From 6f8038813c460b4f0572d5ef595cdfa94af3a94d Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Tue, 21 May 2019 10:20:03 +0100 Subject: gentoo resync : 21.05.2019 --- sci-biology/cufflinks/Manifest | 10 -- sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 57 ---------- .../cufflinks-2.2.1-boost-1.65-tr1-removal.patch | 14 --- .../cufflinks/files/cufflinks-2.2.1-flags.patch | 28 ----- .../files/cufflinks-2.2.1-format-security.patch | 16 --- .../files/cufflinks-2.2.1-gcc5-make_shared.patch | 11 -- .../cufflinks/files/cufflinks-2.2.1-gcc6.patch | 14 --- .../cufflinks/files/cufflinks-2.2.1-gcc7.patch | 121 --------------------- .../files/cufflinks-2.2.1-samtools-legacy.patch | 44 -------- sci-biology/cufflinks/metadata.xml | 8 -- 10 files changed, 323 deletions(-) delete mode 100644 sci-biology/cufflinks/Manifest delete mode 100644 sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild delete mode 100644 sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch delete mode 100644 sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch delete mode 100644 sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch delete mode 100644 sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch delete mode 100644 sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch delete mode 100644 sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch delete mode 100644 sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch delete mode 100644 sci-biology/cufflinks/metadata.xml (limited to 'sci-biology/cufflinks') diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest deleted file mode 100644 index 4c95c2d9efa8..000000000000 --- a/sci-biology/cufflinks/Manifest +++ /dev/null @@ -1,10 +0,0 @@ -AUX cufflinks-2.2.1-boost-1.65-tr1-removal.patch 344 BLAKE2B af0287f43bfd37da352fc330e3f6e06d4c6946851c6d8760302078157c8073591ccf7b508e2debf35747837216cc15e952fd7128bca500547cc180061dc2f780 SHA512 774558e93cf57ca9e9361df2271119474c8726573ff4467af4836db863d87ff0f38fe7048c9287227f18d3541891bb7b433b5fa33567616eeecda2bb5b057e9a -AUX cufflinks-2.2.1-flags.patch 1132 BLAKE2B 675fb86a95425ed0def259b6f316e443eddb0c80a3a4f78e724f85ca3b14e58c29bb59bbc80a61ee7dcfaeb404383ffe0e58669dedc95224913c8d43939fd799 SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12 -AUX cufflinks-2.2.1-format-security.patch 618 BLAKE2B 1a316055af35849333c8ccbd46079a4ee1096becde474151932317bb66f81eff27b80d15306d9432f69a42fa9202a7712f9eff9921b915a92f4094ad2eadc79b SHA512 61a8cfe31988b028636f97db06d6855d9fce4ff3548da70d7e791fde85b38c09376be63714b67a0dc3e112f1d543735a51ebc437fc0b32eff98e9bf13138ff3c -AUX cufflinks-2.2.1-gcc5-make_shared.patch 417 BLAKE2B 99fb3c7135789073089344d0f362088e5d95354b80a43e5a4fd47daa8b38d7c05b18476c491e5945b6b313925e984361915651c0b783c866273eeb4530eb35ea SHA512 81340797fe99aeb0fd118b28f729dfdcfbd3dd1a5efa2a4874a3732a167ad1c8b8d7d3408d1137db35ac5c17319d90dc1351bfd91a15af5c095de746791394d7 -AUX cufflinks-2.2.1-gcc6.patch 344 BLAKE2B 7534c9060e93f074718726e2cbf7df259ba298b447915a4162916977340d33e35a4fddbf3e1b662334b56d42ffb8e0a096c337b465b5952abe27d1248fd6d0f2 SHA512 1e8fc2e717c464e39aecf2c434857e962a809fd2a9f84bfca2b7230d5150d464262b579f1a8c13970767e929562d04994d60002834c98c204e089d2d2a8381c0 -AUX cufflinks-2.2.1-gcc7.patch 4133 BLAKE2B ac2fbf2ebadfe0e90d7163dbd839b2173a3a3a9925b25e2eba8775793545ed8e17e8075c9e562300fa0fae6fd7c35893c8bc892c3e79bd6645b2e3cf51acbdbf SHA512 cbcc2be9e1266e24801dc91ed776aa314761ac682274c103c4f4ad9c37f8ad02b63233f2a16608dd620ca67e89a21028142bdc059cbe5fd2fffdbdb3e38f0af8 -AUX cufflinks-2.2.1-samtools-legacy.patch 1105 BLAKE2B ceeb2236456f30598e0d98ce1eaa4fae908286704fb6912a19ccc008b3d41476b853cacc3fc545450dde7d883593a545110a440c044118875041f56077c963b3 SHA512 80c6eaadcfe6919d61b63efc83d3d618e939c3a1cd5e4977f936c41656a96c7c2dd71a1309d6b0422b1bf248a366643a62f011b30b37b4001efae5da04acaadf -DIST cufflinks-2.2.1.tar.gz 766280 BLAKE2B 200ca88d15cdfca550a12a39cf69d4c41850532c76840d2a86a21654b317e28c7f35d36ba26105490e75d55c5527dd64da1ef3c14f2d467a60379c234a8e9e60 SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b -EBUILD cufflinks-2.2.1-r2.ebuild 1303 BLAKE2B 43a7781892fd664ca50d429ee741233ec4e319a8bccda379cc18a36c8447fb65972a07480bc74dde09d964f8e34f15b5e53204d6da2b1ce9af79fbc39d566103 SHA512 45d0d18bc405809d76f26b348ae90fa0fd9453a9ca1632c052ca6354679b65c9c40460bda40b7f50745549df916704cac3b6e4ed1b833cb9114f61ab002b1640 -MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild deleted file mode 100644 index 3892e03e23b2..000000000000 --- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic python-single-r1 toolchain-funcs - -DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq" -HOMEPAGE="http://cufflinks.cbcb.umd.edu/" -SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - sci-biology/samtools:0.1-legacy - >=dev-libs/boost-1.62.0:= - ${PYTHON_DEPS}" -DEPEND=" - ${RDEPEND} - dev-cpp/eigen:3 - virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}"/${P}-samtools-legacy.patch - "${FILESDIR}"/${P}-flags.patch - "${FILESDIR}"/${P}-gcc6.patch - "${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch - "${FILESDIR}"/${P}-gcc7.patch - "${FILESDIR}"/${P}-format-security.patch - "${FILESDIR}"/${P}-gcc5-make_shared.patch -) - -src_prepare() { - default - python_fix_shebang src/cuffmerge - - eautoreconf -} - -src_configure() { - # keep in sync with Boost - append-cxxflags -std=c++14 - append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) - - econf \ - --disable-optim \ - --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \ - --with-bam="${EPREFIX}/usr/" \ - $(use_enable debug) \ - PYTHON="${PYTHON}" -} diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch deleted file mode 100644 index 42a906e7a83a..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch +++ /dev/null @@ -1,14 +0,0 @@ -Boost 1.65 removed the TR1 headers. -Bug: https://bugs.gentoo.org/show_bug.cgi?id=630654 - ---- a/src/biascorrection.h -+++ b/src/biascorrection.h -@@ -15,7 +15,7 @@ - #include - #include - #include --#include -+#include - #include - #include "common.h" - diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch deleted file mode 100644 index 47784088fab9..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch +++ /dev/null @@ -1,28 +0,0 @@ - configure.ac | 7 ++++--- - 1 file changed, 4 insertions(+), 3 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 96ffbac..e88b8e4 100755 ---- a/configure.ac -+++ b/configure.ac -@@ -61,7 +61,8 @@ AC_CANONICAL_HOST - - # set CFLAGS and CXXFLAGS - user_CFLAGS=${CFLAGS} --generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024" -+generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized" -+generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024" - ext_CFLAGS="" - debug_CFLAGS="" - #echo "${host_cpu}-${host_os}" -@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with - [ext_LDFLAGS="-lprofiler -ltcmalloc"], []) - - CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" --CXXFLAGS="$CFLAGS" --CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" -+CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}" -+CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" - user_LDFLAGS="$LDFLAGS" - LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" - diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch deleted file mode 100644 index fa13f78d8b52..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ -Author: Andreas Tille -Date: Wed, 22 May 2013 13:27:40 +0200 -Description: When building with --format-security (Debhelper 9 hardening) - this patch is needed to build successfully - ---- a/src/locfit/makecmd.c -+++ b/src/locfit/makecmd.c -@@ -200,7 +200,7 @@ char *cmdline; - /* vs is used to store the command line string. */ - sprintf(vn,"=clstr%d",clcount); - vs = createvar(vn,STSYSTEM,1+strlen(cmdline),VCHAR); -- sprintf((char *)vdptr(vs),cmdline); -+ sprintf((char *)vdptr(vs),"%s",cmdline); - - /* va is used to store pointers to the command line fields. */ - sprintf(vn,"=cline%d",clcount); diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch deleted file mode 100644 index 67a28df10249..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/src/differential.cpp -+++ b/src/differential.cpp -@@ -575,7 +575,7 @@ - boost::mutex::scoped_lock lock(meta_data_lock); - #endif - pair p; -- p = meta_data_table.insert(make_pair(description, new SampleDifferenceMetaData())); -+ p = meta_data_table.insert(make_pair(description, boost::make_shared())); - return p.first->second; - } - diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch deleted file mode 100644 index 6ee9bcf456d4..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- a/src/lemon/error.h -+++ b/src/lemon/error.h -@@ -67,9 +67,9 @@ - } - - ExceptionMember& operator=(const ExceptionMember& copy) { -- if (ptr.get() == 0) return; -+ if (ptr.get() == 0) return *this; - try { -- if (!copy.valid()) return; -+ if (!copy.valid()) return *this; - *ptr = copy.get(); - } catch (...) {} - } diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch deleted file mode 100644 index 48fe6e10ac96..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch +++ /dev/null @@ -1,121 +0,0 @@ -Author: Alex Mestiashvili -Origin: https://lists.debian.org/debian-med/2017/09/msg00021.html -Bug-Debian: https://bugs.debian.org/871234 -Description: Fix gcc-7 build issue, thanks to Jeff Epler ---- a/src/GHash.hh -+++ b/src/GHash.hh -@@ -88,7 +88,7 @@ - //nextkey is SET to the corresponding key - GHashEntry* NextEntry() { //returns a pointer to a GHashEntry - register int pos=fCurrentEntry; -- while (pos char* GHash::NextKey() { - register int pos=fCurrentEntry; -- while (pos OBJ* GHash::NextData() { - register int pos=fCurrentEntry; -- while (pos OBJ* GHash::NextData(char* &nextkey) { - register int pos=fCurrentEntry; -- while (pos int GHash::First() const { - register int pos=0; -- while(pos int GHash::Last() const { - register int pos=fCapacity-1; -- while(0<=pos){ if(0<=hash[pos].hash) break; pos--; } -- GASSERT(pos<0 || 0<=hash[pos].hash); -+ while(0<=pos){ if(0<=(hash[pos].hash)) break; pos--; } -+ GASSERT(pos<0 || 0<=(hash[pos].hash)); - return pos; - } - -@@ -474,8 +474,8 @@ - // Find next valid entry - template int GHash::Next(int pos) const { - GASSERT(0<=pos && pos int GHash::Prev(int pos) const { - GASSERT(0<=pos && pos= 0){ if(0<=hash[pos].hash) break; } -- GASSERT(pos<0 || 0<=hash[pos].hash); -+ while(--pos >= 0){ if(0<=(hash[pos].hash)) break; } -+ GASSERT(pos<0 || 0<=(hash[pos].hash)); - return pos; - } - diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch deleted file mode 100644 index 374ce519ef86..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch +++ /dev/null @@ -1,44 +0,0 @@ -Modify the buildsystem to work with the legacy version of samtools, -which can coexist with the most recent version of samtools. -See also: https://bugs.gentoo.org/show_bug.cgi?id=577854 - ---- cufflinks-2.2.1/ax_bam.m4 -+++ cufflinks-2.2.1/ax_bam.m4 -@@ -102,7 +102,7 @@ - - AC_LANG_PUSH(C++) - AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ -- @%:@include -+ @%:@include - ]], [[ - ]])],[ - AC_MSG_RESULT(yes) -@@ -171,7 +171,7 @@ - - AC_LANG_PUSH(C++) - AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ -- @%:@include -+ @%:@include - ]], [[ - ]])],[ - AC_MSG_RESULT(yes) -@@ -189,7 +189,7 @@ - AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).]) - fi - else -- BAM_LIB="-lbam" -+ BAM_LIB="-lbam-0.1-legacy" - AC_SUBST(BAM_CPPFLAGS) - AC_SUBST(BAM_LDFLAGS) - AC_SUBST(BAM_LIB) ---- cufflinks-2.2.1/src/hits.h -+++ cufflinks-2.2.1/src/hits.h -@@ -18,7 +18,7 @@ - - #include - --#include -+#include - - #include "common.h" - #include "multireads.h" diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/cufflinks/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - -- cgit v1.2.3