reinit the tree, so we can have metadata

4 files changed, 100 insertions, 0 deletions

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
new file mode 100644
index 000000000000..42a906e7a83a
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch
@@ -0,0 +1,14 @@
+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
new file mode 100644
index 000000000000..47784088fab9
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
@@ -0,0 +1,28 @@
+ 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-gcc6.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch
new file mode 100644
index 000000000000..6ee9bcf456d4
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch
@@ -0,0 +1,14 @@
+--- 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-samtools-legacy.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
new file mode 100644
index 000000000000..374ce519ef86
--- /dev/null
+++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
@@ -0,0 +1,44 @@
+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"