[med-svn] [Git][med-team/ncbi-vdb][master] 4 commits: Move around kfg files to the place where it used to be in version 2.x
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Feb 25 09:15:47 GMT 2022
Andreas Tille pushed to branch master at Debian Med / ncbi-vdb
Commits:
58549c5a by Andreas Tille at 2022-02-25T06:56:52+01:00
Move around kfg files to the place where it used to be in version 2.x
- - - - -
6df7f300 by Andreas Tille at 2022-02-25T08:24:23+01:00
Remove now unused patches which all were targeting the old build system
- - - - -
07729f6a by Andreas Tille at 2022-02-25T10:13:28+01:00
Library libvdb-sqlite is not provided by upstream any more which builds libsam-extract as new library. Binary packages are adapted accordingly
- - - - -
d0082b21 by Andreas Tille at 2022-02-25T10:15:24+01:00
DEP3
- - - - -
14 changed files:
- debian/changelog
- debian/control
- − debian/libncbi-vdb3.install
- − debian/patches/add_-msse2.patch
- − debian/patches/find_hdf5_serial.patch
- − debian/patches/find_ngs-sdk.patch
- − debian/patches/fix_install_target.patch
- + debian/patches/libsam-extract_shared.patch
- − debian/patches/remove_-m64_flag.patch
- debian/patches/series
- − debian/patches/skip_failing_test.patch
- − debian/patches/use_debian_packaged_libmbedx.patch
- − debian/patches/use_debian_packaged_zlib.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -3,6 +3,9 @@ ncbi-vdb (3.0.0+dfsg-1) UNRELEASED; urgency=medium
* New upstream version
* Switch to cmake build system
* Reflect SONAME bump in package names
+ * Library libvdb-sqlite is not provided by upstream any more which
+ builds libsam-extract as new library. Binary packages are adapted
+ accordingly
-- Andreas Tille <tille at debian.org> Sat, 19 Feb 2022 11:53:03 +0100
=====================================
debian/control
=====================================
@@ -147,12 +147,12 @@ Description: virtual layer update modul of ncbi-vdb library (devel)
.
This is the development package.
-Package: libvdb-sqlite2
+Package: libsam-extract3
Architecture: amd64 arm64 i386 x32
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
-Description: sqlite modul of ncbi-vdb library
+Description: sam-extract modul of ncbi-vdb library
NGS is a new, domain-specific API for accessing reads, alignments and
pileups produced from Next Generation Sequencing. The API itself is
independent from any particular back-end implementation, and supports
@@ -160,15 +160,15 @@ Description: sqlite modul of ncbi-vdb library
building new back-end "engines". The engine for accessing SRA data is
contained within the sister repository ncbi-vdb.
.
- This library is part of the ncbi-vdb package and provides a sqlite
- interface.
+ This library is part of the ncbi-vdb package and provides an interface
+ to extrat sam files.
-Package: libvdb-sqlite-dev
+Package: libsam-extract-dev
Architecture: amd64 arm64 i386 x32
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
- libvdb-sqlite2 (= ${binary:Version})
+ libsam-extract3 (= ${binary:Version})
Description: sqlite modul of ncbi-vdb library (devel)
NGS is a new, domain-specific API for accessing reads, alignments and
pileups produced from Next Generation Sequencing. The API itself is
@@ -177,7 +177,7 @@ Description: sqlite modul of ncbi-vdb library (devel)
building new back-end "engines". The engine for accessing SRA data is
contained within the sister repository ncbi-vdb.
.
- This library is part of the ncbi-vdb package and provides a sqlite
- interface.
+ This library is part of the ncbi-vdb package and provides an interface
+ to extrat sam files.
.
This is the development package.
=====================================
debian/libncbi-vdb3.install deleted
=====================================
@@ -1 +0,0 @@
-libs/kfg/*.kfg /usr/lib/ncbi-vdb/kfg
=====================================
debian/patches/add_-msse2.patch deleted
=====================================
@@ -1,19 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 20 Nov 2021 22:47:22 -0500
-Bug-Debian: https://bugs.debian.org/836128
-Description: Add -msse2 to libs/search on 32-bit x86
-
---- a/libs/search/Makefile
-+++ b/libs/search/Makefile
-@@ -39,6 +39,11 @@ OBJFILES = \
-
- include $(TOP)/build/Makefile.env
-
-+MARCH := $(shell uname -m)
-+ifneq ($(filter i%86, $(MARCH)),)
-+ CFLAGS += -msse2
-+endif
-+
- #-------------------------------------------------------------------------------
- # outer targets
- #
=====================================
debian/patches/find_hdf5_serial.patch deleted
=====================================
@@ -1,30 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
-Description: use hdf5 serial
- May be there is a more elegant way to use hdf5 rather than patching the source
- but I did not found it. Any hints are welcome.
-
---- a/setup/konfigure.perl
-+++ b/setup/konfigure.perl
-@@ -1667,8 +1667,8 @@ sub check_compiler {
- $flags = $n;
- $log = ' int main() { }\n'
- } elsif ($n eq 'hdf5') {
-- $library = '-Wl,-Bstatic -lhdf5 -Wl,-Bdynamic -ldl -lm -lz';
-- $log = '#include <hdf5.h> \n int main() { H5close (); }\n'
-+ $library = '-lhdf5_serial -Wl,-Bdynamic -ldl -lm -lz';
-+ $log = '#include <hdf5/serial/hdf5.h> \n int main() { H5close (); }\n'
- } elsif ($n eq 'fuse') {
- $flags = '-D_FILE_OFFSET_BITS=64';
- $library = '-lfuse';
---- a/libs/hdf5/Makefile
-+++ b/libs/hdf5/Makefile
-@@ -104,7 +104,7 @@ KDF5_OBJ = \
- $(addsuffix .$(LOBX),$(KDF5_SRC))
-
- KDF5_LIB = \
-- -lhdf5 \
-+ -lhdf5_serial \
- -lz \
-
- ifdef HDF5_LIBDIR
=====================================
debian/patches/find_ngs-sdk.patch deleted
=====================================
@@ -1,41 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
-Description: Enable finding ngs-sdk
-
---- a/setup/konfigure.perl
-+++ b/setup/konfigure.perl
-@@ -1396,7 +1396,9 @@ sub find_in_dir {
- print "\tlibraries... " unless ($AUTORUN);
- if ($lib) {
- my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);
-- my $libdir = File::Spec->catdir($builddir, 'lib');
-+ my $buildarch = `dpkg-architecture -qDEB_BUILD_MULTIARCH`;
-+ chomp $buildarch;
-+ my $libdir = File::Spec->catdir($dir, 'lib', $buildarch);
- my $ilibdir = File::Spec->catdir($builddir, 'ilib');
- my $f = File::Spec->catdir($libdir, $lib);
- print "\n\t\tchecking $f\n\t" if ($OPT{'debug'});
-@@ -1477,8 +1479,8 @@ sub find_in_dir {
- }
- }
- if ($jar) {
-- print "\tjar... " unless ($AUTORUN);
-- my $try = "$dir/jar/$jar";
-+ print "\tjar... (seeking for $jar in dir $dir)" unless ($AUTORUN);
-+ my $try = "$dir/$jar";
- if (-e "$try") {
- println $try unless ($AUTORUN);
- $found_lib = $try;
---- a/setup/package.prl
-+++ b/setup/package.prl
-@@ -33,8 +33,8 @@ sub REQ { ( { name => 'ngs-sdk',
- option => 'with-ngs-java-prefix',
- origin => 'I',
- type => 'JO',
-- pkgpath => '/usr/local/ngs/ngs-java',
-- usrpath => '$HOME/ngs/ngs-java',
-+ pkgpath => '/usr/share/java', # grmpf, why is this ignored after it is changed :-(((
-+ usrpath => '/usr/share/java', # try again with same value
- bldpath => '$HOME/ncbi-outdir/ngs-java',
- locbldpath=>'$Bin/../../OUTDIR/ngs-java',
- lib => 'ngs-java.jar',
=====================================
debian/patches/fix_install_target.patch deleted
=====================================
@@ -1,18 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
-Description: Install target tries to install to /usr/lib64 which is broken on
- one hand and on the other hand I have not found a proper method to stop this
- by less invasive means
-
---- a/Makefile
-+++ b/Makefile
-@@ -69,7 +69,8 @@ $(SUBDIRS_STD):
- install:
- @ echo "Checking make status of object libraries..."
- @ $(MAKE) -s --no-print-directory TOP=$(CURDIR) $(SUBDIRS)
-- @ $(MAKE) -s --no-print-directory TOP=$(CURDIR) -f build/Makefile.install install
-+ # Skip useless broken part of install target
-+ #@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) -f build/Makefile.install install
-
- uninstall:
- @ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install uninstall
=====================================
debian/patches/libsam-extract_shared.patch
=====================================
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 19 Feb 2022 11:53:03 +0100
+Description: Upstream creates static library with versioning / linking scheme
+ which looks as it would be intended to create a shared library. This patch
+ really created this shared library (which ends up in a seprate binary package)
+
+--- a/libs/align/CMakeLists.txt
++++ b/libs/align/CMakeLists.txt
+@@ -83,6 +83,7 @@ GenerateStaticLibs( align-access "${ALIG
+
+ GenerateStaticLibs( sam-extract "${SAM_EXTRACT_SRC}" )
+ ExportStatic( sam-extract true )
++ExportShared( sam-extract true "" )
+
+ GenerateStaticLibs( align-reader "${ALIGN_READER_SRC}" )
+
=====================================
debian/patches/remove_-m64_flag.patch deleted
=====================================
@@ -1,59 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 31 Aug 2016 07:55:11 +0200
-Bug-Debian: https://bugs.debian.org/836129
-Description: Enable build on x32 by removing explicit -m32/-m64
-
---- a/build/Makefile.gcc
-+++ b/build/Makefile.gcc
-@@ -51,18 +51,6 @@ ifneq (sun,$(OS))
- WARN += -Wno-variadic-macros
- endif
-
--ifeq (64,$(BITS))
--ifneq (arm64,$(ARCH))
-- CARCH = -m64
--endif
--else
--ifeq (32_64,$(BITS))
-- CARCH = -arch i386 -arch x86_64
--else
-- CARCH = -m32
--endif
--endif
--
- ifeq (prof, $(BUILD))
- PROF = -pg
- endif
---- a/build/Makefile.cc
-+++ b/build/Makefile.cc
-@@ -46,12 +46,6 @@ LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH)
- # tool options
- WARN =
-
--ifeq (64,$(BITS))
-- CARCH = -m64
--else
-- CARCH = -m32
--endif
--
- ifeq (prof, $(BUILD))
- PROF = -xpg
- endif
---- a/build/Makefile.clang
-+++ b/build/Makefile.clang
-@@ -48,15 +48,6 @@ LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH)
- # tool options
- WARN = -Wall -Wno-variadic-macros -Wno-long-long # -Wconversion
- # TODO: Lots of new clang options in later versions (-fsanitize, CFI, CPI, ...)
--ifeq (64,$(BITS))
-- CARCH = -m64
--else
--ifeq (32_64,$(BITS))
-- CARCH = -arch i386 -arch x86_64
--else
-- CARCH = -m32
--endif
--endif
-
- ifeq (prof, $(BUILD))
- PROF = -pg
=====================================
debian/patches/series
=====================================
@@ -1,12 +1,4 @@
-#find_hdf5_serial.patch
-#find_ngs-sdk.patch
-#skip_failing_test.patch
-#fix_install_target.patch
-#use_debian_packaged_zlib.patch
spelling.patch
-#remove_-m64_flag.patch
-#add_-msse2.patch
-#use_debian_packaged_libmbedx.patch
mbedtls_ssl_init.patch
i386-uint64_msbit.patch
fix_path_mbedtls.patch
@@ -15,3 +7,4 @@ zstd.patch
fix_build.patch
fix_cmake.patch
soversion.patch
+libsam-extract_shared.patch
=====================================
debian/patches/skip_failing_test.patch deleted
=====================================
@@ -1,119 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
-Description: Skip some tests that are failing in pbuilder.
- FIXME: There are more tests to skip but I have given up for the moment.
-
---- a/test/kfg/kfgtest.cpp
-+++ b/test/kfg/kfgtest.cpp
-@@ -806,6 +806,7 @@ FIXTURE_TEST_CASE(KConfigImportNgc_Basic
- string ngcPath("./prj_2956.ngc");
- C::t(ngcPath);
- Cleaner cleaner(wd);
-+/* FIXME: This test fails in pbuilder environment
- REQUIRE_RC(KConfigImportNgc(kfg, ngcPath.c_str(), "repos/ngc/", &newRepo));
- TEST_MESSAGE("KConfigImportNgc(" << ngcPath << ")");
- // contents of the input file:
-@@ -872,6 +873,7 @@ FIXTURE_TEST_CASE(KConfigImportNgc_Basic
- REQUIRE_EQ(string(newRepo), string("repos/ngc/"));
-
- REQUIRE_RC(KDirectoryRemove(wd, true, "repos"));
-+*/
- }
- #endif
-
-@@ -881,15 +883,19 @@ FIXTURE_TEST_CASE(KConfigImportNgc_NullL
- CreateAndLoad(GetName(), "\n");
- const char* newRepo;
- Cleaner cleaner(wd);
-+/* FIXME: This test fails in pbuilder environment
- REQUIRE_RC(KConfigImportNgc(kfg, "./prj_2956.ngc", NULL, &newRepo));
- string encDirName = "/ncbi/dbGaP-2956";
- REQUIRE_EQ(string(newRepo).rfind(encDirName), string(newRepo).size() - encDirName.size()); // string(buf) ends with encDirName
-+*/
- }
- FIXTURE_TEST_CASE(KConfigImportNgc_NullLocation_NullNewRepo, KfgFixture)
- {
- CreateAndLoad(GetName(), "\n");
- Cleaner cleaner(wd);
-+/* FIXME: This test fails in pbuilder environment
- REQUIRE_RC(KConfigImportNgc(kfg, "./prj_2956.ngc", NULL, NULL));
-+*/
- }
- #endif
-
---- a/test/kdb/remote_open_test.cpp
-+++ b/test/kdb/remote_open_test.cpp
-@@ -72,11 +72,13 @@ TEST_CASE(KDBManagerVPathOpenDB_Local)
- const KDatabase * db;
- REQUIRE_RC(KDBManagerVPathOpenLocalDBRead ( mgr, &db, path ));
- REQUIRE_NOT_NULL(db);
-+/* FIXME: Fails in pbuilder
- const KTable *tbl;
- REQUIRE_RC(KDatabaseOpenTableRead(db, &tbl, "SEQUENCE"));
- REQUIRE_RC(KTableRelease(tbl));
- REQUIRE_RC(KDatabaseRelease(db));
- REQUIRE_RC(KDBManagerRelease(mgr));
-+*/
- }
-
- REQUIRE_RC(VPathRelease(path));
-@@ -214,59 +216,6 @@ protected:
- string m_cachedFile;
- };
-
--FIXTURE_TEST_CASE(KDBManagerVPathOpenDB_Remote, RemoteDBFixture)
--{
-- Configure(GetName());
-- Resolve("SRR600096");
--
-- KDBManager* mgr;
-- REQUIRE_RC(KDB_MANAGER_MAKE(&mgr, NULL));
-- const KDatabase * db;
-- REQUIRE_RC(KDBManagerVPathOpenRemoteDBRead ( mgr, &db, m_path, m_cache ));
-- REQUIRE_NOT_NULL(db);
--
-- /* read something */
-- const KTable *tbl;
-- REQUIRE_RC(KDatabaseOpenTableRead(db, &tbl, "SEQUENCE"));
-- REQUIRE_RC(KTableRelease(tbl));
--
-- REQUIRE_RC(KDatabaseRelease(db));
-- REQUIRE_RC(KDBManagerRelease(mgr));
--}
--
--FIXTURE_TEST_CASE(KDBManagerVPathOpenDB_Remote_NoCache, RemoteDBFixture)
--{
-- Configure(GetName());
-- Resolve("SRR600096");
--
-- KDBManager* mgr;
-- REQUIRE_RC(KDB_MANAGER_MAKE(&mgr, NULL));
-- const KDatabase * db;
-- REQUIRE_RC(KDBManagerVPathOpenRemoteDBRead ( mgr, &db, m_path, NULL ));
-- REQUIRE_NOT_NULL(db);
--
-- /* read something */
-- const KTable *tbl;
-- REQUIRE_RC(KDatabaseOpenTableRead(db, &tbl, "SEQUENCE"));
-- REQUIRE_RC(KTableRelease(tbl));
--
-- REQUIRE_RC(KDatabaseRelease(db));
-- REQUIRE_RC(KDBManagerRelease(mgr));
--}
--
--FIXTURE_TEST_CASE(KDBManagerVPathOpenDB_Remote_Table, RemoteDBFixture)
--{
-- Configure(GetName());
-- Resolve("SRR000123");
--
-- KDBManager* mgr;
-- REQUIRE_RC(KDB_MANAGER_MAKE(&mgr, NULL));
-- const KDatabase * db;
-- REQUIRE_RC_FAIL(KDBManagerVPathOpenRemoteDBRead ( mgr, &db, m_path, NULL )); // not a database
--
-- REQUIRE_RC(KDBManagerRelease(mgr));
--}
--
- FIXTURE_TEST_CASE(KDBManagerVPathOpenDB_Remote_BadPath, RemoteDBFixture)
- {
- Configure(GetName());
=====================================
debian/patches/use_debian_packaged_libmbedx.patch deleted
=====================================
@@ -1,91 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 04 Nov 2016 08:56:33 +0100
-Description: Somehow Build system expects a copy of libmbedx509.a which is
- in package libmbedtls-dev - just drop it from list of dependencies
-
---- a/libs/ncbi-vdb/Makefile
-+++ b/libs/ncbi-vdb/Makefile
-@@ -127,9 +127,6 @@ VDB_LIB_CMN = \
- vfs \
- cloud \
- $(LIBKXML) \
-- mbedx509 \
-- mbedtls \
-- mbedcrypto \
- kns \
- kfg \
- krypto \
-@@ -155,7 +152,7 @@ VDB_OBJ = \
- $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD)))
-
- VDB_LIB = \
-- $(addprefix -s,$(VDB_LIB_RD))
-+ $(addprefix -s,$(VDB_LIB_RD)) -lmbedx509 -lmbedtls -lmbedcrypto
-
- $(LIBDIR)/libncbi-vdb.$(LIBX): $(VDB_OBJ)
- $(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(VDB_LIB)
-@@ -181,7 +178,7 @@ WVDB_OBJ = \
- $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RDWR)))
-
- WVDB_LIB = \
-- $(addprefix -s,$(VDB_LIB_RDWR))
-+ $(addprefix -s,$(VDB_LIB_RDWR)) -lmbedx509 -lmbedtls -lmbedcrypto
-
- $(LIBDIR)/libncbi-wvdb.$(LIBX): $(WVDB_OBJ)
- $(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(WVDB_LIB)
---- a/libs/kns/Makefile
-+++ b/libs/kns/Makefile
-@@ -109,7 +109,8 @@ KNS_OBJ = \
-
- KNS_LIB = \
- -lkfs \
-- -dklib
-+ -dklib \
-+ -lmbedx509 -lmbedtls -lmbedcrypto
-
- $(ILIBDIR)/libkns.$(LIBX): $(KNS_OBJ)
- $(LD) --slib -o $@ $^ $(KNS_LIB)
---- a/libs/kns/tls-priv.h
-+++ b/libs/kns/tls-priv.h
-@@ -37,7 +37,7 @@
- #include MBEDTLS_CONFIG_FILE
- #endif
-
--#include <mbedtls/net.h>
-+#include <mbedtls/net_sockets.h>
- #include <mbedtls/debug.h>
- #include <mbedtls/ssl.h>
- #include <mbedtls/aes.h>
---- a/libs/kns/tls.c
-+++ b/libs/kns/tls.c
-@@ -60,7 +60,7 @@ struct KTLSStream;
- #include MBEDTLS_CONFIG_FILE
- #endif
-
--#include <mbedtls/net.h>
-+#include <mbedtls/net_sockets.h>
- #include <mbedtls/debug.h>
- #include <mbedtls/ssl.h>
- #include <mbedtls/aes.h>
---- a/libs/hdf5/Makefile
-+++ b/libs/hdf5/Makefile
-@@ -112,7 +112,7 @@ ifdef HDF5_LIBDIR
- endif
-
- $(LIBDIR)/libkdf5.$(SHLX): $(KDF5_OBJ)
-- $(LD) --dlib --vers $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers -o $@ $^ $(KDF5_LIB)
-+ $(LD) --dlib --vers $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers -o $@ $^ $(KDF5_LIB) -lmbedx509 -lmbedtls -lmbedcrypto
-
- $(LIBDIR)/libkdf5.$(LIBX): $(KDF5_OBJ)
- $(LD) --slib --vers $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers -o $@ $^ $(KDF5_LIB)
---- a/libs/vdb-sqlite/Makefile
-+++ b/libs/vdb-sqlite/Makefile
-@@ -85,7 +85,7 @@ VDB_SQLITE_OBJ = \
- $(addsuffix .$(LOBX),$(VDB_SQLITE_SRC))
-
- VDB_SQLITE_LIB = \
-- -sncbi-vdb -lz -lbz2
-+ -sncbi-vdb -lmbedx509 -lmbedtls -lmbedcrypto -lz -lbz2
-
- VDB_SQLITE_VERS = \
- $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers
=====================================
debian/patches/use_debian_packaged_zlib.patch deleted
=====================================
@@ -1,47 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
-Description: External copy of bz2 and zlib are removed - exclude these from
- build system as well.
-
---- a/libs/Makefile
-+++ b/libs/Makefile
-@@ -35,7 +35,6 @@ include $(TOP)/build/Makefile.config
- # default
- #
- MAIN_SUBDIRS = \
-- ext \
- kfc \
- klib \
- kproc \
---- a/libs/ncbi-vdb/Makefile
-+++ b/libs/ncbi-vdb/Makefile
-@@ -138,10 +138,7 @@ VDB_LIB_CMN = \
- klib \
- kproc \
- $(LIBKQ) \
-- kfc \
-- bz2 \
-- z \
-- zstd \
-+ kfc
-
- VDB_LIB_RD = \
- align-reader \
-@@ -199,4 +196,4 @@ fuzz:
- $(TOP)/build/ld.sh linux x86_64 gcc --build dbg --ldflags "-g -m64" --objx o --shlx so --libx a --srcdir $(SRCDIR) --bindir $(BINDIR) --slib -o $(FLIBDIR)/libncbi-vdb.$(LIBX) -L$(FLIBDIR) $(VDB_LIB) $(VDB_NGS_LIB)
-
- cleanfuzz:
-- rm -rf $(FLIBDIR)/*
-\ No newline at end of file
-+ rm -rf $(FLIBDIR)/*
---- a/libs/vdb-sqlite/Makefile
-+++ b/libs/vdb-sqlite/Makefile
-@@ -85,7 +85,7 @@ VDB_SQLITE_OBJ = \
- $(addsuffix .$(LOBX),$(VDB_SQLITE_SRC))
-
- VDB_SQLITE_LIB = \
-- -sncbi-vdb
-+ -sncbi-vdb -lz -lbz2
-
- VDB_SQLITE_VERS = \
- $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers
=====================================
debian/rules
=====================================
@@ -88,8 +88,8 @@ override_dh_auto_install:
$(LIBINSTALLDIR)/libkdf5.so
d-shlibmove $(DSLMFLAGS) \
$(LIBINSTALLDIR)/libncbi-wvdb.so
-# d-shlibmove $(DSLMFLAGS) \
-# $(LIBINSTALLDIR)/libvdb-sqlite.so
+ d-shlibmove $(DSLMFLAGS) \
+ $(LIBINSTALLDIR)/libsam-extract.so
find debian/lib* -name .gitignore -delete
# move schemata from development packages to library packages since these are used in executables
mkdir -p $(SCHEMADIR)
@@ -100,3 +100,6 @@ override_dh_auto_install:
sed -i "s:^include ':&/usr/lib/ncbi-vdb/:" $${schema} ; \
mv $${schema} $(SCHEMADIR)/$${schemadir} ; \
done
+ # Move around kfg files to the place where it used to be in version 2.x
+ mkdir debian/libncbi-vdb3/usr/lib/ncbi-vdb/
+ mv debian/libncbi-vdb-dev/usr/include/ncbi-vdb/kfg/ncbi debian/libncbi-vdb3/usr/lib/ncbi-vdb/kfg
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/6ac3d1c4ea81994fd32052128efd5959d5445a54...d0082b21b63b51bcfb224e693db943cc6db11290
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220225/3ee8cd7a/attachment-0001.htm>
More information about the debian-med-commit
mailing list