[med-svn] [subread] 01/02: d/rules: export -fsigned-char only once d/patches/arch_specific_flags.patch: use -O2 instead of -O9, remove duplicated options d/README.source: merge with d/README.Debian-source describe why powerpc, mips and s390x are excluded

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository subread.

commit 1e72b13c2eed9ee7733a469ad4370c8d07aabef0
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu May 21 17:40:32 2015 +0200

    d/rules: export -fsigned-char only once
    d/patches/arch_specific_flags.patch: use -O2 instead of -O9,
     remove duplicated options
    d/README.source: merge with d/README.Debian-source
     describe why powerpc, mips and s390x are excluded
---
 debian/README.Debian-source              |  2 --
 debian/README.source                     | 15 +++++++++++++++
 debian/patches/arch_specific_flags.patch |  8 ++++----
 debian/rules                             |  1 +
 4 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/debian/README.Debian-source b/debian/README.Debian-source
deleted file mode 100644
index c009f5b..0000000
--- a/debian/README.Debian-source
+++ /dev/null
@@ -1,2 +0,0 @@
- This source package doesn't contain the pdf documentation
- /doc/SubreadUserGuide.pdf shiped with the original tarball.
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..aafb435
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,15 @@
+
+ The source package of subread doesn't include the pdf documentation
+ /doc/SubreadUserGuide.pdf shiped with the original tarball.
+
+ In order to get the +dfsg tarball use get-orig-source target in d/rules
+
+ The subread package is currently build only for the following architectures:
+
+ arm64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 mipsel ppc64elo
+
+ It is possible to built subread also on powerpc, mips and s390x, 
+ but a few core tools of subread suite fail on these architectures.
+ exactSNP can't read the input BAM file and subjunc segfaults.
+
+ -- Alex Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 21 May 2015 16:15:30 +0200
diff --git a/debian/patches/arch_specific_flags.patch b/debian/patches/arch_specific_flags.patch
index bb06253..722caa8 100644
--- a/debian/patches/arch_specific_flags.patch
+++ b/debian/patches/arch_specific_flags.patch
@@ -1,7 +1,7 @@
 Description: inject architecture specific flags:
  for amd64 and i386 add -mtune=generic and -msse3,
- for architectures where char is by default unsigned 
- use -fsigned-char gcc option
+ use -fsigned-char for all architectures
+ change -O9 to -O2 as I couldn't fine -O9 in gcc options
 Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
 --- subread.orig/src/Makefile.Linux
 +++ subread/src/Makefile.Linux
@@ -10,11 +10,11 @@ Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  include makefile.version
  
 -CCFLAGS = -mtune=core2 ${MACOS} -O9 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
-+CCFLAGS = ${EXTRA_CC_FLAGS} -O9 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
++CCFLAGS = ${EXTRA_CC_FLAGS} -O2 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
  #CCFLAGS =  -D_FORTIFY_SOURCE=2 -mtune=core2 ${MACOS} -O2 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  # -DREPORT_ALL_THE_BEST
 -LDFLAGS = ${STATIC_MAKE} -lpthread -lz -lm ${MACOS} -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
 -CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 
-+LDFLAGS = ${STATIC_MAKE} ${EXTRA_LD_FLAGS} -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
++LDFLAGS = ${STATIC_MAKE} ${EXTRA_LD_FLAGS} -lpthread -lz -lm # -DREPORT_ALL_THE_BEST
 +CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0
  
  
diff --git a/debian/rules b/debian/rules
index 16c77ef..cef5aab 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,6 +11,7 @@ bindir := $(CURDIR)/bin
 utildir := $(CURDIR)/bin/utilities
 
 DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
+EXTRA_CC_FLAGS = 
 ifeq ($(DEB_HOST_ARCH),$(filter $(DEB_HOST_ARCH),amd64 i386))
         EXTRA_CC_FLAGS = -mtune=generic -msse3
 endif

-- 
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