From dab9f0b41c94b362dad8c86fb355f5cb9a7cf962 Mon Sep 17 00:00:00 2001 From: Jeffrey Gardner Date: Tue, 2 Oct 2007 04:35:49 +0000 Subject: Testing new revision. svn path=/; revision=84 --- sci-biology/ncbi-tools/ChangeLog | 334 +++++++++++++++++++++ sci-biology/ncbi-tools/Manifest | 38 +++ sci-biology/ncbi-tools/files/21ncbi-r1 | 6 + .../ncbi-tools/files/digest-ncbi-tools-20061015-r1 | 8 + .../ncbi-tools/files/digest-ncbi-tools-20070826 | 8 + .../ncbi-tools/files/ncbi-tools-asn2all.patch | 27 ++ .../ncbi-tools/files/ncbi-tools-extra_vib.patch | 37 +++ sci-biology/ncbi-tools/files/ncbi-tools-lop.patch | 15 + sci-biology/ncbi-tools/files/ncbirc | 2 + sci-biology/ncbi-tools/metadata.xml | 9 + sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild | 200 ++++++++++++ 11 files changed, 684 insertions(+) create mode 100644 sci-biology/ncbi-tools/ChangeLog create mode 100644 sci-biology/ncbi-tools/Manifest create mode 100644 sci-biology/ncbi-tools/files/21ncbi-r1 create mode 100644 sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 create mode 100644 sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 create mode 100644 sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch create mode 100644 sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch create mode 100644 sci-biology/ncbi-tools/files/ncbi-tools-lop.patch create mode 100644 sci-biology/ncbi-tools/files/ncbirc create mode 100644 sci-biology/ncbi-tools/metadata.xml create mode 100644 sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild (limited to 'sci-biology') diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog new file mode 100644 index 0000000..ed0294c --- /dev/null +++ b/sci-biology/ncbi-tools/ChangeLog @@ -0,0 +1,334 @@ +# ChangeLog for sci-biology/ncbi-tools +# Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.53 2007/06/05 11:00:49 armin76 Exp $ + + 05 Jun 2007; Raúl Porcel ncbi-tools-20060507.ebuild: + alpha stable wrt #152292 + + 10 Mar 2007; Olivier Fisette + +files/ncbi-tools-extra_vib.patch: + Added missing patch. Thanks to Walter Meinl for reporting + (bug #170202). + +*ncbi-tools-20061015-r1 (09 Mar 2007) + + 09 Mar 2007; Olivier Fisette + -ncbi-tools-20061015.ebuild, +ncbi-tools-20061015-r1.ebuild: + Install ans2all utility. Added support for compiling/installing arbitrary + NCBI utilities. Thanks to José María Fernández González + for his work (see bug #169822). Pruned old version. + + 03 Nov 2006; Olivier Fisette + -ncbi-tools-20050605-r2.ebuild: + Pruned old version. + +*ncbi-tools-20061015 (03 Nov 2006) + + 03 Nov 2006; Olivier Fisette + +ncbi-tools-20061015.ebuild: + New upstream version. + + 30 Oct 2006; Christian Faulhammer + ncbi-tools-20060507.ebuild: + stable x86 as requested in bug #152292 + + 25 Oct 2006; Lars Weiler ncbi-tools-20060507.ebuild: + Stable on ppc; bug #152292. + + 25 Oct 2006; Fabian Groffen + ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild: + Dropped ppc-macos, see you in prefix. + + 24 Oct 2006; Fabian Groffen + ncbi-tools-20060507.ebuild: + Dropped ppc-macos, we don't have pmake + + 24 Oct 2006; Jeff Gardner ncbi-tools-20060507.ebuild: + Stable on amd64. + + 23 Oct 2006; Markus Rothe ncbi-tools-20060507.ebuild: + Stable on ppc64; bug #152292 + + 23 Oct 2006; Jeff Gardner ncbi-tools-20060507.ebuild: + Stable on sparc - bug #152292 + + 27 Jun 2006; Brent Baude ncbi-tools-20060507.ebuild: + Keywording ncbi-tools-20060507 ~ppc64 for bug #138082 + + 27 Jun 2006; Olivier Fisette + -files/ncbi-tools-20050605-lop.patch, +files/ncbi-tools-lop.patch, + ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild, + ncbi-tools-20060507.ebuild: + Fixed ppc64 lop patch (my mistake). + +*ncbi-tools-20060507 (26 Jun 2006) + + 26 Jun 2006; Olivier Fisette + +files/ncbi-tools-asn2all.patch, +ncbi-tools-20060507.ebuild: + New upstream version. Switched from GNU make to pmake as GNU make 3.81 is + confused by some Makefiles (fixes bug #136904, thanks to Greg Wilson for + reporting). Compile and install asn2all (fixes bug #136206, thanks to José + María Fernández González for the suggestion). Minor bugfixes and ebuild + clean-up. ppc64 keyword dropped as pmake is not available for that arch. + + 01 Feb 2006; Donnie Berkholz ; + ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild: + (#121066) Port to modular X. Add some die messages to -r2 so the die's + aren't completely unhelpful. Fix the path expansion for html docs so it + doesn't break the installation -- not sure how it got committed as is: + {*.html *.gif} is missing a comma. + + 21 Jan 2006; Olivier Fisette + -ncbi-tools-20050605-r1.ebuild: + Removed buggy version. + +*ncbi-tools-20050605-r2 (14 Dec 2005) + + 14 Dec 2005; Olivier Fisette + +ncbi-tools-20050605-r2.ebuild: + Fixed file collisions with "dev-libs/libpcre" (bug #115463). + + 16 Nov 2005; Olivier Fisette + ncbi-tools-20050605-r1.ebuild: + Readded ~sparc (closes bug #111807). + + 15 Nov 2005; Fernando J. Pereda + ncbi-tools-20050605-r1.ebuild: + re-add ~alpha wrt bug #111807 + +*ncbi-tools-20050605-r1 (15 Nov 2005) + + 15 Nov 2005; Olivier Fisette + +ncbi-tools-20050605-r1.ebuild: + Added MPI support for the BLAST family of programs. Thanks to Brady + Catherman for his work (fixes bug #111807). + + 09 Nov 2005; Jason Wever ncbi-tools-20050605.ebuild: + Stable on SPARC wrt bug #108334. + + 22 Oct 2005; Olivier Fisette -files/21ncbi, + -ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20050429.ebuild: + Pruning old versions. + + 22 Oct 2005; Fabian Groffen + ncbi-tools-20050605.ebuild: + Marked ppc-macos per bug #108334 + + 18 Oct 2005; Aron Griffis + ncbi-tools-20050605.ebuild: + Mark 20050605 stable on alpha + + 12 Oct 2005; Michael Hanselmann + ncbi-tools-20050605.ebuild: + Stable on ppc. + + 11 Oct 2005; Luis Medinas + ncbi-tools-20050605.ebuild: + Marked Stable on amd64 + + 09 Oct 2005; Mark Loeser ncbi-tools-20050605.ebuild: + Stable on x86 + + 07 Oct 2005; Brent Baude ncbi-tools-20050605.ebuild: + Marking ncbi-tools-200506 ppc64 stable for bug 108334 + + 19 Sep 2005; Olivier Fisette metadata.xml: + Maintainer changed from Stephen Diener (MIA) to Olivier Fisette. + + 16 Sep 2005; Aron Griffis + ncbi-tools-20050429.ebuild: + Mark 20050429 stable on alpha + + 19 Aug 2005; Michael Hanselmann + ncbi-tools-20050429.ebuild: + Removed from ppc (xlc not available). + + 09 Aug 2005; Brent Baude + +files/ncbi-tools-20050605-lop.patch, + -files/ncbi-tools-20050605-lop.patch.gz, ncbi-tools-20050605.ebuild: + For the ebuild ncbi-tools-20050605, I was asked to remove the gz patch and + submit it as plain text. This commit will remove the gz patch and replace it + with a plain text one. The patch name change is also reflected in the + ebuild. + + 08 Aug 2005; Brent Baude + +files/ncbi-tools-20050605-lop.patch.gz, ncbi-tools-20050605.ebuild: + Added patch for 20050506 which when ppc64, will patch the makefile to use + gcc instead of the default xlc (IBM compiler) which doesnt exist on gentoo. + + 08 Aug 2005; Brent Baude ncbi-tools-20050429.ebuild: + ncbi-tools-20050429.ebuild does not compile on ppc64; will fix later ebuild + +*ncbi-tools-20050605 (06 Aug 2005) + + 06 Aug 2005; Olivier Fisette + -ncbi-tools-20040616.ebuild, ncbi-tools-20050429.ebuild, + +ncbi-tools-20050605.ebuild: + New version. Added 20050429 to x86. Removed old version. + + 09 Jun 2005; Markus Rothe + ncbi-tools-20041020-r1.ebuild: + Stable on ppc64 + + 02 Jun 2005; Olivier Fisette ChangeLog: + Use "virtual/motif" instead of "x11-libs/openmotif". + + 16 May 2005; Olivier Fisette + ncbi-tools-20050429.ebuild: + Fixed CFLAGS not being applied properly (bug #92564). + +*ncbi-tools-20050429 (13 May 2005) + + 13 May 2005; Olivier Fisette + +ncbi-tools-20050429.ebuild: + New version. + + 29 Apr 2005; Markus Rothe + ncbi-tools-20041020-r1.ebuild: + Added ~ppc64 to KEYWORDS + + 24 Apr 2005; Michael Hanselmann + ncbi-tools-20041020-r1.ebuild: + Stable on ppc. + +*ncbi-tools-20041020-r1 (06 Mar 2005) + + 06 Mar 2005; Olivier Fisette +files/21ncbi-r1, + +ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20041020.ebuild: + Added the "BLASTMAT" environment variable to the env.d file. + + 02 Mar 2005; Lina Pezzella ncbi-tools-20041020.ebuild: + Stable ppc-macos + + 01 Mar 2005; Olivier Fisette + ncbi-tools-20041020.ebuild: + Added to x86. + + 02 Feb 2005; Lina Pezzella ncbi-tools-20040616.ebuild: + Stable ppc-macos + + 30 Jan 2005; Olivier Fisette + ncbi-tools-20041020.ebuild: + Ebuild cleanup. + +*ncbi-tools-20041020 (18 Jan 2005) + + 18 Jan 2005; Olivier Fisette + +ncbi-tools-20041020.ebuild: + New version. + + 02 Jan 2005; Olivier Fisette : + Added to x86. Use toolchain-funcs rather than gcc eclass. + + 29 Dec 2004; Ciaran McCreesh : + Change encoding to UTF-8 for GLEP 31 compliance + +*ncbi-tools-20040616 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette +metadata.xml, + +files/21ncbi, +files/ncbirc, +ncbi-tools-20040616.ebuild: + Moved from app-sci/ncbi-tools to sci-biology/ncbi-tools. + + 30 Nov 2004; ncbi-tools-20040616.ebuild: + Keyworded ~ppc-macos. + + 22 Nov 2004; Karol Wojtaszek + ncbi-tools-20040616.ebuild: + Added to ~amd64 + + 14 Oct 2004; Olivier Fisette + ncbi-tools-20040616.ebuild: + Use gcc-getCC from gcc.eclass rather than ${CC}. + + 04 Oct 2004; Olivier Fisette + ncbi-tools-20040616.ebuild: + Fixed potential bug in "SRC_URI". + +*ncbi-tools-20040616 (03 Oct 2004) + + 03 Oct 2004; Olivier Fisette files/21ncbi, + -files/dot-ncbirc, +files/ncbirc, -ncbi-tools-20031103.ebuild, + -ncbi-tools-20040202-r1.ebuild, +ncbi-tools-20040616.ebuild: + Updated version and new ebuild. This fixes bug #65941. + + 02 Jun 2004; Aron Griffis ncbi-tools-20031103.ebuild, + ncbi-tools-20040202-r1.ebuild: + Fix use invocation + + 05 May 2004; Bryan Østergaard + ncbi-tools-20040202-r1.ebuild: + Stable on alpha. + + 19 Apr 2004; Patrick Kursawe + ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, + ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, + ncbi-tools-20040202.ebuild: + Cleanup, removing S=... with no effect + + 30 Mar 2004; Donnie Berkholz ; + ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, + ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, + ncbi-tools-20040202.ebuild: + Change x11-base/xfree dependency to virtual/x11. + + 21 Mar 2004; Martin Holzer + ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild, + ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild, + ncbi-tools-20040202.ebuild: + adding categorie. see 45110 for details + +*ncbi-tools-20040202-r1 (06 Feb 2004) + + 06 Feb 2004; Stephen Diener + ncbi-tools-20040202-r1.ebuild: + Replaced buggy tarball with new one. Bumped revision to propogate. + +*ncbi-tools-20040202 (05 Feb 2004) + + 05 Feb 2004; Stephen Diener + ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003.ebuild, + ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild, + ncbi-tools-20040202.ebuild: + Bumped 20031103 to x86, removed old ebuilds, added new release 20040202 + +*ncbi-tools-20040202 (04 Feb 2004) + + 04 Feb 2004; Stephen Diener + ncbi-tools-20031103.ebuild, ncbi-tools-20040202.ebuild: + Version bump. Changes -O3 -> -O2 so X11 apps will work. + + 11 Jan 2004; Heinrich Wendel + ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003-r2.ebuild, + ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild: + fixed motif dep + +*ncbi-tools-20031103 (13 Dec 2003) + + 13 Dec 2003; Stephen Diener + ncbi-tools-20031103.ebuild: + Added november release of ncbi-tools (blast-2.2.6 included); + Added support for -X + +*ncbi-tools-20030422 (11 Nov 2003) + + 11 Nov 2003; ncbi-tools-20030422.ebuild: + added bl2seq to list of installed binaries; changed date format from 04222003 + to 20030422; renamed files to have date appended to not collide and changed + SRC_URI to mirror://gentoo/ + +*ncbi-tools-04222003-r2 (08 Oct 2003) + + 08 Oct 2003; Robin H. Johnson + ncbi-tools-04222003-r2.ebuild: + modified patch from #30656, corrected two pathes in the postinst message + +*ncbi-tools-04222003-r1 (05 May 2003) + + 05 May 2003; Jon Portnoy ncbi-tools-04222003-r1.ebuild : + A few enhancements from Gontran Zepeda . + +*ncbi-tools-04222003 (03 May 2003) + + 03 May 2003; Jon Portnoy ncbi-tools-04222003 : + Initial important. Ebuild submitted by Steve Diener + . diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest new file mode 100644 index 0000000..58ff038 --- /dev/null +++ b/sci-biology/ncbi-tools/Manifest @@ -0,0 +1,38 @@ +AUX 21ncbi-r1 232 RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b SHA1 5674f379f7a70e71394bca272fedd72a1622a7da SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 +MD5 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232 +RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b files/21ncbi-r1 232 +SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 files/21ncbi-r1 232 +AUX ncbi-tools-asn2all.patch 1190 RMD160 3aaccc677bd8b9bad6c6424f5080c71cdac553d7 SHA1 ae22c77cfcd7d416a89ea3fe1e0331264473669d SHA256 e2fd71fdaa07b9e1c9cf646b2d3aa02c2ec822d41dcd45cadfced4164f458bed +MD5 b89cb833887b3e3efda83d074b4b8edb files/ncbi-tools-asn2all.patch 1190 +RMD160 3aaccc677bd8b9bad6c6424f5080c71cdac553d7 files/ncbi-tools-asn2all.patch 1190 +SHA256 e2fd71fdaa07b9e1c9cf646b2d3aa02c2ec822d41dcd45cadfced4164f458bed files/ncbi-tools-asn2all.patch 1190 +AUX ncbi-tools-extra_vib.patch 1393 RMD160 05e2dcf17b6af9475625eb0aa0be6bc96071a923 SHA1 bb92aeada6786d4573f9ad98e3d50b4a4201ba10 SHA256 b7639937d59c8bd636c6b02a65a4469d188645b9a10fffd0c8680fb861a7a8e1 +MD5 81e003b746faf22d3f1b1df37ffdcf41 files/ncbi-tools-extra_vib.patch 1393 +RMD160 05e2dcf17b6af9475625eb0aa0be6bc96071a923 files/ncbi-tools-extra_vib.patch 1393 +SHA256 b7639937d59c8bd636c6b02a65a4469d188645b9a10fffd0c8680fb861a7a8e1 files/ncbi-tools-extra_vib.patch 1393 +AUX ncbi-tools-lop.patch 701 RMD160 1b9d8d196b1d4f27b090e616c9ac03cb9b4e6a09 SHA1 be28d340be72b9840342b407d95dc2a558e39de9 SHA256 9e5c57e944d23920f196f36912933653c236998729f69f28be8b55964865dfbc +MD5 6b62beda180ee6d7d4d4a52507acc3ff files/ncbi-tools-lop.patch 701 +RMD160 1b9d8d196b1d4f27b090e616c9ac03cb9b4e6a09 files/ncbi-tools-lop.patch 701 +SHA256 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Location of the ".ncbi.rc" file which sets the default path for shared data. +NCBI=/etc/ncbi diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 new file mode 100644 index 0000000..a80231e --- /dev/null +++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1 @@ -0,0 +1,8 @@ +MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096 +RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096 +SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096 +MD5 8eca84753fd7a1d39bab256a4944f65e ncbi-tools-20061015.tar.gz 15772715 +RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 ncbi-tools-20061015.tar.gz 15772715 +SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de ncbi-tools-20061015.tar.gz 15772715 +RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568 +SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568 diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 new file mode 100644 index 0000000..3c82f07 --- /dev/null +++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 @@ -0,0 +1,8 @@ +MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096 +RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096 +SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096 +MD5 c17f7b08c12823e4320661894110dcb1 ncbi-tools-20070826.tar.gz 17076175 +RMD160 00daadd503bf729c15ada0008e305492a076fe15 ncbi-tools-20070826.tar.gz 17076175 +SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8 ncbi-tools-20070826.tar.gz 17076175 +RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568 +SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568 diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch new file mode 100644 index 0000000..1cd7976 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch @@ -0,0 +1,27 @@ +--- ncbi-20050605/make/makedis.csh 2005-05-13 05:42:12.000000000 +0200 ++++ ncbi/make/makedis.csh 2005-09-20 22:02:38.000000000 +0200 +@@ -472,6 +472,24 @@ + + set net_stat = $status + ++if ("$?NCBI_MT_OTHERLIBS" == "1") then ++ set CMD='make $MFLG -f makenet.unx \ ++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ ++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ ++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ ++ THREAD_OBJ=$NCBI_THREAD_OBJ \ ++ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ ++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all' ++else ++ set CMD='make $MFLG -f makenet.unx \ ++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ ++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ ++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ ++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all' ++endif ++eval echo $CMD ++eval echo $CMD | sh ++ + if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then + echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat + cat <