaml-3.10.2[ocamlopt?]
+ dev-libs/gmp"
RDEPEND="${DEPEND}"
-src_prepare(){
- sed -i ${S}/project.mak -e "s:(OCAMLFIND) install:(OCAMLFIND) install -ldconf \$(INSTALLDIR)/ld.conf:g"
+pkg_setup() {
+ OCAMLDIR=$(ocamlc -where)
}
-src_configure(){
- ./configure -installdir "${D}${OCAMLDIR}" || die "configure failed"
+src_prepare(){
+ sed \
+ -e "s:(OCAMLFIND) install:(OCAMLFIND) install -ldconf \$(INSTALLDIR)/ld.conf:g" \
+ -i "${S}"/project.mak || die
}
-src_compile(){
- emake || die "emake failed"
+src_configure(){
+ ./configure -installdir "${D}${OCAMLDIR}" || die
}
src_install(){
- mkdir -p "${D}${OCAMLDIR}"
- cp "${OCAMLDIR}/ld.conf" "${D}${OCAMLDIR}/ld.conf"
- emake install || die "emake install failed"
- rm "${D}${OCAMLDIR}/ld.conf"
+ dodir "${OCAMLDIR}"
+ cp "${OCAMLDIR}/ld.conf" "${D}${OCAMLDIR}/ld.conf" || die
+ emake install
+ rm "${D}${OCAMLDIR}/ld.conf" || die
dodoc Changes README
}
diff --git a/dev-perl/DBIx-DBStag/ChangeLog b/dev-perl/DBIx-DBStag/ChangeLog
index 0d2382ad8..eb258598c 100644
--- a/dev-perl/DBIx-DBStag/ChangeLog
+++ b/dev-perl/DBIx-DBStag/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-perl/DBIx-DBStag
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> DBIx-DBStag-0.12.ebuild,
+ metadata.xml:
+ Fix header and move to EAPI=5
+
*DBIx-DBStag-0.12 (30 Jul 2011)
30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild b/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild
index aaeebfbd5..d9ad03471 100644
--- a/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild
+++ b/dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# This ebuild generated by g-cpan 0.16.4
+# $Header: $
-EAPI="2"
+EAPI=5
MODULE_AUTHOR="SCAIN"
@@ -15,7 +15,8 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=">=dev-perl/DBIx-DBSchema-0.39
+DEPEND="
+ >=dev-perl/DBIx-DBSchema-0.39
dev-perl/libxml-perl
>=dev-perl/Data-Stag-0.11
dev-perl/DBI
diff --git a/dev-perl/DBIx-DBStag/Manifest b/dev-perl/DBIx-DBStag/Manifest
index e37c61258..b5b876d76 100644
--- a/dev-perl/DBIx-DBStag/Manifest
+++ b/dev-perl/DBIx-DBStag/Manifest
@@ -1 +1 @@
-DIST DBIx-DBStag-0.12.tar.gz 142945 RMD160 5163a58fd03a9ef047c89c3e7b197d29bcf5747a SHA1 582505e67eefc184e18c742e69b9127a3b8e0606 SHA256 c2f07f42ffbbfb4256c1b66b4936bf9869acb7f4b058351290bbee4d719b1e67
+DIST DBIx-DBStag-0.12.tar.gz 142945 SHA256 c2f07f42ffbbfb4256c1b66b4936bf9869acb7f4b058351290bbee4d719b1e67
diff --git a/dev-perl/DBIx-DBStag/metadata.xml b/dev-perl/DBIx-DBStag/metadata.xml
index 07b525505..2bc893037 100644
--- a/dev-perl/DBIx-DBStag/metadata.xml
+++ b/dev-perl/DBIx-DBStag/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/dev-perl/Log-Cabin/ChangeLog b/dev-perl/Log-Cabin/ChangeLog
index 75bc1c7ad..a951d1303 100644
--- a/dev-perl/Log-Cabin/ChangeLog
+++ b/dev-perl/Log-Cabin/ChangeLog
@@ -1,7 +1,14 @@
# ChangeLog for dev-perl/Log-Cabin
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> Log-Cabin-0.06.ebuild:
+ Fix header and move to EAPI=5
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> Log-Cabin-0.06.ebuild,
+ metadata.xml:
+ Add ~amd64 or ~x86 keywords for revdeps
+
*Log-Cabin-0.06 (08 Jan 2012)
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild b/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
index 971995df9..1b9975241 100644
--- a/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
+++ b/dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# This ebuild generated by g-cpan 0.16.4
+# $Header: $
-EAPI="2"
+EAPI=5
MODULE_AUTHOR="JORVIS"
@@ -14,6 +14,5 @@ DESCRIPTION="Partial implementation of Log::Log4perl with reduced disk IO."
LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
SLOT="0"
-KEYWORDS="~x86"
+KEYWORDS="~amd64 ~x86"
IUSE=""
-
diff --git a/dev-perl/Log-Cabin/Manifest b/dev-perl/Log-Cabin/Manifest
index 3d9fab49a..a70fd3db5 100644
--- a/dev-perl/Log-Cabin/Manifest
+++ b/dev-perl/Log-Cabin/Manifest
@@ -1 +1 @@
-DIST Log-Cabin-0.06.tar.gz 4425 RMD160 2d5a791cfb22deaadf8fe1d52dd94bc31fdcf0e2 SHA1 d104e17964bbce8c0753276d425472baf0824282 SHA256 220494ed5e237e7263c665c5a4d809ddcd018a2f9e165cc871ef82e796096eb3
+DIST Log-Cabin-0.06.tar.gz 4425 SHA256 220494ed5e237e7263c665c5a4d809ddcd018a2f9e165cc871ef82e796096eb3
diff --git a/dev-perl/Log-Cabin/metadata.xml b/dev-perl/Log-Cabin/metadata.xml
index 07b525505..2bc893037 100644
--- a/dev-perl/Log-Cabin/metadata.xml
+++ b/dev-perl/Log-Cabin/metadata.xml
@@ -1,9 +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>
+ <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
index 21674a4ba..e5a12f4a0 100644
--- a/dev-perl/Text-ParseWords/ChangeLog
+++ b/dev-perl/Text-ParseWords/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-perl/Text-ParseWords
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> Text-ParseWords-3.27.ebuild,
+ metadata.xml:
+ Fix header and move to EAPI=5
+
*Text-ParseWords-3.27 (30 Jul 2011)
30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/dev-perl/Text-ParseWords/Manifest b/dev-perl/Text-ParseWords/Manifest
index 6219202dd..d5a1a30b0 100644
--- a/dev-perl/Text-ParseWords/Manifest
+++ b/dev-perl/Text-ParseWords/Manifest
@@ -1 +1 @@
-DIST Text-ParseWords-3.27.zip 9740 RMD160 0c3344087a5b8fe0270a9d6c8133358bacd5c99e SHA1 12ef6ce2a82cd595a0f50333b8beb9357a5efae2 SHA256 4d4bceae6a957941c758ebd5a47b680f0f8964934b766d13ba2adc3e62b6676d
+DIST Text-ParseWords-3.27.zip 9740 SHA256 4d4bceae6a957941c758ebd5a47b680f0f8964934b766d13ba2adc3e62b6676d
diff --git a/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild b/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild
index 57f8bc5bb..fa643e9bf 100644
--- a/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild
+++ b/dev-perl/Text-ParseWords/Text-ParseWords-3.27.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# This ebuild generated by g-cpan 0.16.4
+# $Header: $
-EAPI="2"
+EAPI=5
MODULE_AUTHOR="CHORNY"
MODULE_A_EXT="zip"
diff --git a/dev-perl/Text-ParseWords/metadata.xml b/dev-perl/Text-ParseWords/metadata.xml
index 07b525505..2bc893037 100644
--- a/dev-perl/Text-ParseWords/metadata.xml
+++ b/dev-perl/Text-ParseWords/metadata.xml
@@ -1,9 +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>
+ <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
index 88eb8ecf5..1ae37a244 100644
--- a/dev-perl/Time-Progress/ChangeLog
+++ b/dev-perl/Time-Progress/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-perl/Time-Progress
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> Time-Progress-1.7.ebuild,
+ metadata.xml:
+ Fix header and move to EAPI=5
+
*Time-Progress-1.7 (30 Jul 2011)
30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/dev-perl/Time-Progress/Manifest b/dev-perl/Time-Progress/Manifest
index 28722c066..4f2e91eb1 100644
--- a/dev-perl/Time-Progress/Manifest
+++ b/dev-perl/Time-Progress/Manifest
@@ -1 +1 @@
-DIST Time-Progress-1.7.tar.gz 4366 RMD160 6af7d39f3f4998ec7185608d26fc37fa7eab3fe7 SHA1 98e7d807141457089657f33f679a5f758552fe9c SHA256 7f823cfa9e294d3c45117ad2a82ef4830deb5689be6fe84fbd72cd37103b7a43
+DIST Time-Progress-1.7.tar.gz 4366 SHA256 7f823cfa9e294d3c45117ad2a82ef4830deb5689be6fe84fbd72cd37103b7a43
diff --git a/dev-perl/Time-Progress/Time-Progress-1.7.ebuild b/dev-perl/Time-Progress/Time-Progress-1.7.ebuild
index 7bb62ec26..8a9d4a184 100644
--- a/dev-perl/Time-Progress/Time-Progress-1.7.ebuild
+++ b/dev-perl/Time-Progress/Time-Progress-1.7.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# This ebuild generated by g-cpan 0.16.4
+# $Header: $
-EAPI="2"
+EAPI=5
MODULE_AUTHOR="CADE"
diff --git a/dev-perl/Time-Progress/metadata.xml b/dev-perl/Time-Progress/metadata.xml
index 07b525505..2bc893037 100644
--- a/dev-perl/Time-Progress/metadata.xml
+++ b/dev-perl/Time-Progress/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/dev-perl/go-perl/ChangeLog b/dev-perl/go-perl/ChangeLog
index 2e162b59e..5d5e94da2 100644
--- a/dev-perl/go-perl/ChangeLog
+++ b/dev-perl/go-perl/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-perl/go-perl
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> go-perl-0.13.ebuild,
+ metadata.xml:
+ Fix header and move to EAPI=5
+
*go-perl-0.13 (30 Jul 2011)
30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/dev-perl/go-perl/Manifest b/dev-perl/go-perl/Manifest
index 05ead67d3..9aac4f306 100644
--- a/dev-perl/go-perl/Manifest
+++ b/dev-perl/go-perl/Manifest
@@ -1 +1 @@
-DIST go-perl-0.13.tar.gz 806739 RMD160 e55c6b0f1647a4087d094b6e83fa3351f7f57624 SHA1 25fa3bda2b8f9654d0552e10c9f8b778de41d6fe SHA256 392835fe0dd201a11b4f257bc10b8774cadc30dd93ef972fb65382b2a3557541
+DIST go-perl-0.13.tar.gz 806739 SHA256 392835fe0dd201a11b4f257bc10b8774cadc30dd93ef972fb65382b2a3557541
diff --git a/dev-perl/go-perl/go-perl-0.13.ebuild b/dev-perl/go-perl/go-perl-0.13.ebuild
index ae9db233b..2fbf7b1f5 100644
--- a/dev-perl/go-perl/go-perl-0.13.ebuild
+++ b/dev-perl/go-perl/go-perl-0.13.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# This ebuild generated by g-cpan 0.16.4
+# $Header: $
-EAPI="2"
+EAPI=5
MODULE_AUTHOR="CMUNGALL"
@@ -15,7 +15,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=">=dev-perl/Data-Stag-0.11
+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
index 07b525505..2bc893037 100644
--- a/dev-perl/go-perl/metadata.xml
+++ b/dev-perl/go-perl/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/dev-python/Forthon/ChangeLog b/dev-python/Forthon/ChangeLog
new file mode 100644
index 000000000..253728161
--- /dev/null
+++ b/dev-python/Forthon/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for dev-python/Forthon
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> Forthon-0.8.11.ebuild,
+ metadata.xml:
+ Correct license name
+
diff --git a/dev-python/Forthon/Forthon-0.8.11.ebuild b/dev-python/Forthon/Forthon-0.8.11.ebuild
index 2383f9bca..3060fa753 100644
--- a/dev-python/Forthon/Forthon-0.8.11.ebuild
+++ b/dev-python/Forthon/Forthon-0.8.11.ebuild
@@ -1,31 +1,32 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
PYTHON_COMPAT=( python{2_5,2_6,2_7,3_1,3_2,3_3} )
-inherit distutils-r1
+inherit eutils distutils-r1
DESCRIPTION="Python interface generator for Fortran based codes"
HOMEPAGE="http://hifweb.lbl.gov/Forthon http://pypi.python.org/pypi/Forthon"
SRC_URI="http://hifweb.lbl.gov/${PN}/${P}.tgz"
-LICENSE="LLNL-BSD"
+LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
python_prepare_all() {
sed -i -e "/data_files/ s/'License.txt',//" setup.py || die
+ epatch "${FILESDIR}"/${P}-fix_options_parser.patch
distutils-r1_python_prepare_all
}
python_install_all() {
dohtml docs/index.html
if use examples ; then
- insinto /usr/share/doc/${PF}
- doins -r {example,example2,simpleexample}
+ docinto /usr/share/doc/${PF}
+ dodoc -r {example,example2,simpleexample}
fi
distutils-r1_python_install_all
}
diff --git a/dev-python/Forthon/files/Forthon-0.8.11-fix_options_parser.patch b/dev-python/Forthon/files/Forthon-0.8.11-fix_options_parser.patch
new file mode 100644
index 000000000..6a5bfc122
--- /dev/null
+++ b/dev-python/Forthon/files/Forthon-0.8.11-fix_options_parser.patch
@@ -0,0 +1,17 @@
+In order to allow for installation of package for multiple versions of Python
+Linux distribution often provide wrappers with correct shebangs tied to specific
+Python implementation, e.g. Forthon-2.7, Forthon-python2.7, etc.
+This patch fixes logic in Forthon_options to take that into account
+
+Patch written by Kacper Kowalik <xarthisius@gentoo.org>
+--- a/Lib/Forthon_options.py
++++ b/Lib/Forthon_options.py
+@@ -92,7 +92,7 @@ class InputError(Exception):
+ # --- Otherwise ignore the arguments. This is needed since for example this
+ # --- module may be imported by the compilers module which is used by some
+ # --- program other than Forthon.
+-if os.path.basename(sys.argv[0]) == 'Forthon' or sys.argv[0] == '-c':
++if os.path.basename(sys.argv[0]).startswith('Forthon') or sys.argv[0] == '-c':
+ (options, args) = parser.parse_args()
+ else:
+ (options, args) = parser.parse_args(args=[])
diff --git a/dev-python/Forthon/metadata.xml b/dev-python/Forthon/metadata.xml
index 6629da3fa..ef58ee263 100644
--- a/dev-python/Forthon/metadata.xml
+++ b/dev-python/Forthon/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>xarthisius@gentoo.org</email>
- <name>Kacper Kowalik</name>
- </maintainer>
+ <maintainer>
+ <email>xarthisius@gentoo.org</email>
+ <name>Kacper Kowalik</name>
+ </maintainer>
</pkgmetadata>
diff --git a/dev-python/GOGrapher/ChangeLog b/dev-python/GOGrapher/ChangeLog
index ab83cc68a..0e2b330ef 100644
--- a/dev-python/GOGrapher/ChangeLog
+++ b/dev-python/GOGrapher/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-python/GOGrapher
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> GOGrapher-9999.ebuild,
+ metadata.xml:
+ Set license to GPL-2
+
*GOGrapher-9999 (08 Jan 2012)
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/dev-python/GOGrapher/GOGrapher-9999.ebuild b/dev-python/GOGrapher/GOGrapher-9999.ebuild
index 5d9e2967e..fbd436778 100644
--- a/dev-python/GOGrapher/GOGrapher-9999.ebuild
+++ b/dev-python/GOGrapher/GOGrapher-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -20,11 +20,11 @@ else
KEYWORDS=""
fi
-LICENSE=""
+LICENSE="GPL-2"
SLOT="0"
IUSE=""
-DEPEND="dev-python/networkx
- dev-python/pygraphviz"
+DEPEND="
+ dev-python/networkx
+ dev-python/pygraphviz"
RDEPEND="${DEPEND}"
-
diff --git a/dev-python/GOGrapher/metadata.xml b/dev-python/GOGrapher/metadata.xml
index 07b525505..2bc893037 100644
--- a/dev-python/GOGrapher/metadata.xml
+++ b/dev-python/GOGrapher/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/dev-python/RecSQL/ChangeLog b/dev-python/RecSQL/ChangeLog
new file mode 100644
index 000000000..16c58e071
--- /dev/null
+++ b/dev-python/RecSQL/ChangeLog
@@ -0,0 +1,18 @@
+# ChangeLog for dev-python/RecSQL
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 26 Mar 2013; Justin Lecher <jlec@gentoo.org> RecSQL-9999.ebuild,
+ metadata.xml:
+ Enhance python r1 eclass usage
+
+ 25 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> -Manifest,
+ -RecSQL-0.7.8.ebuild, RecSQL-9999.ebuild:
+ Update deps
+
+*RecSQL-0.7.8 (23 Mar 2013)
+*RecSQL-9999 (23 Mar 2013)
+
+ 23 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> +RecSQL-0.7.8.ebuild,
+ +RecSQL-9999.ebuild, +metadata.xml:
+ Add RecSQL to tree
diff --git a/dev-python/RecSQL/RecSQL-9999.ebuild b/dev-python/RecSQL/RecSQL-9999.ebuild
new file mode 100644
index 000000000..f823e082a
--- /dev/null
+++ b/dev-python/RecSQL/RecSQL-9999.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+PYTHON_REQ_USE="sqlite"
+
+if [[ $PV = *9999* ]]; then
+ scm_eclass=git-2
+ EGIT_REPO_URI="
+ git://github.com/orbeckst/${PN}.git
+ https://github.com/orbeckst/${PN}.git"
+ SRC_URI=""
+ KEYWORDS=""
+else
+ scm_eclass=vcs-snapshot
+ SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+inherit eutils distutils-r1 ${scm_eclass}
+
+DESCRIPTION="Simple SQL analysis of python records"
+HOMEPAGE="http://orbeckst.github.com/RecSQL/"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}"
diff --git a/dev-python/RecSQL/metadata.xml b/dev-python/RecSQL/metadata.xml
new file mode 100644
index 000000000..098ac091a
--- /dev/null
+++ b/dev-python/RecSQL/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</herd>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-python/asciidata/ChangeLog b/dev-python/asciidata/ChangeLog
deleted file mode 100644
index 69d7889af..000000000
--- a/dev-python/asciidata/ChangeLog
+++ /dev/null
@@ -1,28 +0,0 @@
-# ChangeLog for dev-python/asciidata
-# 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,
- +asciidata-1.1.1-r1.ebuild:
- Fix PYTHON ABI Stuff
-
-*asciidata-1.1.1 (26 Jun 2009)
-
- 26 Jun 2009; Sébastien Fabbro <bicatali@gentoo.org>
- -asciidata-1.1.ebuild, +asciidata-1.1.1.ebuild:
- Version bump
-
- 23 May 2008; Sébastien Fabbro <bicatali@gentoo.org>
- -asciidata-1.0.ebuild, +asciidata-1.1.ebuild:
- Version bump, now depend on numpy
-
-*asciidata-1.0 (15 Oct 2006)
-
- 15 Oct 2006; Sebastien Fabbro <seb@ist.utl.pt>
- +asciidata-1.0.ebuild, +metadata.xml
- Initial import.
diff --git a/dev-python/asciidata/Manifest b/dev-python/asciidata/Manifest
deleted file mode 100644
index e8f7b78de..000000000
--- a/dev-python/asciidata/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST asciidata-1.1.1.tar.gz 482467 SHA256 4dfbf3145ddda8693fb82d97fbaf14ebcddf957557c4e97c789bc6fd1862f11e SHA512 17feb70bf3383a2689322eceae797c3512afb3f6ba0bddd6a161a29b867bc14d290324daa1c9538240a3f852f108c7521dd17ce786f6d7752eade422c21e2534 WHIRLPOOL 6ed01fa43fe3cf2fb60637f9b727d1acab3fdda2ad07c6bd934051e6ef80520a98accd1d731f0af101bd3ee653dffb8295ed63b188422b83c5dec56e0a0c0d8e
diff --git a/dev-python/asciidata/asciidata-1.1.1-r1.ebuild b/dev-python/asciidata/asciidata-1.1.1-r1.ebuild
deleted file mode 100644
index 8c096fda0..000000000
--- a/dev-python/asciidata/asciidata-1.1.1-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-SUPPORT_PYTHON_ABIS="1"
-DISTUTILS_SRC_TEST=setup.py
-RESTRICT_PYTHON_ABIS="3.* 2.7-pypy-*"
-
-inherit distutils
-
-DESCRIPTION="Python module to handle ASCII tables"
-HOMEPAGE="http://www.stecf.org/software/astroasciidata/index.html"
-SRC_URI="http://www.stecf.org/software/PYTHONtools/astro${PN}/source/${P}.tar.gz"
-
-IUSE="doc test"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-LICENSE="GPL-2"
-
-RDEPEND="dev-python/numpy
- dev-python/pyfits"
-DEPEND="doc? ( dev-tex/latex2html )
- test? ( ${RDEPEND} )"
-
-src_compile() {
- distutils_src_compile
- if use doc; then
- pushd doc &> /dev/null
- latex2html ${PN}.tex
- popd &> /dev/null
- fi
-}
-
-src_install() {
- distutils_src_install
- if use doc; then
- dohtml -r doc/${PN}/
- fi
-}
diff --git a/dev-python/asciidata/metadata.xml b/dev-python/asciidata/metadata.xml
deleted file mode 100644
index 804a75129..000000000
--- a/dev-python/asciidata/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-astronomy</herd>
-<longdescription lang="en">
- AsciiData is a Python module to handle ASCII tables. With this
- module it is possible to:
- * read ASCII tables;
- * access its elements for reading and writing;
- * save the ASCII table back to a file;
- * delete/add rows and columns.
-</longdescription>
-</pkgmetadata>
diff --git a/dev-python/astlib/ChangeLog b/dev-python/astlib/ChangeLog
index 7d86e5759..992453036 100644
--- a/dev-python/astlib/ChangeLog
+++ b/dev-python/astlib/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for dev-python/astlib
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*astlib-0.7.0 (29 Apr 2013)
+
+ 29 Apr 2013; Sébastien Fabbro <bicatali@gentoo.org> +astlib-0.7.0.ebuild,
+ -astlib-0.17.1.ebuild, -files/astlib-0.17.1-wcstools.patch, metadata.xml:
+ dev-python/astlib: Version bump
+
*astlib-0.17.1 (06 Sep 2012)
06 Sep 2012; Sébastien Fabbro <bicatali@gentoo.org> +astlib-0.17.1.ebuild,
diff --git a/dev-python/astlib/Manifest b/dev-python/astlib/Manifest
index be7b45e86..462098cb2 100644
--- a/dev-python/astlib/Manifest
+++ b/dev-python/astlib/Manifest
@@ -1 +1 @@
-DIST astLib-0.17.1.tar.gz 547431 SHA256 ff03cab7e9b41b3c9366c56273929b721fee08ec39ae8984606aa71bbaeeb961 SHA512 511282e0794dc72a295678b833cac634f9c3053456fa715b0e936e1de2915e675e614e74adaa68347d0952daf7da7d375deab2c05675cd375e287e1b8edcc0ba WHIRLPOOL c667fa216a50d720c8205fab7b905956c6d600affb9cbd740845f670a64fb3f4f95c858d831c44369f9878bb5e7b48f70f31799e0a1a9751be0a95803f728b44
+DIST astLib-0.7.0.tar.gz 711298 SHA256 c6105a6d86c8fceeb0d0bad217106efcc1f1d12a1fcae2d63c1392f518c18152 SHA512 1984f02b847ef4ce123000f89999a52c6fb1dffa9fb8d1c9ad5c731cb27cab65b4ba735d24f79282f71d64cd8dcff414be1fae9161b04d8be170ed6cb84eb048 WHIRLPOOL 58c40033209cbda7b13e9c4ce83ad31f55b526f224f562d3caa1c237e2a5c763847b452afd995ef2479165eacc64599f6745c188651d013452c304ff6e8b844c
diff --git a/dev-python/astlib/astlib-0.17.1.ebuild b/dev-python/astlib/astlib-0.7.0.ebuild
index 8d5beb6ec..7052b65f0 100644
--- a/dev-python/astlib/astlib-0.17.1.ebuild
+++ b/dev-python/astlib/astlib-0.7.0.ebuild
@@ -1,42 +1,35 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.*"
+PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
-inherit distutils eutils
+inherit distutils-r1
MYPN=astLib
MYP=${MYPN}-${PV}
-DESCRIPTION="Python astronomy modules for coordinate conversion and manipulating FITS images"
+DESCRIPTION="Python astronomy modules for image and coordinate manipulation"
HOMEPAGE="http://astlib.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${MYP}.tar.gz"
-IUSE="doc examples"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
LICENSE="BSD"
-DEPEND="sci-astronomy/wcstools"
+IUSE="doc examples"
+
+DEPEND=""
RDEPEND="${DEPEND}
- dev-python/matplotlib
- dev-python/imaging
- dev-python/pyfits
- sci-libs/scipy"
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ sci-libs/scipy[${PYTHON_USEDEP}]
+ virtual/pyfits[${PYTHON_USEDEP}]"
S="${WORKDIR}/${MYP}"
-src_prepare() {
- epatch "${FILESDIR}"/${PN}-0.17.1-wcstools.patch
- distutils_src_prepare
-}
-
-src_install() {
- distutils_src_install
+python_install_all() {
use doc && dohtml docs/${MYPN}/*
if use examples; then
insinto /usr/share/doc/${PF}
diff --git a/dev-python/astlib/files/astlib-0.17.1-wcstools.patch b/dev-python/astlib/files/astlib-0.17.1-wcstools.patch
deleted file mode 100644
index dac0a6a02..000000000
--- a/dev-python/astlib/files/astlib-0.17.1-wcstools.patch
+++ /dev/null
@@ -1,75 +0,0 @@
---- setup.py.orig 2012-09-06 09:40:12.270646957 -0700
-+++ setup.py 2012-09-06 09:45:04.370193374 -0700
-@@ -13,23 +13,23 @@
- exampleScripts=glob.glob("scripts"+os.path.sep+"*.py")
-
- class build_PyWCSTools_ext(build_ext):
--
-+
- def build_extensions(self):
--
-+
- os.chdir(sourceDir)
--
-+
- cc=distutils.ccompiler.new_compiler()
--
-- WCSToolsCFiles=["actread.c", "binread.c", "ctgread.c", "catutil.c", "cel.c", "daoread.c", "dateutil.c", "distort.c", "dsspos.c",
-+
-+ WCSToolsCFiles=["actread.c", "binread.c", "ctgread.c", "catutil.c", "cel.c", "daoread.c", "dateutil.c", "distort.c", "dsspos.c",
- "fileutil.c", "imutil.c", "findstar.c", "fitsfile.c", "fitswcs.c", "gscread.c", "gsc2read.c", "hget.c", "hput.c", "iget.c",
- "imgetwcs.c", "imhfile.c", "imio.c", "imsetwcs.c", "imrotate.c", "lin.c", "matchstar.c", "platefit.c", "platepos.c",
- "polfit.c", "proj.c", "sdssread.c", "sortstar.c", "sph.c", "tabread.c", "tmcread.c", "tnxpos.c", "ty2read.c", "uacread.c",
- "ubcread.c", "ucacread.c", "ujcread.c", "wcs.c", "wcsinit.c", "wcscon.c", "wcslib.c", "wcstrig.c", "webread.c", "worldpos.c"]
- cc.compile(WCSToolsCFiles)
--
-+
- os.chdir(topDir)
--
-- build_ext.build_extensions(self)
-+
-+ build_ext.build_extensions(self)
-
- setup(name='astLib',
- version='0.17.1',
-@@ -51,35 +51,11 @@
- with World Coordinate System (WCS) information through PyWCSTools - a simple wrapping of WCSTools by Doug Mink.
- PyWCSTools is distributed (and developed) as part of astLib.""",
- packages=['astLib', 'PyWCSTools'],
-- cmdclass={"build_ext": build_PyWCSTools_ext},
- scripts=exampleScripts,
- ext_modules=[
-- Extension('PyWCSTools._wcscon', [sourceDir+"wcscon_wrap.c"],
-- extra_objects=[sourceDir+"actread.o", sourceDir+"binread.o", sourceDir+"ctgread.o", sourceDir+"catutil.o",
-- sourceDir+"cel.o", sourceDir+"daoread.o", sourceDir+"dateutil.o", sourceDir+"distort.o",
-- sourceDir+"dsspos.o", sourceDir+"fileutil.o", sourceDir+"imutil.o", sourceDir+"findstar.o",
-- sourceDir+"fitsfile.o", sourceDir+"fitswcs.o", sourceDir+"gscread.o", sourceDir+"gsc2read.o",
-- sourceDir+"hget.o", sourceDir+"hput.o", sourceDir+"iget.o", sourceDir+"imgetwcs.o",
-- sourceDir+"imhfile.o", sourceDir+"imio.o", sourceDir+"imsetwcs.o", sourceDir+"imrotate.o",
-- sourceDir+"lin.o", sourceDir+"matchstar.o", sourceDir+"platefit.o",
-- sourceDir+"platepos.o", sourceDir+"polfit.o", sourceDir+"proj.o", sourceDir+"sdssread.o",
-- sourceDir+"sortstar.o", sourceDir+"sph.o", sourceDir+"tabread.o", sourceDir+"tmcread.o",
-- sourceDir+"tnxpos.o", sourceDir+"ty2read.o", sourceDir+"uacread.o", sourceDir+"ubcread.o",
-- sourceDir+"ucacread.o", sourceDir+"ujcread.o", sourceDir+"wcs.o", sourceDir+"wcsinit.o",
-- sourceDir+"wcscon.o", sourceDir+"wcslib.o", sourceDir+"wcstrig.o", sourceDir+"webread.o",
-- sourceDir+"worldpos.o"]),
-- Extension('PyWCSTools._wcs', [sourceDir+"wcs_wrap.c"],
-- extra_objects=[sourceDir+"actread.o", sourceDir+"binread.o", sourceDir+"ctgread.o", sourceDir+"catutil.o",
-- sourceDir+"cel.o", sourceDir+"daoread.o", sourceDir+"dateutil.o", sourceDir+"distort.o",
-- sourceDir+"dsspos.o", sourceDir+"fileutil.o", sourceDir+"imutil.o", sourceDir+"findstar.o",
-- sourceDir+"fitsfile.o", sourceDir+"fitswcs.o", sourceDir+"gscread.o", sourceDir+"gsc2read.o",
-- sourceDir+"hget.o", sourceDir+"hput.o", sourceDir+"iget.o", sourceDir+"imgetwcs.o",
-- sourceDir+"imhfile.o", sourceDir+"imio.o", sourceDir+"imsetwcs.o", sourceDir+"imrotate.o",
-- sourceDir+"lin.o", sourceDir+"matchstar.o", sourceDir+"platefit.o",
-- sourceDir+"platepos.o", sourceDir+"polfit.o", sourceDir+"proj.o", sourceDir+"sdssread.o",
-- sourceDir+"sortstar.o", sourceDir+"sph.o", sourceDir+"tabread.o", sourceDir+"tmcread.o",
-- sourceDir+"tnxpos.o", sourceDir+"ty2read.o", sourceDir+"uacread.o", sourceDir+"ubcread.o",
-- sourceDir+"ucacread.o", sourceDir+"ujcread.o", sourceDir+"wcs.o", sourceDir+"wcsinit.o",
-- sourceDir+"wcscon.o", sourceDir+"wcslib.o", sourceDir+"wcstrig.o", sourceDir+"webread.o",
-- sourceDir+"worldpos.o"])]
-+ Extension('PyWCSTools._wcscon', [sourceDir+"wcscon_wrap.c"],
-+ libraries=['wcstools']),
-+ Extension('PyWCSTools._wcs', [sourceDir+"wcs_wrap.c"],
-+ libraries=['wcstools'])]
-+
- )
diff --git a/dev-python/astlib/metadata.xml b/dev-python/astlib/metadata.xml
index 7f08aaee0..306677cbb 100644
--- a/dev-python/astlib/metadata.xml
+++ b/dev-python/astlib/metadata.xml
@@ -9,6 +9,7 @@
images with World Coordinate System (WCS) information through
PyWCSTools - a simple wrapping of WCSTools by Doug Mink. PyWCSTools
is distributed (and developed) as part of astLib.
- In Gentoo, PyWCSTools is using the stock library instead of the bundled one.
+ In Gentoo, PyWCSTools is using the stock library instead of the
+ bundled one.
</longdescription>
</pkgmetadata>
diff --git a/dev-python/pymvpa/ChangeLog b/dev-python/pymvpa/ChangeLog
index 26f976663..19f3e6798 100644
--- a/dev-python/pymvpa/ChangeLog
+++ b/dev-python/pymvpa/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for dev-python/pymvpa
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> pymvpa-0.4.4.ebuild,
+ metadata.xml:
+ Move to new python eclasses
+
25 Jun 2011; Justin Lecher <jlec@gentoo.org> pymvpa-0.4.4.ebuild,
metadata.xml:
Dropped keywords because deps are missing
diff --git a/dev-python/pymvpa/metadata.xml b/dev-python/pymvpa/metadata.xml
index 183179e84..3bfd92ff3 100644
--- a/dev-python/pymvpa/metadata.xml
+++ b/dev-python/pymvpa/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-mathematics</herd>
- <longdescription lang="en">
+ <herd>sci-mathematics</herd>
+ <longdescription lang="en">
Python module to ease pattern classification analyses of large
datasets. It provides high-level abstraction of typical processing
steps (e.g. data preparation, classification, feature selection,
diff --git a/dev-python/pymvpa/pymvpa-0.4.4.ebuild b/dev-python/pymvpa/pymvpa-0.4.4.ebuild
index 88a45808b..606a3d396 100644
--- a/dev-python/pymvpa/pymvpa-0.4.4.ebuild
+++ b/dev-python/pymvpa/pymvpa-0.4.4.ebuild
@@ -1,14 +1,12 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-python/pywavelets/pywavelets-0.2.0.ebuild,v 1.1 2010/04/22 20:14:30 bicatali Exp $
-EAPI=2
+EAPI=5
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.*"
+PYTHON_COMPAT=( python{2_6,2_7} )
-inherit distutils
+inherit distutils-r1
DESCRIPTION="Multivariate pattern analysis with Python"
HOMEPAGE="http://www.pymvpa.org/"
@@ -21,19 +19,23 @@ IUSE="doc examples minimal test"
DEPEND="
dev-lang/swig
- dev-python/lxml
- dev-python/numpy
+ dev-python/lxml[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
sys-apps/help2man
- doc? ( dev-python/sphinx media-gfx/graphviz )
- test? ( dev-python/nose )"
+ doc? (
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ media-gfx/graphviz
+ )
+ test? ( dev-python/nose[${PYTHON_USEDEP}] )"
-RDEPEND="dev-python/numpy
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
!minimal? (
dev-python/hcluster
- dev-python/ipython
- dev-python/matplotlib
+ dev-python/ipython[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/pynifti
- dev-python/rpy
+ dev-python/rpy[${PYTHON_USEDEP}]
sci-libs/afni
sci-libs/fsl
sci-libs/libsvm
diff --git a/dev-python/pythonocc/ChangeLog b/dev-python/pythonocc/ChangeLog
index 94d6ddb41..f130d8d9a 100644
--- a/dev-python/pythonocc/ChangeLog
+++ b/dev-python/pythonocc/ChangeLog
@@ -1,7 +1,22 @@
# ChangeLog for dev-python/pythonocc
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> ChangeLog:
+ Version BUmp; change license; move to new python eclasses
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> ChangeLog:
+ Version BUmp; change license; move to new python eclasses
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> ChangeLog:
+ Version BUmp; change license; move to new python eclasses
+
+*pythonocc-0.5 (03 Mar 2013)
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> -pythonocc-0.4.ebuild,
+ +pythonocc-0.5.ebuild, metadata.xml:
+ Version BUmp; change license; move to new python eclasses
+
14 Mar 2011; Oliver Borm (boroli) <oli.borm@web.de> pythonocc-0.4.ebuild:
dev-python/pythonocc: restrict to opencascade-6.3 dependency
diff --git a/dev-python/pythonocc/Manifest b/dev-python/pythonocc/Manifest
index 42d818058..e9fbe053b 100644
--- a/dev-python/pythonocc/Manifest
+++ b/dev-python/pythonocc/Manifest
@@ -1 +1 @@
-DIST pythonOCC-0.4.tar.gz 4025282 RMD160 6314f793a3c7362abbe5e7514ed1b7d245ffece6 SHA1 193b4b02615565f9c95d5b2615a27b3cc6bab952 SHA256 bbf8ca4bf6b86d65d9221b411aa4d3e61d19184680783963c8367287d7ba00ee
+DIST pythonocc-0.5.tar.gz 13373832 SHA256 6a8e04694e4f4be317df24b223f8913b1cdbba2994bcf38f8045cb510fcb6ffc SHA512 0c0c4156a6272093b7fa9c590fe2b6fee1c82061e99ac5e0f410215734b156310e28cefea29fddf95a9add4c05aae9f6bb63612242a8ca7369668e385388b753 WHIRLPOOL 28c4ddd2ee650bc45449be3e04c6223c00c752d18edf3dd0727240ff4a8a40298f1c8299fa8b270e7581814e63481a219ed26c7302430c8960dc741fb7c0e897
diff --git a/dev-python/pythonocc/metadata.xml b/dev-python/pythonocc/metadata.xml
index d369d068f..897aa2e6b 100644
--- a/dev-python/pythonocc/metadata.xml
+++ b/dev-python/pythonocc/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</herd>
</pkgmetadata>
diff --git a/dev-python/pythonocc/pythonocc-0.4.ebuild b/dev-python/pythonocc/pythonocc-0.5.ebuild
index fd891a68d..ae1e35547 100644
--- a/dev-python/pythonocc/pythonocc-0.4.ebuild
+++ b/dev-python/pythonocc/pythonocc-0.5.ebuild
@@ -1,30 +1,27 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=2
+EAPI=5
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
-inherit distutils
+inherit distutils-r1
MY_PN=pythonOCC
MY_P=${MY_PN}-${PV}
DESCRIPTION="Python Interface to OpenCASCADE CAD library"
HOMEPAGE="http://www.pythonocc.org"
-SRC_URI="http://download.gna.org/${PN}/${PV}/${MY_P}.tar.gz"
+SRC_URI="http://pythonocc.googlecode.com/files/${P}.tar.gz"
-LICENSE="GPL-3"
+LICENSE="LGPL-3"
KEYWORDS="~amd64 ~x86"
SLOT="0"
IUSE=""
-RDEPEND="<sci-libs/opencascade-6.4"
+RDEPEND="sci-libs/opencascade"
DEPEND="${RDEPEND}
dev-lang/swig"
-RESTRICT_PYTHON_ABIS="3.*"
-
-S=${WORKDIR}/${MY_P}/src
+S="${WORKDIR}"/${P}/src
diff --git a/dev-util/VampirTrace/Manifest b/dev-util/VampirTrace/Manifest
new file mode 100644
index 000000000..55591bfc9
--- /dev/null
+++ b/dev-util/VampirTrace/Manifest
@@ -0,0 +1 @@
+DIST dcount.php?package=vampirtrace&get=VampirTrace-5.14.3.tar.gz 5956627 SHA256 d3bc18662ee48c9c02de0b5933c52213849cbb79b21a3b4ec786bc21e3126209 SHA512 2b1faa707d12b672ba12b399f6b1c14c8d3cff0b3f961f70b81adb1e5ba69960a217ae228cbacd1ffd3f54aab1b30697ef66748a4fd604e8684910d98041d458 WHIRLPOOL 2bcf401f25f4ed500e92739e36265979cab1c5c0caebb53555caf6f293411b4ac8c542254bc95cad5a81f3458ccb74126580450873ff53a9df3e944f67cb9d48
diff --git a/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild b/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild
new file mode 100644
index 000000000..02a8faa88
--- /dev/null
+++ b/dev-util/VampirTrace/VampirTrace-5.14.3.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2013-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils cuda
+
+DESCRIPTION="An open source library that allows detailed logging of program execution for parallel applications"
+HOMEPAGE="http://www.tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/software_werkzeuge_zur_unterstuetzung_von_programmierung_und_optimierung/vampirtrace"
+SRC_URI="http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get=${P}.tar.gz"
+
+SLOT="0"
+LICENSE="vampir"
+KEYWORDS="~amd64"
+IUSE="cuda"
+
+DEPEND="
+ virtual/mpi
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.0.0 )"
+
+src_prepare() {
+ use cuda && cuda_src_prepare
+}
+
+src_configure() {
+ econf $(use_with cuda cuda-dir "${EPREFIX}"/opt/cuda)
+}
+
+src_install() {
+ default
+ # avoid collisions with app-text/lcdf-typetools:
+ mv "${D}/usr/bin/otfinfo" "${D}/usr/bin/otfinfo.vampir"
+ mv "${D}/usr/lib/debug/usr/bin/otfinfo.debug" "${D}/usr/lib/debug/usr/bin/otfinfo.vampir.debug"
+ # libtool is already installed:
+ rm "${D}/usr/share/libtool"
+}
diff --git a/dev-util/VampirTrace/metadata.xml b/dev-util/VampirTrace/metadata.xml
new file mode 100644
index 000000000..4c72b4d3b
--- /dev/null
+++ b/dev-util/VampirTrace/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>cluster</herd>
+ <longdescription>
+ VampirTrace is an open source library that allows detailed logging of program execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads). Besides these typical parallelization paradigms, VampirTrace is capable of tracing GPU accelerated applications and generates exact time stamps for all GPU related events.
+ </longdescription>
+ <use>
+ <flag name="cuda">
+ Enable tracing of CUDA calls and GPU kernels.
+ </flag>
+ </use>
+</pkgmetadata>
diff --git a/licenses/ECL-2.0 b/licenses/ECL-2.0
new file mode 100644
index 000000000..012da6c80
--- /dev/null
+++ b/licenses/ECL-2.0
@@ -0,0 +1,97 @@
+Educational Community License, Version 2.0 (ECL-2.0)
+(plain text)
+Educational Community License
+
+Version 2.0, April 2007
+
+http://www.osedu.org/licenses/
+
+The Educational Community License version 2.0 ("ECL") consists of the Apache 2.0 license, modified to change the scope of the patent grant in section 3 to be specific to the needs of the education communities using this license. The original Apache 2.0 license can be found at: http://www.apache.org/licenses/LICENSE-2.0
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
+"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document.
+
+"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License.
+
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+
+"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License.
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+
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+
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+
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+
+"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution."
+
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+
+2. Grant of Copyright License.
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+If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License.
+You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.
+
+5. Submission of Contributions.
+
+Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions.
+
+6. Trademarks.
+
+This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file.
+
+7. Disclaimer of Warranty.
+
+Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License.
+
+8. Limitation of Liability.
+
+In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages.
+
+9. Accepting Warranty or Additional Liability.
+
+While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS
+
+APPENDIX: How to apply the Educational Community License to your work
+
+To apply the Educational Community License to your work, attach
+the following boilerplate notice, with the fields enclosed by
+brackets "[]" replaced with your own identifying information.
+(Don't include the brackets!) The text should be enclosed in the
+appropriate comment syntax for the file format. We also recommend
+that a file or class name and description of purpose be included on
+the same "printed page" as the copyright notice for easier
+identification within third-party archives.
+
+ Copyright [yyyy] [name of copyright owner] Licensed under the
+ Educational Community License, Version 2.0 (the "License"); you may
+ not use this file except in compliance with the License. You may
+ obtain a copy of the License at
+
+http://www.osedu.org/licenses/ECL-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an "AS IS"
+ BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
+ or implied. See the License for the specific language governing
+ permissions and limitations under the License. \ No newline at end of file
diff --git a/licenses/blasr b/licenses/blasr
new file mode 100644
index 000000000..bdd17171c
--- /dev/null
+++ b/licenses/blasr
@@ -0,0 +1,65 @@
+Copyright (c) 2010, Pacific Biosciences of California, Inc.
+
+
+
+All rights reserved.
+
+
+
+Redistribution and use in source and binary forms, with or without
+
+modification, are permitted provided that the following conditions are
+
+met:
+
+
+
+ * Redistributions of source code must retain the above copyright
+
+ notice, this list of conditions and the following disclaimer.
+
+
+
+ * Redistributions in binary form must reproduce the above
+
+ copyright notice, this list of conditions and the following
+
+ disclaimer in the documentation and/or other materials provided
+
+ with the distribution.
+
+
+
+ * Neither the name of Pacific Biosciences nor the names of its
+
+ contributors may be used to endorse or promote products derived
+
+ from this software without specific prior written permission.
+
+
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED
+
+BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND
+
+ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
+
+AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
+
+PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
+
+AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
+
+THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
diff --git a/licenses/mgltools b/licenses/mgltools
new file mode 100644
index 000000000..e252878ab
--- /dev/null
+++ b/licenses/mgltools
@@ -0,0 +1,42 @@
+1. Grant Of Limited License; Software Use Restrictions. The programs
+ received by you will be used only for NON COMMERCIAL purposes.
+ This license is issued to you as an individual.
+
+ For COMMERCIAL use done with the software please contact Michel F.
+ Sanner for details about commercial usage license agreements.
+
+ For any question regarding license agreements, please contact
+ Michel Sanner:
+ TSRI, Molecular Biology Department, TCP 26,
+ 10550 North Torrey Pines Road, La Jolla, CA 92037
+ sanner@scripps.edu
+ tel (858) 784-7742
+ fax (858) 784-2341
+
+ 2. COMMERCIAL USAGE is defined as revenues generating activities. These
+ include using this software for consulting activities and selling
+ applications built on top of, or using this software. Scientific
+ research in an academic environment and teaching are considered
+ NON COMMERCIAL.
+
+ 3. Copying Restrictions. You will not sell or otherwise distribute commercially
+ these programs or derivatives to any other party, whether with or without
+ consideration.
+
+ 4. Ownership of Software. You will not obtain, and will not attempt to
+ obtain copyright coverage thereon without the express purpose written
+ consent of The Scripps Research Institute and Dr. Sanner.
+
+ 5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY
+ FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
+ ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY
+ DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+
+ 6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES,
+ INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE
+ IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE
+ NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
+ MODIFICATIONS.
+
diff --git a/licenses/vampir b/licenses/vampir
new file mode 100644
index 000000000..70f15aa22
--- /dev/null
+++ b/licenses/vampir
@@ -0,0 +1,36 @@
+Copyright (c) 2005-2013, ZIH, TU Dresden, Federal Republic of Germany
+
+Copyright (c) 1998-2005, Forschungszentrum Juelich, Juelich Supercomputing
+ Centre, Federal Republic of Germany
+
+Copyright (c) 2007-2008, High Performance Computing Center Stuttgart,
+ Federal Republic of Germany
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+- Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+- Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+- Neither the name of ZIH, TU Dresden, Forschungszentrum Juelich, Juelich
+Supercomputing Centre, or High Performance Computing Center Stuttgart, nor the
+names of its contributors may be used to endorse or promote products derived
+from this software without pecific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
diff --git a/media-gfx/PhiloGL/ChangeLog b/media-gfx/PhiloGL/ChangeLog
index 55b169465..305d9b9e0 100644
--- a/media-gfx/PhiloGL/ChangeLog
+++ b/media-gfx/PhiloGL/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for media-gfx/PhiloGL
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> PhiloGL-1.4.3.ebuild,
+ metadata.xml:
+ Move to EAPI=5 and fix quoting
+
17 Feb 2012; Kacper Kowalik <xarthisius@gentoo.org> PhiloGL-1.4.2.ebuild:
[media-gfx/PhiloGL] don't mess with paths and follow upstream as close as
possible
diff --git a/media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild b/media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild
index ad07e5bec..9ee4e2183 100644
--- a/media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild
+++ b/media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
DESCRIPTION="WebGL Framework for Data Vis, Creative Coding and Game Development"
HOMEPAGE="http://www.senchalabs.org/philogl/"
@@ -17,7 +17,7 @@ S=${WORKDIR}
src_prepare() {
if use examples ; then
- for f in $(find ${S}/examples -name index.html); do
+ for f in $(find "${S}"/examples -name index.html); do
sed -e "s:../../../build:/usr/share/${PN}/build:g" \
-e "s:../../build:/usr/share/${PN}/build:g" \
-i ${f} || die
diff --git a/media-gfx/PhiloGL/metadata.xml b/media-gfx/PhiloGL/metadata.xml
index 6629da3fa..ef58ee263 100644
--- a/media-gfx/PhiloGL/metadata.xml
+++ b/media-gfx/PhiloGL/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>xarthisius@gentoo.org</email>
- <name>Kacper Kowalik</name>
- </maintainer>
+ <maintainer>
+ <email>xarthisius@gentoo.org</email>
+ <name>Kacper Kowalik</name>
+ </maintainer>
</pkgmetadata>
diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog
index d21056bc0..7b0a6c211 100644
--- a/media-gfx/librecad/ChangeLog
+++ b/media-gfx/librecad/ChangeLog
@@ -1,7 +1,16 @@
# ChangeLog for media-gfx/librecad
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header$
+ 14 Apr 2013; Dongxu Li <dongxuli2011@gmail.com> +librecad-1.0.3.ebuild,
+ +librecad-2.0.0_alpha5.ebuild:
+ Versions bumped to 1.0.3 and 2.0.0beta5
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> -librecad-1.0.1.ebuild,
+ librecad-1.0.2.ebuild, -librecad-2.0.0_alpha3.ebuild,
+ librecad-2.0.0_alpha4.ebuild, librecad-9999.ebuild, metadata.xml:
+ Update to new qt deps names; drop old
+
15 Ju1 2012; Dongxu Li <dongxuli2011@gmail.com> librecad-9999.ebuild,librecad-2.0.0alpha4.ebuild
Dependency fix, bug#426730
diff --git a/media-gfx/librecad/Manifest b/media-gfx/librecad/Manifest
index b735c7dcd..eb9d46229 100644
--- a/media-gfx/librecad/Manifest
+++ b/media-gfx/librecad/Manifest
@@ -1,4 +1,3 @@
-DIST librecad-1.0.1.tar.gz 4717733 SHA256 218d58d66c3b665c0998b79dda2255985c75f5c150611e70c2e7c1b87655c85b SHA512 72ede3094c4f5e8167e67aace2ebc68334fc88b873c11980b345ea1416dc2659673ef4b8867fd00e61593915eae747e8098896fd1c74a5d85f2c85aa875e1cf2 WHIRLPOOL 5189e77dc465e4776b7b536566f359a8b72da802d9080701b33975e585ba63c70dd67006df6f5f857c37d7d36ddc9cf36c9485ebe9e826d6be85c62c3cf4fb26
-DIST librecad-1.0.2.tar.gz 4577653 SHA256 13ee7e401e4f5fbc68c2e017b7189bec788038f4f6e77f559861ceb8cfb1907d SHA512 d3afd967a72e36067634a5ad8bf93ff7ab874f72ed8e86dd13632d4c700ec3f3f3eac40b2a44ba516cadb3a1c117570f091dd92cbfa3957d004ecba933d02f39 WHIRLPOOL 7cd0b2ecba9498ba41ab49c36bbcd49ec2127a7ac0ad235593e58479342f0f0bb859ffa3c2fa7e687859a6a7812b6c5c96b43fdc939f4a18b326cf8e1e4e0f5a
-DIST librecad-2.0.0_alpha3.tar.gz 13830843 SHA256 a66fe79f34fdcf97b25e91001313eb21ec6c33241acf129b7213daf6f9beca97 SHA512 abb58d2adc92bb34e03abb782886ceea0545d5c423a6c9c3974db755ddb5171d5c295f19f22e622f5dedf3fc0bb67196720d8b169c6857ae78815d4012990a54 WHIRLPOOL e2757f7545ef49e40b9c88ef073b778068ea6b8c7d90aee8337fbd902f01b8172a63501bf7ddb526b5e54c4324f177e983ad5245cdde14cae1f610edbb6eab15
-DIST librecad-2.0.0_alpha4.tar.gz 14408276 RMD160 cf8215ad24140dfbd75c52037fc2b10e82b93a2f SHA1 127d8bffbbfb5e964eee7266ec63ee9c93f7efe2 SHA256 b62e5153d1158d1a5d45f8c66b59512bf5ed7404ac2765704d5f70eb057ebbfd SHA512 3f1f447548057e9bee81b40ed0dcce5601c6e55aa427c0488d9a61f7710faa62d4cea4c83e4a424f034581ae9c98a7c10ee7f9d878a2d73cc793a525221b3b32 WHIRLPOOL cfba88d782467f2b6e75ab97b9fc50dff30fb00b50e2ed22f888869573738b0bc6f89884c561478b5f98ea8cbb7a1d32700dbd38be8f69cb6f21a875bd375774
+DIST librecad-1.0.2.tar.gz 4577097 SHA256 f04ad98b6c9bc0e8f748ef99a7052794155f246c36663e09508810d9acebadad SHA512 4cb8732b047ba01e7d796c51bbc1300e4ee3b674a4ca65c6ff3f18acd0107d3d0e83610f45af86dc164cbf22241558dddc2fb77e31bd2fb33425cb6d7b582889 WHIRLPOOL 73099244f56eb3953fb0a7b80aa5ea3a20adcbaa19a40ca51c14501316e7ebec2a44e30bb669e6ed6797a74c42b0640f959e648c3cee8c7865a9a5f3427b1591
+DIST librecad-1.0.3.tar.gz 4578450 SHA256 8c2f5a7e55a4ae41a9bd47e2e7981577c740edd526e1f305cd6cbf581d053f30 SHA512 5a8e6e612bc954f3af0dfc26d1fc19938c80e216ac252fb65a38a13651c6e2313d593a3ee834ecc98bbd72a4dfd28ef1c39dd9ed6a6f9140d28b765edb59bee9 WHIRLPOOL d8157af2021bba2cee626d023125045455a2fe5f453ae065c9660be61f4c0d687a1c72957d1af1aa640cfde3815625bb7d0899dc5541fcb82bfe0eea4cfad6c6
+DIST librecad-2.0.0_beta5.tar.gz 15196079 SHA256 8d21a2b887d65ea28ac7fde1d0dea373f8267767e33ae26c0207ec1f6d42656f SHA512 22ec041a0a36bd9f59d2bf22aa343824b54c83febeb8b6fd836e4e3a821617ae80f2e5b7c38250b5791b946f8494561b49d9a880b49383c52395a04f0cb57547 WHIRLPOOL 20805394d0576c380b491fe7c02af3adfcbf09850ff84dee3155206746746e5f39b9cc2556836e74bd9c9449e7c50757b9f3ff3fcab6083abd140d0a3934ed06
diff --git a/media-gfx/librecad/librecad-1.0.2.ebuild b/media-gfx/librecad/librecad-1.0.2.ebuild
index 0dc61c5ed..c9f90681f 100644
--- a/media-gfx/librecad/librecad-1.0.2.ebuild
+++ b/media-gfx/librecad/librecad-1.0.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -8,7 +8,7 @@ inherit qt4-r2 eutils
DESCRIPTION="An generic 2D CAD program"
HOMEPAGE="http://www.librecad.org/"
-SRC_URI="https://nodeload.github.com/LibreCAD/LibreCAD/tarball/v${PV} -> ${P}.tar.gz"
+SRC_URI="https://github.com/LibreCAD/LibreCAD/archive/v1.0.2.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
@@ -16,9 +16,9 @@ KEYWORDS="~amd64 ~x86"
IUSE="debug doc"
RDEPEND="
- x11-libs/qt-gui[qt3support]
- x11-libs/qt-assistant:4
- x11-libs/qt-qt3support:4
+ dev-qt/qtgui[qt3support]
+ dev-qt/qthelp:4
+ dev-qt/qt3support:4
dev-cpp/muParser
"
diff --git a/media-gfx/librecad/librecad-1.0.1.ebuild b/media-gfx/librecad/librecad-1.0.3.ebuild
index c4006fb16..3c9374764 100644
--- a/media-gfx/librecad/librecad-1.0.1.ebuild
+++ b/media-gfx/librecad/librecad-1.0.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -8,7 +8,7 @@ inherit qt4-r2 eutils
DESCRIPTION="An generic 2D CAD program"
HOMEPAGE="http://www.librecad.org/"
-SRC_URI="https://nodeload.github.com/LibreCAD/LibreCAD/tarball/v${PV} -> ${P}.tar.gz"
+SRC_URI="https://github.com/LibreCAD/LibreCAD/archive/v1.0.3.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
@@ -16,9 +16,12 @@ KEYWORDS="~amd64 ~x86"
IUSE="debug doc"
RDEPEND="
- x11-libs/qt-gui[qt3support]
- x11-libs/qt-assistant:4
- x11-libs/qt-qt3support:4"
+ dev-qt/qtgui[qt3support]
+ dev-qt/qthelp:4
+ dev-qt/qt3support:4
+ dev-cpp/muParser
+ "
+
DEPEND="${RDEPEND}"
src_unpack() {
@@ -27,7 +30,7 @@ src_unpack() {
}
src_prepare() {
-sed -i -e "s:\\\$\+system(git describe --tags):1.0.0:" "${PN}.pro"
+sed -i -e "s:\\\$\+system(git describe --tags):1.0.3:" "${PN}.pro"
}
src_install() {
diff --git a/media-gfx/librecad/librecad-2.0.0_alpha3.ebuild b/media-gfx/librecad/librecad-2.0.0_alpha3.ebuild
deleted file mode 100644
index 99391e82b..000000000
--- a/media-gfx/librecad/librecad-2.0.0_alpha3.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-inherit qt4-r2 eutils flag-o-matic
-
-DESCRIPTION="An generic 2D CAD program"
-HOMEPAGE="http://www.librecad.org/"
-SRC_URI="https://nodeload.github.com/LibreCAD/LibreCAD/tarball/${PV/_/} ->
-${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug doc"
-
-DEPEND="
- x11-libs/qt-assistant:4
- x11-libs/qt-gui:4
- dev-libs/boost
- dev-cpp/muParser
- "
-
-RDEPEND="${DEPEND}"
-
-src_unpack() {
- unpack ${A}
- mv * ${P}
-}
-
-src_prepare() {
- append-cppflags "-std=c++0x"
- sed -i -e '/RS_VECTOR2D/ s/^#//' librecad/src/src.pro
-}
-
-src_install() {
- qt4-r2 eutils_src_install
- dobin unix/librecad
- insinto /usr/share/"${PN}"
- doins -r unix/resources/*
- if use doc ; then
- dohtml -r support/doc/*
- fi
- doicon res/main/"${PN}".png
- make_desktop_entry "${PN}" LibreCAD "${PN}.png" Graphics
-}
diff --git a/media-gfx/librecad/librecad-2.0.0_alpha4.ebuild b/media-gfx/librecad/librecad-2.0.0_beta5.ebuild
index 5c3c639ff..a16e4c8f6 100644
--- a/media-gfx/librecad/librecad-2.0.0_alpha4.ebuild
+++ b/media-gfx/librecad/librecad-2.0.0_beta5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -8,7 +8,7 @@ inherit qt4-r2 eutils flag-o-matic
DESCRIPTION="An generic 2D CAD program"
HOMEPAGE="http://www.librecad.org/"
-SRC_URI="https://nodeload.github.com/LibreCAD/LibreCAD/tarball/${PV/_/} ->
+SRC_URI="https://github.com/LibreCAD/LibreCAD/archive/2.0.0beta5.tar.gz ->
${P}.tar.gz"
LICENSE="GPL-2"
@@ -17,9 +17,9 @@ KEYWORDS="~amd64 ~x86"
IUSE="debug doc"
DEPEND="
- x11-libs/qt-assistant:4
- x11-libs/qt-gui:4
- x11-libs/qt-svg:4
+ dev-qt/qthelp:4
+ dev-qt/qtgui:4
+ dev-qt/qtsvg:4
dev-libs/boost
dev-cpp/muParser
media-libs/freetype
diff --git a/media-gfx/librecad/librecad-9999.ebuild b/media-gfx/librecad/librecad-9999.ebuild
index ef083b360..d3db6f76e 100644
--- a/media-gfx/librecad/librecad-9999.ebuild
+++ b/media-gfx/librecad/librecad-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -15,9 +15,9 @@ IUSE="debug doc"
EGIT_REPO_URI="https://github.com/LibreCAD/LibreCAD.git"
DEPEND="${RDEPEND}
- x11-libs/qt-gui:4
- x11-libs/qt-assistant:4
- x11-libs/qt-svg:4
+ dev-qt/qtgui:4
+ dev-qt/qthelp:4
+ dev-qt/qtsvg:4
dev-libs/boost
dev-cpp/muParser
media-libs/freetype
diff --git a/media-gfx/librecad/metadata.xml b/media-gfx/librecad/metadata.xml
index baf99ed1d..c79d2dfcf 100644
--- a/media-gfx/librecad/metadata.xml
+++ b/media-gfx/librecad/metadata.xml
@@ -1,11 +1,15 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci</herd>
- <maintainer>
- <email>dongxuli2011@gmail.com</email>
- <name>Dongxu Li</name>
- <description>Package maintainer and upstream developer</description>
- </maintainer>
- <longdescription>LibreCAD is a 2D CAD drawing tool based on the community edition of QCad (www.qcad.org). LibreCAD has been re-structured and ported to qt4 and works natively cross platform.</longdescription>
+ <herd>sci</herd>
+ <maintainer>
+ <email>dongxuli2011@gmail.com</email>
+ <name>Dongxu Li</name>
+ <description>Package maintainer and upstream developer</description>
+ </maintainer>
+ <longdescription>
+LibreCAD is a 2D CAD drawing tool based on the community edition of QCad
+(www.qcad.org). LibreCAD has been re-structured and ported to qt4 and
+works natively cross platform.
+</longdescription>
</pkgmetadata>
diff --git a/profiles/arch.list b/profiles/arch.list
index e69de29bb..db7b9fa3a 100644
--- a/profiles/arch.list
+++ b/profiles/arch.list
@@ -0,0 +1,44 @@
+alpha
+amd64
+amd64-fbsd
+arm
+hppa
+ia64
+m68k
+mips
+ppc
+ppc64
+s390
+sh
+sparc
+sparc-fbsd
+x86
+x86-fbsd
+
+# Prefix keywords
+ppc-aix
+x86-freebsd
+x64-freebsd
+sparc64-freebsd
+hppa-hpux
+ia64-hpux
+x86-interix
+amd64-linux
+arm-linux
+ia64-linux
+ppc64-linux
+x86-linux
+ppc-macos
+x86-macos
+x64-macos
+m68k-mint
+x86-netbsd
+ppc-openbsd
+x86-openbsd
+x64-openbsd
+sparc-solaris
+sparc64-solaris
+x64-solaris
+x86-solaris
+x86-winnt
+x86-cygwin
diff --git a/profiles/hardened/package.mask b/profiles/hardened/package.mask
deleted file mode 100644
index 885811b75..000000000
--- a/profiles/hardened/package.mask
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-# When you add an entry to the top of this file, add your name, the date, and
-# an explanation of why something is getting masked. Please be extremely
-# careful not to commit atoms that are not valid, as it can cause large-scale
-# breakage, especially if it ends up in the daily snapshot.
-#
-## Example:
-##
-## # Dev E. Loper <developer@gentoo.org> (28 Jun 2012)
-## # Masking foo USE flag until we can get the
-## # foo stuff to work properly again (bug 12345)
-## =media-video/mplayer-0.90_pre5 foo
-## =media-video/mplayer-0.90_pre5-r1 foo
-#
-
-#--- END OF EXAMPLES ---
-
-# Christoph Junghans <ottxor@gentoo.org> (24 Dec 2012)
-# Needs multilib
-dev-util/ccache-icc
-
-# Justin Lecher <jlec@gentoo.org> (11 Nov 2011)
-# Needs multilib
-sci-chemistry/nmrpipe
diff --git a/profiles/package.mask b/profiles/package.mask
index 094b0dc22..1c816acbe 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -30,6 +30,18 @@
#--- END OF EXAMPLES ---
+# Justin Lecher <jlec@gentoo.org> (03 March 2013)
+# Mask for missing license
+sci-biology/lastz
+sci-biology/phylobayes
+
+# Justin Lecher <jlec@gentoo.org> (03 March 2013)
+# Missing deps
+sci-biology/gbrowse
+sci-mathematics/surfer
+dev-python/pymvpa
+sci-biology/artemis-bin
+
# Nicolas Bock <nicolasbock@gmail.com> (05 July 2012)
# live ebuild
=sci-chemistry/freeon-9999
diff --git a/sci-astronomy/astrometry/ChangeLog b/sci-astronomy/astrometry/ChangeLog
index 1f6a71d65..f0751a374 100644
--- a/sci-astronomy/astrometry/ChangeLog
+++ b/sci-astronomy/astrometry/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-astronomy/astrometry
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> astrometry-0.38.ebuild,
+ metadata.xml:
+ Clean wrong space and blank lines
+
*astrometry-0.38 (09 May 2012)
09 May 2012; Sébastien Fabbro <bicatali@gentoo.org> +astrometry-0.38.ebuild,
diff --git a/sci-astronomy/astrometry/astrometry-0.38.ebuild b/sci-astronomy/astrometry/astrometry-0.38.ebuild
index 35146c249..97ce21611 100644
--- a/sci-astronomy/astrometry/astrometry-0.38.ebuild
+++ b/sci-astronomy/astrometry/astrometry-0.38.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -12,13 +12,13 @@ DESCRIPTION="Automated astrometric calibration programs and service"
HOMEPAGE="http://astrometry.net/"
SRC_URI="${HOMEPAGE}/downloads/${MYP}.tar.bz2"
-LICENSE="GPL-2"
SLOT="0"
-
+LICENSE="GPL-2"
KEYWORDS="~amd64 ~x86"
IUSE=""
-RDEPEND="dev-python/numpy
+RDEPEND="
+ dev-python/numpy
media-libs/libpng
media-libs/netpbm
sci-astronomy/wcslib
@@ -41,7 +41,6 @@ src_prepare() {
"${FILESDIR}"/${PV}-array-bounds.patch
}
-
src_compile() {
emake
emake extra
diff --git a/sci-astronomy/astrometry/metadata.xml b/sci-astronomy/astrometry/metadata.xml
index 0fa913062..df28cb837 100644
--- a/sci-astronomy/astrometry/metadata.xml
+++ b/sci-astronomy/astrometry/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-astronomy</herd>
-<longdescription lang="en">
+ <herd>sci-astronomy</herd>
+ <longdescription lang="en">
If you have astronomical imaging of the sky with celestial
coordinates you do not know—or do not trust—then Astrometry.net is
for you. Input an image and we'll give you back astrometric
diff --git a/sci-astronomy/eye/ChangeLog b/sci-astronomy/eye/ChangeLog
index 69d34e3f3..153dbfcb9 100644
--- a/sci-astronomy/eye/ChangeLog
+++ b/sci-astronomy/eye/ChangeLog
@@ -1,7 +1,9 @@
# ChangeLog for sci-astronomy/eye
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> eye-9999.ebuild, metadata.xml:
+ Clean wrong space and blank lines
*eye-9999 (09 Jul 2012)
diff --git a/sci-astronomy/eye/eye-9999.ebuild b/sci-astronomy/eye/eye-9999.ebuild
index 3a0934122..ee72144ca 100644
--- a/sci-astronomy/eye/eye-9999.ebuild
+++ b/sci-astronomy/eye/eye-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -16,7 +16,6 @@ fi
inherit ${_SVN} autotools
-
DESCRIPTION="Enhance astronomical object extraction with neural network filters"
HOMEPAGE="http://www.astromatic.net/software/eye"
diff --git a/sci-astronomy/eye/metadata.xml b/sci-astronomy/eye/metadata.xml
index 9c2032f73..f5351e412 100644
--- a/sci-astronomy/eye/metadata.xml
+++ b/sci-astronomy/eye/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-astronomy</herd>
-<longdescription lang="en">
+ <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
associate these input stimuli to the corresponding response in one
diff --git a/sci-astronomy/stiff/ChangeLog b/sci-astronomy/stiff/ChangeLog
index 5d562b9e3..702e17376 100644
--- a/sci-astronomy/stiff/ChangeLog
+++ b/sci-astronomy/stiff/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-astronomy/stiff
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-astronomy/stiff/ChangeLog,v 1.7 2011/08/04 18:33:30 bicatali Exp $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> stiff-9999.ebuild, metadata.xml:
+ Move to EAPI=5 and autotools-utils
+
*stiff-9999 (09 Jul 2012)
09 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> +stiff-9999.ebuild,
diff --git a/sci-astronomy/stiff/metadata.xml b/sci-astronomy/stiff/metadata.xml
index 320c9fec8..70689020c 100644
--- a/sci-astronomy/stiff/metadata.xml
+++ b/sci-astronomy/stiff/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-astronomy</herd>
-<longdescription lang="en">
+ <herd>sci-astronomy</herd>
+ <longdescription lang="en">
STIFF is a program that convert scientific FITS images to the
more popular TIFF, in 8 (grayscale) or 24 (true colour: 3 times 8) bits per
pixel.
diff --git a/sci-astronomy/stiff/stiff-9999.ebuild b/sci-astronomy/stiff/stiff-9999.ebuild
index 961d68bf5..8dacd157b 100644
--- a/sci-astronomy/stiff/stiff-9999.ebuild
+++ b/sci-astronomy/stiff/stiff-9999.ebuild
@@ -1,9 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-astronomy/stiff/stiff-2.1.3.ebuild,v 1.1 2011/04/10 14:45:35 bicatali Exp $
-EAPI=4
-
+EAPI=5
if [[ ${PV} == "9999" ]] ; then
_SVN=subversion
@@ -15,7 +14,9 @@ else
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
fi
-inherit ${_SVN} autotools
+AUTOTOOLS_AUTORECONF=true
+
+inherit ${_SVN} autotools-utils
DESCRIPTION="Converts astronomical FITS images to the TIFF format"
HOMEPAGE="http://astromatic.iap.fr/software/stiff"
@@ -24,20 +25,18 @@ LICENSE="GPL-3"
SLOT="0"
IUSE="doc threads"
-RDEPEND="media-libs/tiff
+RDEPEND="
+ media-libs/tiff
virtual/jpeg
sys-libs/zlib"
DEPEND="${RDEPEND}"
-src_prepare() {
- eautoreconf
-}
-
src_configure() {
- econf $(use_enable threads)
+ local myeconfargs=( $(use_enable threads) )
+ autotools-utils_src_configure
}
src_install () {
- default
- use doc && dodoc doc/*
+ use doc && DOCS=( doc/. )
+ autotools-utils_src_install
}
diff --git a/sci-astronomy/zebra/ChangeLog b/sci-astronomy/zebra/ChangeLog
index 72dc7db77..d4e0f1ae8 100644
--- a/sci-astronomy/zebra/ChangeLog
+++ b/sci-astronomy/zebra/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-astronomy/zebra
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 22 Feb 2013; Justin Lecher <jlec@gentoo.org> zebra-1.01.ebuild, metadata.xml:
+ Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
+
*zebra-1.01 (17 May 2012)
17 May 2012; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml,
diff --git a/sci-astronomy/zebra/metadata.xml b/sci-astronomy/zebra/metadata.xml
index b8ef7bb1f..1edf84d77 100644
--- a/sci-astronomy/zebra/metadata.xml
+++ b/sci-astronomy/zebra/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-astronomy</herd>
-<longdescription lang="en">
+ <herd>sci-astronomy</herd>
+ <longdescription lang="en">
The Zurich Extragalactic Bayesian Redshift Analyzer is a software to
compute and analyze photometric redshifts of galaxies.
ZEBRA combines and extends several of the classical approaches to
diff --git a/sci-astronomy/zebra/zebra-1.01.ebuild b/sci-astronomy/zebra/zebra-1.01.ebuild
index 7463821b1..d4f2e76f4 100644
--- a/sci-astronomy/zebra/zebra-1.01.ebuild
+++ b/sci-astronomy/zebra/zebra-1.01.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
-inherit autotools-utils
+inherit autotools-utils toolchain-funcs
DESCRIPTION="Galaxy redhift Bayesian analyzer"
HOMEPAGE="http://www.astro.phys.ethz.ch/exgal_ocosm/zebra/index.html"
@@ -15,20 +15,20 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="doc examples"
-RDEPEND="sci-libs/gsl
+RDEPEND="
+ sci-libs/gsl
sci-libs/lapackpp
virtual/blas
virtual/cblas
virtual/lapack"
-
DEPEND="${RDEPEND}
virtual/pkgconfig"
src_configure() {
myeconfargs+=(
- --with-blas="$(pkg-config --libs blas)"
- --with-cblas="$(pkg-config --libs cblas)"
- --with-lapack="$(pkg-config --libs lapack)"
+ --with-blas="$($(tc-getPKG_CONFIG) --libs blas)"
+ --with-cblas="$($(tc-getPKG_CONFIG) --libs cblas)"
+ --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
)
autotools-utils_src_configure
}
diff --git a/sci-biology/Gambit/ChangeLog b/sci-biology/Gambit/ChangeLog
new file mode 100644
index 000000000..d41e6a52a
--- /dev/null
+++ b/sci-biology/Gambit/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/Gambit
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> Gambit-0.4.145.ebuild,
+ metadata.xml:
+ Update to new qt deps names
+
diff --git a/sci-biology/Gambit/Gambit-0.4.145.ebuild b/sci-biology/Gambit/Gambit-0.4.145.ebuild
index ebc5f6235..52859bfb9 100644
--- a/sci-biology/Gambit/Gambit-0.4.145.ebuild
+++ b/sci-biology/Gambit/Gambit-0.4.145.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -16,8 +16,8 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND="x11-libs/qt-core:4
- x11-libs/qt-gui:4"
+DEPEND="dev-qt/qtcore:4
+ dev-qt/qtgui:4"
RDEPEND="${DEPEND}
sci-biology/samtools"
diff --git a/sci-biology/Gambit/Manifest b/sci-biology/Gambit/Manifest
index 81f4846b6..b53686f60 100644
--- a/sci-biology/Gambit/Manifest
+++ b/sci-biology/Gambit/Manifest
@@ -1,2 +1,2 @@
-DIST GambitDocumentation_v0.4.145.pdf 1061985 RMD160 f24642f26d1f8974e6f7668306f1e9bad6d556f2 SHA1 197508b85911f2175dc777b20d53c0fba5901a94 SHA256 f0d28fedab07007244a2a6f6292b7c445843a336878583ae177c22528ede30c9
-DIST Gambit_v0.4.145_src.tar.gz 246624 RMD160 26ecd68915c1ff48dff28f81ae7d7113a0036ee6 SHA1 c33faf2f89df8dfc6bc22d21031cabc85b397ab0 SHA256 1c1ed7fdb3b9a5007f2daeef2b96033d7145a767dd526339dbb928dd27626268
+DIST GambitDocumentation_v0.4.145.pdf 1061985 SHA256 f0d28fedab07007244a2a6f6292b7c445843a336878583ae177c22528ede30c9
+DIST Gambit_v0.4.145_src.tar.gz 246624 SHA256 1c1ed7fdb3b9a5007f2daeef2b96033d7145a767dd526339dbb928dd27626268
diff --git a/sci-biology/Gambit/metadata.xml b/sci-biology/Gambit/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/Gambit/metadata.xml
+++ b/sci-biology/Gambit/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/YASRA/ChangeLog b/sci-biology/YASRA/ChangeLog
index 17ca0d95f..77b3b5e07 100644
--- a/sci-biology/YASRA/ChangeLog
+++ b/sci-biology/YASRA/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/YASRA
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> YASRA-2.1.ebuild, metadata.xml:
+ Drop keywords as deps are unkeyworded
+
*YASRA-2.1 (17 Jan 2012)
17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +YASRA-2.1.ebuild,
diff --git a/sci-biology/YASRA/YASRA-2.1.ebuild b/sci-biology/YASRA/YASRA-2.1.ebuild
index 3c3e10d58..c8288fc52 100644
--- a/sci-biology/YASRA/YASRA-2.1.ebuild
+++ b/sci-biology/YASRA/YASRA-2.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -10,7 +10,7 @@ SRC_URI="http://www.bx.psu.edu/miller_lab/dist/YASRA-"${PV}".tar.gz"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE=""
DEPEND=""
diff --git a/sci-biology/YASRA/metadata.xml b/sci-biology/YASRA/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/YASRA/metadata.xml
+++ b/sci-biology/YASRA/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 7009cae88..f121b1666 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/amos
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 19 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild:
+ Bump to latest git HEAD, fixes qt problems, #348031
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild, metadata.xml:
+ Update to new qt deps names
+
22 May 2012; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild:
Bump to EAPI=4, remove unnecessary bits
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index ed45785d1..67180f85f 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -1,53 +1,28 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
-[ "$PV" == "9999" ] && CVS=cvs
+[ "$PV" == "9999" ] && VCS=git-2
-inherit eutils ${CVS}
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils ${VCS}
DESCRIPTION="Genome assembly package live cvs sources"
HOMEPAGE="http://sourceforge.net/projects/amos"
-ECVS_SERVER="amos.cvs.sourceforge.net:/cvsroot/amos"
-ECVS_AUTH="pserver"
-ECVS_MODULE="AMOS"
-ECVS_BRANCH="HEAD"
-ECVS_USER="anonymous"
-ECVS_PASS=""
+SRC_URI=""
+EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
-LICENSE="GPL-2"
+LICENSE="Artistic"
SLOT="0"
-IUSE=""
KEYWORDS=""
+IUSE=""
DEPEND="
dev-libs/boost
- x11-libs/qt-qt3support"
+ dev-qt/qtcore:4"
RDEPEND="${DEPEND}
dev-perl/DBI
sci-biology/mummer"
-
-S="${DISTDIR}"/cvs-src/AMOS/AMOS/
-
-src_unpack() {
- ECVS_TOP_DIR="${DISTDIR}/cvs-src/${ECVS_MODULE}"
- cvs_src_unpack
-}
-
-src_prepare(){
- epatch "${FILESDIR}"/amos.m4.patch
-}
-
-src_configure() {
- ./bootstrap || die
- #CFLAGS=$CFLAGS' -I/usr/include/qt4/Qt' CXXFLAGS=$CXXFLAGS' -I/usr/include/qt4/Qt' econf --enable-all --with-Qt-include-dir=/usr/include/qt4 --with-Qt-lib-dir=/usr/lib/qt4 --with-Qt-bin-dir=/usr/bin --with-Qt-lib=Qt3Support
- econf --enable-all
- einfo "No hawkeye and other Qt3-based apps installed, sorry, no qt3 anynore on Gentoo"
-}
-
-src_compile() {
- # TODO: force MAKEOPTS=-j1 because it seems -j6 is exploting some dependency issue in Makefiles
- MAKEOPTS=-j1 emake DESTDIR="${D}"
-}
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
index b6e8ca8b0..973202fc7 100644
--- a/sci-biology/amos/metadata.xml
+++ b/sci-biology/amos/metadata.xml
@@ -1,10 +1,15 @@
<?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>
- <longdescription>AMOS is collection of tools and class interfaces for the assembly of DNA sequencing reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation</longdescription>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <longdescription>
+AMOS is collection of tools and class interfaces for the assembly of DNA
+sequencing reads. The package includes a robust infrastructure, modular assembly
+pipelines, and tools for overlapping, consensus generation, contigging, and
+assembly manipulation
+</longdescription>
</pkgmetadata>
diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog
index 9659b9085..9885717fd 100644
--- a/sci-biology/artemis-bin/ChangeLog
+++ b/sci-biology/artemis-bin/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/artemis-bin
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> artemis-bin-13.2.12.ebuild,
+ metadata.xml:
+ Clean whitespace errors
+
*artemis-bin-13.2.12 (08 Jan 2012)
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/artemis-bin/Manifest b/sci-biology/artemis-bin/Manifest
index a423d4495..db279ac09 100644
--- a/sci-biology/artemis-bin/Manifest
+++ b/sci-biology/artemis-bin/Manifest
@@ -1 +1 @@
-DIST artemis_compiled_v13.2.12.tar.gz 8935513 RMD160 b795ed5c1fa8418634d46ed269decec20cc74f5b SHA1 ef5652515efe0756c23e08c6694d77ea361efdd2 SHA256 71e8304947ecda531a7e2a8b2cce84a75c5ada19be43c854eb524012c872a094
+DIST artemis_compiled_v13.2.12.tar.gz 8935513 SHA256 71e8304947ecda531a7e2a8b2cce84a75c5ada19be43c854eb524012c872a094
diff --git a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild b/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
index a62f70001..e457ac8ad 100644
--- a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -19,4 +19,3 @@ DEPEND="sci-biology/samtools
sci-biology/bamview"
RDEPEND="${DEPEND}
>=virtual/jre-1.5"
-
diff --git a/sci-biology/artemis-bin/metadata.xml b/sci-biology/artemis-bin/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/artemis-bin/metadata.xml
+++ b/sci-biology/artemis-bin/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/blasr/ChangeLog b/sci-biology/blasr/ChangeLog
index f10ba2293..7a26c1b35 100644
--- a/sci-biology/blasr/ChangeLog
+++ b/sci-biology/blasr/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/blasr
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> blasr-9999.ebuild:
+ correct license
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> blasr-9999.ebuild, metadata.xml:
+ Migrate to git2 eclass and EAPI=5
+
*blasr-9999 (22 Mar 2012)
22 Mar 2012; Andrey Kislyuk <weaver@gentoo.org> +blasr-9999.ebuild,
diff --git a/sci-biology/blasr/Manifest b/sci-biology/blasr/Manifest
deleted file mode 100644
index f0cffa05b..000000000
--- a/sci-biology/blasr/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-EBUILD blasr-9999.ebuild 754 RMD160 ada0b6b464ddccfe5dc9e785814812321a747580 SHA1 45f6852797f5b4b7bc3119a833da677cfb49a36c SHA256 276896a1e64d5940abd3b500a34a4b26e88be72974e7b3733c2d21e9725ce38c
-MISC ChangeLog 269 RMD160 d21a6fc5e4aad19cb2c7f551588aabfe06ee36cb SHA1 ea4a5afd80d0c4bc409e52ba14d4cd73c60004bc SHA256 0941218f7fd828b2662b2bbae81f1baead5cb6702dacd48ae2e77603a79079a1
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
index 94e874fa1..9d620badb 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -1,21 +1,20 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-9999.ebuild,v 1.1 2011/10/31 21:18:17 weaver Exp $
-EAPI=4
+EAPI=5
MY_HASH=885c33a
-EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
-
-inherit git
+inherit git-2
DESCRIPTION="The PacBio long read aligner"
HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
SRC_URI=""
+EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
-LICENSE="as-is"
+LICENSE="blasr"
SLOT="0"
IUSE=""
KEYWORDS=""
@@ -29,5 +28,5 @@ ASSEMBLY_HOME="${D}/usr"
src_install() {
dodir /usr/bin
- make install ASSEMBLY_HOME="${D}/usr" || die
+ emake install ASSEMBLY_HOME="${ED}/usr" || die
}
diff --git a/sci-biology/blasr/metadata.xml b/sci-biology/blasr/metadata.xml
index 3302123e5..fc7c76942 100644
--- a/sci-biology/blasr/metadata.xml
+++ b/sci-biology/blasr/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- </maintainer>
- <herd>sci-biology</herd>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/cluster/ChangeLog b/sci-biology/cluster/ChangeLog
index 9a490de51..5924d8d77 100644
--- a/sci-biology/cluster/ChangeLog
+++ b/sci-biology/cluster/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/cluster
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> cluster-1.50.ebuild,
+ cluster-1.50-r1.ebuild, metadata.xml:
+ Correct motif dep naming
+
09 Jun 2012; Justin Lecher <jlec@gentoo.org> cluster-1.50.ebuild,
cluster-1.50-r1.ebuild:
Correct masking, #419999
diff --git a/sci-biology/cluster/cluster-1.50-r1.ebuild b/sci-biology/cluster/cluster-1.50-r1.ebuild
index 37589b677..8e6150988 100644
--- a/sci-biology/cluster/cluster-1.50-r1.ebuild
+++ b/sci-biology/cluster/cluster-1.50-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -13,7 +13,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="X"
-DEPEND="X? ( x11-libs/openmotif )"
+DEPEND="X? ( x11-libs/motif )"
RDEPEND="
X? ( x11-misc/xdg-utils app-text/mupdf )"
diff --git a/sci-biology/cluster/cluster-1.50.ebuild b/sci-biology/cluster/cluster-1.50.ebuild
index 9e388579f..b9195f866 100644
--- a/sci-biology/cluster/cluster-1.50.ebuild
+++ b/sci-biology/cluster/cluster-1.50.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -13,7 +13,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="X"
-DEPEND="X? ( x11-libs/openmotif )"
+DEPEND="X? ( x11-libs/motif )"
RDEPEND="
!>=media-gfx/graphviz-2.28.0
X? ( x11-misc/xdg-utils app-text/mupdf )"
diff --git a/sci-biology/cluster/metadata.xml b/sci-biology/cluster/metadata.xml
index 94729cbd6..11a0b2b82 100644
--- a/sci-biology/cluster/metadata.xml
+++ b/sci-biology/cluster/metadata.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
- <maintainer>
- <email>je_fro@gentoo.org</email>
- <name>Jeff Gardner</name>
- </maintainer>
- <longdescription lang="en">
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>je_fro@gentoo.org</email>
+ <name>Jeff Gardner</name>
+ </maintainer>
+ <longdescription lang="en">
Cluster provides an interface to access methods of gene expression data
analysis.
</longdescription>
diff --git a/sci-biology/consed-bin/ChangeLog b/sci-biology/consed-bin/ChangeLog
new file mode 100644
index 000000000..11c1fa713
--- /dev/null
+++ b/sci-biology/consed-bin/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/consed-bin
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> consed-bin-20.ebuild,
+ metadata.xml:
+ Correct motif dep naming
+
diff --git a/sci-biology/consed-bin/Manifest b/sci-biology/consed-bin/Manifest
index f5f0c6afa..3ec34e37f 100644
--- a/sci-biology/consed-bin/Manifest
+++ b/sci-biology/consed-bin/Manifest
@@ -1,2 +1,2 @@
-DIST consed-bin-20-linux.tar.gz 31407408 RMD160 8ab84f5216bb433884c75806738a6f7f20dea915 SHA1 9ccf1a2db890e30f042188d20e52098e1e37987a SHA256 ebde602163743d018ac8bf49f04ff0afbd0cccb3b7ef065a154943a68e95ad27
-DIST consed-bin-20-sources.tar.gz 31407408 RMD160 8ab84f5216bb433884c75806738a6f7f20dea915 SHA1 9ccf1a2db890e30f042188d20e52098e1e37987a SHA256 ebde602163743d018ac8bf49f04ff0afbd0cccb3b7ef065a154943a68e95ad27
+DIST consed-bin-20-linux.tar.gz 31407408 SHA256 ebde602163743d018ac8bf49f04ff0afbd0cccb3b7ef065a154943a68e95ad27
+DIST consed-bin-20-sources.tar.gz 31407408 SHA256 ebde602163743d018ac8bf49f04ff0afbd0cccb3b7ef065a154943a68e95ad27
diff --git a/sci-biology/consed-bin/consed-bin-20.ebuild b/sci-biology/consed-bin/consed-bin-20.ebuild
index ef4c886b9..9f5acb7a2 100644
--- a/sci-biology/consed-bin/consed-bin-20.ebuild
+++ b/sci-biology/consed-bin/consed-bin-20.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.2 2010/10/10 21:20:04 ulm Exp $
@@ -16,7 +16,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=">=x11-libs/openmotif-2.3:0"
+DEPEND=">=x11-libs/motif-2.3:0"
RDEPEND="${DEPEND}
>=sci-biology/phred-000925
>=sci-biology/phrap-1.080721
diff --git a/sci-biology/consed-bin/metadata.xml b/sci-biology/consed-bin/metadata.xml
index 3302123e5..fc7c76942 100644
--- a/sci-biology/consed-bin/metadata.xml
+++ b/sci-biology/consed-bin/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- </maintainer>
- <herd>sci-biology</herd>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/estscan/ChangeLog b/sci-biology/estscan/ChangeLog
index 5dc0f1250..de16cc83c 100644
--- a/sci-biology/estscan/ChangeLog
+++ b/sci-biology/estscan/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/estscan
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ Add local USE to metadata.xml
+
12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
estscan-3.0.3.ebuild:
remove offending double-quotes
diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest
index 28750b886..9129d27ce 100644
--- a/sci-biology/estscan/Manifest
+++ b/sci-biology/estscan/Manifest
@@ -1,9 +1,9 @@
-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
-DIST Dr.smat.gz 8813 RMD160 d59a9439300c8fbe38f94efa6325be655690eb5e SHA1 2ce056fc8a347720dd0832fa1a0af32a298193e5 SHA256 7f3f2f77310be208efebd79d9fb861f815748cd5ce0ffd7889aa606e54a0794f
-DIST Hs.smat.gz 62935 RMD160 90f5e045a7aafbb8bdd4e43eb64f7d60a40e8d65 SHA1 acc1cde028167c9dbf68b621985fb2222239c6fb SHA256 53d34b4e0934c9e3baf3c2e221a4bdd6153314564fd20023d8aef9d454aa3c44
-DIST Mm.smat.gz 62711 RMD160 30cf8dd0d944afcae7dd05b30bc08820e303c7c4 SHA1 2d0d50292bc39df2b086ddcc8482ba3b58ed2f6e SHA256 d04f3acd9ae6f8817dbfc9318ebee163e50669c1d2ccc6c048377054866c67da
-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
+DIST At.smat.gz 32314 SHA256 7f41329858b19ea13809becf58c7262b48dd8070dc38894b8ad7c55adcdd4c2a
+DIST BTLib-0.19.tar.gz 36283 SHA256 0acd6446031222b8fd5bd11eb3ec6c3164bc50491feef765c052689d9c3ee302
+DIST Dm.smat.gz 31711 SHA256 1f741836aa2b4ed96ab9ea6adb883eaa4d8d95610bd7a1ac484193ab30afca1d
+DIST Dr.smat.gz 8813 SHA256 7f3f2f77310be208efebd79d9fb861f815748cd5ce0ffd7889aa606e54a0794f
+DIST Hs.smat.gz 62935 SHA256 53d34b4e0934c9e3baf3c2e221a4bdd6153314564fd20023d8aef9d454aa3c44
+DIST Mm.smat.gz 62711 SHA256 d04f3acd9ae6f8817dbfc9318ebee163e50669c1d2ccc6c048377054866c67da
+DIST Rn.smat.gz 32388 SHA256 2e0a9b3347a8d216a026f98e38243d207e683bc50ac5be35c4c24f5ee1803cb8
+DIST estscan-3.0.3.tar.gz 46412 SHA256 037dc8770681ed12406a789ea292462a4ce5d89b0e906a1a3340aa4debc71e2f
+DIST user_guide_fev_07.pdf 327005 SHA256 416998f9fc282a53679fd56585b468ccebc4463e61ee5e989d9b426ed6f725fd
diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml
index 07b525505..14aff5c6f 100644
--- a/sci-biology/estscan/metadata.xml
+++ b/sci-biology/estscan/metadata.xml
@@ -1,9 +1,15 @@
<?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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <use>
+ <flag name="icc">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="ifc">Undocumented USE</flag>
+ </use>
</pkgmetadata>
diff --git a/sci-biology/hydra-sv/ChangeLog b/sci-biology/hydra-sv/ChangeLog
new file mode 100644
index 000000000..426bf05d2
--- /dev/null
+++ b/sci-biology/hydra-sv/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/hydra-sv
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> hydra-sv-0.5.3.ebuild,
+ +metadata.xml:
+ Add metadata.xml; move to EAPI=5; cleaned ebuild syntax
+
diff --git a/sci-biology/hydra-sv/Manifest b/sci-biology/hydra-sv/Manifest
index 0ebd049fa..ce0abb311 100644
--- a/sci-biology/hydra-sv/Manifest
+++ b/sci-biology/hydra-sv/Manifest
@@ -1 +1 @@
-DIST Hydra.v0.5.3.tar.gz 228772 RMD160 c926616bc422bad52fcb3c5e205b459e1ed590f8 SHA1 31d180da2b0ec842bd37d943d1a3ee44ae562dbd SHA256 0d03168f1ab6cec69108730c5747d310ff54023294bba67de77a9d3eebdcfacd
+DIST Hydra.v0.5.3.tar.gz 228772 SHA256 0d03168f1ab6cec69108730c5747d310ff54023294bba67de77a9d3eebdcfacd
diff --git a/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild b/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild
index 84dd6edcd..fc2f46308 100644
--- a/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild
+++ b/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $
-EAPI=4
+EAPI=5
DESCRIPTION="Detection of structural variation breakpoints in unique and duplicated genomic regions"
HOMEPAGE="http://code.google.com/p/hydra-sv/"
@@ -13,16 +13,13 @@ SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
-DEPEND=""
-RDEPEND=""
-
S="${WORKDIR}/Hydra-Version-${PV}"
src_compile() {
emake clean
- emake
+ default
}
src_install() {
- dobin bin/* scripts/* || die
+ dobin bin/* scripts/*
}
diff --git a/sci-libs/csrosetta-angless/metadata.xml b/sci-biology/hydra-sv/metadata.xml
index efb490d78..897aa2e6b 100644
--- a/sci-libs/csrosetta-angless/metadata.xml
+++ b/sci-biology/hydra-sv/metadata.xml
@@ -1,8 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
+ <herd>sci</herd>
</pkgmetadata>
diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog
index 163f6a460..66c444c00 100644
--- a/sci-biology/manatee-igs/ChangeLog
+++ b/sci-biology/manatee-igs/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/manatee-igs
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> manatee-igs-2.23.1.ebuild,
+ metadata.xml:
+ Shorten DESCRIPTION
+
*manatee-igs-2.23.1 (08 Jan 2012)
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/manatee-igs/Manifest b/sci-biology/manatee-igs/Manifest
index 778b235c6..23b52dc41 100644
--- a/sci-biology/manatee-igs/Manifest
+++ b/sci-biology/manatee-igs/Manifest
@@ -1,2 +1,2 @@
-DIST README_Linux.txt 9628 RMD160 0a8d8892469ebf2c4b464fdc6074be3b25991959 SHA1 9380f72792ad9c5d272a883f6481294173099138 SHA256 b08bf592d0e81595eba5354e942051e159d3c0a27a8a24a6a78ddc760b4433e3
-DIST manatee-2.23.1_linux.tgz 19879146 RMD160 0bd7e892f20ef91082e48335692548cb757aff27 SHA1 fca80384727ce6683f3b8dcd6a375ad76d4a1530 SHA256 2fca0e6662c2ac56add013a200096d550911dca7ebc83c5932517edad4181533
+DIST README_Linux.txt 9628 SHA256 b08bf592d0e81595eba5354e942051e159d3c0a27a8a24a6a78ddc760b4433e3
+DIST manatee-2.23.1_linux.tgz 19879146 SHA256 2fca0e6662c2ac56add013a200096d550911dca7ebc83c5932517edad4181533
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index b2f4e39a9..d97e8debc 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=3
-DESCRIPTION="IGS-modified version of the genome annotation tool that can view, modify and store annotation for prokaryotic and eukaryotic genomes."
+DESCRIPTION="IGS-modified version of the genome annotation tool"
HOMEPAGE="http://manatee.sourceforge.net/igs"
SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/manatee-igs/metadata.xml
+++ b/sci-biology/manatee-igs/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 4cd234f7e..68b66f6c8 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,7 +1,15 @@
# ChangeLog for sci-biology/mira
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mira-3.4.1.1 (22 Feb 2013)
+*mira-3.9.9 (22 Feb 2013)
+
+ 22 Feb 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +files/mira-3.4.0.2-boost-1.50.patch, +mira-3.4.1.1.ebuild,
+ +mira-3.9.9.ebuild:
+ sci-biology/mira: current stable and development version bumps
+
22 May 2012; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r2.ebuild,
-mira-3.2.1.17-r1.ebuild, -mira-3.2.1.20.ebuild, mira-3.4.0.1.ebuild:
Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop
@@ -15,4 +23,3 @@
fixed that in a different way, the still applicable part of the patch is
however provided under files/ but is just a cosmetic change (hence not really
needed)
-
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index 2bebb9aa7..ea16e44d1 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -1,2 +1,5 @@
-DIST mira-3.4.0.1.tar.bz2 10262667 RMD160 dc008eeb8dd291f9255f7b50ec5e0f888004cddd SHA1 a993c4e30d85b063768d3c5c1af7c3a5d5ff2aa4 SHA256 cafe45601b3c143ac142c022e1fc0a21544e880bb226897824de5dbf6d516d7e
-DIST mira_3rdparty_09-09-2011.tar.bz2 31285 RMD160 9c890ed445b75c2caf46c91adfb7040e7e9309c1 SHA1 c650b903861218854b8976bf3ebe977ec06afe99 SHA256 0e00cd0efff5601d559ee8d40d29b8d3b87db3f4cd5b7bfa5970501ea43f840b
+DIST mira-3.4.0.1.tar.bz2 10262667 SHA256 cafe45601b3c143ac142c022e1fc0a21544e880bb226897824de5dbf6d516d7e SHA512 b42924d75042c9953e084fb2512518fa8ca0b3bc11e67550c53bc4b15422e8a78fc0c8a993a84683b07bcc6e65b45f6956dd5d3c1fbfaf060d6b888f8227df05 WHIRLPOOL 3421299f091c92a34aae2e230ac24f117b1a29cd3557bf0a32f1b78a266dba405d00853a0625dd9526e8b31d80d451ff72ea1c6120608370553b5f2b05e45c83
+DIST mira-3.4.1.1.tar.gz 11665587 SHA256 d523a75ea499886564c2f698397c21d49e970e3d4f773b7fd13098f8f20ccce8 SHA512 f7ecf942b168f0a7b32505dfbc625c6fbded00084ae7511e59d0b236ca8b76deba712ea09239d12aeb3190daf6faecce714cd6bceb02edcbc5df44d021bf36f3 WHIRLPOOL 44bc92e5b02536cbdd09fb08566e7d885cab75a6841d8826450ef1a7e7dcf797a4c77e482c3fadedc8422e93292ea7781705a16a6bc3d848675b717ca60e722f
+DIST mira-3.9.9.tar.bz2 10356020 SHA256 d80929a9e7807bd0c160301c26d12b94fffd6439f8fea178b550c189da28848b SHA512 da2de917e99ac3825ac45ace7ae72b85d352eb75195db9f87679b45b3fe1a284aa6d53f5c6f3d45e1caa95e0dba20cf7a979bd97df67b65239f0aeb6e8af80d8 WHIRLPOOL 9d3a7b4e78e26b0eeb0f2e3cec804c0a99b9dbe260796f783214cf0c6b71da40fb5fd5480a4ec730e3bd3b0566b53f6e61ae1badee63460bfb4ceef006ac461c
+DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
+DIST mira_3rdparty_09-09-2011.tar.bz2 31285 SHA256 0e00cd0efff5601d559ee8d40d29b8d3b87db3f4cd5b7bfa5970501ea43f840b SHA512 de000592c0ffcf834dc31d33603107bac4ab8ed29cdb4db8e6e8e73d024214a641718c2a917bd7c73b50c4047201d629fc1f82c1618487e62589d0b276f7462f WHIRLPOOL 94c2723218dd6378352b365d36cd488269abeadf09dd544f1fc40c3af31de5b6149a32f97c7365f1df8b947e7a6738fef0448f39a5d74b398e98c1a14f3ef4f3
diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
new file mode 100644
index 000000000..427192294
--- /dev/null
+++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
@@ -0,0 +1,24 @@
+ config/m4/ax_boost_regex.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
+index 1ac06af..5b7be93 100644
+--- a/config/m4/ax_boost_regex.m4
++++ b/config/m4/ax_boost_regex.m4
+@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
+ for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+ [link_regex="no"])
+ done
+ if test "x$link_regex" != "xyes"; then
+ for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
+ ax_lib=${libextension}
+ AC_CHECK_LIB($ax_lib, exit,
+- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
+ [link_regex="no"])
+ done
+ fi
diff --git a/sci-biology/mira/mira-3.4.1.1.ebuild b/sci-biology/mira/mira-3.4.1.1.ebuild
new file mode 100644
index 000000000..5260ee14a
--- /dev/null
+++ b/sci-biology/mira/mira-3.4.1.1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
+
+EAPI=4
+
+MIRA_3RDPARTY_PV="06-07-2012"
+
+inherit autotools base multilib
+
+DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
+HOMEPAGE="http://www.chevreux.org/projects_mira.html"
+SRC_URI="
+ http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/${P}.tar.gz
+ mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
+
+CDEPEND="
+ dev-libs/boost
+ dev-util/google-perftools"
+DEPEND="${CDEPEND}
+ app-editors/vim-core
+ dev-libs/expat"
+RDEPEND="${CDEPEND}"
+
+DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
+ THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
+
+src_prepare() {
+ find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
+ epatch \
+ "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch
+ AT_M4DIR="config/m4" eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-thread=boost_thread-mt
+}
+
+#src_compile() {
+# base_src_compile
+# # TODO: resolve docbook incompatibility for building docs
+# #if use doc; then emake -C doc clean docs || die; fi
+#}
+
+src_install() {
+ base_src_install
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+}
+
+pkg_postinst() {
+ einfo "Documentation is no longer built, you can find it at:"
+ einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
+}
diff --git a/sci-biology/mira/mira-3.9.9.ebuild b/sci-biology/mira/mira-3.9.9.ebuild
new file mode 100644
index 000000000..0deeb871d
--- /dev/null
+++ b/sci-biology/mira/mira-3.9.9.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
+
+EAPI=4
+
+MIRA_3RDPARTY_PV="06-07-2012"
+
+inherit autotools base multilib
+
+DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
+HOMEPAGE="http://www.chevreux.org/projects_mira.html"
+SRC_URI="
+ http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
+ mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
+
+CDEPEND="
+ dev-libs/boost
+ dev-util/google-perftools"
+DEPEND="${CDEPEND}
+ app-editors/vim-core
+ dev-libs/expat"
+RDEPEND="${CDEPEND}"
+
+DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
+ THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
+
+src_prepare() {
+ find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
+ epatch \
+ "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch
+ AT_M4DIR="config/m4" eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
+ --with-boost-thread=boost_thread-mt
+}
+
+#src_compile() {
+# base_src_compile
+# # TODO: resolve docbook incompatibility for building docs
+# #if use doc; then emake -C doc clean docs || die; fi
+#}
+
+src_install() {
+ base_src_install
+ dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
+}
+
+pkg_postinst() {
+ einfo "Documentation is no longer built, you can find it at:"
+ einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
+}
diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
new file mode 100644
index 000000000..234411af5
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -0,0 +1,21 @@
+# ChangeLog for sci-biology/ncbi-tools++
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
+ Some Prefix love
+
+ 01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
+ Some Prefix love
+
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ Document USE
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0.ebuild,
+ ncbi-tools++-9.0.0-r1.ebuild:
+ Clean whitespace errors
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> +metadata.xml:
+ Add metadata.xml
+
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
index 610ee24ab..f5d6a3d67 100644
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch
@@ -1,135 +1,184 @@
- src/algo/align/ngalign/Makefile.xngalign.lib | 2 ++
- src/algo/blast/api/Makefile.xblast.lib | 2 +-
- src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +-
- src/algo/blast/core/Makefile.blast.lib | 2 ++
- src/algo/cobalt/Makefile.cobalt.lib | 2 ++
- src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++
- src/algo/sequence/Makefile.xalgoseq.lib | 2 ++
- src/algo/structure/struct_dp/Makefile.xstruct_dp.lib | 2 ++
- src/algo/structure/struct_util/Makefile.xstruct_util.lib | 2 ++
- src/algo/structure/threader/Makefile.xstruct_thread.lib | 2 ++
- src/algo/winmask/Makefile.xalgowinmask.lib | 1 +
- src/cgi/Makefile.cgi.lib | 2 ++
- src/cgi/Makefile.fcgi.lib | 2 ++
- src/connect/Makefile.connssl.lib | 2 ++
- src/connect/Makefile.xconnect.lib | 4 ++++
- src/connect/Makefile.xthrserv.lib | 2 +-
- src/connect/Makefile.xxconnect.lib | 2 ++
- src/connect/services/Makefile.ncbi_xcache_netcache.lib | 2 +-
- src/connect/services/Makefile.xconnserv.lib | 2 +-
- src/connect/test/Makefile.conntest.lib | 2 ++
- src/corelib/Makefile.test_boost.lib | 2 ++
- src/corelib/Makefile.test_mt.lib | 2 ++
- src/corelib/test/Makefile.pbacktest.lib | 2 ++
- src/db/bdb/Makefile.bdb.lib | 4 ++++
- src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +-
- src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++
- src/dbapi/Makefile.dbapi.lib | 5 +++++
- src/dbapi/driver/Makefile.dbapi_driver.lib | 2 ++
- src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib | 2 ++
- src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib | 2 +-
- src/dbapi/simple/Makefile.sdbapi.lib | 1 +
- src/html/Makefile.html.lib | 2 ++
- src/objects/access/Makefile.access.lib | 1 +
- src/objects/biblio/Makefile.biblio.lib | 2 ++
- src/objects/biotree/Makefile.biotree.lib | 2 ++
- src/objects/blast/Makefile.blast.lib | 2 ++
- src/objects/blast/Makefile.xnetblastcli.lib | 2 ++
- src/objects/blastdb/Makefile.blastdb.lib | 2 ++
- src/objects/blastxml/Makefile.blastxml.lib | 2 ++
- src/objects/cdd/Makefile.cdd.lib | 2 ++
- src/objects/cn3d/Makefile.cn3d.lib | 2 ++
- src/objects/docsum/Makefile.docsum.lib | 2 ++
- src/objects/entrez2/Makefile.entrez2.lib | 2 ++
- src/objects/entrez2/Makefile.entrez2cli.lib | 2 ++
- src/objects/entrezgene/Makefile.entrezgene.lib | 2 ++
- src/objects/featdef/Makefile.featdef.lib | 2 ++
- src/objects/gbseq/Makefile.gbseq.lib | 2 ++
- src/objects/general/Makefile.general.lib | 2 ++
- src/objects/genomecoll/Makefile.genome_collection.lib | 2 ++
- src/objects/homologene/Makefile.homologene.lib | 2 ++
- src/objects/id1/Makefile.id1.lib | 2 ++
- src/objects/id1/Makefile.id1cli.lib | 2 ++
- src/objects/id2/Makefile.id2.lib | 2 ++
- src/objects/id2/Makefile.id2cli.lib | 2 ++
- src/objects/insdseq/Makefile.insdseq.lib | 2 ++
- src/objects/macro/Makefile.macro.lib | 2 ++
- src/objects/medlars/Makefile.medlars.lib | 2 ++
- src/objects/medline/Makefile.medline.lib | 2 ++
- src/objects/mim/Makefile.mim.lib | 2 ++
- src/objects/mla/Makefile.mla.lib | 2 ++
- src/objects/mla/Makefile.mlacli.lib | 2 ++
- src/objects/mmdb/Makefile.mmdb.lib | 2 ++
- src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++
- src/objects/objprt/Makefile.objprt.lib | 2 ++
- src/objects/omssa/Makefile.omssa.lib | 2 ++
- src/objects/pcassay/Makefile.pcassay.lib | 2 ++
- src/objects/pcsubstance/Makefile.pcsubstance.lib | 2 ++
- src/objects/proj/Makefile.proj.lib | 2 ++
- src/objects/pub/Makefile.pub.lib | 2 ++
- src/objects/pubmed/Makefile.pubmed.lib | 2 ++
- src/objects/remap/Makefile.remap.lib | 2 ++
- src/objects/remap/Makefile.remapcli.lib | 2 ++
- src/objects/scoremat/Makefile.scoremat.lib | 2 ++
- src/objects/seq/Makefile.seq.lib | 2 ++
- src/objects/seqcode/Makefile.seqcode.lib | 2 ++
- src/objects/seqedit/Makefile.seqedit.lib | 1 +
- src/objects/seqset/Makefile.seqset.lib | 1 +
- src/objects/seqsplit/Makefile.seqsplit.lib | 2 ++
- src/objects/seqtest/Makefile.seqtest.lib | 2 ++
- src/objects/submit/Makefile.submit.lib | 1 +
- src/objects/taxon1/Makefile.taxon1.lib | 2 ++
- src/objects/taxon3/Makefile.taxon3.lib | 2 ++
- src/objects/tinyseq/Makefile.tinyseq.lib | 2 ++
- src/objects/valerr/Makefile.valerr.lib | 2 ++
- src/objects/valid/Makefile.valid.lib | 2 ++
- src/objects/variation/Makefile.variation.lib | 1 +
- src/objmgr/split/Makefile.id2_split.lib | 2 +-
- src/objmgr/util/Makefile.util.lib | 1 +
- src/objtools/align_format/Makefile.align_format.lib | 2 ++
- src/objtools/alnmgr/Makefile.alnmgr.lib | 1 +
- src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 2 ++
- src/objtools/blast/gene_info_reader/Makefile.gene_info.lib | 2 ++
- src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib | 2 ++
- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 ++
- src/objtools/blast/seqdb_writer/Makefile.writedb.lib | 2 ++
- src/objtools/blast/services/Makefile.blast_services.lib | 1 +
- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++
- src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +-
- src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++
- src/objtools/edit/Makefile.edit.lib | 2 ++
- src/objtools/eutils/egquery/Makefile.egquery.lib | 2 ++
- src/objtools/eutils/ehistory/Makefile.ehistory.lib | 2 ++
- src/objtools/eutils/einfo/Makefile.einfo.lib | 2 ++
- src/objtools/eutils/elink/Makefile.elink.lib | 2 ++
- src/objtools/eutils/epost/Makefile.epost.lib | 2 ++
- src/objtools/eutils/esearch/Makefile.esearch.lib | 2 ++
- src/objtools/eutils/espell/Makefile.espell.lib | 2 ++
- src/objtools/eutils/esummary/Makefile.esummary.lib | 2 ++
- src/objtools/eutils/linkout/Makefile.linkout.lib | 2 ++
- src/objtools/format/Makefile.xformat.lib | 2 ++
- src/objtools/lds/Makefile.lds.lib | 2 +-
- src/objtools/manip/Makefile.xobjmanip.lib | 2 ++
- src/objtools/readers/Makefile.xobjread.lib | 3 +--
- src/objtools/readers/Makefile.xobjreadex.lib | 2 +-
- src/objtools/simple/Makefile.xobjsimple.lib | 1 +
- src/objtools/validator/Makefile.validator.lib | 2 ++
- src/objtools/writers/Makefile.xobjwrite.lib | 1 +
- src/serial/Makefile.serial.lib | 2 ++
- src/serial/soap/Makefile.soap.lib | 2 ++
- src/serial/soap/Makefile.soap_server.lib | 2 ++
- src/serial/test/Makefile.we_cpp.lib | 1 +
- src/sra/sdk/libs/align/Makefile.align-writer.lib | 2 +-
- src/util/Makefile.util.lib | 2 ++
- src/util/compress/api/Makefile.compress.lib | 2 +-
- src/util/qparse/Makefile.xqueryparse.lib | 2 ++
- src/util/regexp/Makefile.regexp.lib | 2 ++
- src/util/sequtil/Makefile.sequtil.lib | 2 ++
- src/util/xregexp/Makefile.xregexp.lib | 2 +-
- 128 files changed, 237 insertions(+), 16 deletions(-)
+ src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib | 2 ++
+ src/algo/align/ngalign/Makefile.xngalign.lib | 2 ++
+ src/algo/align/nw/Makefile.xalgoalignnw.lib | 2 ++
+ src/algo/align/prosplign/Makefile.prosplign.lib | 2 ++
+ src/algo/align/splign/Makefile.xalgoalignsplign.lib | 2 ++
+ src/algo/blast/api/Makefile.xblast.lib | 2 +-
+ src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +-
+ src/algo/blast/core/Makefile.blast.lib | 2 ++
+ src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib | 2 ++
+ src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib | 2 ++
+ src/algo/blast/format/Makefile.xblastformat.lib | 2 +-
+ src/algo/blast/gumbel_params/Makefile.gumbelparams.lib | 1 +
+ src/algo/cobalt/Makefile.cobalt.lib | 2 ++
+ src/algo/dustmask/Makefile.xalgodustmask.lib | 1 +
+ src/algo/gnomon/Makefile.gnomon.lib | 2 +-
+ src/algo/ms/formats/pepxml/Makefile.pepXML.lib | 2 ++
+ src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++
+ src/algo/phy_tree/Makefile.xalgophytree.lib | 2 +-
+ src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib | 2 ++
+ src/algo/segmask/Makefile.xalgosegmask.lib | 1 +
+ src/algo/seqqa/Makefile.xalgoseqqa.lib | 2 ++
+ src/algo/sequence/Makefile.xalgoseq.lib | 2 ++
+ src/algo/structure/bma_refine/Makefile.xbma_refiner.lib | 3 +++
+ src/algo/structure/cd_utils/Makefile.xcd_utils.lib | 2 +-
+ src/algo/structure/struct_dp/Makefile.xstruct_dp.lib | 2 ++
+ src/algo/structure/struct_util/Makefile.xstruct_util.lib | 2 ++
+ src/algo/structure/threader/Makefile.xstruct_thread.lib | 2 ++
+ src/algo/text/Makefile.xalgotext.lib | 2 ++
+ src/algo/volume_merge/Makefile.xalgovmerge.lib | 2 ++
+ src/algo/winmask/Makefile.xalgowinmask.lib | 2 ++
+ src/cgi/Makefile.cgi.lib | 2 ++
+ src/cgi/Makefile.fcgi.lib | 2 ++
+ src/connect/Makefile.connssl.lib | 2 ++
+ src/connect/Makefile.xconnect.lib | 4 ++++
+ src/connect/Makefile.xthrserv.lib | 2 +-
+ src/connect/Makefile.xxconnect.lib | 2 ++
+ src/connect/services/Makefile.ncbi_xcache_netcache.lib | 2 +-
+ src/connect/services/Makefile.xconnserv.lib | 2 +-
+ src/connect/test/Makefile.conntest.lib | 2 ++
+ src/corelib/Makefile.test_boost.lib | 2 ++
+ src/corelib/Makefile.test_mt.lib | 2 ++
+ src/corelib/test/Makefile.pbacktest.lib | 2 ++
+ src/db/bdb/Makefile.bdb.lib | 4 ++++
+ src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +-
+ src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++
+ src/dbapi/Makefile.dbapi.lib | 5 +++++
+ src/dbapi/driver/Makefile.dbapi_driver.lib | 2 ++
+ src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib | 2 ++
+ src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib | 2 +-
+ src/dbapi/simple/Makefile.sdbapi.lib | 1 +
+ src/html/Makefile.html.lib | 2 ++
+ src/misc/cgi_redirect/Makefile.cgi_redirect.lib | 2 ++
+ src/misc/grid_cgi/Makefile.xgridcgi.lib | 2 ++
+ src/objects/access/Makefile.access.lib | 1 +
+ src/objects/biblio/Makefile.biblio.lib | 2 ++
+ src/objects/biotree/Makefile.biotree.lib | 2 ++
+ src/objects/blast/Makefile.blast.lib | 2 ++
+ src/objects/blast/Makefile.xnetblastcli.lib | 2 ++
+ src/objects/blastdb/Makefile.blastdb.lib | 2 ++
+ src/objects/blastxml/Makefile.blastxml.lib | 2 ++
+ src/objects/cdd/Makefile.cdd.lib | 2 ++
+ src/objects/cn3d/Makefile.cn3d.lib | 2 ++
+ src/objects/docsum/Makefile.docsum.lib | 2 ++
+ src/objects/entrez2/Makefile.entrez2.lib | 2 ++
+ src/objects/entrez2/Makefile.entrez2cli.lib | 2 ++
+ src/objects/entrezgene/Makefile.entrezgene.lib | 2 ++
+ src/objects/featdef/Makefile.featdef.lib | 2 ++
+ src/objects/gbseq/Makefile.gbseq.lib | 2 ++
+ src/objects/general/Makefile.general.lib | 2 ++
+ src/objects/genomecoll/Makefile.genome_collection.lib | 2 ++
+ src/objects/homologene/Makefile.homologene.lib | 2 ++
+ src/objects/id1/Makefile.id1.lib | 2 ++
+ src/objects/id1/Makefile.id1cli.lib | 2 ++
+ src/objects/id2/Makefile.id2.lib | 2 ++
+ src/objects/id2/Makefile.id2cli.lib | 2 ++
+ src/objects/insdseq/Makefile.insdseq.lib | 2 ++
+ src/objects/macro/Makefile.macro.lib | 2 ++
+ src/objects/medlars/Makefile.medlars.lib | 2 ++
+ src/objects/medline/Makefile.medline.lib | 2 ++
+ src/objects/mim/Makefile.mim.lib | 2 ++
+ src/objects/mla/Makefile.mla.lib | 2 ++
+ src/objects/mla/Makefile.mlacli.lib | 2 ++
+ src/objects/mmdb/Makefile.mmdb.lib | 2 ++
+ src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++
+ src/objects/objprt/Makefile.objprt.lib | 2 ++
+ src/objects/omssa/Makefile.omssa.lib | 2 ++
+ src/objects/pcassay/Makefile.pcassay.lib | 2 ++
+ src/objects/pcsubstance/Makefile.pcsubstance.lib | 2 ++
+ src/objects/proj/Makefile.proj.lib | 2 ++
+ src/objects/pub/Makefile.pub.lib | 2 ++
+ src/objects/pubmed/Makefile.pubmed.lib | 2 ++
+ src/objects/remap/Makefile.remap.lib | 2 ++
+ src/objects/remap/Makefile.remapcli.lib | 2 ++
+ src/objects/scoremat/Makefile.scoremat.lib | 2 ++
+ src/objects/seq/Makefile.seq.lib | 2 ++
+ src/objects/seqcode/Makefile.seqcode.lib | 2 ++
+ src/objects/seqedit/Makefile.seqedit.lib | 1 +
+ src/objects/seqset/Makefile.seqset.lib | 1 +
+ src/objects/seqsplit/Makefile.seqsplit.lib | 2 ++
+ src/objects/seqtest/Makefile.seqtest.lib | 2 ++
+ src/objects/submit/Makefile.submit.lib | 1 +
+ src/objects/taxon1/Makefile.taxon1.lib | 2 ++
+ src/objects/taxon3/Makefile.taxon3.lib | 2 ++
+ src/objects/tinyseq/Makefile.tinyseq.lib | 2 ++
+ src/objects/valerr/Makefile.valerr.lib | 2 ++
+ src/objects/valid/Makefile.valid.lib | 2 ++
+ src/objects/variation/Makefile.variation.lib | 1 +
+ src/objmgr/split/Makefile.id2_split.lib | 2 +-
+ src/objmgr/util/Makefile.util.lib | 1 +
+ src/objtools/align/Makefile.xalntool.lib | 2 ++
+ src/objtools/align_format/Makefile.align_format.lib | 2 ++
+ src/objtools/alnmgr/Makefile.alnmgr.lib | 1 +
+ src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 2 ++
+ src/objtools/blast/gene_info_reader/Makefile.gene_info.lib | 2 ++
+ src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib | 2 ++
+ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 ++
+ src/objtools/blast/seqdb_writer/Makefile.writedb.lib | 2 ++
+ src/objtools/blast/services/Makefile.blast_services.lib | 1 +
+ src/objtools/cddalignview/Makefile.cddalignview.lib | 2 ++
+ src/objtools/cleanup/Makefile.cleanup.lib | 2 +-
+ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++
+ .../data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib | 2 ++
+ src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib | 2 ++
+ src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +-
+ src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++
+ src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib | 2 ++
+ src/objtools/data_loaders/trace/Makefile.xloader_trace.lib | 2 ++
+ src/objtools/edit/Makefile.edit.lib | 2 ++
+ src/objtools/eutils/api/Makefile.eutils.lib | 2 ++
+ src/objtools/eutils/egquery/Makefile.egquery.lib | 2 ++
+ src/objtools/eutils/ehistory/Makefile.ehistory.lib | 2 ++
+ src/objtools/eutils/einfo/Makefile.einfo.lib | 2 ++
+ src/objtools/eutils/elink/Makefile.elink.lib | 2 ++
+ src/objtools/eutils/epost/Makefile.epost.lib | 2 ++
+ src/objtools/eutils/esearch/Makefile.esearch.lib | 2 ++
+ src/objtools/eutils/espell/Makefile.espell.lib | 2 ++
+ src/objtools/eutils/esummary/Makefile.esummary.lib | 2 ++
+ src/objtools/eutils/linkout/Makefile.linkout.lib | 2 ++
+ src/objtools/eutils/uilist/Makefile.uilist.lib | 2 ++
+ src/objtools/format/Makefile.xformat.lib | 2 ++
+ src/objtools/lds/Makefile.lds.lib | 2 +-
+ src/objtools/manip/Makefile.xobjmanip.lib | 2 ++
+ src/objtools/readers/Makefile.xobjread.lib | 3 +--
+ src/objtools/readers/Makefile.xobjreadex.lib | 2 +-
+ src/objtools/seqmasks_io/Makefile.seqmasks_io.lib | 2 +-
+ src/objtools/simple/Makefile.xobjsimple.lib | 1 +
+ src/objtools/snputil/Makefile.snputil.lib | 2 ++
+ src/objtools/validator/Makefile.validator.lib | 2 ++
+ src/objtools/writers/Makefile.xobjwrite.lib | 1 +
+ src/sample/app/asn/Makefile.sample_asn.lib | 2 ++
+ src/sample/app/soap/Makefile.soap_dataobj.lib | 2 ++
+ src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib | 2 ++
+ src/sample/lib/basic/Makefile.basic_sample_lib.lib | 2 ++
+ src/sample/lib/dtd/Makefile.dtd_sample_lib.lib | 2 ++
+ src/sample/lib/xsd/Makefile.xsd_sample_lib.lib | 2 ++
+ src/serial/Makefile.serial.lib | 2 ++
+ src/serial/soap/Makefile.soap.lib | 2 ++
+ src/serial/soap/Makefile.soap_server.lib | 2 ++
+ src/serial/test/Makefile.we_cpp.lib | 1 +
+ src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib | 2 +-
+ src/sra/sdk/libs/align/Makefile.align-writer.lib | 2 +-
+ src/util/Makefile.util.lib | 2 ++
+ src/util/compress/api/Makefile.compress.lib | 2 +-
+ src/util/qparse/Makefile.xqueryparse.lib | 2 ++
+ src/util/regexp/Makefile.regexp.lib | 2 ++
+ src/util/sequtil/Makefile.sequtil.lib | 2 ++
+ src/util/xregexp/Makefile.xregexp.lib | 2 +-
+ 167 files changed, 307 insertions(+), 23 deletions(-)
+diff --git a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
+index c8851d8..35ae629 100644
+--- a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
++++ b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib
+@@ -10,3 +10,5 @@ LIB = xalgocontig_assembly
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
++
++DLL_LIB = align_format blastinput dbapi_driver seq xalgoalignnw xalgodustmask xalnmgr xblast xncbi xobjmgr xobjutil xser # axf
diff --git a/src/algo/align/ngalign/Makefile.xngalign.lib b/src/algo/align/ngalign/Makefile.xngalign.lib
-index d163f7c..f9c79ba 100644
+index d163f7c..ade88ce 100644
--- a/src/algo/align/ngalign/Makefile.xngalign.lib
+++ b/src/algo/align/ngalign/Makefile.xngalign.lib
@@ -15,3 +15,5 @@ LIB = xngalign
@@ -137,9 +186,39 @@ index d163f7c..f9c79ba 100644
CXXFLAGS = $(FAST_CXXFLAGS) -I./.
LDFLAGS = $(FAST_LDFLAGS)
+
-+DLL_LIB = seq xalgoalignutil xncbi blastinput
++DLL_LIB = seq xalgoalignutil xncbi blastinput xalgoalignnw align_format xcgi ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2
+diff --git a/src/algo/align/nw/Makefile.xalgoalignnw.lib b/src/algo/align/nw/Makefile.xalgoalignnw.lib
+index acc1ddf..acba81c 100644
+--- a/src/algo/align/nw/Makefile.xalgoalignnw.lib
++++ b/src/algo/align/nw/Makefile.xalgoalignnw.lib
+@@ -15,3 +15,5 @@ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+ WATCHERS = kiryutin
++
++DLL_LIB = access align_format dbapi_driver general seq writedb xncbi xser # axf
+diff --git a/src/algo/align/prosplign/Makefile.prosplign.lib b/src/algo/align/prosplign/Makefile.prosplign.lib
+index 248ee37..73143ad 100644
+--- a/src/algo/align/prosplign/Makefile.prosplign.lib
++++ b/src/algo/align/prosplign/Makefile.prosplign.lib
+@@ -10,3 +10,5 @@ LIB = prosplign
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
++
++DLL_LIB = align_format blastinput dbapi_driver general igblast seq xalgoalignutil xalnmgr xncbi xobjmgr xobjutil xser # axf
+diff --git a/src/algo/align/splign/Makefile.xalgoalignsplign.lib b/src/algo/align/splign/Makefile.xalgoalignsplign.lib
+index d67680b..3d56789 100644
+--- a/src/algo/align/splign/Makefile.xalgoalignsplign.lib
++++ b/src/algo/align/splign/Makefile.xalgoalignsplign.lib
+@@ -10,3 +10,5 @@ LIB = xalgoalignsplign
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
++
++DLL_LIB = access align_format blastinput dbapi_driver gene_info general seq seqdb xalgoalignnw xalgoalignutil xalgoseq xblast xncbi xobjmgr xobjutil xser xutil # axf prosplign
diff --git a/src/algo/blast/api/Makefile.xblast.lib b/src/algo/blast/api/Makefile.xblast.lib
-index 073973b..3be07ae 100644
+index 073973b..c6a4c2c 100644
--- a/src/algo/blast/api/Makefile.xblast.lib
+++ b/src/algo/blast/api/Makefile.xblast.lib
@@ -78,7 +78,7 @@ SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
@@ -147,12 +226,12 @@ index 073973b..3be07ae 100644
LIB = xblast
-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
-+DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread
++DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xnetblastcli xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread
CFLAGS = $(FAST_CFLAGS)
# Strict gcc flags
diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib
-index bfb315c..6f56c5a 100644
+index bfb315c..2cd809a 100644
--- a/src/algo/blast/blastinput/Makefile.blastinput.lib
+++ b/src/algo/blast/blastinput/Makefile.blastinput.lib
@@ -24,7 +24,7 @@ SRC = $(SRC_CXX)
@@ -160,7 +239,7 @@ index bfb315c..6f56c5a 100644
LIB = blastinput
-DLL_LIB = xblast $(OBJMGR_LIBS)
-+DLL_LIB = seqdb ncbi_xloader_blastdb $(OBJMGR_LIBS)
++DLL_LIB = seqdb ncbi_xloader_blastdb ncbi_xloader_blastdb_rmt align_format xalnmgr xblast xcgi xobjread xobjutil ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2 xalnmgr xcgi
# should be redundant, given the above :-/
ASN_DEP = seqset xnetblast
@@ -174,8 +253,49 @@ index 8e889a7..1326aee 100644
WATCHERS = coulouri maning madden camacho
+
+DLL_LIB = xutil
+diff --git a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+index fcfb9f9..0e762b4 100644
+--- a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
++++ b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+@@ -14,3 +14,5 @@ LDFLAGS = $(FAST_LDFLAGS)
+ ASN_DEP = seqset
+
+ WATCHERS = morgulis
++
++DLL_LIB = dbapi_driver seq seqdb seqset xncbi xobjmgr xobjread xobjutil xser xutil # axf
+diff --git a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
+index e64f111..475f4a1 100644
+--- a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
++++ b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
+@@ -10,3 +10,5 @@ LDFLAGS = $(FAST_LDFLAGS)
+ ASN_DEP = seqset
+
+ WATCHERS = morgulis
++
++DLL_LIB = dbapi_driver xncbi xobjmgr # axf
+diff --git a/src/algo/blast/format/Makefile.xblastformat.lib b/src/algo/blast/format/Makefile.xblastformat.lib
+index f7da067..9920332 100644
+--- a/src/algo/blast/format/Makefile.xblastformat.lib
++++ b/src/algo/blast/format/Makefile.xblastformat.lib
+@@ -7,6 +7,6 @@ SRC = blastfmtutil blastxml_format blast_format data4xmlformat build_archive vec
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+
+-DLL_LIB = blastxml xhtml xcgi
++DLL_LIB = blastxml xhtml xcgi align_format general scoremat seq seqdb xalnmgr xblast xnetblast xobjmgr xobjutil blast_services ncbi_xloader_genbank xcgi # cobalt
+
+ WATCHERS = jianye zaretska madden camacho fongah2
+diff --git a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
+index 316d4fa..844de85 100644
+--- a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
++++ b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
+@@ -11,3 +11,4 @@ LDFLAGS = $(FAST_LDFLAGS)
+
+ WATCHERS = boratyng madden camacho
+
++DLL_LIB = dbapi_driver xncbi xutil # axf
diff --git a/src/algo/cobalt/Makefile.cobalt.lib b/src/algo/cobalt/Makefile.cobalt.lib
-index e618f67..32905ca 100644
+index e618f67..b406cc5 100644
--- a/src/algo/cobalt/Makefile.cobalt.lib
+++ b/src/algo/cobalt/Makefile.cobalt.lib
@@ -14,3 +14,5 @@ ASN_DEP = seq seqset biotree xnetblast blastdb
@@ -183,9 +303,41 @@ index e618f67..32905ca 100644
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
+
-+DLL_LIB = align_format
++DLL_LIB = align_format dbapi_driver general igblast seq seqdb seqset xalgoalignnw xalgophytree xblast xncbi xnetblast xobjmgr xobjutil xser fastme # axf
+diff --git a/src/algo/dustmask/Makefile.xalgodustmask.lib b/src/algo/dustmask/Makefile.xalgodustmask.lib
+index 84e2568..3632356 100644
+--- a/src/algo/dustmask/Makefile.xalgodustmask.lib
++++ b/src/algo/dustmask/Makefile.xalgodustmask.lib
+@@ -11,3 +11,4 @@ SRC = symdust
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = dbapi_driver seq xncbi xobjmgr # axf
+diff --git a/src/algo/gnomon/Makefile.gnomon.lib b/src/algo/gnomon/Makefile.gnomon.lib
+index af363c0..3235647 100644
+--- a/src/algo/gnomon/Makefile.gnomon.lib
++++ b/src/algo/gnomon/Makefile.gnomon.lib
+@@ -6,7 +6,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) \
+ gnomon_engine gnomon_objmgr score gnomon_model parse hmm gnomon_seq asn1 chainer id_handler \
+ annot select_alignments_alt
+ LIB = xalgognomon
+-DLL_LIB = xobjutil $(SOBJMGR_LIBS)
++DLL_LIB = xobjutil $(SOBJMGR_LIBS) xalgoseq
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+diff --git a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
+index 686dd70..98f57b2 100644
+--- a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
++++ b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib
+@@ -2,3 +2,5 @@ WATCHERS = lewisg slottad
+
+ LIB = pepXML
+ SRC = pepXML__ pepXML___
++
++DLL_LIB = access align_format dbapi_driver xncbi xser # axf
diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib
-index 872b92e..24fcff3 100644
+index 872b92e..78261eb 100644
--- a/src/algo/ms/omssa/Makefile.xomssa.lib
+++ b/src/algo/ms/omssa/Makefile.xomssa.lib
@@ -19,3 +19,5 @@ LIB = xomssa
@@ -193,9 +345,51 @@ index 872b92e..24fcff3 100644
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
+
-+DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast
++DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast xregexp
+diff --git a/src/algo/phy_tree/Makefile.xalgophytree.lib b/src/algo/phy_tree/Makefile.xalgophytree.lib
+index 5964ef4..8163366 100644
+--- a/src/algo/phy_tree/Makefile.xalgophytree.lib
++++ b/src/algo/phy_tree/Makefile.xalgophytree.lib
+@@ -6,7 +6,7 @@ ASN_DEP = biotree
+
+ SRC = bio_tree phy_node dist_methods lex.newick newick.tab tree_to_dist_mat phytree_calc
+ LIB = xalgophytree
+-DLL_LIB = biotree
++DLL_LIB = biotree seq xalnmgr xobjutil # fastme
+
+ # The -I flag is necessary because filenames in #line directives throw
+ # off some compilers (GCC 2.95 at least). :-/
+diff --git a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
+index 15d7440..fab9207 100644
+--- a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
++++ b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib
+@@ -10,3 +10,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
+ ASN_DEP = biotree seqset taxon1
+
+ WATCHERS = boratyng
++
++DLL_LIB = access align_format biotree dbapi_driver fastme gene_info seq taxon1 xalgophytree xncbi xobjmgr xobjutil xser # axf
+diff --git a/src/algo/segmask/Makefile.xalgosegmask.lib b/src/algo/segmask/Makefile.xalgosegmask.lib
+index bd011c1..97281ec 100644
+--- a/src/algo/segmask/Makefile.xalgosegmask.lib
++++ b/src/algo/segmask/Makefile.xalgosegmask.lib
+@@ -11,3 +11,4 @@ SRC = segmask
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = align_format xobjmgr
+diff --git a/src/algo/seqqa/Makefile.xalgoseqqa.lib b/src/algo/seqqa/Makefile.xalgoseqqa.lib
+index b1bea47..a0e5b1b 100644
+--- a/src/algo/seqqa/Makefile.xalgoseqqa.lib
++++ b/src/algo/seqqa/Makefile.xalgoseqqa.lib
+@@ -12,3 +12,5 @@ LIB = xalgoseqqa
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
++
++DLL_LIB = access align_format dbapi_driver entrez2cli gene_info general seq seqtest xalgognomon xalgoseq xalnmgr xncbi xobjmgr xobjutil xser # axf
diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib
-index 51f4cd7..0c20790 100644
+index 51f4cd7..724e939 100644
--- a/src/algo/sequence/Makefile.xalgoseq.lib
+++ b/src/algo/sequence/Makefile.xalgoseq.lib
@@ -13,3 +13,5 @@ LDFLAGS = $(FAST_LDFLAGS)
@@ -203,7 +397,30 @@ index 51f4cd7..0c20790 100644
WATCHERS = dicuccio
+
-+DLL_LIB = taxon1 xalnmgr
++DLL_LIB = taxon1 xalnmgr xregexp align_format seqset xobjmgr xobjutil
+diff --git a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
+index 5562f82..68d3a87 100644
+--- a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
++++ b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib
+@@ -24,3 +24,6 @@ SRC = RowSelector \
+ RefinerTrial \
+ RefinerEngine \
+ Interface
++
++DLL_LIB = blastinput cdd ncbi_xcache_bdb xcd_utils xncbi xser xutil
++
+diff --git a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
+index eda71f8..8d3a96a 100644
+--- a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
++++ b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib
+@@ -68,6 +68,6 @@ SRC = \
+ cuTaxTree \
+ cuUtils
+
+-DLL_LIB = xobjread
++DLL_LIB = xobjread blastdb blast_services cdd entrez2cli id1cli mmdb ncbimime scoremat taxon1 xblast xobjmgr xregexp
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
diff --git a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib b/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib
index 676a8dd..3d3e4c9 100644
--- a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib
@@ -234,15 +451,36 @@ index c06a2c0..9f1ff25 100644
LIB = xstruct_thread
+
+DLL_LIB = xutil
+diff --git a/src/algo/text/Makefile.xalgotext.lib b/src/algo/text/Makefile.xalgotext.lib
+index 81ba0e6..f25073e 100644
+--- a/src/algo/text/Makefile.xalgotext.lib
++++ b/src/algo/text/Makefile.xalgotext.lib
+@@ -10,3 +10,5 @@ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+ ASN_DEP = general
++
++DLL_LIB = align_format blastinput ncbi_xcache_bdb xcompress xncbi xutil # axf
+diff --git a/src/algo/volume_merge/Makefile.xalgovmerge.lib b/src/algo/volume_merge/Makefile.xalgovmerge.lib
+index 499861a..3ffb80b 100644
+--- a/src/algo/volume_merge/Makefile.xalgovmerge.lib
++++ b/src/algo/volume_merge/Makefile.xalgovmerge.lib
+@@ -10,3 +10,5 @@ SRC = volume_merge
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++
++DLL_LIB = xncbi
diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib
-index afaf676..7344871 100644
+index afaf676..ad2c1fe 100644
--- a/src/algo/winmask/Makefile.xalgowinmask.lib
+++ b/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,3 +21,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
+@@ -21,3 +21,5 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
-+DLL_LIB = seqmasks_io
++DLL_LIB = seqmasks_io xobjread xobjutil
++
diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib
index a990390..edf40aa 100644
--- a/src/cgi/Makefile.cgi.lib
@@ -479,6 +717,26 @@ index a57c1e3..0005299 100644
WATCHERS = ivanov
+
+DLL_LIB = xncbi xutil
+diff --git a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
+index 6d7a4af..332e5d0 100644
+--- a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
++++ b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib
+@@ -7,3 +7,5 @@ SRC = redirect
+ LIB = xcgi_redirect
+
+ WATCHERS = ivanov
++
++DLL_LIB = axf dbapi_driver xcgi xhtml xncbi
+diff --git a/src/misc/grid_cgi/Makefile.xgridcgi.lib b/src/misc/grid_cgi/Makefile.xgridcgi.lib
+index c9ef138..8e25cbe 100644
+--- a/src/misc/grid_cgi/Makefile.xgridcgi.lib
++++ b/src/misc/grid_cgi/Makefile.xgridcgi.lib
+@@ -9,3 +9,5 @@ LIB = xgridcgi
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+
+ WATCHERS = vakatov
++
++DLL_LIB = xncbi xcgi xconnserv xhtml
diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib
index 11421d9..e7900a1 100644
--- a/src/objects/access/Makefile.access.lib
@@ -545,14 +803,14 @@ index d18eb78..f90501d 100644
+
+DLL_LIB = xser
diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib
-index 978cae9..2365261 100644
+index 978cae9..24b726c 100644
--- a/src/objects/cdd/Makefile.cdd.lib
+++ b/src/objects/cdd/Makefile.cdd.lib
@@ -1,2 +1,4 @@
LIB = cdd
SRC = cdd__ cdd___
+
-+DLL_LIB = mmdb xser scoremat
++DLL_LIB = mmdb xser scoremat cn3d
diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib
index 1af5d1d..ecd31b2 100644
--- a/src/objects/cn3d/Makefile.cn3d.lib
@@ -1006,8 +1264,18 @@ index 90eeee0..138e836 100644
WATCHERS = ucko vasilche
+DLL_LIB = xser xobjmgr
+diff --git a/src/objtools/align/Makefile.xalntool.lib b/src/objtools/align/Makefile.xalntool.lib
+index cb9846d..9c2a8f9 100644
+--- a/src/objtools/align/Makefile.xalntool.lib
++++ b/src/objtools/align/Makefile.xalntool.lib
+@@ -6,3 +6,5 @@ ASN_DEP = seqset
+
+ LIB = xalntool
+ SRC = alngraphic
++
++DLL_LIB = access dbapi_driver general seq xhtml xncbi xobjmgr xobjutil xser # align_format axf blastinput
diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib
-index 4b3e59e..d8e9345 100644
+index 4b3e59e..c67c352 100644
--- a/src/objtools/align_format/Makefile.align_format.lib
+++ b/src/objtools/align_format/Makefile.align_format.lib
@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -1015,18 +1283,18 @@ index 4b3e59e..d8e9345 100644
WATCHERS = zaretska jianye madden camacho
+
-+DLL_LIB = seqdb blastdb xser
++DLL_LIB = seqdb blastdb xser xhtml gene_info xnetblast blast_services ncbi_xloader_genbank xalnmgr xcgi xobjread xobjutil
diff --git a/src/objtools/alnmgr/Makefile.alnmgr.lib b/src/objtools/alnmgr/Makefile.alnmgr.lib
-index e32c351..1702b90 100644
+index e32c351..41355ff 100644
--- a/src/objtools/alnmgr/Makefile.alnmgr.lib
+++ b/src/objtools/alnmgr/Makefile.alnmgr.lib
@@ -12,3 +12,4 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial \
WATCHERS = todorov dicuccio grichenk
-+DLL_LIB = tables
++DLL_LIB = tables dbapi_driver ncbi_xcache_bdb seq seqset sequtil xncbi xobjmgr xobjutil xser # align_format axf
diff --git a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-index d8177ed..f7beead 100644
+index d8177ed..aa4d8e4 100644
--- a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+++ b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
@@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -1034,7 +1302,7 @@ index d8177ed..f7beead 100644
#
# LIB_OR_DLL = dll
+
-+DLL_LIB = xncbi xser xobjutil seq
++DLL_LIB = xncbi xser xobjutil seq seqdb
diff --git a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib b/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
index bf5fd1b..c32aca4 100644
--- a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
@@ -1084,6 +1352,29 @@ index 10a878c..7a70b22 100644
LDFLAGS = $(FAST_LDFLAGS)
+DLL_LIB = xncbi xser xnetblast xnetblastcli
+diff --git a/src/objtools/cddalignview/Makefile.cddalignview.lib b/src/objtools/cddalignview/Makefile.cddalignview.lib
+index 8e39baa..f4d3a35 100644
+--- a/src/objtools/cddalignview/Makefile.cddalignview.lib
++++ b/src/objtools/cddalignview/Makefile.cddalignview.lib
+@@ -11,3 +11,5 @@ SRC = \
+ cav_seqset
+
+ LIB = xcddalignview
++
++DLL_LIB = cdd dbapi_driver general ncbimime seq seqset xncbi xser # align_format axf ncbi_xloader_bam
+diff --git a/src/objtools/cleanup/Makefile.cleanup.lib b/src/objtools/cleanup/Makefile.cleanup.lib
+index 663d755..ad7b3cf 100644
+--- a/src/objtools/cleanup/Makefile.cleanup.lib
++++ b/src/objtools/cleanup/Makefile.cleanup.lib
+@@ -10,7 +10,7 @@ SRC = autogenerated_cleanup cleanup \
+ cleanup_utils \
+ newcleanupp
+
+-DLL_LIB = xregexp $(PCRE_LIB)
++DLL_LIB = xregexp $(PCRE_LIB) access biblio general pub seq seqset sequtil submit xobjmgr xobjutil xser
+ LIB = xcleanup
+
+ LIBS = $(PCRE_LIBS)
diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
index 80af69f..704ed7a 100644
--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
@@ -1095,6 +1386,26 @@ index 80af69f..704ed7a 100644
+
+DLL_LIB = seqdb
+
+diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+index 80abb48..2ddec92 100644
+--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+@@ -6,3 +6,5 @@ SRC = bdbloader_rmt remote_blastdb_adapter
+ ASN_DEP = blastdb xnetblast
+
+ WATCHERS = camacho
++
++DLL_LIB = blast_services ncbi_xloader_blastdb xobjmgr
+diff --git a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
+index a51042b..fa92fc9 100644
+--- a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
++++ b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib
+@@ -9,3 +9,5 @@ LIB = ncbi_xloader_cdd
+ SRC = cdd
+
+ ASN_DEP = seqset
++
++DLL_LIB = dbapi_driver general seq seqset xconnect xncbi xobjmgr xser # align_format axf ncbi_xloader_bam
diff --git a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
index f2b2b49..864e4b1 100644
--- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
@@ -1108,7 +1419,7 @@ index f2b2b49..864e4b1 100644
WATCHERS = vasilche
diff --git a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-index 0a29cbf..015ac93 100644
+index 0a29cbf..74c30dc 100644
--- a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+++ b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
@@ -15,3 +15,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
@@ -1116,7 +1427,27 @@ index 0a29cbf..015ac93 100644
WATCHERS = vasilche
+
-+DLL_LIB = xncbi
++DLL_LIB = xncbi gene_info id2 ncbi_xreader xconnect xser
+diff --git a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
+index 8d09d8c..d6040ed 100644
+--- a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
++++ b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib
+@@ -7,3 +7,5 @@ ASN_DEP = seq seqset seqedit
+
+
+ WATCHERS = vasilche
++
++DLL_LIB = dbapi_driver seq seqedit seqset xncbi xobjmgr xser # axf
+diff --git a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
+index d2debd5..33fed34 100644
+--- a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
++++ b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib
+@@ -9,3 +9,5 @@ LIB = ncbi_xloader_trace
+ SRC = trace_chgr
+
+ ASN_DEP = id1
++
++DLL_LIB = dbapi_driver general id1 id1cli seq xncbi xobjmgr xser # align_format axf
diff --git a/src/objtools/edit/Makefile.edit.lib b/src/objtools/edit/Makefile.edit.lib
index 7ce0d11..f5458c5 100644
--- a/src/objtools/edit/Makefile.edit.lib
@@ -1127,6 +1458,16 @@ index 7ce0d11..f5458c5 100644
WATCHERS = bollin
+
+DLL_LIB = xncbi seq xobjutil xobjmgr
+diff --git a/src/objtools/eutils/api/Makefile.eutils.lib b/src/objtools/eutils/api/Makefile.eutils.lib
+index da71ea9..b444e72 100644
+--- a/src/objtools/eutils/api/Makefile.eutils.lib
++++ b/src/objtools/eutils/api/Makefile.eutils.lib
+@@ -10,3 +10,5 @@ ASN_DEP = einfo esearch egquery epost elink esummary espell uilist \
+ ehistory
+
+ WATCHERS = grichenk
++
++DLL_LIB = dbapi_driver xconnect xncbi xser # align_format axf ncbi_xloader_bam
diff --git a/src/objtools/eutils/egquery/Makefile.egquery.lib b/src/objtools/eutils/egquery/Makefile.egquery.lib
index 82b4ed0..7030a29 100644
--- a/src/objtools/eutils/egquery/Makefile.egquery.lib
@@ -1217,8 +1558,18 @@ index 19b2b8a..77dcc3c 100644
WATCHERS = grichenk
+
+DLL_LIB = xser
+diff --git a/src/objtools/eutils/uilist/Makefile.uilist.lib b/src/objtools/eutils/uilist/Makefile.uilist.lib
+index b49c3c5..2ee63f0 100644
+--- a/src/objtools/eutils/uilist/Makefile.uilist.lib
++++ b/src/objtools/eutils/uilist/Makefile.uilist.lib
+@@ -4,3 +4,5 @@ SRC = uilist__ uilist___
+ LIB = uilist
+
+ WATCHERS = grichenk
++
++DLL_LIB = access dbapi_driver xncbi xser # align_format axf
diff --git a/src/objtools/format/Makefile.xformat.lib b/src/objtools/format/Makefile.xformat.lib
-index a4fc469..0203fea 100644
+index a4fc469..fa58b3c 100644
--- a/src/objtools/format/Makefile.xformat.lib
+++ b/src/objtools/format/Makefile.xformat.lib
@@ -19,3 +19,5 @@ SRC = accession_item basecount_item comment_item contig_item date_item \
@@ -1226,7 +1577,7 @@ index a4fc469..0203fea 100644
WATCHERS = ludwigf dicuccio kornbluh
+
-+DLL_LIB = submit connect xncbi gbseq xobjmgr
++DLL_LIB = submit connect xncbi gbseq xobjmgr xobjutil xalnmgr xconnect
diff --git a/src/objtools/lds/Makefile.lds.lib b/src/objtools/lds/Makefile.lds.lib
index e371035..689cfb4 100644
--- a/src/objtools/lds/Makefile.lds.lib
@@ -1270,6 +1621,18 @@ index 85eefe2..9f317ae 100644
-DLL_LIB = xobjread
+DLL_LIB = xobjread xncbi xutil seq xobjmgr xobjutil
+diff --git a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+index 687af1e..f48568c 100644
+--- a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
++++ b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+@@ -11,6 +11,6 @@ mask_writer_seqloc \
+ mask_writer_blastdb_maskinfo
+
+ ASN_DEP = seqset
+-DLL_LIB = seqdb blastdb
++DLL_LIB = seqdb blastdb xobjread xobjutil
+
+ WATCHERS = morgulis camacho
diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib
index dab25d6..f676dc7 100644
--- a/src/objtools/simple/Makefile.xobjsimple.lib
@@ -1279,6 +1642,16 @@ index dab25d6..f676dc7 100644
SRC = simple_om
+DLL_LIB = xobjmgr ncbi_xloader_genbank
+diff --git a/src/objtools/snputil/Makefile.snputil.lib b/src/objtools/snputil/Makefile.snputil.lib
+index 15abef3..5ad1560 100644
+--- a/src/objtools/snputil/Makefile.snputil.lib
++++ b/src/objtools/snputil/Makefile.snputil.lib
+@@ -9,3 +9,5 @@ SRC = snp_utils snp_bitfield \
+ ASN_DEP = seqset
+
+ WATCHERS = rudnev
++
++DLL_LIB = general seq xncbi xobjmgr xser
diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib
index 80a74d8..6eec94b 100644
--- a/src/objtools/validator/Makefile.validator.lib
@@ -1298,6 +1671,66 @@ index cd6596b..a7d0c01 100644
WATCHERS = ludwigf boukn
+DLL_LIB = xobjutil xalnmgr
+diff --git a/src/sample/app/asn/Makefile.sample_asn.lib b/src/sample/app/asn/Makefile.sample_asn.lib
+index 0db9ebd..26e6ad9 100644
+--- a/src/sample/app/asn/Makefile.sample_asn.lib
++++ b/src/sample/app/asn/Makefile.sample_asn.lib
+@@ -10,3 +10,5 @@ LIB = sample_asn
+ ASN_DEP = general
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver general xncbi xser
+diff --git a/src/sample/app/soap/Makefile.soap_dataobj.lib b/src/sample/app/soap/Makefile.soap_dataobj.lib
+index 4b87f51..c398ded 100644
+--- a/src/sample/app/soap/Makefile.soap_dataobj.lib
++++ b/src/sample/app/soap/Makefile.soap_dataobj.lib
+@@ -2,3 +2,5 @@ LIB = soap_dataobj
+ SRC = soap_dataobj__ soap_dataobj___
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
+index f9d6103..4c22831 100644
+--- a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
++++ b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = asn_sample_lib
+ SRC = asn_sample_lib__ asn_sample_lib___
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/basic/Makefile.basic_sample_lib.lib b/src/sample/lib/basic/Makefile.basic_sample_lib.lib
+index a6ba11a..364d9fc 100644
+--- a/src/sample/lib/basic/Makefile.basic_sample_lib.lib
++++ b/src/sample/lib/basic/Makefile.basic_sample_lib.lib
+@@ -5,3 +5,5 @@ SRC = basic_sample_lib
+
+
+ WATCHERS = gouriano
++
++DLL_LIB = xncbi
+diff --git a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
+index d2a27ef..a63a7e8 100644
+--- a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
++++ b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = dtd_sample_lib
+ SRC = dtd_sample_lib__ dtd_sample_lib___
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
+diff --git a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
+index 4b7b6e2..838e8ea 100644
+--- a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
++++ b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib
+@@ -2,3 +2,5 @@ LIB = xsd_sample_lib
+ SRC = xsd_sample_lib__ xsd_sample_lib___
+
+ WATCHERS = gouriano
++
++DLL_LIB = access align_format axf dbapi_driver xncbi xser
diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib
index 2563b5f..efad054 100644
--- a/src/serial/Makefile.serial.lib
@@ -1337,6 +1770,19 @@ index 9877691..599ef5d 100644
WATCHERS = gouriano
+DLL_LIB = xncbi xutil xser
+diff --git a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
+index 4896661..8e2ad56 100644
+--- a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
++++ b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib
+@@ -12,7 +12,7 @@ ASN_DEP = seqset seq
+
+ LIB_OR_DLL = both
+
+-DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB)
++DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB) xobjreadex
+ LIBS = $(CMPRS_LIBS) $(ORIG_LIBS)
+
+ CPPFLAGS = $(SRA_INCLUDE) -DNCBI_XLOADER_BAM_EXPORTS $(ORIG_CPPFLAGS)
diff --git a/src/sra/sdk/libs/align/Makefile.align-writer.lib b/src/sra/sdk/libs/align/Makefile.align-writer.lib
index f2a2f58..f61b25a 100644
--- a/src/sra/sdk/libs/align/Makefile.align-writer.lib
diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml
new file mode 100644
index 000000000..250e06858
--- /dev/null
+++ b/sci-biology/ncbi-tools++/metadata.xml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="boost">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="cppunit">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="freetype">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="ftds">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="mesa">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="muparser">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="sablotron">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="xerces">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="xalan">Undocumented USE</flag>
+ </use>
+ <use>
+ <flag name="xslt">Undocumented USE</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 439e91722..9a2f8da09 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $
@@ -12,7 +12,6 @@ MY_PV="9_0_0"
MY_P="ncbi_cxx--${MY_PV}"
#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
-
DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
SRC_URI="
@@ -24,7 +23,7 @@ SLOT="0"
IUSE="
debug static-libs static threads pch
test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -90,7 +89,6 @@ src_prepare() {
# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
@@ -106,6 +104,8 @@ src_prepare() {
epatch ${PATCHES[@]}
tc-export CXX CC
+
+
# cd src/build-system || die
# eaclocal -I.
# eautoconf
@@ -186,9 +186,9 @@ src_configure() {
# --with-sssutils
# --with-sssdb
# --with-included-sss
- --with-z="${EPREFIX}"/usr
- --with-bz2="${EPREFIX}"/usr
- --with-muparser="${EPREFIX}"/usr
+ --with-z="${EPREFIX}/usr"
+ --with-bz2="${EPREFIX}/usr"
+ --with-muparser="${EPREFIX}/usr"
--without-sybase
--with-autodep
# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
@@ -201,41 +201,41 @@ src_configure() {
$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
$(use_with test check)
$(use_with pch)
- $(use_with lzo lzo "${EPREFIX}"/usr)
- $(use_with pcre pcre "${EPREFIX}"/usr)
- $(use_with gnutls gnutls "${EPREFIX}"/usr)
- $(use_with ssl openssl "${EPREFIX}"/usr)
- $(use_with ftds ftds "${EPREFIX}"/usr)
- $(use_with mysql mysql "${EPREFIX}"/usr)
- $(use_with fltk fltk "${EPREFIX}"/usr)
- $(use_with opengl opengl "${EPREFIX}"/usr)
- $(use_with mesa mesa "${EPREFIX}"/usr)
- $(use_with opengl glut "${EPREFIX}"/usr)
- $(use_with opengl glew "${EPREFIX}"/usr)
+ $(use_with lzo lzo "${EPREFIX}/usr")
+ $(use_with pcre pcre "${EPREFIX}/usr")
+ $(use_with gnutls gnutls "${EPREFIX}/usr")
+ $(use_with ssl openssl "${EPREFIX}/usr")
+ $(use_with ftds ftds "${EPREFIX}/usr")
+ $(use_with mysql mysql "${EPREFIX}/usr")
+ $(use_with fltk fltk "${EPREFIX}/usr")
+ $(use_with opengl opengl "${EPREFIX}/usr")
+ $(use_with mesa mesa "${EPREFIX}/usr")
+ $(use_with opengl glut "${EPREFIX}/usr")
+ $(use_with opengl glew "${EPREFIX}/usr")
$(use_with opengl glew-mx)
- $(use_with wxwidgets wxwidgets "${EPREFIX}"/usr)
+ $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
- $(use_with freetype freetype "${EPREFIX}"/usr)
- $(use_with fastcgi fastcgi "${EPREFIX}"/usr)
- $(use_with berkdb bdb "${EPREFIX}"/usr)
- $(use_with odbc odbc "${EPREFIX}"/usr)
- $(use_with python python "${EPREFIX}"/usr)
- $(use_with boost boost "${EPREFIX}"/usr)
- $(use_with sqlite sqlite3 "${EPREFIX}"/usr)
- $(use_with icu icu "${EPREFIX}"/usr)
- $(use_with expat expat "${EPREFIX}"/usr)
- $(use_with xml libxml "${EPREFIX}"/usr)
- $(use_with xml libxslt "${EPREFIX}"/usr)
- $(use_with xerces xerces "${EPREFIX}"/usr)
- $(use_with hdf5 hdf5 "${EPREFIX}"/usr)
- $(use_with xalan xalan "${EPREFIX}"/usr)
-# $(use_with gif gif "${EPREFIX}"/usr)
- $(use_with jpeg jpeg "${EPREFIX}"/usr)
- $(use_with tiff tiff "${EPREFIX}"/usr)
- $(use_with png png "${EPREFIX}"/usr)
- $(use_with xpm xpm "${EPREFIX}"/usr)
- $(use_with curl curl "${EPREFIX}"/usr)
-# $(use_with X x "${EPREFIX}"/usr)
+ $(use_with freetype freetype "${EPREFIX}/usr")
+ $(use_with fastcgi fastcgi "${EPREFIX}/usr")
+ $(use_with berkdb bdb "${EPREFIX}/usr")
+ $(use_with odbc odbc "${EPREFIX}/usr")
+ $(use_with python python "${EPREFIX}/usr")
+ $(use_with boost boost "${EPREFIX}/usr")
+ $(use_with sqlite sqlite3 "${EPREFIX}/usr")
+ $(use_with icu icu "${EPREFIX}/usr")
+ $(use_with expat expat "${EPREFIX}/usr")
+ $(use_with xml libxml "${EPREFIX}/usr")
+ $(use_with xml libxslt "${EPREFIX}/usr")
+ $(use_with xerces xerces "${EPREFIX}/usr")
+ $(use_with hdf5 hdf5 "${EPREFIX}/usr")
+ $(use_with xalan xalan "${EPREFIX}/usr")
+# $(use_with gif gif "${EPREFIX}/usr")
+ $(use_with jpeg jpeg "${EPREFIX}/usr")
+ $(use_with tiff tiff "${EPREFIX}/usr")
+ $(use_with png png "${EPREFIX}/usr")
+ $(use_with xpm xpm "${EPREFIX}/usr")
+ $(use_with curl curl "${EPREFIX}/usr")
+# $(use_with X x "${EPREFIX}/usr")
$(use_with X x)
)
@@ -243,17 +243,17 @@ src_configure() {
use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
# TODO
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+ # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
- einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}"/usr --libdir=/usr/lib64 ${myconf[@]}"
+ einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
# bash \
# ./src/build-system/configure \
# cd src/build-system || die
econf \
--srcdir="${S}" \
- --prefix="${EPREFIX}"/usr \
+ --prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
${myconf[@]} || die
#--without-debug \
@@ -280,7 +280,14 @@ src_compile() {
}
src_install() {
- emake install || die
+ rm -rvf "${S}"_build/lib/ncbi || die
+ emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
+
+# dobin "${S}"_build/bin/*
+# dolib.so "${S}"_build/lib/*so*
+# dolib.a "${S}"_build/lib/*.a
+# doheader "${S}"_build/inc/*
+
# File collisions with sci-biology/ncbi-tools
rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index f93b1aa86..09f183a93 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $
@@ -12,7 +12,6 @@ MY_PV="9_0_0"
MY_P="ncbi_cxx--${MY_PV}"
#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
-
DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
SRC_URI="
@@ -148,7 +147,6 @@ src_prepare() {
# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
@@ -271,7 +269,7 @@ src_configure() {
fi
# TODO
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+ # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
"${S}"/configure --without-debug \
diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index a57b68364..38b6c289d 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/sra_sdk
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> sra_sdk-2.1.9.ebuild,
+ sra_sdk-2.2.2a.ebuild, metadata.xml:
+ Drop useless blank line
+
*sra_sdk-2.2.2a (28 Dec 2012)
28 Dec 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/sra_sdk/metadata.xml b/sci-biology/sra_sdk/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/sra_sdk/metadata.xml
+++ b/sci-biology/sra_sdk/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
index bfbb5772c..db790500d 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -78,8 +78,6 @@ src_install(){
#doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp --preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done
-
-
# install the main libs and the ncbi/vdb-copy.kfg file
insinto /usr/lib/ncbi
doins "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi/*
@@ -87,8 +85,6 @@ src_install(){
# zap the subdirectory so that copying below does not fail
rm -rf "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi
-
-
# BUG: neither the dolib nor cp --preserve=all work
#insinto /usr/lib64
#dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
index c759f57b6..dee4cdeb6 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -80,8 +80,6 @@ src_install(){
#doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
for f in "${OBJDIR}"/bin/*; do cp --preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done
-
-
# install the main libs and the ncbi/vdb-copy.kfg file
insinto /usr/lib/ncbi
doins "${OBJDIR}"/lib/ncbi/*
@@ -89,8 +87,6 @@ src_install(){
# zap the subdirectory so that copying below does not fail
rm -rf "${OBJDIR}"/lib/ncbi
-
-
# BUG: neither the dolib nor cp --preserve=all work
#insinto /usr/lib64
#dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
diff --git a/sci-biology/wcd/ChangeLog b/sci-biology/wcd/ChangeLog
index 19bb05dc9..be44eea7e 100644
--- a/sci-biology/wcd/ChangeLog
+++ b/sci-biology/wcd/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/wcd
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> wcd-0.6.0.ebuild,
+ +files/wcd-0.6.0-impl-decl.patch, +files/wcd-0.6.0-ldflags.patch,
+ metadata.xml:
+ Add missing multilib.eclass; move to EAPI=5 and autotools-utils.eclass;
+ simplify ebuild syntax; fix for ld.gold; fix implicid declarations
+
*wcd-0.6.0 (25 Jun 2011)
25 Jun 2011; Justin Lecher <jlec@gentoo.org> -wcd-0.6.0_beta.ebuild,
diff --git a/sci-biology/wcd/Manifest b/sci-biology/wcd/Manifest
index c272d244a..108729131 100644
--- a/sci-biology/wcd/Manifest
+++ b/sci-biology/wcd/Manifest
@@ -1 +1 @@
-DIST wcd-0.6.0.tar.gz 595214 RMD160 eda5edf8215f0b723c5d1e970f36cb3e97b09e6f SHA1 988f944d4a6cd0894a864fa990f0f6eaab3b94bd SHA256 58a02677a0d89f9c2ff89f6f0ef9f5ce9caa487ff3f85a0a73fb9da0ec138509
+DIST wcd-0.6.0.tar.gz 595214 SHA256 58a02677a0d89f9c2ff89f6f0ef9f5ce9caa487ff3f85a0a73fb9da0ec138509 SHA512 e810ab6517d93bd473e88d60e687710df7eab72e53750f4ef4d0e19566d3f02a28e863b026ed6de5dc1672a750abb93fd49b35ed5767af092d2fb404d1453ace WHIRLPOOL 7f19d149d2d6b70b5880fea43b623e9009ae6995438b921fd4f3d04ee74689bba119e247783c00229f557d7321817da3687bffc33190f961a76c4768cea65aac
diff --git a/sci-biology/wcd/files/wcd-0.6.0-impl-decl.patch b/sci-biology/wcd/files/wcd-0.6.0-impl-decl.patch
new file mode 100644
index 000000000..15d851577
--- /dev/null
+++ b/sci-biology/wcd/files/wcd-0.6.0-impl-decl.patch
@@ -0,0 +1,15 @@
+ src/auxcluster.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/auxcluster.c b/src/auxcluster.c
+index ac00a0f..e98f19f 100644
+--- a/src/auxcluster.c
++++ b/src/auxcluster.c
+@@ -2,6 +2,7 @@
+
+ #include "common.h"
+ #include "strings.h"
++#include <string.h>
+ #include "assert.h"
+
+ extern SeqInfoPtr seqInfo;
diff --git a/sci-biology/wcd/files/wcd-0.6.0-ldflags.patch b/sci-biology/wcd/files/wcd-0.6.0-ldflags.patch
new file mode 100644
index 000000000..d697d00b7
--- /dev/null
+++ b/sci-biology/wcd/files/wcd-0.6.0-ldflags.patch
@@ -0,0 +1,16 @@
+ src/Makefile.am | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Makefile.am b/src/Makefile.am
+index e986a91..ff87e29 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -7,7 +7,7 @@ wcd_CFLAGS += -DMPI
+ endif
+ if PTHREADS
+ wcd_CFLAGS += -DPTHREADS
+-wcd_LDFLAGS += -lpthread
++wcd_LDADD = -lpthread
+ endif
+ if !COMPILER
+ wcd_CFLAGS += -DNOINLINE
diff --git a/sci-biology/wcd/metadata.xml b/sci-biology/wcd/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/wcd/metadata.xml
+++ b/sci-biology/wcd/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/wcd/wcd-0.6.0.ebuild b/sci-biology/wcd/wcd-0.6.0.ebuild
index 3367cc404..2557e3166 100644
--- a/sci-biology/wcd/wcd-0.6.0.ebuild
+++ b/sci-biology/wcd/wcd-0.6.0.ebuild
@@ -1,10 +1,12 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
-inherit eutils flag-o-matic
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils flag-o-matic multilib
DESCRIPTION="Sequence clustering by either of: d2 function, edit distance, common word heuristics"
HOMEPAGE="http://code.google.com/p/wcdest/"
@@ -18,35 +20,26 @@ IUSE="doc mpi threads"
DEPEND="mpi? ( sys-cluster/mpich2 )"
RDEPEND=""
-S="${WORKDIR}"/wcd-0.6.0
+PATCHES=(
+ "${FILESDIR}"/${P}-ldflags.patch
+ "${FILESDIR}"/${P}-impl-decl.patch
+ )
src_configure(){
- local myconf=""
- if use mpi; then
- myconf="${myconf} --enable-mpi"
- fi
+ local myeconfargs=()
+ use mpi && myeconfargs+=( --enable-mpi )
- if use threads; then
- myconf="${myconf} --enable-pthreads"
- fi
+ use threads && myeconfargs+=( --enable-pthreads )
- econf ${myconf}
+ autotools-utils_src_configure
}
src_compile() {
- emake
- if use doc; then
- emake pdf info html
- fi
+ autotools-utils_src_compile
+ use doc && autotools-utils_src_compile pdf info html
}
src_install() {
- local f
- emake PREFIX=/usr DESTDIR="${D}" LIBDIR="${D}"usr/$(get_libdir) install
-
- if use doc; then
- for f in README doc/wcd.html doc/wcd.pdf doc/wcd.texi; do
- dodoc ${f}
- done
- fi
+ use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi )
+ autotools-utils_src_install PREFIX=/usr LIBDIR="${D}"usr/$(get_libdir)
}
diff --git a/sci-chemistry/GromacsWrapper/ChangeLog b/sci-chemistry/GromacsWrapper/ChangeLog
new file mode 100644
index 000000000..f8c6e3290
--- /dev/null
+++ b/sci-chemistry/GromacsWrapper/ChangeLog
@@ -0,0 +1,25 @@
+# ChangeLog for sci-chemistry/GromacsWrapper
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 26 Mar 2013; Justin Lecher <jlec@gentoo.org> GromacsWrapper-9999.ebuild:
+ Drop py 2.5 support
+
+ 26 Mar 2013; Justin Lecher <jlec@gentoo.org> GromacsWrapper-9999.ebuild:
+ Enhance python r1 eclass usage
+
+ 26 Mar 2013; Justin Lecher <jlec@gentoo.org> -GromacsWrapper-0.3.1.ebuild,
+ metadata.xml:
+ Drop in tree version
+
+ 23 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org>
+ +files/0001-Drop-chmod-hack.patch, GromacsWrapper-0.3.1.ebuild,
+ GromacsWrapper-9999.ebuild:
+ Add patch to fix hack
+
+*GromacsWrapper-0.3.1 (23 Mar 2013)
+*GromacsWrapper-9999 (23 Mar 2013)
+
+ 23 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> +GromacsWrapper-0.3.1.ebuild,
+ +GromacsWrapper-9999.ebuild, +metadata.xml:
+ Add Gromacs Python wrapper
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild
new file mode 100644
index 000000000..4d8864dca
--- /dev/null
+++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+if [[ $PV = *9999* ]]; then
+ scm_eclass=git-2
+ EGIT_REPO_URI="
+ git://github.com/orbeckst/${PN}.git
+ https://github.com/orbeckst/${PN}.git"
+ EGIT_BRANCH="develop"
+ SRC_URI=""
+ KEYWORDS=""
+else
+ scm_eclass=vcs-snapshot
+ SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+inherit eutils distutils-r1 ${scm_eclass}
+
+DESCRIPTION="Python framework for Gromacs"
+HOMEPAGE="http://orbeckst.github.com/GromacsWrapper/"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND="
+ >=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}]
+ >=dev-python/RecSQL-0.3[${PYTHON_USEDEP}]
+ >=sci-libs/scipy-0.9[${PYTHON_USEDEP}]
+ "
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/0001-Drop-chmod-hack.patch"
+)
diff --git a/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch
new file mode 100644
index 000000000..8645df77b
--- /dev/null
+++ b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch
@@ -0,0 +1,28 @@
+From 49b8d9662365e0e9b0725682b8a8479de402b272 Mon Sep 17 00:00:00 2001
+From: Alexey Shvetsov <alexxy@gentoo.org>
+Date: Sat, 23 Mar 2013 16:40:04 +0400
+Subject: [PATCH] Drop chmod hack.
+
+It doesnt work if wrapper installed system-wide
+
+Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>
+---
+ gromacs/config.py | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/gromacs/config.py b/gromacs/config.py
+index cece6fc..2e686e7 100644
+--- a/gromacs/config.py
++++ b/gromacs/config.py
+@@ -619,8 +619,6 @@ del g
+ # Must extract because it is part of a zipped python egg;
+ # see http://peak.telecommunity.com/DevCenter/PythonEggs#accessing-package-resources
+ GridMAT_MD = resource_filename(__name__,'external/GridMAT-MD_v1.0.2/GridMAT-MD.pl')
+-os.chmod(GridMAT_MD, 0755)
+-
+
+ #: 3rd party bundled analysis scripts and tools; this is a list of triplets of
+ #:
+--
+1.8.1.5
+
diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml
new file mode 100644
index 000000000..098ac091a
--- /dev/null
+++ b/sci-chemistry/GromacsWrapper/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</herd>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index 9799e4374..f4d3a9da3 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -1,7 +1,19 @@
# ChangeLog for sci-chemistry/ambertools
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> ambertools-1.5-r4.ebuild:
+ Add missing multilib.eclass
+
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> -ambertools-1.5-r2.ebuild,
+ -ambertools-1.5-r3.ebuild, ambertools-12.ebuild:
+ Add missing multilib.eclass
+
+ 22 Feb 2013; Justin Lecher <jlec@gentoo.org> ambertools-1.5-r2.ebuild,
+ ambertools-1.5-r3.ebuild, ambertools-1.5-r4.ebuild, ambertools-12.ebuild,
+ metadata.xml:
+ Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
+
08 Nov 2012; Justin Lecher <jlec@gentoo.org> ambertools-12.ebuild,
metadata.xml:
Add another fix for blas/lapack
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild
deleted file mode 100644
index 39413fdcb..000000000
--- a/sci-chemistry/ambertools/ambertools-1.5-r2.ebuild
+++ /dev/null
@@ -1,156 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
-
-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-${PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="openmp X"
-
-RESTRICT="fetch"
-
-RDEPEND="
- virtual/cblas
- virtual/lapack
- sci-libs/clapack
- sci-libs/arpack
- sci-libs/cifparse-obj
- sci-chemistry/mopac7
- sci-libs/netcdf
- sci-libs/fftw:2.1
- sci-chemistry/reduce
- virtual/fortran"
-DEPEND="${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 \
- "${FILESDIR}/${P}-bugfix_1-21.patch" \
- "${FILESDIR}/${P}-gentoo2.patch"
- cd "${S}"/AmberTools/src
- rm -r \
- arpack \
- blas \
- byacc \
- lapack \
- fftw-2.1.5 \
- fftw-3.2.2 \
- c9x-complex \
- cifparse \
- netcdf \
- pnetcdf \
- reduce \
- ucpp-1.3 \
- || die
-}
-
-src_configure() {
- cd "${S}"/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:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
- -e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
- -e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
- -e "s:GENTOO_LDFLAGS:${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" \
- -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="${myconf} -noX11"
-
- use openmp && myconf="${myconf} -openmp"
-
- ./configure \
- ${myconf} \
- -nobintraj \
- -nomdgx \
- -nomtkpp \
- -nopython \
- -nosleap \
- gnu
-}
-
-src_compile() {
- cd "${S}"/AmberTools/src
- emake || die
-}
-
-src_test() {
- cd "${S}"/AmberTools/test
- make test || die
-}
-
-src_install() {
- rm -r bin/chemistry bin/MMPBSA_mods
- rm bin/ante-MMPBSA.py bin/extractFrcmod.py
-
- for x in bin/*
- do dobin ${x} || die
- done
-
- dobin AmberTools/src/antechamber/mopac.sh
- sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
- -i "${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}"
-
- 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-r3.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild
deleted file mode 100644
index 44bd0599a..000000000
--- a/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild
+++ /dev/null
@@ -1,158 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
-
-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-${PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="openmp X"
-
-RESTRICT="fetch"
-
-RDEPEND="
- virtual/cblas
- virtual/lapack
- sci-libs/clapack
- sci-libs/arpack
- sci-libs/cifparse-obj
- sci-chemistry/mopac7
- sci-libs/netcdf
- sci-libs/fftw:2.1
- sci-chemistry/reduce
- virtual/fortran"
-DEPEND="${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 \
- "${FILESDIR}/${P}-bugfix_1-21.patch" \
- "${FILESDIR}/${P}-bugfix_22-27.patch" \
- "${FILESDIR}/${P}-gentoo2.patch" \
- "${FILESDIR}/${P}-overflow.patch"
- cd "${S}"/AmberTools/src
- rm -r \
- arpack \
- blas \
- byacc \
- lapack \
- fftw-2.1.5 \
- fftw-3.2.2 \
- c9x-complex \
- cifparse \
- netcdf \
- pnetcdf \
- reduce \
- ucpp-1.3 \
- || die
-}
-
-src_configure() {
- cd "${S}"/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:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
- -e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
- -e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
- -e "s:GENTOO_LDFLAGS:${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" \
- -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="${myconf} -noX11"
-
- use openmp && myconf="${myconf} -openmp"
-
- ./configure \
- ${myconf} \
- -nobintraj \
- -nomdgx \
- -nomtkpp \
- -nopython \
- -nosleap \
- gnu
-}
-
-src_compile() {
- cd "${S}"/AmberTools/src
- emake || die
-}
-
-src_test() {
- cd "${S}"/AmberTools/test
- make test || die
-}
-
-src_install() {
- rm -r bin/chemistry bin/MMPBSA_mods
- rm bin/ante-MMPBSA.py bin/extractFrcmod.py
-
- for x in bin/*
- do dobin ${x} || die
- done
-
- dobin AmberTools/src/antechamber/mopac.sh
- sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
- -i "${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}"
-
- 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-r4.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
index d689579f9..2ac4b2fd6 100644
--- a/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
+++ b/sci-chemistry/ambertools/ambertools-1.5-r4.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
EAPI=4
-inherit eutils fortran-2 toolchain-funcs
+inherit eutils fortran-2 multilib toolchain-funcs
DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
HOMEPAGE="http://ambermd.org/#AmberTools"
@@ -76,8 +76,8 @@ src_prepare() {
src_configure() {
cd "${S}"/AmberTools/src
sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
- -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
- -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+ -e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+ -e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
@@ -85,7 +85,7 @@ src_configure() {
-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
-e "s:fc=g77:fc=$(tc-getFC):g" \
- -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+ -e "s:\$netcdflib:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
-i configure || die
sed -e "s:arsecond_:arscnd_:g" \
diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild
index ea7dfdb00..70ea7f3c3 100644
--- a/sci-chemistry/ambertools/ambertools-12.ebuild
+++ b/sci-chemistry/ambertools/ambertools-12.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
-inherit eutils fortran-2 toolchain-funcs
+inherit eutils fortran-2 multilib toolchain-funcs
DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
HOMEPAGE="http://ambermd.org/#AmberTools"
@@ -73,18 +73,18 @@ src_configure() {
cd "${S}"/AmberTools/src
sed \
-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
- -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
- -e "s:-llapack:$(pkg-config lapack --libs) -lclapack:g" \
- -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
- -e "s:-lblas:$(pkg-config blas cblas --libs):g" \
+ -e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+ -e "s:-llapack:$($(tc-getPKG_CONFIG) lapack --libs) -lclapack:g" \
+ -e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
+ -e "s:-lblas:$($(tc-getPKG_CONFIG) blas cblas --libs):g" \
-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
- -e "s:GENTOO_FFTW3_LIBS:$(pkg-config fftw3 --libs):" \
+ -e "s:GENTOO_FFTW3_LIBS:$($(tc-getPKG_CONFIG) fftw3 --libs):" \
-e "s:fc=g77:fc=$(tc-getFC):g" \
- -e "s:\$netcdfflag:$(pkg-config netcdf --libs):g" \
+ -e "s:\$netcdfflag:$($(tc-getPKG_CONFIG) netcdf --libs):g" \
-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
-i configure2 || die
sed -e "s:arsecond_:arscnd_:g" \
diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml
index b2558d8c6..13ef0bf5a 100644
--- a/sci-chemistry/ambertools/metadata.xml
+++ b/sci-chemistry/ambertools/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>alexxy@gentoo.org</email>
- <name>Alexey Shvetsov</name>
- </maintainer>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-chemistry/ball/ChangeLog b/sci-chemistry/ball/ChangeLog
index 851aa6fc7..7e0be39f5 100644
--- a/sci-chemistry/ball/ChangeLog
+++ b/sci-chemistry/ball/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-chemistry/ball
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> ball-9999.ebuild, metadata.xml:
+ Update to new qt deps names
+
25 Mar 2012; Justin Lecher <jlec@gentoo.org> ball-9999.ebuild,
+files/ball-9999-libsvm.patch, +files/ball-9999-multilib.patch:
Fix patches to be in line with tree
diff --git a/sci-chemistry/ball/ball-9999.ebuild b/sci-chemistry/ball/ball-9999.ebuild
index 4fac56b8d..8cab0732c 100644
--- a/sci-chemistry/ball/ball-9999.ebuild
+++ b/sci-chemistry/ball/ball-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -28,15 +28,15 @@ RDEPEND="
sci-mathematics/lpsolve
virtual/opengl
x11-libs/libX11
- x11-libs/qt-core
- x11-libs/qt-gui
- x11-libs/qt-opengl
- x11-libs/qt-test
- x11-libs/qt-webkit
+ dev-qt/qtcore
+ dev-qt/qtgui
+ dev-qt/qtopengl
+ dev-qt/qttest
+ dev-qt/qtwebkit
cuda? ( dev-util/nvidia-cuda-toolkit )
mpi? ( virtual/mpi )
- sql? ( x11-libs/qt-sql )
- webkit? ( x11-libs/qt-webkit )"
+ sql? ( dev-qt/qtsql )
+ webkit? ( dev-qt/qtwebkit )"
DEPEND="${RDEPEND}
dev-python/sip
sys-devel/bison
diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml
index 8c954a23a..95b15413c 100644
--- a/sci-chemistry/ball/metadata.xml
+++ b/sci-chemistry/ball/metadata.xml
@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci</herd>
- <maintainer>
- <email>jlec@gentoo.org</email>
- </maintainer>
- <longdescription>
+ <herd>sci</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ </maintainer>
+ <longdescription>
Rapid Software Prototyping can significantly reduce development times in the
field of Computational Molecular Biology and Molecular Modeling.
BALL (Biochemical Algorithms Library) is an application framework in C++ that
@@ -24,9 +24,9 @@ Based on BALL we have developed a stand-alone tool for molecular visualization,
BALLView . BALLView makes the broad functionality available through an
integrated user-friendly GUI.
</longdescription>
- <use>
- <flag name="sql">Include SQL database support</flag>
- <flag name="cuda">Include cuda support</flag>
- <flag name="webkit">Uses <pkg>x11-libs/qt-webkit</pkg> for drawing</flag>
- </use>
+ <use>
+ <flag name="sql">Include SQL database support</flag>
+ <flag name="cuda">Include cuda support</flag>
+ <flag name="webkit">Uses <pkg>x11-libs/qt-webkit</pkg> for drawing</flag>
+ </use>
</pkgmetadata>
diff --git a/sci-chemistry/burrow-owl/ChangeLog b/sci-chemistry/burrow-owl/ChangeLog
index 8377c8ba5..ad72a3754 100644
--- a/sci-chemistry/burrow-owl/ChangeLog
+++ b/sci-chemistry/burrow-owl/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-chemistry/burrow-owl
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> burrow-owl-9999.ebuild,
+ metadata.xml:
+ Bump to EPAI=5 and move to virtual/pkgconfig
+
19 Feb 2012; Justin Lecher <jlec@gentoo.org> burrow-owl-9999.ebuild:
Drop Keywords
diff --git a/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild b/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild
index 42615b4d6..0b8c025e9 100644
--- a/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild
+++ b/sci-chemistry/burrow-owl/burrow-owl-9999.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
AUTOTOOLS_AUTORECONF="true"
@@ -28,7 +28,7 @@ RDEPEND="
x11-libs/gtk+:2"
DEPEND="${RDEPEND}
dev-util/indent
- dev-util/pkgconfig
+ virtual/pkgconfig
doc? ( app-doc/doxygen )
"
diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml
index 31da0a681..15f3d5ac1 100644
--- a/sci-chemistry/burrow-owl/metadata.xml
+++ b/sci-chemistry/burrow-owl/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>sci-chemistry@gentoo.org</email>
- </maintainer>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>sci-chemistry@gentoo.org</email>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-chemistry/camshift/ChangeLog b/sci-chemistry/camshift/ChangeLog
index 40e7c22e9..7e6131da7 100644
--- a/sci-chemistry/camshift/ChangeLog
+++ b/sci-chemistry/camshift/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-chemistry/camshift
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 22 Feb 2013; Justin Lecher <jlec@gentoo.org> +files/1.35.0-gcc47.patch,
+ files/1.35.0-gentoo.patch, camshift-1.35.0.ebuild, metadata.xml:
+ Bump to EAPI=5; add missing deps; fix for gcc-4.7
+
*camshift-1.35.0 (27 Jan 2011)
27 Jan 2011; Justin Lecher <jlec@gentoo.org> +files/1.35.0-gentoo.patch,
diff --git a/sci-chemistry/camshift/Manifest b/sci-chemistry/camshift/Manifest
index 213b6311c..f950434d1 100644
--- a/sci-chemistry/camshift/Manifest
+++ b/sci-chemistry/camshift/Manifest
@@ -1 +1 @@
-DIST camshift-1.35.0.tar.gz 6297498 RMD160 79d389b7c2533b87b8333be89b76a1901556c2de SHA1 0c6dbaabcddfb9de65bc0500bd0a9f18a1eefa8a SHA256 21d64fa08b51f01fb8526592fb4b382060e20fd677ec1c31aff14e5d7eef3316
+DIST camshift-1.35.0.tar.gz 6297498 SHA256 21d64fa08b51f01fb8526592fb4b382060e20fd677ec1c31aff14e5d7eef3316 SHA512 78cf5e257c00f0f025052fddd9066c6ef404765d106df72737ed360a269e1106c19ff25ec4962fc8faf2be9af935e0230506c55d2ff4e521c2ad955771b3396c WHIRLPOOL b435e895f9b0c2d2d6bf4216744fc86ac62211792da2fb570d43c228f9a32e957d7e27ebac9cd0cbceb09c996f4162d399954ec3cdd653deb95dd1a431e14585
diff --git a/sci-chemistry/camshift/camshift-1.35.0.ebuild b/sci-chemistry/camshift/camshift-1.35.0.ebuild
index c4adb6026..78196ea0b 100644
--- a/sci-chemistry/camshift/camshift-1.35.0.ebuild
+++ b/sci-chemistry/camshift/camshift-1.35.0.ebuild
@@ -1,12 +1,14 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="3"
+EAPI=5
-inherit autotools eutils flag-o-matic
+AUTOTOOLS_AUTORECONF=true
-sDESCRIPTION="Structure based prediction of protein chemical shifts"
+inherit autotools-utils flag-o-matic
+
+DESCRIPTION="Structure based prediction of protein chemical shifts"
HOMEPAGE="http://www-vendruscolo.ch.cam.ac.uk/camshift/camshift.php"
SRC_URI="http://www-vendruscolo.ch.cam.ac.uk/${PN}/${P}.tar.gz"
@@ -15,35 +17,36 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="sse"
-RDEPEND="virtual/blas"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${PV}-gentoo.patch
+RDEPEND="
+ virtual/blas
+ virtual/lapack"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
- eautoreconf
-}
+PATCHES=(
+ "${FILESDIR}"/${PV}-gcc47.patch
+ "${FILESDIR}"/${PV}-gentoo.patch )
src_configure(){
- econf \
- --with-lapack \
- --with-external-blas \
+ local myeconfargs=(
+ --with-lapack
+ --with-external-blas
$(use_enable sse mkasm)
+ )
+ autotools-utils_src_configure
}
src_compile() {
- emake \
+ autotools-utils_src_compile \
CFLAGS="${CFLAGS}" \
CXXFLAGS="${CXXFLAGS}" \
- LDFLAGS="${LDFLAGS}" || \
- die "make failed"
+ LDFLAGS="${LDFLAGS}"
}
src_install() {
- dobin bin/${PN} || die
+ dobin "${BUILD_DIR}"/bin/${PN}
insinto /usr/share/${PN}
- doins -r data || die
- dodoc README NEWS ChangeLog AUTHORS || die
+ doins -r data
+ dodoc README NEWS ChangeLog AUTHORS
}
diff --git a/sci-chemistry/camshift/files/1.35.0-gcc47.patch b/sci-chemistry/camshift/files/1.35.0-gcc47.patch
new file mode 100644
index 000000000..7e9d4b973
--- /dev/null
+++ b/sci-chemistry/camshift/files/1.35.0-gcc47.patch
@@ -0,0 +1,148 @@
+ include/almost/forcefield/intern/angleenergy.h | 14 ++++-----
+ include/almost/forcefield/intern/bondenergy.h | 2 +-
+ include/almost/kernel/molecule.h | 2 +-
+ include/almost/kernel/rmsd.h | 42 +++++++++++++-------------
+ src/lib/io/formostream.cpp | 4 +--
+ 5 files changed, 32 insertions(+), 32 deletions(-)
+
+diff --git a/include/almost/forcefield/intern/angleenergy.h b/include/almost/forcefield/intern/angleenergy.h
+index 75308ca..a9bc70c 100644
+--- a/include/almost/forcefield/intern/angleenergy.h
++++ b/include/almost/forcefield/intern/angleenergy.h
+@@ -419,7 +419,7 @@ namespace Almost {
+ int f = Coor<float_type>::DIM*this->first_[i];
+ int m = Coor<float_type>::DIM*this->middle_[i];
+ int l = Coor<float_type>::DIM*this->last_[i];
+- dangle = angle(coor,f,m,l);
++ dangle = this->angle(coor,f,m,l);
+ ene += this->ka_[i]*(dangle-this->a0_[i])*(dangle-this->a0_[i]);
+ }
+ return ene;
+@@ -444,9 +444,9 @@ namespace Almost {
+ vkj[2] = coor.coor[l+2]-coor.coor[m+2];
+
+
+- float_type nij = norm(vij);
+- float_type nkj = norm(vkj);
+- float_type n = scal(vij,vkj);
++ float_type nij = this->norm(vij);
++ float_type nkj = this->norm(vkj);
++ float_type n = this->scal(vij,vkj);
+ float_type cosd = n/(nij*nkj);;
+ float_type dangle = acos(cosd);
+ float_type sind = sqrt(1-cosd*cosd);
+@@ -513,9 +513,9 @@ namespace Almost {
+ vkj[2] = coor.coor[l+2]-coor.coor[m+2];
+
+
+- float_type nij = norm(vij);
+- float_type nkj = norm(vkj);
+- float_type n = scal(vij,vkj);
++ float_type nij = this->norm(vij);
++ float_type nkj = this->norm(vkj);
++ float_type n = this->scal(vij,vkj);
+ float_type cosd = n/(nij*nkj);;
+ float_type dangle = acos(cosd);
+ float_type sind = sqrt(1-cosd*cosd);
+diff --git a/include/almost/forcefield/intern/bondenergy.h b/include/almost/forcefield/intern/bondenergy.h
+index f60d99c..d6977f2 100644
+--- a/include/almost/forcefield/intern/bondenergy.h
++++ b/include/almost/forcefield/intern/bondenergy.h
+@@ -242,7 +242,7 @@ namespace Almost {
+ float_type d;
+ int f = this->first_[i];
+ int s = this->second_[i];
+- d = sqrt(distanceP2(coor.coor+Coor<float_type>::DIM*f,
++ d = sqrt(this->distanceP2(coor.coor+Coor<float_type>::DIM*f,
+ coor.coor+Coor<float_type>::DIM*s));
+ e +=this->kb_[i]*(d-this->b0_[i])*(d-this->b0_[i]);
+ }
+diff --git a/include/almost/kernel/molecule.h b/include/almost/kernel/molecule.h
+index e399d8d..0ea1d28 100644
+--- a/include/almost/kernel/molecule.h
++++ b/include/almost/kernel/molecule.h
+@@ -1100,7 +1100,7 @@ namespace Kernel {
+ if(this->fragment_atoms_[i][j]>=gpos) ++this->fragment_atoms_[i][j];
+
+
+- return add_atom_(fd,atom,pos);
++ return this->add_atom_(fd,atom,pos);
+ }
+
+
+diff --git a/include/almost/kernel/rmsd.h b/include/almost/kernel/rmsd.h
+index 0947666..210f53e 100644
+--- a/include/almost/kernel/rmsd.h
++++ b/include/almost/kernel/rmsd.h
+@@ -172,6 +172,27 @@ namespace Almost {
+ /*====================================================================*/
+
+ template <typename float_type>
++ float_type EPpythag(float_type a,float_type b)
++ {
++ /* finds sqrt(a*a+b*b) without overflow or destructive underflow */
++
++ float_type p,r,s,t,u;
++
++ p=(abs(a) > abs(b) ? abs(a) : abs(b));
++ if (p>0) {
++ r=(abs(a)<abs(b)?abs(a):abs(b))/p;
++ r=r*r;
++ for (t=4.0+r;t!=4.0;t=4.0+r) {
++ s=r/t;
++ u=1.0+2.0*s;
++ p=u*p;
++ r=(s/u)*(s/u)*r;
++ }
++ }
++ return(p);
++ }
++
++ template <typename float_type>
+ int EPimtql2(int n,float_type *d,float_type *e,float_type **z)
+ {
+ int i,j,k,l,m,ii,mml;
+@@ -316,27 +337,6 @@ namespace Almost {
+
+ /*====================================================================*/
+
+- template <typename float_type>
+- float_type EPpythag(float_type a,float_type b)
+- {
+- /* finds sqrt(a*a+b*b) without overflow or destructive underflow */
+-
+- float_type p,r,s,t,u;
+-
+- p=(abs(a) > abs(b) ? abs(a) : abs(b));
+- if (p>0) {
+- r=(abs(a)<abs(b)?abs(a):abs(b))/p;
+- r=r*r;
+- for (t=4.0+r;t!=4.0;t=4.0+r) {
+- s=r/t;
+- u=1.0+2.0*s;
+- p=u*p;
+- r=(s/u)*(s/u)*r;
+- }
+- }
+- return(p);
+- }
+-
+ template<typename float_type>
+ inline float_type rmsd_dist(const Almost::Coor<float_type> & ref,
+ const Almost::Coor<float_type> & to_move,
+diff --git a/src/lib/io/formostream.cpp b/src/lib/io/formostream.cpp
+index 9a98154..1469b8a 100644
+--- a/src/lib/io/formostream.cpp
++++ b/src/lib/io/formostream.cpp
+@@ -1572,9 +1572,9 @@ PDBOStream & operator<<(PDBOStream & pdb, const Molecules & molecules){
+
+ for(int i=0;i<molecules.solvent_size();i++){
+ pdb<<molecules.solvent(i);
+- int i = molecules.solvent_size()-1;
++ int j = molecules.solvent_size()-1;
+ sprintf(buff,
+- "%-6s%5i\n","TER",molecules.solvent(i).atom_size()
++ "%-6s%5j\n","TER",molecules.solvent(i).atom_size()
+ +molecules.solvent(i).atom_offset());
+ pdb.stream()<<buff;
+
diff --git a/sci-chemistry/camshift/files/1.35.0-gentoo.patch b/sci-chemistry/camshift/files/1.35.0-gentoo.patch
index 4fd9ee25c..845325713 100644
--- a/sci-chemistry/camshift/files/1.35.0-gentoo.patch
+++ b/sci-chemistry/camshift/files/1.35.0-gentoo.patch
@@ -1,3 +1,19 @@
+ bin/Makefile.am | 2 +-
+ configure.in | 18 +++---------------
+ src/forcefield/Makefile.am | 4 ++--
+ src/lib/Makefile.am | 2 +-
+ 4 files changed, 7 insertions(+), 19 deletions(-)
+
+diff --git a/bin/Makefile.am b/bin/Makefile.am
+index c9f5f40..0f1d790 100644
+--- a/bin/Makefile.am
++++ b/bin/Makefile.am
+@@ -1,4 +1,4 @@
+-INCLUDES = -I../.. -I../include/almost
++INCLUDES = -I$(top_srcdir) -I$(top_srcdir)/include/almost
+ bin_PROGRAMS=camshift
+
+ if LIBBZ2
diff --git a/configure.in b/configure.in
index e0d186d..9b15335 100644
--- a/configure.in
@@ -45,3 +61,25 @@ index e0d186d..9b15335 100644
echo ${host} ${host-cpu} ${host-vendor} ${host-os} $ix86 $powerpc
AC_OUTPUT(
almost.h
+diff --git a/src/forcefield/Makefile.am b/src/forcefield/Makefile.am
+index 8d143ab..4b72814 100644
+--- a/src/forcefield/Makefile.am
++++ b/src/forcefield/Makefile.am
+@@ -1,4 +1,4 @@
+-INCLUDES = -I../../include/almost
++INCLUDES = -I$(top_srcdir)/include/almost
+
+ lib_LIBRARIES= libnbimpl.a
+-libnbimpl_a_SOURCES=enefunc.c enefuncvdw.c pbcenefunc.c forcefunc.c forcefuncvdw.c pbcforcefunc.c sasaenefunc.c pbcsasaenefunc.c sasaforcefunc.c pbcsasaforcefunc.c eneforcefunc.c enefunchs.c forcefunchs.c enefuncsoft.c forcefuncsoft.c qvdwfunc.c $(ASMF)
+\ No newline at end of file
++libnbimpl_a_SOURCES=enefunc.c enefuncvdw.c pbcenefunc.c forcefunc.c forcefuncvdw.c pbcforcefunc.c sasaenefunc.c pbcsasaenefunc.c sasaforcefunc.c pbcsasaforcefunc.c eneforcefunc.c enefunchs.c forcefunchs.c enefuncsoft.c forcefuncsoft.c qvdwfunc.c $(ASMF)
+diff --git a/src/lib/Makefile.am b/src/lib/Makefile.am
+index 02ee6ee..0e9001f 100644
+--- a/src/lib/Makefile.am
++++ b/src/lib/Makefile.am
+@@ -1,4 +1,4 @@
+-INCLUDES=-I../../include/almost
++INCLUDES=-I$(top_srcdir)/include/almost
+ lib_LIBRARIES=libAlm.a
+ PBDSOURCES = pdb/pdbatomline.cpp \
+ pdb/pdbauthorline.cpp \
diff --git a/sci-chemistry/camshift/metadata.xml b/sci-chemistry/camshift/metadata.xml
index 0fbe927f0..d410f1573 100644
--- a/sci-chemistry/camshift/metadata.xml
+++ b/sci-chemistry/camshift/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>sci@gentoo.org</email>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-chemistry/chooch/ChangeLog b/sci-chemistry/chooch/ChangeLog
index d06136ebf..1c397d3c2 100644
--- a/sci-chemistry/chooch/ChangeLog
+++ b/sci-chemistry/chooch/ChangeLog
@@ -1,7 +1,12 @@
# ChangeLog for sci-chemistry/chooch
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 22 Feb 2013; Justin Lecher <jlec@gentoo.org> chooch-5.0.2-r1.ebuild,
+ metadata.xml:
+ Bump to EAPI=5; add missing deps; drop additional virtual which aren't
+ needed; move to autotools-utils
+
*chooch-5.0.2-r1 (13 May 2009)
13 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/chooch/Manifest b/sci-chemistry/chooch/Manifest
index 9d4067824..e5b6d9eaa 100644
--- a/sci-chemistry/chooch/Manifest
+++ b/sci-chemistry/chooch/Manifest
@@ -1 +1 @@
-DIST chooch-5.0.2.tar.gz 3057641 RMD160 5eb6d2b33f58e3a0b6379713184cd0c11d3a5956 SHA1 ec6cefd5044487c79e8099329c9f6eb3061e047d SHA256 ad80d5d296bfbd2bb8f9fac930df5a4e9ba583e23b2de298209b7a6925240643
+DIST chooch-5.0.2.tar.gz 3057641 SHA256 ad80d5d296bfbd2bb8f9fac930df5a4e9ba583e23b2de298209b7a6925240643 SHA512 028d0b57e5f8e17a23e7573e9ce4d187cde6fc546ea83e43e3e497f769ac99b60a21ea811d3fa41180089b3bd05df535d536504f0ee677d09c385c37d97b0818 WHIRLPOOL fd1193cfd2c991ca34ad9fa45a681c5bbb5917e20c6219d47fa0571550b1bd235041641a65982d793b55e9f438505d3a4130481c2bf6d8f051a83bae144baf84
diff --git a/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild b/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild
index 2ddd7a2e6..42c08fd57 100644
--- a/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild
+++ b/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild
@@ -1,10 +1,12 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="2"
+EAPI=5
-inherit autotools eutils multilib toolchain-funcs
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils multilib toolchain-funcs
DESCRIPTION="a program that will automatically determine values of the anomalous scattering factors"
HOMEPAGE="http://www.gwyndafevans.co.uk/id2.html"
@@ -15,38 +17,35 @@ LICENSE="GPL-2"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
-RDEPEND="sci-libs/gsl
+RDEPEND="
+ sci-libs/gsl
sci-libs/Cgraph
- virtual/blas
- virtual/cblas
sci-libs/pgplot"
DEPEND="${RDEPEND}"
S="${WORKDIR}"/${PN}/${P}
-src_prepare() {
- epatch "${FILESDIR}"/${PV}-Makefile.am.patch
- epatch "${FILESDIR}"/${PV}-aclocal.patch
- AT_M4DIR="${S}" eautoreconf
-}
+PATCHES=(
+ "${FILESDIR}"/${PV}-Makefile.am.patch
+ "${FILESDIR}"/${PV}-aclocal.patch
+)
-src_configure() {
- econf \
- --with-pgplot-prefix="/usr" \
- --with-cgraph-prefix="/usr" \
- --with-gsl-prefix="/usr" \
- --disable-gsltest || \
- die
-}
+AT_M4DIR="${S}"
+
+DOCS=( doc/${PN}.pdf )
-src_compile() {
- emake \
- all || die
+src_configure() {
+ local myeconfargs=(
+ --with-pgplot-prefix="${EPREFIX}/usr"
+ --with-cgraph-prefix="${EPREFIX}/usr"
+ --with-gsl-prefix="${EPREFIX}/usr"
+ --disable-gsltest
+ )
+ autotools-utils_src_configure
}
src_install() {
- emake DESTDIR="${D}" install || die "installation failed"
- dodoc doc/${PN}.pdf || die "nothing to read"
+ autotools-utils_src_install
if use examples; then
insinto /usr/share/${PN}
diff --git a/sci-chemistry/chooch/metadata.xml b/sci-chemistry/chooch/metadata.xml
index 0fbe927f0..d410f1573 100644
--- a/sci-chemistry/chooch/metadata.xml
+++ b/sci-chemistry/chooch/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>sci@gentoo.org</email>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-chemistry/concoord/ChangeLog b/sci-chemistry/concoord/ChangeLog
index 2297c3ea4..0cc1262e8 100644
--- a/sci-chemistry/concoord/ChangeLog
+++ b/sci-chemistry/concoord/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-chemistry/concoord
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*concoord-2.1.2 (11 Mar 2013)
+
+ 11 Mar 2013; Justin Lecher <jlec@gentoo.org> concoord-2.1.ebuild,
+ +concoord-2.1.2.ebuild, metadata.xml:
+ Version Bump; switch license to all-rights-reserved
+
24 Jul 2012; Justin Lecher <jlec@gentoo.org> concoord-2.1.ebuild:
Use QA_PREBUILT for binary packages
diff --git a/sci-chemistry/concoord/Manifest b/sci-chemistry/concoord/Manifest
index be73d1173..781e917b9 100644
--- a/sci-chemistry/concoord/Manifest
+++ b/sci-chemistry/concoord/Manifest
@@ -1,2 +1,4 @@
DIST concoord2.1_linux_i386.tgz 2948256 SHA256 12c39d870bc90069d2dbc05db3299ff58c8850caad988b4cac7c430b9aa347ff SHA512 2af10b14f24305dbea4ff12df86ca9bc5e8d2957873756b2f9b5ee57fc7b8db91a787ff09d70ce70a1c3d9278a142474c893250944aa3b8c83862311ed3e3cef WHIRLPOOL 8905669c310b7a44d7d65c3112dd246c4b7c70c3b2c15284ebb19cb337fd45a9ac090801b91575c6a137eb2d7022b1690ec0162f10dbb421fdc4c3cffb5d24b8
DIST concoord2.1_linux_x86_64.tgz 3352731 SHA256 1cd86640e900d01800dc497509a1030add5d8f0e33f19dcd7c7d4e6e887e3d1a SHA512 cfb30d7d0950e5978ea0a908a0e607b675333e267ee7da6103ead1b27ceb4dedde42daef3f7027c47e40e01cd247f3e57c5fa13eb76c0f3ac7fa1868f5fb8bf5 WHIRLPOOL 027dfb15865d0a4fb633c61c872246765df80e0a97eb7296a5d4f8875e4a8e613cd3ae81090c895bb601155174d41671a04e3ca6a32e6a2f26e985e49d4fbd9a
+DIST concoord_2.1.2_linux32.tgz 1193266 SHA256 b71302903dec80c4578a3be595002695d2aada5a6f43e21f0a10f572ececbf34 SHA512 d74f2fdbb6184f79d3c0770cfa01324dd52448f3a865f5fb379a51431024b843537b8de551aacd2b0117736f7cb2412379cf23e765716969c1ab3069e6e75ea2 WHIRLPOOL a3bcd1d4bfd73e661b0368b43a18ae8718aba0ca145d1fe60e3e38580c59f5879538843c96d2fc78efec9240bc8e6f3a52e3ec8475e54b57f0867e3a91d67551
+DIST concoord_2.1.2_linux64.tgz 1431558 SHA256 f8fe46a88622f70f01a783b9c462678ad1756305e2f815010625723c3e72a1ff SHA512 e625e10ebe2e5ef6a84af3fe665e792d59ffed3df009f19d66ec0972bd88ec91167e3ec0eee9a72b1c35ba0a85ec70fa5420a7718b83e238b167ad31d95303cf WHIRLPOOL 9c3725d9877058de6df89664ace5910deba7e27d3d309104b7abe16054e98397c1d45028bbf4fac1116678798fc8f217d98d67a267c1f9e64504d51f78b04ce1
diff --git a/sci-chemistry/concoord/concoord-2.1.2.ebuild b/sci-chemistry/concoord/concoord-2.1.2.ebuild
new file mode 100644
index 000000000..b36801f0d
--- /dev/null
+++ b/sci-chemistry/concoord/concoord-2.1.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Method to generate protein conformations around a known structure based on geometric restrictions"
+HOMEPAGE="http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html"
+SRC_URI="
+ amd64? ( http://www3.mpibpc.mpg.de/groups/de_groot/${PN}/${PN}_${PV}_linux64.tgz )
+ x86? ( http://www3.mpibpc.mpg.de/groups/de_groot/${PN}/${PN}_${PV}_linux32.tgz )"
+
+SLOT="0"
+KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="all-rights-reserved"
+IUSE=""
+
+QA_PREBUILT="opt/${PN}/bin/*"
+
+S="${WORKDIR}"/${PN}_${PV}
+
+src_install() {
+ insinto /opt/${PN}/
+ doins -r lib
+ exeinto /opt/${PN}/bin
+ doexe bin/*
+ cat >> "${T}"/60${PN} <<- EOF
+ CONCOORDLIB="${EPREFIX}/opt/${PN}/lib"
+ CONCOORDBIN="${EPREFIX}/opt/${PN}/bin"
+ PATH="${EPREFIX}/opt/${PN}/bin"
+ EOF
+ doenvd "${T}"/60${PN}
+}
diff --git a/sci-chemistry/concoord/concoord-2.1.ebuild b/sci-chemistry/concoord/concoord-2.1.ebuild
index 84f3d884d..a1f95c513 100644
--- a/sci-chemistry/concoord/concoord-2.1.ebuild
+++ b/sci-chemistry/concoord/concoord-2.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -12,7 +12,7 @@ SRC_URI="
SLOT="0"
KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="as-is"
+LICENSE="all-rights-reserved"
IUSE=""
QA_PREBUILT="opt/${PN}/bin/*"
diff --git a/sci-chemistry/concoord/metadata.xml b/sci-chemistry/concoord/metadata.xml
index 210ad0db0..5ef07a39e 100644
--- a/sci-chemistry/concoord/metadata.xml
+++ b/sci-chemistry/concoord/metadata.xml
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci</herd>
- <maintainer>
- <email>jlec@gentoo.org</email>
- </maintainer>
+ <herd>sci</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-chemistry/cs-rosetta/ChangeLog b/sci-chemistry/cs-rosetta/ChangeLog
new file mode 100644
index 000000000..bc0a70efa
--- /dev/null
+++ b/sci-chemistry/cs-rosetta/ChangeLog
@@ -0,0 +1,18 @@
+# ChangeLog for sci-chemistry/cs-rosetta
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 22 Mar 2013; Justin Lecher <jlec@gentoo.org>
+ cs-rosetta-1.01.2009.1109.11.ebuild:
+ Missing exec bit for pdbrms
+
+ 21 Mar 2013; Justin Lecher <jlec@gentoo.org>
+ cs-rosetta-1.01.2009.1109.11.ebuild:
+ Use Fortran eclass
+
+*cs-rosetta-1.01.2009.1109.11 (20 Mar 2013)
+
+ 20 Mar 2013; Justin Lecher <jlec@gentoo.org>
+ +cs-rosetta-1.01.2009.1109.11.ebuild, +metadata.xml:
+ New addition
+
diff --git a/sci-chemistry/cs-rosetta/Manifest b/sci-chemistry/cs-rosetta/Manifest
new file mode 100644
index 000000000..b4198cc93
--- /dev/null
+++ b/sci-chemistry/cs-rosetta/Manifest
@@ -0,0 +1,3 @@
+DIST cs-rosetta-1.01.2009.1109.11-changelog 953 SHA256 cb6bca3c3365ef74b9d68f7e38dd808dce309cfce7685a61ea15f29f5e724fd9 SHA512 dee6ffdb448dbd35f26f9fc1d1db4095fe445c833bd7c5d7a6aa37edc1ae526d6ba6e851aa83ee8204e5aa262b01c88684161f507f5db5eff6ac8d008dd09012 WHIRLPOOL efed7173beb9ff05d39d9107684d06ab5987d524431614bb65cb28771cb4b899e758787d4bdd473fea2b92d2373a50c5439201254fcd1b3447d51b1b39abb093
+DIST cs-rosetta-1.01.2009.1109.11-install.com 12420 SHA256 f9977454ce9216aae0daccca5b788123b4786a5ca118368bfbd9e1ab6e6001bc SHA512 dc7ae15bef5fe591a5a11418c5eb203a39fba961da0a130ea6960e16a5c678af1b3a94cb7aef2c5ca3faa600fe9d1b8e31440b35b68b1f090597e261f8de76c9 WHIRLPOOL ec938b6da46470189f94ee4eaf47f9724d2b8ef57563c7d867de9eea99dfbc210f95216686531be43c84b11c187cef1533fa793ad1d824faa51ca14f61fbbb2d
+DIST cs-rosetta-1.01.2009.1109.11.tar.Z 15461998 SHA256 db20c16b7a6f0e8ff8dbea54b6245d6d8d64dc6cbd4ed49b8bdf3b0e0d0eabe1 SHA512 6c4872ca7e7fffa1de99b6c8447953bceaf226f24e02ceb4a2e6019aaaa52d6ae0393c55a8276b060e317980b051da19943879e5341020ec1ab2b42175e42aa1 WHIRLPOOL 3dca3fc9b6627d52b407322077dd838445b50b7e7f0c7bc7b795e0edd325a1483c695347c4cb42e45e3b971aac6381ae41011d9d136c3ee64696598ebff82189
diff --git a/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild b/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild
new file mode 100644
index 000000000..1f294c392
--- /dev/null
+++ b/sci-chemistry/cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild
@@ -0,0 +1,104 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="System for chemical shifts based protein structure prediction using ROSETTA"
+HOMEPAGE="http://spin.niddk.nih.gov/bax/software/CSROSETTA/"
+SRC_URI="
+ http://spin.niddk.nih.gov/bax/software/CSROSETTA/install.com -> ${P}-install.com
+ http://spin.niddk.nih.gov/bax/software/CSROSETTA/CSRosetta.tar.Z -> ${P}.tar.Z
+ http://spin.niddk.nih.gov/bax/software/CSROSETTA/changeLog -> ${P}-changelog"
+
+SLOT="0"
+LICENSE="all-rights-reserved"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="custom-cflags"
+
+RDEPEND="
+ dev-lang/perl
+ sci-biology/ncbi-tools++
+ sci-biology/profphd
+ sci-biology/psipred
+ sci-biology/samtools
+ ~sci-libs/cs-rosetta-db-${PV}
+ sci-chemistry/nmrpipe
+ sci-chemistry/rosetta"
+DEPEND=""
+
+S="${WORKDIR}"
+
+src_unpack() {
+ unpack ${P}.tar.Z
+}
+
+src_prepare() {
+ cat >> "${T}"/39${PN} <<- EOF
+ rosetta3="${EPREFIX}/usr/bin/AbinitioRelax"
+ rosetta3_extpdbs="${EPREFIX}/usr/bin/extract_pdbs"
+ rosetta3DB="${EPREFIX}/usr/share/rosetta-db"
+ csrosettaDir="${EPREFIX}/opt/${PN}"
+ csrosettaCom="${EPREFIX}/opt/${PN}/com"
+ PATH="${EPREFIX}/opt/${PN}/com"
+ MFR="${EPREFIX}/opt/${PN}/com/mfr.tcl"
+ EOF
+
+ # needs more love
+ sed \
+ -e "s:CSROSETTA_DIR/src/nnmake/pNNMAKE.gnu:${EPREFIX}/opt/${PN}/src/nnmake/pNNMAKE:g" \
+ -i com/make_fragments_2000.pl || die
+
+ append-fflags -ffixed-line-length-132
+}
+
+src_compile() {
+ use custom-cflags || CXXFLAGS="-pipe -ffor-scope -fno-exceptions -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000"
+
+ compilation() {
+ if [[ -f dipolar_nn.f ]]; then
+ sed \
+ -e '/write/s:(i,6f6.3):(i3,6(1x,f6.3)):g' \
+ -i dipolar_nn.f || die
+ fi
+
+ sed \
+ -e '/LDFLAGS/s: = : ?= :g' \
+ -e '/CCFLAGS/s: = : += :g' \
+ -e 's:$(OBJECT) $(LDFLAGS):$(LDFLAGS) $(OBJECT) -lm -o:g' \
+ -e 's:$(FFLAGS) -o:$(FFLAGS) $(LDFLAGS) -o:g' \
+ -e '/make.system/d' \
+ -i *akefile || die
+ emake \
+ CC=$(tc-getCXX) \
+ CCFLAGS="${CXXFLAGS}"
+
+ if [[ -f pNNMAKE. ]]; then
+ mv pNNMAKE{.,} || die
+ emake almostsuperclean
+ else
+ emake clean
+ fi
+ }
+
+ for i in src/{mfr2rosetta,SPARTA/src,pdbrms,TALOS,rosettaFrag2csFrag,nnmake}; do
+ pushd ${i} > /dev/null
+ compilation
+ popd > /dev/null
+ done
+}
+
+src_install() {
+ insinto /opt/${PN}/
+ doins -r *
+ chmod 755 \
+ "${ED}"/opt/${PN}/com/* \
+ "${ED}"/opt/${PN}/src/{mfr2rosetta/mfr2rosetta,SPARTA/src/SPARTA,pdbrms/pdbrms,TALOS/TALOS,rosettaFrag2csFrag/rosettaFrag2csFrag,nnmake/pNNMAKE} \
+ || die
+
+ dosym make_fragments_2000.pl /opt/${PN}/com/make_fragment_2000.pl
+
+ doenvd "${T}"/39${PN}
+}
diff --git a/sci-libs/csrosetta-cs/metadata.xml b/sci-chemistry/cs-rosetta/metadata.xml
index efb490d78..897aa2e6b 100644
--- a/sci-libs/csrosetta-cs/metadata.xml
+++ b/sci-chemistry/cs-rosetta/metadata.xml
@@ -1,8 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
+ <herd>sci</herd>
</pkgmetadata>
diff --git a/sci-chemistry/curvefit/ChangeLog b/sci-chemistry/curvefit/ChangeLog
index 8f46e69a4..d972ffb0b 100644
--- a/sci-chemistry/curvefit/ChangeLog
+++ b/sci-chemistry/curvefit/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-chemistry/curvefit
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> curvefit-1.40.ebuild,
+ metadata.xml:
+ Correct lib name of ref blas
+
14 Sep 2012; Justin Lecher <jlec@gentoo.org> curvefit-1.40.ebuild:
Quote sed correctly
diff --git a/sci-chemistry/curvefit/curvefit-1.40.ebuild b/sci-chemistry/curvefit/curvefit-1.40.ebuild
index 5429531ac..0e0c6ceb0 100644
--- a/sci-chemistry/curvefit/curvefit-1.40.ebuild
+++ b/sci-chemistry/curvefit/curvefit-1.40.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
inherit multilib
@@ -42,7 +42,7 @@ src_install() {
doexe batch_curve curveplot ${_exe}
- dosym ../../usr/$(get_libdir)/libblas.so /opt/${PN}/libblas.so.3
+ dosym ../../usr/$(get_libdir)/librefblas.so /opt/${PN}/libblas.so.3
dodoc Versions
dohtml curvefit_manual.html
diff --git a/sci-chemistry/curvefit/metadata.xml b/sci-chemistry/curvefit/metadata.xml
index d369d068f..897aa2e6b 100644
--- a/sci-chemistry/curvefit/metadata.xml
+++ b/sci-chemistry/curvefit/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</herd>
</pkgmetadata>
diff --git a/sci-chemistry/freeon/ChangeLog b/sci-chemistry/freeon/ChangeLog
index e96fe68a5..25af9d785 100644
--- a/sci-chemistry/freeon/ChangeLog
+++ b/sci-chemistry/freeon/ChangeLog
@@ -1,7 +1,12 @@
# ChangeLog for sci-chemistry/freeon
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 22 Feb 2013; Justin Lecher <jlec@gentoo.org> freeon-9999.ebuild,
+ metadata.xml:
+ Add missing dep on virtual/pkgconfig; bump to eapi=5; use pkg-config to
+ detect blas
+
14 Jul 2012; Christoph Junghans <ottxor@gentoo.org> freeon-9999.ebuild:
clean up
diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild
index 5514e13ae..2fe44e90d 100644
--- a/sci-chemistry/freeon/freeon-9999.ebuild
+++ b/sci-chemistry/freeon/freeon-9999.ebuild
@@ -1,38 +1,41 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+
+FORTRAN_STANDARD=90
inherit autotools-utils fortran-2 git-2
DESCRIPTION="an experimental suite of programs for linear scaling quantum chemistry."
HOMEPAGE="http://www.freeon.org"
+SRC_URI=""
EGIT_REPO_URI="http://git.savannah.gnu.org/r/freeon.git"
EGIT_BOOTSTRAP="fix_localversion.sh"
-AUTOTOOLS_AUTORECONF=1
-
-FORTRAN_STANDARD=90
-
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="static-libs"
-DEPEND="
+RDEPEND="
sys-libs/zlib
sci-libs/hdf5
- virtual/fortran
+ virtual/blas
virtual/lapack"
-RDEPEND="${DEPEND}"
+DEPEND="${DEPEND}
+ virtual/pkgconfig"
src_configure() {
local myeconfargs=(
--disable-internal-hdf5
--disable-static-binaries
--disable-internal-lapack
+ --with-lapacklibs="$($(tc-getPKG_CONFIG) --libs lapack)"
)
#TODO mv BasisSets from /usr to /usr/share/freeon/
autotools-utils_src_configure
diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml
index 16d631946..bf041ec0c 100644
--- a/sci-chemistry/freeon/metadata.xml
+++ b/sci-chemistry/freeon/metadata.xml
@@ -1,12 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <longdescription lang="en">
+ <longdescription lang="en">
FreeON is an experimental, open source (GPL) suite of programs for linear scaling quantum chemistry.
</longdescription>
- <herd>sci-chemistry</herd>
- <maintainer>
- <email>nicolasbock@gmail.com</email>
- <name>Nicolas Bock</name>
- </maintainer>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>nicolasbock@gmail.com</email>
+ <name>Nicolas Bock</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-chemistry/gamess/ChangeLog b/sci-chemistry/gamess/ChangeLog
index d8e4e94d0..fc9a8d706 100644
--- a/sci-chemistry/gamess/ChangeLog
+++ b/sci-chemistry/gamess/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-chemistry/gamess
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 27 Feb 2013; Justin Lecher <jlec@gentoo.org> gamess-20120501.1.ebuild,
+ files/gamess-20120501.1.gentoo.patch, metadata.xml:
+ Use PKG_CONFIG instead of generic pkg-config
+
*gamess-20120501.1 (27 Oct 2012)
27 Oct 2012; Reinis Danne <rei4dan@gmail.com> +gamess-20120501.1.ebuild,
diff --git a/sci-chemistry/gamess/files/gamess-20120501.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20120501.1.gentoo.patch
index 22deab3b8..423ed63d0 100644
--- a/sci-chemistry/gamess/files/gamess-20120501.1.gentoo.patch
+++ b/sci-chemistry/gamess/files/gamess-20120501.1.gentoo.patch
@@ -187,7 +187,7 @@ diff -urN gamess.orig/lked gamess/lked
- else
- set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
- endif
-+ set MATHLIBS=`pkg-config --libs blas`
++ set MATHLIBS=`${PKG_CONFIG} --libs blas`
set BLAS=' '
breaksw
@@ -216,7 +216,7 @@ diff -urN gamess.orig/lked gamess/lked
- else
- set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
- endif
-+ set MATHLIBS=`pkg-config --libs blas`
++ set MATHLIBS=`${PKG_CONFIG} --libs blas`
set BLAS=' '
breaksw
diff --git a/sci-chemistry/gamess/gamess-20120501.1.ebuild b/sci-chemistry/gamess/gamess-20120501.1.ebuild
index 45013c53b..7dc9c4d85 100644
--- a/sci-chemistry/gamess/gamess-20120501.1.ebuild
+++ b/sci-chemistry/gamess/gamess-20120501.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -103,6 +103,7 @@ src_unpack() {
}
src_prepare() {
+ tc-export PKG_CONFIG
# apply LINUX-arch patches to gamess makesfiles
epatch "${FILESDIR}/${P}.gentoo.patch"
# select arch
diff --git a/sci-chemistry/gamess/metadata.xml b/sci-chemistry/gamess/metadata.xml
index 6ea2f9c7e..65e218a68 100644
--- a/sci-chemistry/gamess/metadata.xml
+++ b/sci-chemistry/gamess/metadata.xml
@@ -1,14 +1,14 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>alexxy@gentoo.org</email>
- <name>Alexey Shvetsov</name>
- </maintainer>
- <herd>sci-chemistry</herd>
- <use>
- <flag name='neo'>Enable NEO for nuclear basis support</flag>
- <flag name='pax_kernel'>Make this package work on PAX kernels</flag>
- <flag name='qmmm-tinker'>Enable tinker qmmm code</flag>
- </use>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+ <herd>sci-chemistry</herd>
+ <use>
+ <flag name="neo">Enable NEO for nuclear basis support</flag>
+ <flag name="pax_kernel">Make this package work on PAX kernels</flag>
+ <flag name="qmmm-tinker">Enable tinker qmmm code</flag>
+ </use>
</pkgmetadata>
diff --git a/sci-chemistry/gnome-chemistry-utils/ChangeLog b/sci-chemistry/gnome-chemistry-utils/ChangeLog
new file mode 100644
index 000000000..b71a1a2f3
--- /dev/null
+++ b/sci-chemistry/gnome-chemistry-utils/ChangeLog
@@ -0,0 +1,20 @@
+# ChangeLog for sci-chemistry/gnome-chemistry-utils
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 06 Apr 2013; Karl Linden (lilrc) <lilrc@users.sourceforge.net>
+ gnome-chemistry-utils-0.14.2.ebuild:
+ Migrate to gnome2 eclass.
+ Add slots where suitable.
+ Sort inherits alphabetically.
+
+ 06 Apr 2013; Karl Linden (lilrc) <lilrc@users.sourceforge.net>
+ gnome-chemistry-utils-0.14.2.ebuild:
+ Add missing inherit.
+
+*gnome-chemistry-utils-0.14.2 (05 Apr 2013)
+
+ 05 Apr 2013; Karl Linden (lilrc) <lilrc@users.sourceforge.net>
+ +gnome-chemistry-utils-0.14.2.ebuild, +metadata.xml:
+ Initial ebuild.
+
diff --git a/sci-chemistry/gnome-chemistry-utils/Manifest b/sci-chemistry/gnome-chemistry-utils/Manifest
new file mode 100644
index 000000000..dc5f37098
--- /dev/null
+++ b/sci-chemistry/gnome-chemistry-utils/Manifest
@@ -0,0 +1 @@
+DIST gnome-chemistry-utils-0.14.2.tar.bz2 6348310 SHA256 f09e9c5db6160f673fc8d0a52e6dd888a5096994f6168eacb909cc265178a43c SHA512 61e76be0cf4277b542c550d01dcf27229b0844d280946fa7d2e420194e97f657582c892dc12b48546ad35df08c2c9c6ab5a2539e3984b1170a76a0fbb655e681 WHIRLPOOL e7a4838725bfdd87a08dd54dbf9547d93d150d00defdc55723092b83dbff85fef489cee2998f5623383e16988e3bb140880d6971cd061a3a694911a32b0f3049
diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild
new file mode 100644
index 000000000..cbaeea866
--- /dev/null
+++ b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="5"
+
+GCONF_DEBUG="no"
+inherit gnome2 versionator
+
+DESCRIPTION="Programs and library containing GTK widgets and C++ classes related to chemistry"
+HOMEPAGE="http://gchemutils.nongnu.org/"
+SRC_URI="http://download.savannah.gnu.org/releases/gchemutils/$(get_version_component_range 1-2)/${P}.tar.bz2"
+RESTRICT="mirror"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="GPL-3 FDL-1.3"
+IUSE="gnumeric nls"
+
+RDEPEND="
+ >=dev-libs/glib-2.26.0:2
+ >=dev-libs/libxml2-2.4.16:2
+ >=gnome-extra/libgsf-1.14.9
+ >=sci-chemistry/bodr-5
+ >=sci-chemistry/chemical-mime-data-0.1.94
+ >=sci-chemistry/openbabel-2.1.0
+ >=x11-libs/cairo-1.6.0
+ >=x11-libs/gdk-pixbuf-2.22.0
+ >=x11-libs/goffice-0.10.0
+ x11-libs/gtk+:3
+ >=x11-libs/libX11-1.0.0
+ gnumeric? ( >=app-office/gnumeric-1.11.6 )"
+DEPEND="
+ virtual/pkgconfig
+ app-doc/doxygen"
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable nls)
+ --disable-mozilla-plugin
+ --disable-update-databases
+ )
+ gnome2_src_configure ${myeconfargs[@]}
+}
diff --git a/sci-chemistry/gnome-chemistry-utils/metadata.xml b/sci-chemistry/gnome-chemistry-utils/metadata.xml
new file mode 100644
index 000000000..5a8da44f4
--- /dev/null
+++ b/sci-chemistry/gnome-chemistry-utils/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <longdescription lang="en">
+ The Gnome Chemistry Utils provide some programs and library containing
+ GTK widgets and some C++ classes related to chemistry.
+ </longdescription>
+ <use>
+ <flag name="gnumeric">Build pluging for gnumeric</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 7672a1eec..1cba1c5d4 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -2,6 +2,24 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+ nvcc flags dont needed anymore here
+
+ 15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-9999.ebuild:
+ Fix build with cuda enabled
+
+ 10 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ added cuda build fix from gx86
+
+ 09 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fixed deps + doc build on darwin
+
+ 06 Mar 2013; Christoph Junghans <ottxor@gentoo.org> -Manifest,
+ -gromacs-4.5.9999.ebuild, gromacs-4.6.9999.ebuild, gromacs-9999.ebuild,
+ metadata.xml:
+ sync with gx86 + clean up
+
12 Feb 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
gromacs-9999.ebuild, metadata.xml:
sse41 -> sse4_1 (bug #456886) + ninja has missing keywords
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
deleted file mode 100644
index e3ce97c64..000000000
--- a/sci-chemistry/gromacs/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST gmxtest-4.0.4.tgz 14845017 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361 SHA512 f8165ef1d7e2ed69db0a069a1c85fc5fa440d66e96aa54b474392a6331d2327b60f76b8dceb02f9233ce06eb6b7a4e7c448fc71f666e244efa571cf94f1e86ec WHIRLPOOL dbb122736a588deb7931204b29142dd3d9b074691e94341b04dcad2cdf428eb0aae739aa37ef6f61d1dcd6fb96ddcc1292e76f267694f3c18ee67d17352bfd9b
-DIST gromacs-manual-4.5.4.pdf 2463242 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252 SHA512 957995333163f6f28568a18d5423a75dc6c315215692da94d0916f09b6221e2a875c5ff4b05385ad6604bd8ae38f0cb61c740cd734c76b360aa4b598cd2c3380 WHIRLPOOL 07077d81ea89bc02207e45e56c77a668375a7284bf6f4a3cc7fe637f1f53ce4ab687c722f13f208cdd2c056b9d766ebfcbe5ea9579ce7649ec9e088371e7db8d
diff --git a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
deleted file mode 100644
index c1a0dd60f..000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.9999.ebuild
+++ /dev/null
@@ -1,238 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )"
-
-if [ "${PV%9999}" != "${PV}" ]; then
- EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git"
- EGIT_BRANCH="release-4-5-patches"
- inherit git-2
-else
- SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
- X? (
- x11-libs/libX11
- x11-libs/libSM
- x11-libs/libICE
- )
- blas? ( virtual/blas )
- fftw? ( sci-libs/fftw:3.0 )
- fkernels? ( virtual/fortran )
- gsl? ( sci-libs/gsl )
- lapack? ( virtual/lapack )
- mpi? ( virtual/mpi )
- xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-RDEPEND="${CDEPEND}
- app-shells/tcsh"
-
-RESTRICT="test"
-
-pkg_setup() {
- use fkernels && fortran-2_pkg_setup
-}
-
-src_prepare() {
- #add user patches from /etc/portage/patches/sci-chemistry/gromacs
- epatch_user
-
- if use mpi && use threads; then
- elog "mdrun uses only threads OR mpi, and gromacs favours the"
- elog "use of mpi over threads, so a mpi-version of mdrun will"
- elog "be compiled. If you want to run mdrun on shared memory"
- elog "machines only, you can safely disable mpi"
- fi
-
- GMX_DIRS=""
- use single-precision && GMX_DIRS+=" float"
- use double-precision && GMX_DIRS+=" double"
- #if neither single-precision nor double-precision is enabled
- #build at least default (single)
- [ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
- for x in ${GMX_DIRS}; do
- mkdir -p "${WORKDIR}/${P}_${x}" || die
- use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
- done
-}
-
-src_configure() {
- local mycmakeargs_pre=( )
- #from gromacs configure
- if use fftw; then
- mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
- else
- mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
- ewarn "WARNING: The built-in FFTPACK routines are slow."
- ewarn "Are you sure you don\'t want to use FFTW?"
- ewarn "It is free and much faster..."
- fi
-
- if [[ $(gcc-version) == "4.1" ]]; then
- eerror "gcc 4.1 is not supported by gromacs"
- eerror "please run test suite"
- die
- fi
-
- #note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
- #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
- if use fkernels; then
- ewarn "Fortran kernels are usually not faster than C kernels and assembly"
- ewarn "I hope, you know what are you doing..."
- fi
-
- if use double-precision ; then
- #from gromacs manual
- elog
- elog "For most simulations single precision is accurate enough. In some"
- elog "cases double precision is required to get reasonable results:"
- elog
- elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
- elog " and the calculation and diagonalization of the Hessian "
- elog "-calculation of the constraint force between two large groups of atoms"
- elog "-energy conservation: this can only be done without temperature coupling and"
- elog " without cutoffs"
- elog
- fi
-
- if use mpi ; then
- elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
- elog "we configure/compile gromacs twice (with and without mpi) and only"
- elog "install mdrun with mpi support. In addtion you will get libgmx and"
- elog "libmd with and without mpi support."
- fi
-
- #go from slowest to fasterest acceleration
- local acce="none"
- use fkernels && acce="fortran"
- use altivec && acce="altivec"
- use ia64 && acce="ia64"
- use sse2 && acce="sse"
-
- mycmakeargs_pre+=(
- $(cmake-utils_use X GMX_X11)
- $(cmake-utils_use blas GMX_EXTERNAL_BLAS)
- $(cmake-utils_use gsl GMX_GSL)
- $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
- $(cmake-utils_use threads GMX_THREADS)
- $(cmake-utils_use xml GMX_XML)
- -DGMX_DEFAULT_SUFFIX=off
- -DGMX_ACCELERATION="$acce"
- -DGMXLIB="$(get_libdir)"
- )
-
- for x in ${GMX_DIRS}; do
- einfo "Configuring for ${x} precision"
- local suffix=""
- #if we build single and double - double is suffixed
- use double-precision && use single-precision && \
- [ "${x}" = "double" ] && suffix="_d"
- local p
- [ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
- -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
- use mpi || continue
- einfo "Configuring for ${x} precision with mpi"
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
- done
-}
-
-src_compile() {
- for x in ${GMX_DIRS}; do
- einfo "Compiling for ${x} precision"
- BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
- use mpi || continue
- einfo "Compiling for ${x} precision with mpi"
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile mdrun
- done
-}
-
-src_test() {
- for x in ${GMX_DIRS}; do
- local oldpath="${PATH}"
- export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
- cd "${WORKDIR}/${P}_${x}"
- emake -j1 tests || die "${x} Precision test failed"
- export PATH="${oldpath}"
- done
-}
-
-src_install() {
- for x in ${GMX_DIRS}; do
- BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
- use mpi || continue
- #cmake-utils_src_install does not support args
- #using cmake-utils_src_compile instead
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_make install-mdrun DESTDIR="${D}"
- done
-
- sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
- echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
- doenvd "${T}/80gromacs"
- rm -f "${ED}"/usr/bin/GMXRC*
-
- newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
- if use zsh-completion ; then
- insinto /usr/share/zsh/site-functions
- newins "${ED}"/usr/bin/completion.zsh _${PN}
- fi
- rm -f "${ED}"/usr/bin/completion.*
-
- # Fix typos in a couple of files.
- sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
- || die "Failed to fixup demo script."
-
- cd "${S}"
- dodoc AUTHORS INSTALL* README*
- if use doc; then
- newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
- dohtml -r "${ED}usr/share/gromacs/html/"
- fi
- rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
- einfo
- einfo "Please read and cite:"
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
- einfo "http://dx.doi.org/10.1021/ct700301q"
- einfo
- einfo $(g_luck)
- einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
- einfo
- elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 5e52c9f20..7babac633 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -4,10 +4,12 @@
EAPI=5
-TEST_PV="4.6"
-MANUAL_PV="4.6"
+TEST_PV="4.6.1"
+MANUAL_PV="4.6.1"
-inherit bash-completion-r1 cmake-utils cuda eutils multilib toolchain-funcs
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -16,10 +18,17 @@ if [[ $PV = *9999* ]]; then
http://repo.or.cz/r/gromacs.git"
EGIT_BRANCH="release-4-6"
inherit git-2
+ LIVE_DEPEND="doc? (
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ sys-apps/coreutils
+ )"
else
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
+ LIVE_DEPEND=""
fi
ACCE_IUSE="sse2 sse4_1 avx128fma avx256"
@@ -32,7 +41,7 @@ HOMEPAGE="http://www.gromacs.org/"
# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
SLOT="0/${PV}"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
CDEPEND="
@@ -54,11 +63,7 @@ CDEPEND="
)"
DEPEND="${CDEPEND}
virtual/pkgconfig
- doc? (
- dev-texlive/texlive-latex
- media-gfx/imagemagick
- sys-apps/coreutils
- )"
+ ${LIVE_DEPEND}"
RDEPEND="${CDEPEND}"
REQUIRED_USE="
@@ -68,7 +73,7 @@ REQUIRED_USE="
mkl? ( !blas !fftw !lapack )
!openmm" #broken, but https://gerrit.gromacs.org/#/c/2087/
-DOCS=( AUTHORS INSTALL.cmake README )
+DOCS=( AUTHORS README )
HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
pkg_pretend() {
@@ -101,8 +106,7 @@ src_prepare() {
#notes/todos
# -on apple: there is framework support
- #add user patches from /etc/portage/patches/sci-chemistry/gromacs
- epatch_user
+ cmake-utils_src_prepare
use cuda && cuda_src_prepare
@@ -117,9 +121,7 @@ src_prepare() {
done
fi
- if use openmm; then
- sed -i '/option.*GMX_OPENMM/s/^#//' src/contrib/CMakeLists.txt || die
- fi
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
}
src_configure() {
@@ -179,10 +181,11 @@ src_configure() {
[[ ${x} = "double" ]] && suffix="_d"
local p
[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
- local cuda=$(cmake-utils_use cuda GMX_GPU)
- [[ ${x} = "double" ]] && use cuda && cuda="-DGMX_GPU=OFF"
+ local cuda=( "-DGMX_GPU=OFF" )
+ [[ ${x} = "float" ]] && use cuda && \
+ cuda=( -DGMX_GPU=ON )
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
- $(cmake-utils_use threads GMX_THREAD_MPI) ${cuda} -DGMX_OPENMM=OFF
+ $(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
@@ -190,6 +193,7 @@ src_configure() {
einfo "Configuring for openmm build"
mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON
+ -DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins"
-DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" )
BUILD_DIR="${WORKDIR}/${P}_openmm" \
OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure
@@ -240,7 +244,10 @@ src_install() {
mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
BUILD_DIR="${WORKDIR}"/manual_build \
CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
+ [[ ${CHOST} = *-darwin* ]] && \
+ export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
+ [[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
@@ -258,6 +265,8 @@ src_install() {
rm -rf "${ED}"usr/share/gromacs/html
rm -f "${ED}"usr/bin/g_options*
rm -f "${ED}"usr/bin/GMXRC*
+
+ readme.gentoo_create_doc
}
pkg_postinst() {
@@ -271,5 +280,5 @@ pkg_postinst() {
einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
fi
einfo
- elog "Gromacs can use sci-chemistry/vmd to read additional file formats"
+ readme.gentoo_print_elog
}
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b9af3c0fe..36a6d2df8 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -18,7 +18,6 @@ inherit bash-completion-r1 cmake-utils eutils git-2 multilib toolchain-funcs
DESCRIPTION="The ultimate molecular dynamics simulation package"
HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
LICENSE="GPL-2"
SLOT="0/${PV}"
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 8a88d53da..880233ecb 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -11,7 +11,6 @@
<flag name="double-precision">More precise calculations at the expense of speed</flag>
<flag name="single-precision">Single precision version of gromacs (default)</flag>
<!-- acceleration optimization flags -->
- <flag name="fkernels">Enable building of Fortran Kernels for platforms that dont have assembly loops</flag>
<flag name="sse4_1">Enable sse4.1 acceleration</flag>
<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
diff --git a/sci-chemistry/hydronmr/ChangeLog b/sci-chemistry/hydronmr/ChangeLog
new file mode 100644
index 000000000..ea1667daa
--- /dev/null
+++ b/sci-chemistry/hydronmr/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/hydronmr
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*hydronmr-7c (08 Apr 2013)
+
+ 08 Apr 2013; Justin Lecher <jlec@gentoo.org> +hydronmr-7c.ebuild,
+ +metadata.xml:
+ New addition
+
diff --git a/sci-chemistry/hydronmr/Manifest b/sci-chemistry/hydronmr/Manifest
new file mode 100644
index 000000000..d1e0b65db
--- /dev/null
+++ b/sci-chemistry/hydronmr/Manifest
@@ -0,0 +1,13 @@
+DIST 6lyz.pdb 117590 SHA256 ab3b0903048ad0cf5738fbf0b9efc561a400186dc25e2c1ba45dd15197a6c62c SHA512 f1e6814528e290556ab31ec81ff14a42b3bca03b417b462fd43a5ed6c154eb278deb8bd79ffe6af474f07e43258b250e4a188625d27e7eac3cbcd653e0976db4 WHIRLPOOL 8b423e6d8ee973cfdf56a19c6d1e13b4913bf740e6a87ab1e1fd2f53a50371e9fa16ccbb241e5fed56e7d220b3684c055e3c48708504cf4ef602588ce580bda5
+DIST fast-hydronmr-1.pdf 80922 SHA256 506abcd79d9ce6fcbb7c6b5c803d6e6cd48d410083f92b8da75fc1e32f0a7ec8 SHA512 9698d3f2ab0cab996e67cf5a3484e77ceeaacdaa89c0ad33ea76ace873c5f3f60ad2f2ff4f0af2811909a8bab92fd0bf40f98f3b0bba0f3d7286803368b802c0 WHIRLPOOL b8fe34a5d286dd69f7e19e5105b24fb32021100ae11759a256f0633abaf31da5cc5461a52597d7838a31f0c30363376e03cfdd8db4dc51d2b736ff154c81a8ab
+DIST fast-hydronmr-2.pdf 148950 SHA256 fc22633779f0443de423b29b0387177b6bfae009feae9599a8f056a3cc87326e SHA512 ff8ab25fbf90e8245fce039cf8ea866f77a0bf752ed9627c9f7fc008cdaa4ca313336467c01eb25323634e9ca2e5eaf24ffe8f1a4548b09488b0b85590c31ca8 WHIRLPOOL c77af61751d3da0a26f212b21917ff180b0ec9f71873f01276f31e956ec773126dd26cc0395590bed7f4138567cc8a215c9ab04653444844caa13d9cbc06a021
+DIST fast-hydronmr7c2lnx.exe 418849 SHA256 6df46e2dd0f94341549d18d8412de5af722414ae54dea774cc788ecb4bae9aac SHA512 47280c5f8eea689a12c1309a1e2039a6477cff68ba07a1398ed0a4a0be1848ae1427b54d26057f7781304ab8708b041a44f1ed675e624eaa41637f523c94206e WHIRLPOOL 99018b63e4a5074e03300a74e0f610aee9d05bf8a4ea29c1becf2f535dae55e2917cd81bb1cb0abadf2316c9e7e15641e4320e9fac594ba4dfcbd7cf68d80c66
+DIST hydronmr.dat 898 SHA256 61b85b25a8f8c61b411aa96ae5ee73e8f1a630a0b3a3c14a846f4fa9bea50267 SHA512 bc37da9cd82fcb958bad3a38923732a7ae952d9780b5be13ace57a10aa4383e118bfc42594def1232e27f39687f9956feae3096709c