gentoo resync : 21.05.2019

10 files changed, 0 insertions, 323 deletions

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 <vector>
- #include <list>
- #include <string>
--#include <boost/tr1/unordered_map.hpp>
-+#include <boost/unordered_map.hpp>
- #include <boost/thread.hpp>
- #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 <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);
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<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;
- }
- 
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 <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;
-   }
- 
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 <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"
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 @@
-<?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>