# Removal in 30 days. Bug #650256, #673672.
sys-cluster/moosefs
-# David Seifert <soap@gentoo.org> (20 Apr 2019)
-# Completely broken build system, massive maintenance
-# burden, no new release since 2014.
-# Removal in 30 days. Bug #671432.
-sci-biology/cufflinks
-
# James Le Cuirot <chewi@gentoo.org> (20 Apr 2019)
# Ancient and long dead upstream. Use app-emulation/fs-uae
# instead. Removal in 30 days. Bugs #432092, #602966.
+++ /dev/null
-DIST cufflinks-2.2.1.tar.gz 766280 BLAKE2B 200ca88d15cdfca550a12a39cf69d4c41850532c76840d2a86a21654b317e28c7f35d36ba26105490e75d55c5527dd64da1ef3c14f2d467a60379c234a8e9e60 SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b
+++ /dev/null
-# 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}"
-}
+++ /dev/null
-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 <vector>
- #include <list>
- #include <string>
--#include <boost/tr1/unordered_map.hpp>
-+#include <boost/unordered_map.hpp>
- #include <boost/thread.hpp>
- #include "common.h"
-
+++ /dev/null
- 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}"
-
+++ /dev/null
-Author: Andreas Tille <tille@debian.org>
-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);
+++ /dev/null
---- a/src/differential.cpp
-+++ b/src/differential.cpp
-@@ -575,7 +575,7 @@
- boost::mutex::scoped_lock lock(meta_data_lock);
- #endif
- pair<SampleDiffMetaDataTable::iterator, bool> p;
-- p = meta_data_table.insert(make_pair(description, new SampleDifferenceMetaData()));
-+ p = meta_data_table.insert(make_pair(description, boost::make_shared<SampleDifferenceMetaData>()));
- return p.first->second;
- }
-
+++ /dev/null
---- 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 (...) {}
- }
+++ /dev/null
-Author: Alex Mestiashvili <mailatgoogl@gmail.com>
-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 <jepler@unpythonic.net>
---- 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<fCapacity && hash[pos].hash<0) pos++;
-+ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
- if (pos==fCapacity) {
- fCurrentEntry=fCapacity;
- return NULL;
-@@ -186,7 +186,7 @@
- x=HASH2(h,n);
- GASSERT(1<=x && x<n);
- while(k[p].hash!=-1) p=(p+x)%n;
-- GASSERT(k[p].hash<0);
-+ GASSERT((k[p].hash)<0);
- k[p]=hash[i];
- }
- }
-@@ -225,7 +225,7 @@
- GTRACE(("GHash::insert: key=\"%s\"\n",ky));
- //GMessage("GHash::insert: key=\"%s\"\n",ky);
- GASSERT(0<=i && i<fCapacity);
-- GASSERT(hash[i].hash<0);
-+ GASSERT((hash[i].hash)<0);
- hash[i].hash=h;
- hash[i].mark=mrk;
- hash[i].key=Gstrdup(ky);
-@@ -266,7 +266,7 @@
- GTRACE(("GHash::insert: key=\"%s\"\n",ky));
- //GMessage("GHash::insert: key=\"%s\"\n",ky);
- GASSERT(0<=i && i<fCapacity);
-- GASSERT(hash[i].hash<0);
-+ GASSERT((hash[i].hash)<0);
- hash[i].hash=h;
- hash[i].mark=mrk;
- hash[i].key=(char *)ky;
-@@ -310,7 +310,7 @@
- if(i==-1) i=p;
- GTRACE(("GHash::replace: %08x: inserting: \"%s\"\n",this,ky));
- GASSERT(0<=i && i<fCapacity);
-- GASSERT(hash[i].hash<0);
-+ GASSERT((hash[i].hash)<0);
- hash[i].hash=h;
- hash[i].mark=mrk;
- hash[i].key=Gstrdup(ky);
-@@ -412,7 +412,7 @@
-
- template <class OBJ> char* GHash<OBJ>::NextKey() {
- register int pos=fCurrentEntry;
-- while (pos<fCapacity && hash[pos].hash<0) pos++;
-+ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
- if (pos==fCapacity) {
- fCurrentEntry=fCapacity;
- return NULL;
-@@ -425,7 +425,7 @@
-
- template <class OBJ> OBJ* GHash<OBJ>::NextData() {
- register int pos=fCurrentEntry;
-- while (pos<fCapacity && hash[pos].hash<0) pos++;
-+ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
- if (pos==fCapacity) {
- fCurrentEntry=fCapacity;
- return NULL;
-@@ -439,7 +439,7 @@
-
- template <class OBJ> OBJ* GHash<OBJ>::NextData(char* &nextkey) {
- register int pos=fCurrentEntry;
-- while (pos<fCapacity && hash[pos].hash<0) pos++;
-+ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
- if (pos==fCapacity) {
- fCurrentEntry=fCapacity;
- nextkey=NULL;
-@@ -457,16 +457,16 @@
- // Get first non-empty entry
- template <class OBJ> int GHash<OBJ>::First() const {
- register int pos=0;
-- while(pos<fCapacity){ if(0<=hash[pos].hash) break; pos++; }
-- GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
-+ while(pos<fCapacity){ if(0<=(hash[pos].hash)) break; pos++; }
-+ GASSERT(fCapacity<=pos || 0<=(hash[pos].hash));
- return pos;
- }
-
- // Get last non-empty entry
- template <class OBJ> int GHash<OBJ>::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 <class OBJ> int GHash<OBJ>::Next(int pos) const {
- GASSERT(0<=pos && pos<fCapacity);
-- while(++pos <= fCapacity-1){ if(0<=hash[pos].hash) break; }
-- GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
-+ while(++pos <= fCapacity-1){ if(0<=(hash[pos].hash)) break; }
-+ GASSERT(fCapacity<=pos || 0<=(hash[pos].hash));
- return pos;
- }
-
-@@ -483,8 +483,8 @@
- // Find previous valid entry
- template <class OBJ> int GHash<OBJ>::Prev(int pos) const {
- GASSERT(0<=pos && pos<fCapacity);
-- while(--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;
- }
-
+++ /dev/null
-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 <bam/bam.h>
-+ @%:@include <bam-0.1-legacy/bam.h>
- ]], [[
- ]])],[
- AC_MSG_RESULT(yes)
-@@ -171,7 +171,7 @@
-
- AC_LANG_PUSH(C++)
- AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
-- @%:@include <bam/version.hpp>
-+ @%:@include <bam-0.1-legacy/version.hpp>
- ]], [[
- ]])],[
- 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 <boost/shared_ptr.hpp>
-
--#include <bam/sam.h>
-+#include <bam-0.1-legacy/sam.h>
-
- #include "common.h"
- #include "multireads.h"
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
projects / gentoo.git / commitdiff