[med-svn] [sra-sdk] 03/03: Finally sort out the issue where a wrong tarball (ncbi-vdb insetad of sra-sdk= was imported.
Andreas Tille
tille at debian.org
Fri Jul 22 13:24:05 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 ced7dafb02f45759a457628447df36143060da80
Author: Andreas Tille <tille at debian.org>
Date: Fri Jul 22 14:13:21 2016 +0200
Finally sort out the issue where a wrong tarball (ncbi-vdb insetad of sra-sdk= was imported.
---
debian/changelog | 2 +-
debian/patches/10_portability.patch | 6 ++--
debian/patches/find_ncbi-vdb.patch | 20 +++++++++---
debian/patches/find_ngs-sdk.patch | 17 ++++++----
debian/patches/hardening.patch | 9 +++---
debian/patches/lib_hdf5.patch | 44 --------------------------
debian/patches/link_debian_packaged_libz.patch | 14 ++------
debian/patches/series | 1 -
8 files changed, 37 insertions(+), 76 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 7df07fe..8d3f3d1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-sra-sdk (2.7.0+dfsg-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 1430620..84dd9b3 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
-@@ -46,12 +47,17 @@ endif
+@@ -51,12 +52,17 @@ 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)
-@@ -92,6 +98,10 @@ else
+@@ -105,6 +111,10 @@ else
ARCHITECTURES = sparc64 sparc32
endif
endif
@@ -42,7 +42,7 @@ Description: Drop redundant -m32/-m64 option to enable build
ARCH = $(HOST_ARCH)
REMOTE_ARCH = $(ARCH)
-@@ -161,16 +171,4 @@ ifeq (yes,$(HAS_RHOST))
+@@ -174,16 +184,4 @@ ifeq (yes,$(HAS_RHOST))
endif
# determine BITS
diff --git a/debian/patches/find_ncbi-vdb.patch b/debian/patches/find_ncbi-vdb.patch
index e3bf52b..74c249d 100644
--- a/debian/patches/find_ncbi-vdb.patch
+++ b/debian/patches/find_ncbi-vdb.patch
@@ -1,7 +1,19 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
-Description: Make sure ncbi-vdb will be found
-
+--- a/setup/package.prl
++++ b/setup/package.prl
+@@ -33,10 +33,10 @@ sub REQ { (
+ boption => 'with-ncbi-vdb-build',
+ origin => 'I',
+ type => 'SB',
+- srcpath => '../ncbi-vdb',
+- pkgpath => '/usr/local/ncbi/ncbi-vdb',
++ srcpath => '/usr/include',
++ pkgpath => '/usr',
+ usrpath => '$HOME/ncbi/ncbi-vdb',
+- bldpath => '$HOME/ncbi-outdir/ncbi-vdb',
++ bldpath => '/usr',
+ locbldpath=>'$Bin/../../OUTDIR/ncbi-vdb',
+ include => 'klib/rc.h',
+ src => 'libs/kfg/default.kfg',
--- a/setup/konfigure.perl
+++ b/setup/konfigure.perl
@@ -1301,6 +1301,9 @@ sub find_in_dir {
diff --git a/debian/patches/find_ngs-sdk.patch b/debian/patches/find_ngs-sdk.patch
index da5b0c5..2645695 100644
--- a/debian/patches/find_ngs-sdk.patch
+++ b/debian/patches/find_ngs-sdk.patch
@@ -1,7 +1,3 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
-Description: Make sure ngs-sdk will be found
-
--- a/setup/konfigure.perl
+++ b/setup/konfigure.perl
@@ -435,6 +435,7 @@ if ($TOOLS =~ /gcc$/) {
@@ -34,10 +30,19 @@ Description: Make sure ngs-sdk will be found
print "\n\t\tchecking $f\n\t" if ($OPT{'debug'});
--- a/setup/package.prl
+++ b/setup/package.prl
-@@ -17,7 +17,7 @@ sub REQ { ( { name => 'ngs-sdk',
+@@ -7,7 +7,7 @@ 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' , },
+@@ -19,7 +19,7 @@ sub REQ { (
option => 'with-ngs-sdk-prefix',
origin => 'I',
- type => 'IDQ',
+ type => 'L',
- 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 1bdd0b3..f811c6f 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
-@@ -127,11 +127,11 @@ $(RHOSTS):
+@@ -155,11 +155,11 @@ $(RHOSTS):
@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.env rebuild-dirlinks config
$(PASSTHRUS):
@@ -25,16 +25,15 @@ Description: Propagate Debian hardening options into build system
--- a/build/Makefile.env
+++ b/build/Makefile.env
-@@ -330,10 +330,10 @@ DLLX ?= $(SHLX)
+@@ -350,9 +350,9 @@ 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)
- # 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)
+-LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
++LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS) $(DEB_LDFLAGS)
#-------------------------------------------------------------------------------
# runtests
diff --git a/debian/patches/lib_hdf5.patch b/debian/patches/lib_hdf5.patch
deleted file mode 100644
index 9d84e52..0000000
--- a/debian/patches/lib_hdf5.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
-Description: Use hdf5_serial
-
---- a/libs/hdf5/hdf5arrayfile-priv.h
-+++ b/libs/hdf5/hdf5arrayfile-priv.h
-@@ -40,7 +40,7 @@ extern "C" {
- #endif
-
- #ifndef _HDF5_H
--#include <hdf5.h>
-+#include <hdf5/serial/hdf5.h>
- #endif
-
- /* object structure */
-@@ -76,4 +76,4 @@ struct HDF5ArrayFile
- }
- #endif
-
--#endif /* _h_hdf5arrayfile_priv_ */
-\ No newline at end of file
-+#endif /* _h_hdf5arrayfile_priv_ */
---- a/libs/hdf5/hdf5dir.c
-+++ b/libs/hdf5/hdf5dir.c
-@@ -32,7 +32,7 @@ typedef struct HDF5Dir HDF5Dir;
-
- #include <kfs/extern.h> /* may need to be changed */
- #include <kfs/impl.h>
--#include <hdf5.h>
-+#include <hdf5/serial/hdf5.h>
- #include <klib/rc.h>
- #include <klib/namelist.h>
- #include <klib/text.h>
---- a/libs/hdf5/Makefile
-+++ b/libs/hdf5/Makefile
-@@ -104,7 +104,7 @@ KDF5_OBJ = \
- $(addsuffix .$(LOBX),$(KDF5_SRC))
-
- KDF5_LIB = \
-- -lhdf5 \
-+ -lhdf5_serial \
- -lz \
-
- ifdef HDF5_LIBDIR
diff --git a/debian/patches/link_debian_packaged_libz.patch b/debian/patches/link_debian_packaged_libz.patch
index 726c9cf..95e6a6b 100644
--- a/debian/patches/link_debian_packaged_libz.patch
+++ b/debian/patches/link_debian_packaged_libz.patch
@@ -5,8 +5,8 @@ Description: Since libncbi-vdb is dynamically linked against zlib and libbz2
--- a/build/ld.linux.exe.sh
+++ b/build/ld.linux.exe.sh
-@@ -300,6 +300,9 @@ then
- CMD="$CMD -lm"
+@@ -319,6 +319,9 @@ then
+ CMD="$CMD -Wl,-Bdynamic -lm"
fi
+echo "+++++++++++++++++++++++++ adding zlib +++++++++++++++++++++++++++++++++++++++"
@@ -15,13 +15,3 @@ Description: Since libncbi-vdb is dynamically linked against zlib and libbz2
# produce shared library
echo $CMD
$CMD || exit $?
---- a/libs/Makefile
-+++ b/libs/Makefile
-@@ -35,7 +35,6 @@ include $(TOP)/build/Makefile.config
- # default
- #
- SUBDIRS = \
-- ext \
- kfc \
- klib \
- kproc \
diff --git a/debian/patches/series b/debian/patches/series
index 67022ca..1da8794 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,4 +5,3 @@ find_hdf5_serial.patch
find_ngs-sdk.patch
find_ncbi-vdb.patch
link_debian_packaged_libz.patch
-lib_hdf5.patch
--
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