[med-svn] [Git][med-team/ncbi-vdb][master] 3 commits: Start work on ncbi-vdb 3.0.0+dfsg2-2 for more tuneups.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Fri Aug 26 05:30:09 BST 2022
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb
Commits:
4065ac7a by Aaron M. Ucko at 2022-08-25T23:53:17-04:00
Start work on ncbi-vdb 3.0.0+dfsg2-2 for more tuneups.
- - - - -
7ff20193 by Aaron M. Ucko at 2022-08-25T23:56:50-04:00
Accommodate builds covering only arch-(in)dependent packages.
* debian/.gitignore: Also ignore common-install-stamp.
* debian/control: Split out Build-Depends-Arch, for nearly everything.
* debian/rules: Accommodate builds covering only architecture-dependent
or architecture-independent packages, with the help of a new
debian/common-install-stamp target.
- - - - -
dac54376 by Aaron M. Ucko at 2022-08-26T00:04:09-04:00
fix_cmake.patch: Link libncbi-(w)vdb.so against all dependencies.
Leave the test subtree's COMMON_LIBS_* settings alone because tests
link statically.
- - - - -
5 changed files:
- debian/.gitignore
- debian/changelog
- debian/control
- debian/patches/fix_cmake.patch
- debian/rules
Changes:
=====================================
debian/.gitignore
=====================================
@@ -1,4 +1,5 @@
.debhelper
+common-install-stamp
debhelper-build-stamp
files
lib*3
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+ncbi-vdb (3.0.0+dfsg2-2) UNRELEASED; urgency=medium
+
+ * NOT RELEASED YET.
+ * debian/.gitignore: Also ignore common-install-stamp.
+ * debian/control: Split out Build-Depends-Arch, for nearly everything.
+ * debian/patches/fix_cmake.patch: Link libncbi-(w)vdb.so against all
+ dependencies. (Leave the test subtree's COMMON_LIBS_* settings alone
+ because tests link statically.)
+ * debian/rules: Accommodate builds covering only architecture-dependent
+ or architecture-independent packages, with the help of a new
+ debian/common-install-stamp target.
+
+ -- Aaron M. Ucko <ucko at debian.org> Fri, 26 Aug 2022 00:04:08 -0400
+
ncbi-vdb (3.0.0+dfsg2-1) experimental; urgency=medium
* Merge (or port, as appropriate) changes from 2.11.2+dfsg-5.
=====================================
debian/control
=====================================
@@ -5,7 +5,8 @@ Uploaders: Andreas Tille <tille at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- d-shlibs (>= 0.104),
+ d-shlibs (>= 0.104)
+Build-Depends-Arch:
cmake,
libbz2-dev,
libxml2-dev,
=====================================
debian/patches/fix_cmake.patch
=====================================
@@ -3,6 +3,8 @@ Last-Update: 2022-02-21 09:28:30 +0100
Origin: https://lists.debian.org/debian-med/2022/02/msg00094.html
Description: Set linker flags properly
+Index: ncbi-vdb/libs/CMakeLists.txt
+===================================================================
--- ncbi-vdb.orig/libs/CMakeLists.txt
+++ ncbi-vdb/libs/CMakeLists.txt
@@ -32,7 +32,6 @@ add_subdirectory(axf) # sra tools depend
@@ -66,3 +68,23 @@ Index: ncbi-vdb/libs/ncbi-vdb/CMakeLists.txt
)
if( LibXml2_FOUND )
+Index: ncbi-vdb/libs/ncbi-vdb/CMakeLists.posix.txt
+===================================================================
+--- ncbi-vdb.orig/libs/ncbi-vdb/CMakeLists.posix.txt
++++ ncbi-vdb/libs/ncbi-vdb/CMakeLists.posix.txt
+@@ -32,7 +32,7 @@ endforeach()
+
+ add_library( ncbi-vdb STATIC "${VDB_LIB_RD}" )
+ ExportStatic( ncbi-vdb true )
+-ExportShared( ncbi-vdb true "${LIBXML2};m;dl;pthread")
++ExportShared( ncbi-vdb true "${LIBXML2};mbedtls;z;bz2;zstd;m;dl;pthread")
+
+ ################################
+ set( VDB_LIB_RDWR "" )
+@@ -42,5 +42,5 @@ endforeach()
+
+ add_library( ncbi-wvdb STATIC "${VDB_LIB_RDWR}" )
+ ExportStatic( ncbi-wvdb true )
+-ExportShared( ncbi-wvdb true "${LIBXML2};m;dl;pthread")
++ExportShared( ncbi-wvdb true "${LIBXML2};mbedtls;z;bz2;zstd;m;dl;pthread")
+
=====================================
debian/rules
=====================================
@@ -39,6 +39,7 @@ override_dh_auto_clean:
rm -f libs/ngs-jni/jni.h
rm -f libs/ngs-jni/jni_md.h
rm -f build/ld.linux.exe_cmd.sh
+ rm -f debian/common-install-stamp
rm -f test/cloud/cloud-kfg/.aws/c*
rm -f test/kdb/root/sra/SRR600096.sra.cache
rm -f test/kdb/user-settings.mkfg
@@ -48,7 +49,9 @@ override_dh_auto_clean:
rm -f test/vfs/user-settings.mkfg
rm -f test/vxf/local_config/user-settings.mkfg
-override_dh_auto_build:
+override_dh_auto_configure-indep:;
+
+override_dh_auto_build-arch:
dh_auto_build --no-parallel -- NO_VDB3=1
# we need to make really sure that no 'vdb_'-prefixed functions will remain ...
if find . \( -name "*.so" -o -name "*.a" \) -exec strings \{\} \; | tee | grep -q vdb_mbedtls ; then \
@@ -58,7 +61,9 @@ override_dh_auto_build:
false ; \
fi
-override_dh_auto_test:
+override_dh_auto_build-indep:;
+
+override_dh_auto_test-arch:
ifeq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS)))
# FIXME: some tests keep on failing despite debian/patches/skip_failing_test.patch - needs to be sorted out later
dh_auto_test -- NO_VDB3=1 || true
@@ -66,10 +71,28 @@ else
echo "Skip testing which takes a long time"
endif
+override_dh_auto_test-indep:;
+
override_dh_prep:
dh_prep -Xdebian/tmp
-override_dh_auto_install:
+debian/common-install-stamp:
+ mkdir -p debian/libncbi-vdb-dev/usr/include/$(DEB_SOURCE)
+ cp -a interfaces/* debian/libncbi-vdb-dev/usr/include/$(DEB_SOURCE)
+ # move schemata from development packages to library packages since these are used in executables
+ mkdir -p $(SCHEMADIR)
+ for schema in `find debian/libncbi-vdb-dev/usr/include/$(DEB_SOURCE) -name "*.vschema"` ; do \
+ schemafile=`basename $${schema}` ; \
+ schemadir=`basename $$(dirname $${schema})` ; \
+ mkdir -p $(SCHEMADIR)/$${schemadir} ; \
+ sed -i "s:^include ':&/usr/lib/ncbi-vdb/:" $${schema} ; \
+ mv $${schema} $(SCHEMADIR)/$${schemadir} ; \
+ done
+ # Move around kfg files to the place where it used to be in version 2.x
+ mv debian/libncbi-vdb-dev/usr/include/ncbi-vdb/kfg/ncbi $(SCHEMADIR)/kfg
+ touch $@
+
+override_dh_auto_install-arch: debian/common-install-stamp
dh_auto_install -- NO_VDB3=1
find $(LIBINSTALLDIR) -name "*-static.a" -delete
# upstream installs versioned *.a libs - we only want a single version
@@ -90,7 +113,6 @@ override_dh_auto_install:
--movedev $(LIBINSTALLDIR)/libtui_cpp.a usr/lib/$(MULTIARCH) \
--movedev obj-*/ilib/libkapp-norsrc.a usr/lib/$(MULTIARCH) \
$(LIBINSTALLDIR)/libncbi-vdb.so
- dh_install -p libncbi-vdb-dev interfaces usr/include/$(DEB_SOURCE)
# json-response.h and services-priv.h are needed by sra-sdk, but
# the latter shouldn't replace interfaces/vfs/services-priv.h.
dh_install -plibncbi-vdb-dev libs/vfs/json-response.h usr/include/ncbi-vdb/vfs
@@ -103,15 +125,6 @@ override_dh_auto_install:
d-shlibmove $(DSLMFLAGS) \
$(LIBINSTALLDIR)/libsam-extract.so
find debian/lib* -name .gitignore -delete
- # move schemata from development packages to library packages since these are used in executables
- mkdir -p $(SCHEMADIR)
- for schema in `find debian/libncbi-vdb-dev/usr/include/$(DEB_SOURCE) -name "*.vschema"` ; do \
- schemafile=`basename $${schema}` ; \
- schemadir=`basename $$(dirname $${schema})` ; \
- mkdir -p $(SCHEMADIR)/$${schemadir} ; \
- sed -i "s:^include ':&/usr/lib/ncbi-vdb/:" $${schema} ; \
- mv $${schema} $(SCHEMADIR)/$${schemadir} ; \
- done
- # Move around kfg files to the place where it used to be in version 2.x
- mv debian/libncbi-vdb-dev/usr/include/ncbi-vdb/kfg/ncbi $(SCHEMADIR)/kfg
chrpath --delete debian/libkdf5-3/usr/lib/x86_64-linux-gnu/libkdf5.so.3.0.0
+
+override_dh_auto_install-indep: debian/common-install-stamp
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/9ed1364d15a3ba469bd32e961d0d177395d1ab1e...dac5437686e2d5b2aa311c9b0a901e64aecbb692
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/9ed1364d15a3ba469bd32e961d0d177395d1ab1e...dac5437686e2d5b2aa311c9b0a901e64aecbb692
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