[med-svn] [Git][med-team/ncbi-vdb][master] 8 commits: Formally start work on ncbi-vdb 2.10.6+dfsg-2.
Aaron M. Ucko
gitlab at salsa.debian.org
Wed May 20 03:54:28 BST 2020
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb
Commits:
5bf59d5a by Aaron M. Ucko at 2020-05-18T22:24:08-04:00
Formally start work on ncbi-vdb 2.10.6+dfsg-2.
- - - - -
a99de6a3 by Aaron M. Ucko at 2020-05-18T22:24:50-04:00
libs/vfs/services-priv.h -> .../services-priv-internal.h.
Install libs/vfs/services-priv.h as .../services-priv-internal.h to
distinguish it from interfaces/vfs/services-priv.h. (Neither can
stand in for the other.)
- - - - -
0e09b496 by Aaron M. Ucko at 2020-05-19T22:12:02-04:00
Formally refresh patches that developed offsets.
- - - - -
d660898e by Aaron M. Ucko at 2020-05-19T22:40:43-04:00
Always include libmbedx509-0 quirk per new DSLMFLAGS macro.
Factor out a new DSLMFLAGS macro for common d-shlibmove flags; include
the libmbedx509-0 quirk there since it will soon be needed everywhere.
- - - - -
ab68936c by Aaron M. Ucko at 2020-05-19T22:44:39-04:00
Fix system (mbed*/z/bz2) library linkage (#952623, #952627, #953897)
Address remaining underlinkage of system libraries (mbed*, z, bz2).
At this point, the only remaining unresolved references are of libkdf5
against symbols that could come from either libncbi-vdb or libncbi-wvdb.
- - - - -
1fe42a58 by Aaron M. Ucko at 2020-05-19T22:47:23-04:00
Copy headers rather than moving them to allow for consecutive builds.
- - - - -
042c1188 by Aaron M. Ucko at 2020-05-19T22:50:02-04:00
Fix typo in override_dh_missing name; supply debian/not-installed.
- - - - -
78ecbf0f by Aaron M. Ucko at 2020-05-19T22:51:28-04:00
Add myself (A. Ucko) to Uploaders.
- - - - -
8 changed files:
- debian/changelog
- debian/control
- + debian/not-installed
- debian/patches/fix_linking.patch
- 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
=====================================
@@ -1,3 +1,22 @@
+ncbi-vdb (2.10.6+dfsg-2) UNRELEASED; urgency=medium
+
+ * NOT RELEASED YET.
+ * Install libs/vfs/services-priv.h as .../services-priv-internal.h to
+ distinguish it from interfaces/vfs/services-priv.h. (Neither can
+ stand in for the other.)
+ * Formally refresh patches that developed offsets.
+ * Factor out a new DSLMFLAGS macro for common d-shlibmove flags; include
+ the libmbedx509-0 quirk there since it will soon be needed everywhere.
+ * Address remaining underlinkage of system libraries (mbed*, z, bz2).
+ At this point, the only remaining unresolved references are of libkdf5
+ against symbols that could come from either libncbi-vdb or libncbi-wvdb.
+ (Closes: #952623, #952627, #953897.)
+ * Copy headers rather than moving them to allow for consecutive builds.
+ * Fix typo in override_dh_missing name; supply debian/not-installed.
+ * Add myself to Uploaders.
+
+ -- Aaron M. Ucko <ucko at debian.org> Tue, 19 May 2020 22:51:09 -0400
+
ncbi-vdb (2.10.6+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,6 +1,6 @@
Source: ncbi-vdb
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Aaron M. Ucko <ucko at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
=====================================
debian/not-installed
=====================================
@@ -0,0 +1,5 @@
+/usr/ncbi-vdb/*/gcc/*/dbg/bin/ncbi/*.kfg
+/usr/ncbi-vdb/*/gcc/*/dbg/ilib/*
+/usr/ncbi-vdb/*/gcc/*/dbg/lib/libdiagnose.*
+/usr/ncbi-vdb/*/gcc/*/dbg/lib/ncbi/*.kfg
+/usr/ncbi-vdb/*/gcc/*/dbg/obj/libs/*/*
=====================================
debian/patches/fix_linking.patch
=====================================
@@ -22,7 +22,7 @@ Last-Update: Tue, 28 Aug 2018 07:55:59 +0200
$(LD) --slib --vers $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers -o $@ $^ $(KDF5_LIB)
--- a/libs/ncbi-vdb/Makefile
+++ b/libs/ncbi-vdb/Makefile
-@@ -124,7 +124,7 @@ VDB_LIB = \
+@@ -125,7 +125,7 @@ VDB_LIB = \
$(LIBDIR)/libncbi-vdb.$(SHLX): $(VDB_OBJ)
echo $(SRCDIR)
=====================================
debian/patches/skip_failing_test.patch
=====================================
@@ -5,7 +5,7 @@ Description: Skip some tests that are failing in pbuilder.
--- ncbi-vdb.orig/test/kfg/kfgtest.cpp
+++ ncbi-vdb/test/kfg/kfgtest.cpp
-@@ -759,6 +759,7 @@
+@@ -804,6 +804,7 @@
string ngcPath("./prj_2956.ngc");
C::t(ngcPath);
Cleaner cleaner(wd);
@@ -13,7 +13,7 @@ Description: Skip some tests that are failing in pbuilder.
REQUIRE_RC(KConfigImportNgc(kfg, ngcPath.c_str(), "repos/ngc/", &newRepo));
TEST_MESSAGE("KConfigImportNgc(" << ngcPath << ")");
// contents of the input file:
-@@ -825,6 +826,7 @@
+@@ -870,6 +871,7 @@
REQUIRE_EQ(string(newRepo), string("repos/ngc/"));
REQUIRE_RC(KDirectoryRemove(wd, true, "repos"));
@@ -21,7 +21,7 @@ Description: Skip some tests that are failing in pbuilder.
}
#endif
-@@ -833,15 +835,19 @@
+@@ -878,15 +880,19 @@
CreateAndLoad(GetName(), "\n");
const char* newRepo;
Cleaner cleaner(wd);
=====================================
debian/patches/use_debian_packaged_libmbedx.patch
=====================================
@@ -15,18 +15,34 @@ Description: Somehow Build system expects a copy of libmbedx509.a which is
kns \
kfg \
krypto \
-@@ -128,7 +125,7 @@
+@@ -124,7 +121,7 @@
+ $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD)))
+
+ VDB_LIB = \
+- $(addprefix -s,$(VDB_LIB_RD))
++ $(addprefix -s,$(VDB_LIB_RD)) -lmbedx509 -lmbedtls -lmbedcrypto
$(LIBDIR)/libncbi-vdb.$(SHLX): $(VDB_OBJ)
echo $(SRCDIR)
-- $(LD) --dlib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(VDB_LIB)
-+ $(LD) --dlib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(VDB_LIB) -lmbedx509 -lmbedtls -lmbedcrypto
+@@ -150,7 +147,7 @@
+ $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RDWR)))
+
+ WVDB_LIB = \
+- $(addprefix -s,$(VDB_LIB_RDWR))
++ $(addprefix -s,$(VDB_LIB_RDWR)) -lmbedx509 -lmbedtls -lmbedcrypto
+
+ $(LIBDIR)/libncbi-wvdb.$(SHLX): $(WVDB_OBJ)
+ $(LD) --dlib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(WVDB_LIB)
+@@ -165,4 +162,4 @@
+ $(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)
- $(LIBDIR)/libncbi-vdb.$(LIBX): $(VDB_OBJ)
- $(LD) --slib --vers $(SRCDIR)/libncbi-vdb.vers -o $@ $(VDB_LIB)
+ cleanfuzz:
+- rm -rf $(FLIBDIR)/*
+\ No newline at end of file
++ rm -rf $(FLIBDIR)/*
--- ncbi-vdb.orig/libs/kns/Makefile
+++ ncbi-vdb/libs/kns/Makefile
-@@ -108,7 +108,8 @@
+@@ -109,7 +109,8 @@
KNS_LIB = \
-lkfs \
@@ -69,3 +85,14 @@ Description: Somehow Build system expects a copy of libmbedx509.a which is
$(LIBDIR)/libkdf5.$(LIBX): $(KDF5_OBJ)
$(LD) --slib --vers $(SRCDIR)/../ncbi-vdb/libncbi-vdb.vers -o $@ $^ $(KDF5_LIB)
+--- ncbi-vdb.orig/libs/vdb-sqlite/Makefile
++++ ncbi-vdb/libs/vdb-sqlite/Makefile
+@@ -85,7 +85,7 @@
+ $(addsuffix .$(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
=====================================
@@ -3,8 +3,6 @@ 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.
-Index: ncbi-vdb/libs/Makefile
-===================================================================
--- ncbi-vdb.orig/libs/Makefile
+++ ncbi-vdb/libs/Makefile
@@ -35,7 +35,6 @@ include $(TOP)/build/Makefile.config
@@ -15,8 +13,6 @@ Index: ncbi-vdb/libs/Makefile
kfc \
klib \
kproc \
-Index: ncbi-vdb/libs/ncbi-vdb/Makefile
-===================================================================
--- ncbi-vdb.orig/libs/ncbi-vdb/Makefile
+++ ncbi-vdb/libs/ncbi-vdb/Makefile
@@ -104,9 +104,7 @@ VDB_LIB_CMN = \
@@ -30,3 +26,14 @@ Index: ncbi-vdb/libs/ncbi-vdb/Makefile
VDB_LIB_RD = \
align-reader \
+--- ncbi-vdb.orig/libs/vdb-sqlite/Makefile
++++ ncbi-vdb/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
=====================================
@@ -17,6 +17,8 @@ VDB_ARCH := $(word 1, $(subst -, ,$(DEB_HOST_MULTIARCH)))
LIBINSTALLDIR := debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/$(VDB_ARCH)/dbg/lib
LIBPKG := libncbi-vdb2
SCHEMADIR := debian/$(LIBPKG)/usr/lib/$(DEB_SOURCE)
+DSLMFLAGS := --commit --multiarch --devunversioned --exclude-la \
+ --override s/libmbedx509-0-dev/libmbedtls-dev/
# See debian/patches/fix-linking
# export DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs -Wl,--as-needed
@@ -71,11 +73,7 @@ override_dh_auto_install:
mv $(LIBINSTALLDIR)/`readlink $$slib` $$slib ; \
mv $(LIBINSTALLDIR)/`readlink $$slib` $$slib ; \
done
- d-shlibmove --commit \
- --multiarch \
- --devunversioned \
- --exclude-la \
- --override s/libmbedx509-0-dev/libmbedtls-dev/ \
+ d-shlibmove $(DSLMFLAGS) \
--movedev debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/lib/libncbi-ngs-c++.a usr/lib/$(MULTIARCH) \
--movedev debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/ilib/libkapp.a usr/lib/$(MULTIARCH) \
--movedev debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/ilib/libkapp-norsrc.a usr/lib/$(MULTIARCH) \
@@ -86,28 +84,19 @@ override_dh_auto_install:
--movedev debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/ilib/libload.a usr/lib/$(MULTIARCH) \
--movedev debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/ilib/libtui.a usr/lib/$(MULTIARCH) \
--movedev debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/ilib/libtui_cpp.a usr/lib/$(MULTIARCH) \
- --movedev interfaces usr/include \
debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/lib/libncbi-vdb.so
- mv debian/libncbi-vdb-dev/usr/include/interfaces debian/libncbi-vdb-dev/usr/include/$(DEB_SOURCE)
- # json-response.h and services-priv.h are needed by sra-sdk
+ install -d debian/libncbi-vdb-dev/usr/include
+ cp -a interfaces debian/libncbi-vdb-dev/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
- dh_install -plibncbi-vdb-dev libs/vfs/services-priv.h usr/include/ncbi-vdb/vfs
- d-shlibmove --commit \
- --multiarch \
- --devunversioned \
- --exclude-la \
+ cp libs/vfs/services-priv.h debian/libncbi-vdb-dev/usr/include/ncbi-vdb/vfs/services-priv-internal.h
+ d-shlibmove $(DSLMFLAGS) \
--override s/libhdf5_serial[0-9]*-dev/libhdf5-dev/ \
- --override s/libmbedx509-0-dev/libmbedtls-dev/ \
debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/lib/libkdf5.so
- d-shlibmove --commit \
- --multiarch \
- --devunversioned \
- --exclude-la \
+ d-shlibmove $(DSLMFLAGS) \
debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/lib/libncbi-wvdb.so
- d-shlibmove --commit \
- --multiarch \
- --devunversioned \
- --exclude-la \
+ d-shlibmove $(DSLMFLAGS) \
debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/*/dbg/lib/libvdb-sqlite.so
find debian/lib* -name .gitignore -delete
# move schemata from development packages to library packages since these are used in executables
@@ -121,5 +110,5 @@ override_dh_auto_install:
mv $${schema} $(SCHEMADIR)/$${schemadir} ; \
done
-override_missing:
+override_dh_missing:
dh_missing --fail-missing
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/56bfd08586628125124401f9c42067ef0715cdb3...78ecbf0f4d929b2402091d98718f86c469df6492
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/56bfd08586628125124401f9c42067ef0715cdb3...78ecbf0f4d929b2402091d98718f86c469df6492
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