[med-svn] [sra-sdk] 04/04: Adapt patches to new version

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository sra-sdk.

commit 089dbf05942ce37d74d9a998fc194e343b99260b
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 30 08:52:20 2015 +0100

    Adapt patches to new version
---
 debian/patches/10_portability.patch      | 15 -------------
 debian/patches/find_configure_libs.patch | 37 ++++++++------------------------
 debian/patches/hardening.patch           | 10 ++++-----
 3 files changed, 14 insertions(+), 48 deletions(-)

diff --git a/debian/patches/10_portability.patch b/debian/patches/10_portability.patch
index f9b56b8..1430620 100644
--- a/debian/patches/10_portability.patch
+++ b/debian/patches/10_portability.patch
@@ -3,21 +3,6 @@ LastChanged: Tue, 10 Jan 2012 09:06:14 +0900
 Description: Drop redundant -m32/-m64 option to enable build
              on all Debian architectures
 
---- a/build/Makefile.gcc
-+++ b/build/Makefile.gcc
-@@ -55,12 +55,6 @@ ifeq (linux,$(OS))
-     NO_ARRAY_BOUNDS_WARNING = -Wno-array-bounds
- endif
- 
--ifeq (64,$(BITS))
--	CARCH = -m64
--else
--	CARCH = -m32
--endif
--
- ifeq (prof, $(BUILD))
- 	PROF = -pg
- endif
 --- a/build/Makefile.shell
 +++ b/build/Makefile.shell
 @@ -30,6 +30,7 @@ endif
diff --git a/debian/patches/find_configure_libs.patch b/debian/patches/find_configure_libs.patch
index 09b05d4..9feab6f 100644
--- a/debian/patches/find_configure_libs.patch
+++ b/debian/patches/find_configure_libs.patch
@@ -2,33 +2,14 @@ Author: Andreas Tille <tille at debian.org>
 Last-Changed: Mon, 02 Feb 2015 22:00:07 +0100
 Description: Help configure finding Debian packaged libraries
 
---- a/konfigure.perl
-+++ b/konfigure.perl
-@@ -997,7 +997,7 @@ sub find_lib {
-         my ($library, $log);
- 
-         if ($n eq 'hdf5') {
+--- a/setup/konfigure.perl
++++ b/setup/konfigure.perl
+@@ -1442,7 +1442,7 @@ sub check_compiler {
+             $flags = $n;
+             $log = '                      int main() {                     }\n'
+         } elsif ($n eq 'hdf5') {
 -            $library = '-lhdf5';
 +            $library = '-lhdf5_serial';
-             $log = '#include <hdf5.h>            \n main() { H5close     (); }';
-         } elsif ($n eq 'xml2') {
-             $library = '-lxml2';
---- a/package.pm
-+++ b/package.pm
-@@ -9,7 +9,7 @@ sub PKG { ( LNG   => 'C',
-             OUT   => 'ncbi-outdir',
-             PATH  => '/usr/local/ncbi/sra-tools',
-             UPATH =>      '$HOME/ncbi/sra-tools', ) }
--sub DEPENDS      { ( { name => 'hdf5' , },
-+sub DEPENDS      { ( { name => 'hdf5' , Include => '/usr/include/hdf5/serial/'},
-                      { name => 'magic', Include => '/usr/include'        , },
-                      { name => 'xml2' , Include => '/usr/include/libxml2', } ) }
- sub REQ { (
-@@ -47,6 +47,6 @@ sub REQ { (
-               pkgpath => '/usr',
-               usrpath => '$HOME',
-               include => 'hdf5.h',
--              lib => 'libhdf5.a',
-+              lib => 'libhdf5_serial.a',
-         } ) }
- 1
+             $log = '#include <hdf5.h>  \n int main() { H5close         (); }\n'
+         } elsif ($n eq 'fuse') {
+             $flags = '-D_FILE_OFFSET_BITS=64';
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 2469346..b9832cd 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -8,7 +8,7 @@ Description: Propagate Debian hardening options into build system
 
 --- a/Makefile
 +++ b/Makefile
-@@ -115,11 +115,11 @@ $(RHOSTS):
+@@ -120,11 +120,11 @@ $(RHOSTS):
  	@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
  
  $(PASSTHRUS):
@@ -25,15 +25,15 @@ Description: Propagate Debian hardening options into build system
  
 --- a/build/Makefile.env
 +++ b/build/Makefile.env
-@@ -324,9 +324,9 @@ DLLX ?= $(SHLX)
- ARCHDEFS = -D_ARCH_BITS=$(BITS) -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)
+@@ -345,9 +345,9 @@ DLLX ?= $(SHLX)
+ ARCHDEFS = -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=$(LPFX) -DSHLIBEXT=$(DLLX)
  
  # default tool parameters
 -CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
 +CFLAGS	= $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS) $(DEB_CFLAGS)
  CPFLAGS = $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
--LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT)
-+LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(DEB_LDFLAGS)
+-LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
++LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS) $(DEB_LDFLAGS)
  
  #-------------------------------------------------------------------------------
  # runtests

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git