[med-svn] [sra-sdk] 01/04: Try to apply patches for new upstream version (not working yet)
Andreas Tille
tille at debian.org
Tue Jan 10 15:30:05 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit 67dbdf6f8a46b4025ed16af8ae0d2c850d0ac74b
Author: Andreas Tille <tille at debian.org>
Date: Tue Jan 10 16:26:05 2017 +0100
Try to apply patches for new upstream version (not working yet)
---
debian/control | 2 +-
debian/patches/10_portability.patch | 6 ++--
debian/patches/do_not_link_statically.patch | 11 -------
debian/patches/find_hdf5_serial.patch | 42 --------------------------
debian/patches/find_ncbi-vdb.patch | 20 ++++++------
debian/patches/find_ngs-sdk.patch | 14 ++++-----
debian/patches/hardening.patch | 9 +++---
debian/patches/link_debian_packaged_libz.patch | 4 +--
8 files changed, 27 insertions(+), 81 deletions(-)
diff --git a/debian/control b/debian/control
index 75c0b3c..7972a83 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
libngs-sdk-dev (>= 1.2.4),
- libncbi-vdb-dev (>= 2.7.0+dfsg-4)
+ libncbi-vdb-dev (>= 2.8.0+dfsg-1)
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sra-sdk.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/sra-sdk.git
diff --git a/debian/patches/10_portability.patch b/debian/patches/10_portability.patch
index 84dd9b3..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)
-@@ -105,6 +111,10 @@ 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 = $(ARCH)
-@@ -174,16 +184,4 @@ ifeq (yes,$(HAS_RHOST))
+@@ -161,16 +171,4 @@ ifeq (yes,$(HAS_RHOST))
endif
# determine BITS
diff --git a/debian/patches/do_not_link_statically.patch b/debian/patches/do_not_link_statically.patch
index 39b77f4..2e3cc02 100644
--- a/debian/patches/do_not_link_statically.patch
+++ b/debian/patches/do_not_link_statically.patch
@@ -13,14 +13,3 @@ Description: Do not link statically
LD_DYNAMIC="-Wl,-Bdynamic"
LD_ALL_SYMBOLS="-Wl,-whole-archive"
LD_REF_SYMBOLS="-Wl,-no-whole-archive"
---- a/build/ld.linux.exe.sh
-+++ b/build/ld.linux.exe.sh
-@@ -304,7 +304,7 @@ then
- XMLLIBDIR="-L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')"
- else
- ##### Link libxml2 statically on all linux-es except Ubuntu
-- XMLLIBDIR="-Wl,-Bstatic -L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')"
-+ XMLLIBDIR="-L$(grep XML2_LIBDIR ${BUILD_DIR}/Makefile.config.linux.$ARCH | perl -e'while(<>){if(/XML2_LIBDIR = (.+)/){print $1}}')"
- fi
- fi
- if [ $HAVE_XML -ne 0 ]
diff --git a/debian/patches/find_hdf5_serial.patch b/debian/patches/find_hdf5_serial.patch
index 04f21e8..eefb304 100644
--- a/debian/patches/find_hdf5_serial.patch
+++ b/debian/patches/find_hdf5_serial.patch
@@ -13,45 +13,3 @@ Description: Debian has several flavours of hdf5 - use serial here
} elsif ($n eq 'fuse') {
$flags = '-D_FILE_OFFSET_BITS=64';
$library = '-lfuse';
---- a/tools/pacbio-load/Makefile
-+++ b/tools/pacbio-load/Makefile
-@@ -105,7 +105,7 @@ PACBIO_LOAD_LIB = \
- -stk-version \
- -skdf5 \
- -sload \
-- -shdf5 \
-+ -shdf5_serial \
- -sncbi-wvdb \
- -sm \
-
---- a/test/general-loader/Makefile
-+++ b/test/general-loader/Makefile
-@@ -58,7 +58,7 @@ TEST_GEN_LOAD_OBJ = \
- $(addsuffix .$(OBJX),$(TEST_GEN_LOAD_SRC))
-
- TEST_GEN_LOAD_LIB = \
-- -sncbi-wvdb-static \
-+ -sncbi-wvdb \
- -sload \
- -skapp \
- -sktst \
-@@ -121,7 +121,7 @@ setup:
-
- $(TEST_BINDIR)/makeinputs: makeinputs.cpp
- @# generate numbered input streams for tool tests
-- $(CXX) makeinputs.cpp testsource.cpp -o $(TEST_BINDIR)/makeinputs -I$(INCDIRS) -L$(VDB_LIBDIR) -lncbi-vdb-static
-+ $(CXX) makeinputs.cpp testsource.cpp -o $(TEST_BINDIR)/makeinputs -I$(INCDIRS) -L$(VDB_LIBDIR) -lncbi-vdb
-
- tool-tests: $(TEST_BINDIR)/makeinputs
- @mkdir -p input && $(TEST_BINDIR)/makeinputs && rm $(TEST_BINDIR)/makeinputs
---- a/tools/general-loader/Makefile
-+++ b/tools/general-loader/Makefile
-@@ -121,7 +121,7 @@ GEN_LOAD_OBJ = \
- $(addsuffix .$(OBJX),$(GEN_LOAD_SRC))
-
- GEN_LOAD_LIBS = \
-- -sncbi-wvdb-static \
-+ -sncbi-wvdb \
- -sload \
- -skapp \
- -stk-version \
diff --git a/debian/patches/find_ncbi-vdb.patch b/debian/patches/find_ncbi-vdb.patch
index a0c201e..c670dde 100644
--- a/debian/patches/find_ncbi-vdb.patch
+++ b/debian/patches/find_ncbi-vdb.patch
@@ -4,20 +4,18 @@ Description: Make sure libncbi-vdb will be found
--- a/setup/package.prl
+++ b/setup/package.prl
-@@ -33,10 +33,10 @@ sub REQ { (
- boption => 'with-ncbi-vdb-build',
+@@ -18,9 +18,9 @@ sub REQ { ( { name => 'ngs-sdk',
origin => 'I',
- type => 'SB',
-- srcpath => '../ncbi-vdb',
-- pkgpath => '/usr/local/ncbi/ncbi-vdb',
-+ srcpath => '/usr/include',
+ type => 'IDQ',
+ srcpath => '/usr/include',
+- pkgpath => '/usr/local/ngs/ngs-sdk',
+ pkgpath => '/usr',
- usrpath => '$HOME/ncbi/ncbi-vdb',
-- bldpath => '$HOME/ncbi-outdir/ncbi-vdb',
+ usrpath => '$HOME/ngs/ngs-sdk',
+- bldpath => '$HOME/ncbi-outdir/ngs-sdk',
+ bldpath => '/usr',
- locbldpath=>'$Bin/../../OUTDIR/ncbi-vdb',
- include => 'klib/rc.h',
- src => 'libs/kfg/default.kfg',
+ locbldpath=>'$Bin/../../OUTDIR/ngs-sdk',
+ include => 'ngs/itf/Refcount.h',
+ lib => 'libngs-sdk.$SHLX',
--- 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 708bdd5..ace0c82 100644
--- a/debian/patches/find_ngs-sdk.patch
+++ b/debian/patches/find_ngs-sdk.patch
@@ -38,15 +38,15 @@ Description: ngs-sdk header files are in /usr/include
sub PKG { ( LNG => 'C',
OUT => 'ncbi-outdir',
LOCOUT=> '../../OUTDIR',
-- PATH => '/usr/local/ncbi/sra-tools',
-+ PATH => '/usr/bin/sra-tools',
- UPATH => '$HOME/ncbi/sra-tools', ) }
- sub DEPENDS { ( { name => 'fuse' , Include => '/usr/include' , },
- { name => 'hdf5' , Include => '/usr/include' , },
-@@ -19,7 +19,7 @@ sub REQ { (
+- PATH => '/usr/local/ncbi/ncbi-vdb',
++ PATH => '/usr/lib/ncbi/ncbi-vdb',
+ UPATH => '$HOME/ncbi/ncbi-vdb', ) }
+ sub DEPENDS { ( { name => 'hdf5' , Include => '/usr/include' , },
+ { name => 'magic', Include => '/usr/include' , },
+@@ -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 f811c6f..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
-@@ -155,11 +155,11 @@ $(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
-@@ -350,9 +350,9 @@ 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) $(DEB_LDFLAGS)
#-------------------------------------------------------------------------------
# runtests
diff --git a/debian/patches/link_debian_packaged_libz.patch b/debian/patches/link_debian_packaged_libz.patch
index 88f2d41..8589410 100644
--- a/debian/patches/link_debian_packaged_libz.patch
+++ b/debian/patches/link_debian_packaged_libz.patch
@@ -5,8 +5,8 @@ Description: Since libncbi-vdb is dynamically linked against zlib and libbz2
--- a/build/ld.linux.exe.sh
+++ b/build/ld.linux.exe.sh
-@@ -319,6 +319,9 @@ then
- CMD="$CMD -Wl,-Bdynamic -lm"
+@@ -300,6 +300,9 @@ then
+ CMD="$CMD -lm"
fi
+echo "+++++++++++++++++++++++++ adding zlib +++++++++++++++++++++++++++++++++++++++"
--
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