commit: 159437c4bc58b8fcd12cc33bb11d8a4fef437f1b Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Tue Dec 20 15:47:48 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Tue Dec 20 17:35:42 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=159437c4
sci-biology/abyss: Remove old Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3183 sci-biology/abyss/Manifest | 3 -- sci-biology/abyss/abyss-1.3.3.ebuild | 42 ----------------- sci-biology/abyss/abyss-1.3.6-r1.ebuild | 54 ---------------------- sci-biology/abyss/abyss-1.9.0-r1.ebuild | 53 --------------------- .../abyss/files/abyss-1.3.3-ac_prog_ar.patch | 18 -------- sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch | 15 ------ .../abyss/files/abyss-1.3.6-ac_prog_ar.patch | 18 -------- sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch | 15 ------ sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40 ---------------- .../abyss/files/abyss-1.9.0-ac_prog_ar.patch | 18 -------- sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch | 34 -------------- 11 files changed, 310 deletions(-) diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest index f19563b..4c3779e 100644 --- a/sci-biology/abyss/Manifest +++ b/sci-biology/abyss/Manifest @@ -1,4 +1 @@ -DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914 -DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07 -DIST abyss-1.9.0.tar.gz 985480 SHA256 82e4050766a9c7fb87fd736f94724a02388efb1df847b40870a0fbf842917239 SHA512 d9da19f004bb97f9301f3be83ceb5361eb70f42139a1ef17129de99e03bda5de7680d718d76aed26d26f24c1d26c37e050801ff343acad007b76d2214955b83f WHIRLPOOL bd322afa9bf99a53aec177c79ca9618f39043cda606eb4e3d5dcfb46c26298d218fc154e2c46efadac59febb69dd625fe597101a1efbccc62ab8228b555596cc DIST abyss-2.0.2.tar.gz 1036135 SHA256 6482b81eb5439703c0dbf6cd7ac25cd0df7541d9e04ef7865343b241e21db460 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30 WHIRLPOOL 23447cb00b0bb9b5b8a724ba44f8d7193d9640ccd19956b42bbbd83b67557b66b7c68141d6f292c4ab11ab523286471d5ee1c938f22749a61162de056a0d903e diff --git a/sci-biology/abyss/abyss-1.3.3.ebuild b/sci-biology/abyss/abyss-1.3.3.ebuild deleted file mode 100644 index 62b79f6..00000000 --- a/sci-biology/abyss/abyss-1.3.3.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI="4" - -inherit autotools eutils toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"; -SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"; - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp" -KEYWORDS="amd64 x86" - -DEPEND=" - dev-cpp/sparsehash - dev-libs/boost - mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -src_prepare() { - tc-export AR - epatch \ - "${FILESDIR}"/${P}-gcc-4.7.patch \ - "${FILESDIR}"/${P}-ac_prog_ar.patch - - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - econf \ - --docdir="${EPREFIX}/usr/share/doc/${PF}" \ - $(use_enable openmp) -} diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild b/sci-biology/abyss/abyss-1.3.6-r1.ebuild deleted file mode 100644 index a4327b0..00000000 --- a/sci-biology/abyss/abyss-1.3.6-r1.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=6 - -inherit autotools toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"; -SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"; - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost - misc-haskell? ( dev-libs/gmp:0= - virtual/libffi:0= - ) - mpi? ( virtual/mpi ) -" -DEPEND="${RDEPEND} - misc-haskell? ( dev-lang/ghc - dev-haskell/mmap ) -" - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -PATCHES=( - "${FILESDIR}"/${P}-gcc-4.7.patch - "${FILESDIR}"/${P}-ac_prog_ar.patch - "${FILESDIR}"/${P}-samtoafg.patch -) - -src_prepare() { - default - tc-export AR - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - econf $(use_enable openmp) -} diff --git a/sci-biology/abyss/abyss-1.9.0-r1.ebuild b/sci-biology/abyss/abyss-1.9.0-r1.ebuild deleted file mode 100644 index 32af453..00000000 --- a/sci-biology/abyss/abyss-1.9.0-r1.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=6 - -inherit autotools toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"; -SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost:= - misc-haskell? ( dev-libs/gmp:0= - virtual/libffi:0= - ) - mpi? ( virtual/mpi ) -" -DEPEND="${RDEPEND} - misc-haskell? ( dev-lang/ghc - dev-haskell/mmap ) -" - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -PATCHES=( - "${FILESDIR}"/${P}-ac_prog_ar.patch - "${FILESDIR}"/${P}-gcc-6.patch -) - -src_prepare() { - default - tc-export AR - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - econf $(use_enable openmp) -} diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch deleted file mode 100644 index 300868f..00000000 --- a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch +++ /dev/null @@ -1,18 +0,0 @@ - configure.ac | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/configure.ac b/configure.ac -index 5c6cb92..b99bedd 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -12,6 +12,10 @@ AC_PROG_CPP - AC_PROG_CXX - AC_PROG_INSTALL - AC_PROG_RANLIB -+AN_MAKEVAR([AR], [AC_PROG_AR]) -+AN_PROGRAM([ar], [AC_PROG_AR]) -+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) -+AC_PROG_AR - - # Checks for header files. - AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \ diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch deleted file mode 100644 index 42066f7..00000000 --- a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - ParseAligns/abyss-fixmate.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc -index 506ea0c..a0a403c 100644 ---- a/ParseAligns/abyss-fixmate.cc -+++ b/ParseAligns/abyss-fixmate.cc -@@ -15,6 +15,7 @@ - #include <iterator> - #include <sstream> - #include <string> -+#include <unistd.h> - - using namespace std; - diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch deleted file mode 100644 index 158e9b1..00000000 --- a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch +++ /dev/null @@ -1,18 +0,0 @@ - configure.ac | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/configure.ac b/configure.ac -index 9d4bb66..aa94364 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -12,6 +12,10 @@ AC_PROG_CPP - AC_PROG_CXX - AC_PROG_INSTALL - AC_PROG_RANLIB -+AN_MAKEVAR([AR], [AC_PROG_AR]) -+AN_PROGRAM([ar], [AC_PROG_AR]) -+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) -+AC_PROG_AR - AC_CHECK_TOOL(GHC, ghc) - AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) - diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch deleted file mode 100644 index c2cc35c..00000000 --- a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - ParseAligns/abyss-fixmate.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc -index 1a169cf..36cc05b 100644 ---- a/ParseAligns/abyss-fixmate.cc -+++ b/ParseAligns/abyss-fixmate.cc -@@ -16,6 +16,7 @@ - #include <iterator> - #include <sstream> - #include <string> -+#include <unistd.h> - - using namespace std; - diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch deleted file mode 100644 index cb7dfb0..00000000 --- a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch +++ /dev/null @@ -1,40 +0,0 @@ -Hello, - -I see Shaun Jackmans' (abyss-)sam2afg script is available within the -Amos source repository. I find this very useful for coercing output from -assemblers which which don't track read location into amos by remapping -reads against the assembly and converting to afg - not ideal but better -than nothing when you don't have the 'real' read locations to work with. - -This fails, however when reads are aligned with 'bwa mem', which can -output multi-part alignments. sam2afg checks for reuse of the same read -id (presumably to prevent the generation of non-unique eid values), -consequently encountering multiple alignments for a read causes it to die. - -The following one-line patch allows sam2afg to skip these secondary -alignments present in 'bwa mem' output, provided bwa mem has been run -with the '-M' argument which sets the SAM 'secondary alignment' flag on -the alignments in question. - -Hopefully this will also be of use to others... - -Best Regards, -James - --- -Dr. James Abbott -Lead Bioinformatician -Bioinformatics Support Service -Imperial College, London - - ---- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200 -+++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200 -@@ -105,6 +105,7 @@ - die unless defined $qqual; - - $tstart--; # convert to zero-based coordinate -+ next if $flag & 0x100; # secondary alignment - $qid .= "/1" if $flag & 0x40; #FREAD1 - $qid .= "/2" if $flag & 0x80; #FREAD2 - diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch deleted file mode 100644 index 158e9b1..00000000 --- a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch +++ /dev/null @@ -1,18 +0,0 @@ - configure.ac | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/configure.ac b/configure.ac -index 9d4bb66..aa94364 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -12,6 +12,10 @@ AC_PROG_CPP - AC_PROG_CXX - AC_PROG_INSTALL - AC_PROG_RANLIB -+AN_MAKEVAR([AR], [AC_PROG_AR]) -+AN_PROGRAM([ar], [AC_PROG_AR]) -+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) -+AC_PROG_AR - AC_CHECK_TOOL(GHC, ghc) - AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) - diff --git a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch deleted file mode 100644 index 49a30f9..00000000 --- a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch +++ /dev/null @@ -1,34 +0,0 @@ -diff --git a/DataBase/db-csv.cc b/DataBase/db-csv.cc -index 05cac19..48e3b44 100644 ---- a/DataBase/db-csv.cc -+++ b/DataBase/db-csv.cc -@@ -18,11 +18,11 @@ static const char TABLE_LIST[] = - typedef vector<string> vs; - - static bool existFile(const char* f) - { - ifstream file(f); -- return file; -+ return bool(file); - } - - template <typename D> - static bool existTable( - D& db, const string& t) -diff --git a/SimpleGraph/SimpleGraph.cpp b/SimpleGraph/SimpleGraph.cpp -index 373ec70..0a9ebd3 100644 ---- a/SimpleGraph/SimpleGraph.cpp -+++ b/SimpleGraph/SimpleGraph.cpp -@@ -645,11 +645,11 @@ static void* worker(void* pArg) - for (;;) { - /** Lock the input stream. */ - static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER; - pthread_mutex_lock(&inMutex); - EstimateRecord er; -- bool good = (*arg.in) >> er; -+ bool good = bool((*arg.in) >> er); - pthread_mutex_unlock(&inMutex); - if (!good) - break; - - // Flip the anterior distance estimates.
