[med-svn] [sra-sdk] 05/13: Try to adapt patches to version 2.8.0
Andreas Tille
tille at debian.org
Fri Nov 25 18:19:07 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 b06c4081c27dc353ca170da77ebd8bdace522d95
Author: Andreas Tille <tille at debian.org>
Date: Fri Nov 25 14:07:31 2016 +0100
Try to adapt patches to version 2.8.0
---
debian/patches/10_portability.patch | 6 +-
debian/patches/absolute_vschema_path_in_test.patch | 16 --
debian/patches/do_not_link_statically.patch | 11 --
debian/patches/dont_use_static_lib.patch | 90 ----------
debian/patches/find_hdf5_serial.patch | 42 -----
debian/patches/find_ncbi-vdb.patch | 20 +--
debian/patches/find_ngs-sdk.patch | 14 +-
debian/patches/fix_tests.patch | 21 ---
debian/patches/hardening.patch | 9 +-
.../ignore_failing_tests_for_the_moment.patch | 72 --------
debian/patches/link_debian_packaged_libz.patch | 4 +-
debian/patches/link_debian_packaged_lmagic.patch | 15 --
debian/patches/series | 6 -
debian/patches/set_explicit_path_to_schemata.patch | 190 ---------------------
14 files changed, 26 insertions(+), 490 deletions(-)
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,$(HAS_RHOST))
endif
# determine BITS
diff --git a/debian/patches/absolute_vschema_path_in_test.patch b/debian/patches/absolute_vschema_path_in_test.patch
deleted file mode 100644
index af858ca..0000000
--- a/debian/patches/absolute_vschema_path_in_test.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 06 Jun 2016 11:24:46 +0200
-Description: We need to set absolute pathes also in the test
- (test fails anyway for different reasons and is excluded later)
-
---- a/test/vcf-loader/test-vcf-loader.cpp
-+++ b/test/vcf-loader/test-vcf-loader.cpp
-@@ -669,7 +669,7 @@ protected:
- const char VcfDatabaseFixture::schema_text[] =
- "version 1; "
-
--"include 'align/align.vschema';"
-+"include '/usr/lib/ncbi-vdb/align/align.vschema';"
-
- " table variant #1 { "
- " extern column U32 ref_id = .ref_id;"
diff --git a/debian/patches/do_not_link_statically.patch b/debian/patches/do_not_link_statically.patch
index 39b77f4..2e3cc02 100644
--- a/debian/patches/do_not_link_statically.patch
+++ b/debian/patches/do_not_link_statically.patch
@@ -13,14 +13,3 @@ Description: Do not link statically
LD_DYNAMIC="-Wl,-Bdynamic"
LD_ALL_SYMBOLS="-Wl,-whole-archive"
LD_REF_SYMBOLS="-Wl,-no-whole-archive"
---- a/build/ld.linux.exe.sh
-+++ b/build/ld.linux.exe.sh
-@@ -304,7 +304,7 @@ then
- XMLLIBDIR="-L$(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/dont_use_static_lib.patch b/debian/patches/dont_use_static_lib.patch
deleted file mode 100644
index ccbd1e3..0000000
--- a/debian/patches/dont_use_static_lib.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 06 Jun 2016 11:24:46 +0200
-Description: Don't use static library
-
---- a/test/fuse/Makefile
-+++ b/test/fuse/Makefile
-@@ -52,7 +52,7 @@ REMOTE_FUSER_TEST_OBJ = \
- $(addsuffix .$(OBJX),$(REMOTE_FUSER_TEST_SRC))
-
- REMOTE_FUSER_TEST_LIB = \
-- -sncbi-vdb-static \
-+ -sncbi-vdb \
- -skapp
-
- $(TEST_BINDIR)/remote-fuser-test: $(REMOTE_FUSER_TEST_OBJ)
---- a/test/ngs-pileup/Makefile
-+++ b/test/ngs-pileup/Makefile
-@@ -52,7 +52,7 @@ TEST_NGS_PILEUP_OBJ = \
- TEST_NGS_PILEUP_LIB = \
- -sngs-c++ \
- -sncbi-ngs-c++ \
-- -sncbi-vdb-static \
-+ -sncbi-vdb \
- -skapp \
- -sktst \
-
---- a/tools/fastq-dump/Makefile
-+++ b/tools/fastq-dump/Makefile
-@@ -72,7 +72,7 @@ clean: stdclean
- DUMP_LIBS = \
- -lncbi-ngs-c++ \
- -lngs-c++ \
-- -lncbi-vdb-static \
-+ -lncbi-vdb \
- -lkapp \
- -stk-version
-
---- a/tools/ngs-pileup/Makefile
-+++ b/tools/ngs-pileup/Makefile
-@@ -72,7 +72,7 @@ NGS_PILEUP_OBJ = \
-
- NGS_PILEUP_LIBS = \
- -sncbi-ngs-c++ \
-- -sncbi-vdb-static \
-+ -sncbi-vdb \
- -sngs-c++ \
- -skapp \
- -stk-version \
---- a/tools/pileup-stats/Makefile
-+++ b/tools/pileup-stats/Makefile
-@@ -71,7 +71,7 @@ PILEUP_STATS_LIB = \
- -L$(NGS_LIBDIR) \
- -sgeneral-writer \
- -sncbi-ngs-c++ \
-- -sncbi-vdb-static \
-+ -sncbi-vdb \
- -sngs-c++ \
- -skapp \
- -stk-version \
---- a/tools/ref-variation/Makefile
-+++ b/tools/ref-variation/Makefile
-@@ -74,7 +74,7 @@ REF_VARIATION_OBJ = \
-
- REF_VARIATION_LIB = \
- -sncbi-ngs-c++ \
-- -sncbi-vdb-static \
-+ -sncbi-vdb \
- -sngs-c++ \
- -skapp \
- -stk-version \
-@@ -101,7 +101,7 @@ VAR_EXPAND_OBJ = \
-
- VAR_EXPAND_LIB = \
- -sncbi-ngs-c++ \
-- -sncbi-vdb-static \
-+ -sncbi-vdb \
- -sngs-c++ \
- -skapp \
- -stk-version \
---- a/tools/sra-seq-count/Makefile
-+++ b/tools/sra-seq-count/Makefile
-@@ -65,7 +65,7 @@ TOOL_LIBS = \
- -stk-version \
- -sncbi-ngs-c++ \
- -sngs-c++ \
-- -sncbi-vdb-static
-+ -sncbi-vdb
-
- #-------------------------------------------------------------------------------
- # fastq-dump
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/fix_tests.patch b/debian/patches/fix_tests.patch
deleted file mode 100644
index 096f79c..0000000
--- a/debian/patches/fix_tests.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 06 Jun 2016 11:24:46 +0200
-Description: ncbi is not installed in /root/ncbi so this test would fail ... skipping
- No idea at what place VDB_INCDIR is really used.
-
---- a/test/fastq-loader/Makefile
-+++ b/test/fastq-loader/Makefile
-@@ -89,11 +89,11 @@ tfl:
- runtests: set_schema smalltests
-
- set_schema: $(BINDIR)/vdb-config
-- find $(HOME)/ncbi -size +9999c -exec ls -l {} \; | sort -nk5 | tail
-+ # find $(HOME)/ncbi -size +9999c -exec ls -l {} \; | sort -nk5 | tail
- echo HOST=`hostname`
- echo OS=$(OS)
- echo USER=$(USER)
-- $(BINDIR)/vdb-config -s vdb/schema/paths="$(VDB_INCDIR)"
-+ echo Fails for user root/superuser: $(BINDIR)/vdb-config -s vdb/schema/paths="$(VDB_INCDIR)"
-
- SMALLRUN = @ $(SRCDIR)/runtestcase.sh $(BINDIR) $(SRCDIR)
- smalltests: $(TEST_TOOLS)
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/ignore_failing_tests_for_the_moment.patch b/debian/patches/ignore_failing_tests_for_the_moment.patch
deleted file mode 100644
index e32e149..0000000
--- a/debian/patches/ignore_failing_tests_for_the_moment.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 06 Jun 2016 11:24:46 +0200
-Description: Exclude failing tests
-
---- a/test/fastq-loader/Makefile
-+++ b/test/fastq-loader/Makefile
-@@ -106,7 +106,7 @@ smalltests: $(TEST_TOOLS)
- # 1.2 phred 64
- $(SMALLRUN) 1.2 0 $(SRCDIR)/input/1.2.fastq --quality PHRED_64
- # 1.3 phred 33, decimal qualities
-- $(SMALLRUN) 1.3 3 $(SRCDIR)/input/1.3.fastq --quality PHRED_33
-+ # $(SMALLRUN) 1.3 3 $(SRCDIR)/input/1.3.fastq --quality PHRED_33
- # 1.4 logodds 64
- $(SMALLRUN) 1.4 0 $(SRCDIR)/input/1.4.fastq --quality LOGODDS
- #
-@@ -133,9 +133,9 @@ smalltests: $(TEST_TOOLS)
- # 2.8.1 handling of N in reads, ALTREAD is a physical column
- $(SMALLRUN) 2.8.1 0 $(SRCDIR)/input/2.8.1.fastq --quality PHRED_33
- # 2.9 mismatching length of sequence and quality (qualities shorter)
-- $(SMALLRUN) 2.9 3 $(SRCDIR)/input/2.9.fastq --quality PHRED_33
-+ # $(SMALLRUN) 2.9 3 $(SRCDIR)/input/2.9.fastq --quality PHRED_33
- # 2.9.1 mismatching length of sequence and quality (qualities longer)
-- $(SMALLRUN) 2.9.1 3 $(SRCDIR)/input/2.9.1.fastq --quality PHRED_33
-+ # $(SMALLRUN) 2.9.1 3 $(SRCDIR)/input/2.9.1.fastq --quality PHRED_33
- #
- # Multiple files
- # 3.1 reads+qualities together
-@@ -155,19 +155,19 @@ smalltests: $(TEST_TOOLS)
- # 4.3 --cache-size handled correctly
- @echo "running 4.3"; export LD_LIBRARY_PATH=$(LIBDIR);$(BINDIR)/latf-load $(SRCDIR)/input/4.fastq --cache-size 10 -v -o actual/4.1.obj --quality PHRED_33 | grep "Cache size: 10M" >/dev/null
- # 4.3.1 --cache-size rejected if invalid
-- $(SMALLRUN) 4.3.1 3 $(SRCDIR)/input/4.fastq --cache-size BIG --quality PHRED_33
-+ # $(SMALLRUN) 4.3.1 3 $(SRCDIR)/input/4.fastq --cache-size BIG --quality PHRED_33
- # 4.4 --max-rec-count stops at the specified record #
- $(SMALLRUN) 4.4 0 $(SRCDIR)/input/4.4.fastq --max-rec-count 3 --quality PHRED_33
- # 4.5 --max-err-count stops after the specified # of errors
-- $(SMALLRUN) 4.5 3 $(SRCDIR)/input/4.5.fastq --max-err-count 2 --quality PHRED_33
-+ # $(SMALLRUN) 4.5 3 $(SRCDIR)/input/4.5.fastq --max-err-count 2 --quality PHRED_33
- # 4.5.1 --max-err-pct fails if % of error records is too high
-- $(SMALLRUN) 4.5.1 3 $(SRCDIR)/input/4.5.1.fastq --quality PHRED_33 --max-err-count 10 --max-err-pct 20
-+ # $(SMALLRUN) 4.5.1 3 $(SRCDIR)/input/4.5.1.fastq --quality PHRED_33 --max-err-count 10 --max-err-pct 20
- # 4.6 --platform saves correct value in the PLATFORM column
- $(SMALLRUN) 4.6 0 $(SRCDIR)/input/4.fastq -p LS454 --quality PHRED_33
- # 4.6.1 --platform rejects invalid values
-- $(SMALLRUN) 4.6.1 3 $(SRCDIR)/input/4.fastq -p SOMETHINGELSE --quality PHRED_33
-+ # $(SMALLRUN) 4.6.1 3 $(SRCDIR)/input/4.fastq -p SOMETHINGELSE --quality PHRED_33
- # 4.7 input file missing
-- $(SMALLRUN) 4.7 3 $(SRCDIR)/input/not_there --quality PHRED_33
-+ # $(SMALLRUN) 4.7 3 $(SRCDIR)/input/not_there --quality PHRED_33
- # Gzipped input
- $(SMALLRUN) 5.0 0 $(SRCDIR)/input/5.0.fastq.gz --quality PHRED_33
- # Misparsed quality
-@@ -179,7 +179,7 @@ smalltests: $(TEST_TOOLS)
- # secondary read numbers other than 3
- $(SMALLRUN) 8.0 0 $(SRCDIR)/input/8.0.fastq --quality PHRED_33
- # reject inconsistent secondary read numbers
-- $(SMALLRUN) 8.1 3 $(SRCDIR)/input/8.1.fastq --quality PHRED_33
-+ # $(SMALLRUN) 8.1 3 $(SRCDIR)/input/8.1.fastq --quality PHRED_33
- # newest Illumina tag line variation ("_" instead of " /")
- $(SMALLRUN) 9.0 0 $(SRCDIR)/input/9.0.fastq --quality PHRED_33
- # accepting ascii quality values up to 126
---- a/test/Makefile
-+++ b/test/Makefile
-@@ -36,7 +36,7 @@ include $(TOP)/build/Makefile.config
- #
- SUBDIRS = \
- fastq-loader \
-- vcf-loader \
-+ # vcf-loader \
- kget \
- general-loader \
- vschema \
diff --git a/debian/patches/link_debian_packaged_libz.patch b/debian/patches/link_debian_packaged_libz.patch
index 88f2d41..8589410 100644
--- a/debian/patches/link_debian_packaged_libz.patch
+++ b/debian/patches/link_debian_packaged_libz.patch
@@ -5,8 +5,8 @@ Description: Since libncbi-vdb is dynamically linked against zlib and libbz2
--- a/build/ld.linux.exe.sh
+++ b/build/ld.linux.exe.sh
-@@ -319,6 +319,9 @@ then
- CMD="$CMD -Wl,-Bdynamic -lm"
+@@ -300,6 +300,9 @@ then
+ CMD="$CMD -lm"
fi
+echo "+++++++++++++++++++++++++ adding zlib +++++++++++++++++++++++++++++++++++++++"
diff --git a/debian/patches/link_debian_packaged_lmagic.patch b/debian/patches/link_debian_packaged_lmagic.patch
deleted file mode 100644
index e0b7e15..0000000
--- a/debian/patches/link_debian_packaged_lmagic.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-LastChanged: Thu, 21 Jul 2016 14:19:27 +0200
-Description: link against Debian packages libmagic
-
---- a/tools/copycat/Makefile
-+++ b/tools/copycat/Makefile
-@@ -92,7 +92,7 @@ COPYCAT_LIB = \
- -stk-version \
- -sncbi-vdb \
- -skff \
-- -smagic-static
-+ -smagic
-
-
- $(BINDIR)/copycat: $(COPYCAT_OBJ)
diff --git a/debian/patches/series b/debian/patches/series
index 857d5a5..e2a8a93 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,10 +5,4 @@ find_hdf5_serial.patch
find_ngs-sdk.patch
find_ncbi-vdb.patch
link_debian_packaged_libz.patch
-link_debian_packaged_lmagic.patch
-dont_use_static_lib.patch
-fix_tests.patch
-set_explicit_path_to_schemata.patch
-absolute_vschema_path_in_test.patch
-ignore_failing_tests_for_the_moment.patch
do_not_link_statically.patch
diff --git a/debian/patches/set_explicit_path_to_schemata.patch b/debian/patches/set_explicit_path_to_schemata.patch
deleted file mode 100644
index cd93661..0000000
--- a/debian/patches/set_explicit_path_to_schemata.patch
+++ /dev/null
@@ -1,190 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 06 Jun 2016 11:24:46 +0200
-Description: In Debian */*.vschema is installed to /usr/lib/ncbi-vdb/
-
---- a/test/fastq-loader/test-fastq-loader.cpp
-+++ b/test/fastq-loader/test-fastq-loader.cpp
-@@ -146,7 +146,7 @@ public:
- string dbName;
- };
- const string TempFileFixture::TempDir = "./tmp";
--const string TempFileFixture::SchemaPath = "align/align.vschema";
-+const string TempFileFixture::SchemaPath = "/usr/lib/ncbi-vdb/align/align.vschema";
- const string TempFileFixture::DbType = "NCBI:align:db:alignment_unsorted";
-
- ///////////////////////////////////////////////// FASTQ-based tests for CommonWriter
---- a/test/general-loader/test-general-loader.cpp
-+++ b/test/general-loader/test-general-loader.cpp
-@@ -488,7 +488,7 @@ FIXTURE_TEST_CASE ( BadSchemaFileName_Lo
-
- FIXTURE_TEST_CASE ( BadSchemaName, GeneralLoaderFixture )
- {
-- SetUpStream ( GetName(), "align/align.vschema", "bad schema name" );
-+ SetUpStream ( GetName(), "/usr/lib/ncbi-vdb/align/align.vschema", "bad schema name" );
- m_source . OpenStreamEvent();
-
- REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) );
-@@ -496,7 +496,7 @@ FIXTURE_TEST_CASE ( BadSchemaName, Gener
-
- FIXTURE_TEST_CASE ( BadSchemaName_Long, GeneralLoaderFixture )
- {
-- SetUpStream ( GetName(), "align/align.vschema", string ( GeneralLoader :: MaxPackedString + 1, 'x' ) );
-+ SetUpStream ( GetName(), "/usr/lib/ncbi-vdb/align/align.vschema", string ( GeneralLoader :: MaxPackedString + 1, 'x' ) );
- m_source . OpenStreamEvent();
-
- REQUIRE ( Run ( m_source . MakeSource (), SILENT_RC ( rcVDB, rcMgr, rcCreating, rcSchema, rcNotFound ) ) );
---- a/test/general-loader/makeinputs.cpp
-+++ b/test/general-loader/makeinputs.cpp
-@@ -69,7 +69,7 @@ OneTableOneColumnWithDefaults( const str
- TestSource source;
- TestSource::packed = p_packed;
-
-- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
- source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-
- source . NewTableEvent ( 1, tableName );
-@@ -104,7 +104,7 @@ ErrorMessage( const string& p_caseId, bo
- TestSource source;
- TestSource::packed = p_packed;
-
-- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
- source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-
- source . NewTableEvent ( 1, tableName );
-@@ -123,7 +123,7 @@ EmptyDefaultValue( const string& p_caseI
- TestSource source;
- TestSource::packed = p_packed;
-
-- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
- source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-
- source . NewTableEvent ( 1, tableName );
-@@ -143,7 +143,7 @@ MoveAhead( const string& p_caseId, bool
- TestSource source;
- TestSource::packed = p_packed;
-
-- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
- source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-
- source . NewTableEvent ( 1, tableName );
-@@ -172,7 +172,7 @@ IntegerCompression( const string& p_case
- TestSource source;
- TestSource::packed = true;
-
-- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
- source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-
- source . NewTableEvent ( 1, tableName );
-@@ -194,7 +194,7 @@ SoftwareIdString( const string& p_caseId
- TestSource source;
- TestSource::packed = true;
-
-- source . SchemaEvent ( "align/align.vschema", "NCBI:align:db:alignment_sorted" );
-+ source . SchemaEvent ( "/usr/lib/ncbi-vdb/align/align.vschema", "NCBI:align:db:alignment_sorted" );
- source . DatabaseEvent ( DatabasePath ( p_caseId, p_packed ) );
-
- source . SoftwareNameEvent ( string ( "some software" ), string ( "9.8.7654" ) );
---- a/tools/fastq-loader/fastq-loader.c
-+++ b/tools/fastq-loader/fastq-loader.c
-@@ -253,7 +253,7 @@ rc_t CC Usage (const Args * args)
-
- /* MARK: Definitions and Globals */
-
--#define SCHEMAFILE "align/align.vschema"
-+#define SCHEMAFILE "/usr/lib/ncbi-vdb/align/align.vschema"
-
- CommonWriterSettings G;
-
---- a/tools/bam-loader/bam-loader.c
-+++ b/tools/bam-loader/bam-loader.c
-@@ -553,7 +553,7 @@ rc_t CC Usage (const Args * args)
-
- /* MARK: Definitions and Globals */
-
--#define SCHEMAFILE "align/align.vschema"
-+#define SCHEMAFILE "/usr/lib/ncbi-vdb/align/align.vschema"
-
- Globals G;
-
---- a/tools/sra-sort/run.c
-+++ b/tools/sra-sort/run.c
-@@ -78,7 +78,7 @@ bool map_typename_builtin ( const ctx_t
-
- #define ALIGN_EVIDENCE_MAP "NCBI:align:db:alignment_evidence_sorted"
- #define ALIGN_UNSORTED_MAP "NCBI:align:db:alignment_sorted"
--#define ALIGN_SRC "align/align.vschema"
-+#define ALIGN_SRC "/usr/lib/ncbi-vdb/align/align.vschema"
-
- if ( strcmp ( out, "NCBI/align/db/alignment_evidence" ) == 0 )
- copied = string_copy ( out, size, ALIGN_EVIDENCE_MAP, sizeof ALIGN_EVIDENCE_MAP - 1 );
---- a/tools/cg-load/cg-load.c
-+++ b/tools/cg-load/cg-load.c
-@@ -1073,7 +1073,7 @@ rc_t CC KMain( int argc, char* argv[] )
- const XMLLogger* xml_logger = NULL;
- SParam params;
- memset(¶ms, 0, sizeof(params));
-- params.schema = "align/align.vschema";
-+ params.schema = "/usr/lib/ncbi-vdb/align/align.vschema";
-
- params.argv0 = argv[0];
-
---- a/tools/util/sortreadtest.c
-+++ b/tools/util/sortreadtest.c
-@@ -21,11 +21,11 @@
-
- /*
-
-- default file is "ncbi/seq.vschema"
-+ default file is "/usr/lib/ncbi-vdb/ncbi/seq.vschema"
- default table-spec "NCBI:tbl:base_space#2"
-
- */
--#define SCHEMASPEC "ncbi/seq.vschema"
-+#define SCHEMASPEC "/usr/lib/ncbi-vdb/ncbi/seq.vschema"
- #define TYPESPEC "NCBI:tbl:base_space#2"
-
- const char UsageDefaultName[] = "sortreadtest";
---- a/tools/vdb-copy/vdb-copy.kfg
-+++ b/tools/vdb-copy/vdb-copy.kfg
-@@ -25,11 +25,11 @@
- # matching legacy-tables with schema's to write to for vdb-copy
-
- # ILLUMINA
--/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/schema = "sra/illumina.vschema"
-+/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/schema = "/usr/lib/ncbi-vdb/sra/illumina.vschema"
- #/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:q4:v2"
- #/VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:q1:v2"
- /VDBCOPY/NCBI_SRA_Illumina_tbl_v0a_1/tab = "NCBI:SRA:Illumina:tbl:phred:v2"
--/VDBCOPY/_ILLUMINA_/schema = "sra/illumina.vschema"
-+/VDBCOPY/_ILLUMINA_/schema = "/usr/lib/ncbi-vdb/sra/illumina.vschema"
- /VDBCOPY/_ILLUMINA_/tab = "NCBI:SRA:Illumina:tbl:phred:v2"
-
-
-@@ -41,9 +41,9 @@
-
-
- # ABSOLID
--/VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/schema = "sra/abi.vschema"
-+/VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/schema = "/usr/lib/ncbi-vdb/sra/abi.vschema"
- /VDBCOPY/NCBI_SRA_ABI_tbl_v1_1/tab = "NCBI:SRA:ABI:tbl:v2"
--/VDBCOPY/_ABSOLID_/schema = "sra/abi.vschema"
-+/VDBCOPY/_ABSOLID_/schema = "/usr/lib/ncbi-vdb/sra/abi.vschema"
- /VDBCOPY/_ABSOLID_/tab = "NCBI:SRA:ABI:tbl:v2"
-
-
---- a/tools/pacbio-load/pl-context.h
-+++ b/tools/pacbio-load/pl-context.h
-@@ -52,7 +52,7 @@ extern "C" {
- #define ALIAS_WITH_PROGRESS "p"
- #define ALIAS_OUTPUT "o"
-
--#define DFLT_SCHEMA "sra/pacbio.vschema"
-+#define DFLT_SCHEMA "/usr/lib/ncbi-vdb/sra/pacbio.vschema"
- #define PACBIO_SCHEMA_DB "NCBI:SRA:PacBio:smrt:db"
-
-
--
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