[med-svn] [sra-sdk] 06/06: New upstream version
Andreas Tille
tille at debian.org
Thu Jul 21 15:51:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit 33d2462f21418defb805a622ac183c7808359f9d
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 21 17:26:35 2016 +0200
New upstream version
---
debian/changelog | 2 +-
debian/patches/10_portability.patch | 6 +++---
debian/patches/find_configure_libs.patch | 2 +-
debian/patches/find_hdf5_serial.patch | 2 +-
debian/patches/find_ncbi-vdb.patch | 20 ++------------------
debian/patches/find_ngs-sdk.patch | 19 +++++--------------
debian/patches/hardening.patch | 9 +++++----
debian/patches/link_debian_packaged_libz.patch | 4 ++--
8 files changed, 20 insertions(+), 44 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 6cfe65b..8d3f3d1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-sra-sdk (2.6.3-1) UNRELEASED; urgency=medium
+sra-sdk (2.7.0-1) UNRELEASED; urgency=medium
TODO: packaging of https://github.com/ncbi/ncbi-vdb
diff --git a/debian/patches/10_portability.patch b/debian/patches/10_portability.patch
index 9b5bc56..1430620 100644
--- a/debian/patches/10_portability.patch
+++ b/debian/patches/10_portability.patch
@@ -13,7 +13,7 @@ Description: Drop redundant -m32/-m64 option to enable build
ifeq (Darwin, $(UNAME))
HOST_OS = mac
endif
-@@ -51,12 +52,17 @@ endif
+@@ -46,12 +47,17 @@ endif
ifeq (xMINGW, $(findstring xMINGW,x$(UNAME)))
HOST_OS = win
endif
@@ -31,7 +31,7 @@ Description: Drop redundant -m32/-m64 option to enable build
ARCHITECTURES = default
ifeq (mac,$(HOST_OS))
HOST_ARCH = $(shell $(TOP)/build/mac.arch.sh)
-@@ -104,6 +110,10 @@ else
+@@ -92,6 +98,10 @@ else
ARCHITECTURES = sparc64 sparc32
endif
endif
@@ -42,7 +42,7 @@ Description: Drop redundant -m32/-m64 option to enable build
ARCH = $(HOST_ARCH)
REMOTE_ARCH = $(ARCH)
-@@ -173,16 +183,4 @@ ifeq (yes,$(HAS_RHOST))
+@@ -161,16 +171,4 @@ ifeq (yes,$(HAS_RHOST))
endif
# determine BITS
diff --git a/debian/patches/find_configure_libs.patch b/debian/patches/find_configure_libs.patch
index 3d345c8..423bcb4 100644
--- a/debian/patches/find_configure_libs.patch
+++ b/debian/patches/find_configure_libs.patch
@@ -4,7 +4,7 @@ Description: Help configure finding Debian packaged libraries
--- a/setup/konfigure.perl
+++ b/setup/konfigure.perl
-@@ -1481,7 +1481,7 @@ sub check_compiler {
+@@ -1484,7 +1484,7 @@ sub check_compiler {
$flags = $n;
$log = ' int main() { }\n'
} elsif ($n eq 'hdf5') {
diff --git a/debian/patches/find_hdf5_serial.patch b/debian/patches/find_hdf5_serial.patch
index f59c34d..d9f1c35 100644
--- a/debian/patches/find_hdf5_serial.patch
+++ b/debian/patches/find_hdf5_serial.patch
@@ -1,6 +1,6 @@
--- a/setup/konfigure.perl
+++ b/setup/konfigure.perl
-@@ -1482,7 +1482,7 @@ sub check_compiler {
+@@ -1485,7 +1485,7 @@ sub check_compiler {
$log = ' int main() { }\n'
} elsif ($n eq 'hdf5') {
$library = '-lhdf5_serial';
diff --git a/debian/patches/find_ncbi-vdb.patch b/debian/patches/find_ncbi-vdb.patch
index e2a132e..ab27d40 100644
--- a/debian/patches/find_ncbi-vdb.patch
+++ b/debian/patches/find_ncbi-vdb.patch
@@ -1,22 +1,6 @@
---- a/setup/package.prl
-+++ b/setup/package.prl
-@@ -34,10 +34,10 @@ sub REQ { (
- boption => 'with-ncbi-vdb-build',
- origin => 'I',
- type => 'SB',
-- srcpath => '../ncbi-vdb',
-- pkgpath => '/usr/local/ncbi/ncbi-vdb',
-+ srcpath => '/usr/include',
-+ pkgpath => '/usr',
- usrpath => '$HOME/ncbi/ncbi-vdb',
-- bldpath => '$HOME/ncbi-outdir/ncbi-vdb',
-+ bldpath => '/usr',
- locbldpath=>'$Bin/../../OUTDIR/ncbi-vdb',
- include => 'klib/rc.h',
- lib => 'libncbi-vdb.a',
--- a/setup/konfigure.perl
+++ b/setup/konfigure.perl
-@@ -1305,6 +1305,9 @@ sub find_in_dir {
+@@ -1301,6 +1301,9 @@ sub find_in_dir {
} elsif (-e "$dir/interfaces/$include") {
println $dir unless ($AUTORUN);
$found_inc = "$dir/interfaces";
@@ -26,7 +10,7 @@
} else {
print "$dir: " if ($OPT{'debug'});
println 'no' unless ($AUTORUN);
-@@ -1318,7 +1321,7 @@ sub find_in_dir {
+@@ -1313,7 +1316,7 @@ sub find_in_dir {
my $buildarch = `dpkg-architecture -qDEB_BUILD_MULTIARCH`;
chomp $buildarch;
my $libdir = File::Spec->catdir($dir, 'lib', $buildarch);
diff --git a/debian/patches/find_ngs-sdk.patch b/debian/patches/find_ngs-sdk.patch
index c0b2199..5d770c8 100644
--- a/debian/patches/find_ngs-sdk.patch
+++ b/debian/patches/find_ngs-sdk.patch
@@ -1,6 +1,6 @@
--- a/setup/konfigure.perl
+++ b/setup/konfigure.perl
-@@ -439,6 +439,7 @@ if ($TOOLS =~ /gcc$/) {
+@@ -435,6 +435,7 @@ if ($TOOLS =~ /gcc$/) {
my @dependencies;
@@ -8,7 +8,7 @@
my %DEPEND_OPTIONS;
foreach my $href (DEPENDS()) {
$_ = $href->{name};
-@@ -936,7 +937,7 @@ EndText
+@@ -931,7 +932,7 @@ EndText
if ($PKG{LNG} eq 'JAVA') {
L($F,
@@ -17,7 +17,7 @@
}
print $F <<EndText;
-@@ -1314,7 +1315,9 @@ sub find_in_dir {
+@@ -1309,7 +1310,9 @@ sub find_in_dir {
print "\tlibraries... " unless ($AUTORUN);
if ($lib) {
my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);
@@ -30,19 +30,10 @@
print "\n\t\tchecking $f\n\t" if ($OPT{'debug'});
--- a/setup/package.prl
+++ b/setup/package.prl
-@@ -8,7 +8,7 @@ sub CONFIG_OUT { 'build' }
- sub PKG { ( LNG => 'C',
- OUT => 'ncbi-outdir',
- LOCOUT=> '../../OUTDIR',
-- PATH => '/usr/local/ncbi/sra-tools',
-+ PATH => '/usr/bin/sra-tools',
- UPATH => '$HOME/ncbi/sra-tools', ) }
- sub DEPENDS { ( { name => 'fuse' , Include => '/usr/include' , },
- { name => 'hdf5' , Include => '/usr/include' , },
-@@ -20,7 +20,7 @@ sub REQ { (
+@@ -17,7 +17,7 @@ sub REQ { ( { name => 'ngs-sdk',
option => 'with-ngs-sdk-prefix',
origin => 'I',
- type => 'L',
+ type => 'IDQ',
- srcpath => '../ngs/ngs-sdk',
+ srcpath => '/usr/include',
pkgpath => '/usr/local/ngs/ngs-sdk',
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 54ab6c5..1bdd0b3 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
-@@ -154,11 +154,11 @@ $(RHOSTS):
+@@ -127,11 +127,11 @@ $(RHOSTS):
@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
$(PASSTHRUS):
@@ -25,15 +25,16 @@ Description: Propagate Debian hardening options into build system
--- a/build/Makefile.env
+++ b/build/Makefile.env
-@@ -345,9 +345,9 @@ DLLX ?= $(SHLX)
+@@ -330,10 +330,10 @@ 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) $(LDPATHS)
-+LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS) $(DEB_LDFLAGS)
+ # some LDFLAGS may have been specified in $(CONFIG_FILE)
+-LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT)
++LDFLAGS += $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(DEB_LDFLAGS)
#-------------------------------------------------------------------------------
# runtests
diff --git a/debian/patches/link_debian_packaged_libz.patch b/debian/patches/link_debian_packaged_libz.patch
index 95e6a6b..5f56663 100644
--- a/debian/patches/link_debian_packaged_libz.patch
+++ b/debian/patches/link_debian_packaged_libz.patch
@@ -5,8 +5,8 @@ Description: Since libncbi-vdb is dynamically linked against zlib and libbz2
--- a/build/ld.linux.exe.sh
+++ b/build/ld.linux.exe.sh
-@@ -319,6 +319,9 @@ then
- CMD="$CMD -Wl,-Bdynamic -lm"
+@@ -300,6 +300,9 @@ then
+ CMD="$CMD -lm"
fi
+echo "+++++++++++++++++++++++++ adding zlib +++++++++++++++++++++++++++++++++++++++"
--
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