[med-svn] [sra-sdk] 03/06: Adapt patches
Andreas Tille
tille at debian.org
Wed Jan 11 10:11:34 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 9abe735f2f86ab41eee5c4d74a150d0a92311304
Author: Andreas Tille <tille at debian.org>
Date: Wed Jan 11 08:02:35 2017 +0100
Adapt patches
---
debian/patches/10_portability.patch | 6 +--
debian/patches/dont_use_static_lib.patch | 20 -------
...enable_build_using_ncbi-vdb_version_2.8.0.patch | 39 --------------
debian/patches/find_configure_libs.patch | 2 +-
debian/patches/find_hdf5_serial.patch | 2 +-
debian/patches/find_ncbi-vdb.patch | 10 ++--
debian/patches/find_ngs-sdk.patch | 18 +++----
debian/patches/fix_tests.patch | 21 --------
debian/patches/hardening.patch | 9 ++--
.../ignore_failing_tests_for_the_moment.patch | 59 ++++++++++++++++----
debian/patches/link_debian_packaged_libz.patch | 4 +-
debian/patches/series | 2 -
debian/patches/set_explicit_path_to_schemata.patch | 63 +++++++++++++++-------
13 files changed, 117 insertions(+), 138 deletions(-)
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/dont_use_static_lib.patch b/debian/patches/dont_use_static_lib.patch
index ccbd1e3..c14e1da 100644
--- a/debian/patches/dont_use_static_lib.patch
+++ b/debian/patches/dont_use_static_lib.patch
@@ -57,26 +57,6 @@ Description: Don't use static library
-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 = \
diff --git a/debian/patches/enable_build_using_ncbi-vdb_version_2.8.0.patch b/debian/patches/enable_build_using_ncbi-vdb_version_2.8.0.patch
deleted file mode 100644
index 54b32a9..0000000
--- a/debian/patches/enable_build_using_ncbi-vdb_version_2.8.0.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-LastChanged: Fri, 25 Nov 2016 12:41:49 +0100
-Description: Enable build using ncbi-vdb version 2.8.0
-
---- a/tools/kget/kget.c
-+++ b/tools/kget/kget.c
-@@ -646,32 +646,6 @@ static rc_t check_cache_completeness( KD
-
- /* -------------------------------------------------------------------------------------------------------------------- */
-
--/* this is 'borrowed' from libs/kns/http-priv.h :
-- - this is a private header inside the source-directory
-- - without it KNSManagerMakeClientHttp( ... ) a public function cannot be used
-- ( or the user writes it's own URL-parsing )
--*/
--
--typedef enum
--{
-- st_NONE,
-- st_HTTP,
-- st_S3
--} SchemeType;
--
--typedef struct URLBlock URLBlock;
--struct URLBlock
--{
-- String scheme;
-- String host;
-- String path; /* Path includes any parameter portion */
-- String query;
-- String fragment;
--
-- uint32_t port;
--
-- SchemeType scheme_type;
--};
- extern void URLBlockInit ( URLBlock *self );
- extern rc_t ParseUrl ( URLBlock * b, const char * url, size_t url_size );
-
diff --git a/debian/patches/find_configure_libs.patch b/debian/patches/find_configure_libs.patch
index 423bcb4..4a53036 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
-@@ -1484,7 +1484,7 @@ sub check_compiler {
+@@ -1487,7 +1487,7 @@ 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 eefb304..401e18f 100644
--- a/debian/patches/find_hdf5_serial.patch
+++ b/debian/patches/find_hdf5_serial.patch
@@ -4,7 +4,7 @@ Description: Debian has several flavours of hdf5 - use serial here
--- a/setup/konfigure.perl
+++ b/setup/konfigure.perl
-@@ -1485,7 +1485,7 @@ sub check_compiler {
+@@ -1488,7 +1488,7 @@ sub check_compiler {
$log = ' int main() { }\n'
} elsif ($n eq 'hdf5') {
$library = '-lhdf5_serial';
diff --git a/debian/patches/find_ncbi-vdb.patch b/debian/patches/find_ncbi-vdb.patch
index c670dde..4dcd957 100644
--- a/debian/patches/find_ncbi-vdb.patch
+++ b/debian/patches/find_ncbi-vdb.patch
@@ -4,9 +4,9 @@ Description: Make sure libncbi-vdb will be found
--- a/setup/package.prl
+++ b/setup/package.prl
-@@ -18,9 +18,9 @@ sub REQ { ( { name => 'ngs-sdk',
+@@ -20,9 +20,9 @@ sub REQ { (
origin => 'I',
- type => 'IDQ',
+ type => 'L',
srcpath => '/usr/include',
- pkgpath => '/usr/local/ngs/ngs-sdk',
+ pkgpath => '/usr',
@@ -15,10 +15,10 @@ Description: Make sure libncbi-vdb will be found
+ bldpath => '/usr',
locbldpath=>'$Bin/../../OUTDIR/ngs-sdk',
include => 'ngs/itf/Refcount.h',
- lib => 'libngs-sdk.$SHLX',
+ lib => 'libngs-c++.a',
--- a/setup/konfigure.perl
+++ b/setup/konfigure.perl
-@@ -1301,6 +1301,9 @@ sub find_in_dir {
+@@ -1304,6 +1304,9 @@ sub find_in_dir {
} elsif (-e "$dir/interfaces/$include") {
println $dir unless ($AUTORUN);
$found_inc = "$dir/interfaces";
@@ -28,7 +28,7 @@ Description: Make sure libncbi-vdb will be found
} else {
print "$dir: " if ($OPT{'debug'});
println 'no' unless ($AUTORUN);
-@@ -1313,7 +1316,7 @@ sub find_in_dir {
+@@ -1316,7 +1319,7 @@ 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 ace0c82..8e6cf76 100644
--- a/debian/patches/find_ngs-sdk.patch
+++ b/debian/patches/find_ngs-sdk.patch
@@ -12,7 +12,7 @@ Description: ngs-sdk header files are in /usr/include
my %DEPEND_OPTIONS;
foreach my $href (DEPENDS()) {
$_ = $href->{name};
-@@ -931,7 +932,7 @@ EndText
+@@ -934,7 +935,7 @@ EndText
if ($PKG{LNG} eq 'JAVA') {
L($F,
@@ -21,7 +21,7 @@ Description: ngs-sdk header files are in /usr/include
}
print $F <<EndText;
-@@ -1309,7 +1310,9 @@ sub find_in_dir {
+@@ -1312,7 +1313,9 @@ sub find_in_dir {
print "\tlibraries... " unless ($AUTORUN);
if ($lib) {
my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);
@@ -38,15 +38,15 @@ Description: ngs-sdk header files are in /usr/include
sub PKG { ( LNG => 'C',
OUT => 'ncbi-outdir',
LOCOUT=> '../../OUTDIR',
-- PATH => '/usr/local/ncbi/ncbi-vdb',
-+ PATH => '/usr/lib/ncbi/ncbi-vdb',
- UPATH => '$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',
+- PATH => '/usr/local/ncbi/sra-tools',
++ PATH => '/usr/lib/ncbi/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/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 1bdd0b3..e50d00e 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)
+@@ -356,9 +356,9 @@ 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/ignore_failing_tests_for_the_moment.patch b/debian/patches/ignore_failing_tests_for_the_moment.patch
index e32e149..ba76818 100644
--- a/debian/patches/ignore_failing_tests_for_the_moment.patch
+++ b/debian/patches/ignore_failing_tests_for_the_moment.patch
@@ -4,16 +4,16 @@ 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
+@@ -104,7 +104,7 @@ 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)
+ #
+@@ -131,9 +131,9 @@ 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)
@@ -25,9 +25,9 @@ Description: Exclude failing tests
#
# 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
+@@ -161,19 +161,19 @@ smalltests: $(TEST_TOOLS)
+ -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
@@ -39,7 +39,7 @@ Description: Exclude failing tests
# 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
+ # 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
@@ -50,10 +50,10 @@ Description: Exclude failing tests
# Gzipped input
$(SMALLRUN) 5.0 0 $(SRCDIR)/input/5.0.fastq.gz --quality PHRED_33
# Misparsed quality
-@@ -179,7 +179,7 @@ smalltests: $(TEST_TOOLS)
+@@ -185,7 +185,7 @@ 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
+ # 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 " /")
@@ -70,3 +70,42 @@ Description: Exclude failing tests
kget \
general-loader \
vschema \
+--- a/test/fastq-loader/Makefile.rej
++++ /dev/null
+@@ -1,36 +0,0 @@
+---- test/fastq-loader/Makefile
+-+++ test/fastq-loader/Makefile
+-@@ -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 $(SRCDIR)/input/9.0.fastq --quality PHRED_33
+- # accepting ascii quality values up to 126
diff --git a/debian/patches/link_debian_packaged_libz.patch b/debian/patches/link_debian_packaged_libz.patch
index 8589410..88f2d41 100644
--- a/debian/patches/link_debian_packaged_libz.patch
+++ b/debian/patches/link_debian_packaged_libz.patch
@@ -5,8 +5,8 @@ Description: Since libncbi-vdb is dynamically linked against zlib and libbz2
--- a/build/ld.linux.exe.sh
+++ b/build/ld.linux.exe.sh
-@@ -300,6 +300,9 @@ then
- CMD="$CMD -lm"
+@@ -319,6 +319,9 @@ then
+ CMD="$CMD -Wl,-Bdynamic -lm"
fi
+echo "+++++++++++++++++++++++++ adding zlib +++++++++++++++++++++++++++++++++++++++"
diff --git a/debian/patches/series b/debian/patches/series
index 22ff44b..e71691d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,10 +7,8 @@ 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
link_debian_packaged_libmbed.patch
-enable_build_using_ncbi-vdb_version_2.8.0.patch
diff --git a/debian/patches/set_explicit_path_to_schemata.patch b/debian/patches/set_explicit_path_to_schemata.patch
index cd93661..64e458a 100644
--- a/debian/patches/set_explicit_path_to_schemata.patch
+++ b/debian/patches/set_explicit_path_to_schemata.patch
@@ -13,26 +13,6 @@ Description: In Debian */*.vschema is installed to /usr/lib/ncbi-vdb/
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
@@ -188,3 +168,46 @@ Description: In Debian */*.vschema is installed to /usr/lib/ncbi-vdb/
#define PACBIO_SCHEMA_DB "NCBI:SRA:PacBio:smrt:db"
+--- 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/test-general-loader.cpp.rej
++++ /dev/null
+@@ -1,20 +0,0 @@
+---- test/general-loader/test-general-loader.cpp
+-+++ 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 ) ) );
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git
More information about the debian-med-commit
mailing list