[med-svn] [Git][med-team/ncbi-vdb][master] 5 commits: Leave mbedtls quirk handling to d-shlibs (>= 0.104). (#999788)
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Sun Nov 21 04:16:18 GMT 2021
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb
Commits:
6dd7fe7a by Aaron M. Ucko at 2021-11-20T21:50:03-05:00
Leave mbedtls quirk handling to d-shlibs (>= 0.104). (#999788)
- - - - -
cc9d3f8a by Aaron M. Ucko at 2021-11-20T21:55:23-05:00
Skip VDB3, at least for now.
It FTBFS on i386, and has so far just been an uninstalled technology
preview.
- - - - -
245c8c82 by Aaron M. Ucko at 2021-11-20T23:00:32-05:00
Enable arm64 builds.
To that end:
* add_-msse2.patch: Limit -msse2 to 32-bit x86. (Redundant on 64-bit
x86, invalid elsewhere.)
* debian/rules: Wildcard upstream architecture name (VDB_ARCH), no
longer consistently aligned with any single dpkg-architecture variable.
- - - - -
bc744627 by Aaron M. Ucko at 2021-11-20T23:02:28-05:00
debian/watch: Track tags rather than releases
... of which GitHub no longer lists any(!).
- - - - -
182e49d8 by Aaron M. Ucko at 2021-11-20T23:11:55-05:00
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/add_-msse2.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,17 @@
-ncbi-vdb (2.11.2+dfsg-3) UNRELEASED; urgency=medium
-
- TODO: drop d-shlibs override once version 0.104 is out
- -> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=999788#17
-
- -- Andreas Tille <tille at debian.org> Wed, 17 Nov 2021 14:06:43 +0100
+ncbi-vdb (2.11.2+dfsg-3) unstable; urgency=medium
+
+ * Leave mbedtls quirk handling to d-shlibs (>= 0.104). (Closes: #999788.)
+ * Skip VDB3, at least for now -- it FTBFS on i386, and has so far just
+ been an uninstalled technology preview.
+ * Enable arm64 builds. To that end:
+ - add_-msse2.patch: Limit -msse2 to 32-bit x86. (Redundant on 64-bit
+ x86, invalid elsewhere.)
+ - debian/rules: Wildcard upstream architecture name (VDB_ARCH), no
+ longer consistently aligned with any single dpkg-architecture variable.
+ * debian/watch: Track tags rather than releases, of which GitHub no
+ longer lists any(!).
+
+ -- Aaron M. Ucko <ucko at debian.org> Sat, 20 Nov 2021 23:06:09 -0500
ncbi-vdb (2.11.2+dfsg-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- d-shlibs,
+ d-shlibs (>= 0.104),
cmake,
libbz2-dev,
libxml2-dev,
@@ -24,7 +24,7 @@ Homepage: https://github.com/ncbi/ncbi-vdb
Rules-Requires-Root: no
Package: libncbi-vdb2
-Architecture: amd64 i386 x32
+Architecture: amd64 arm64 i386 x32
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
@@ -42,7 +42,7 @@ Description: libraries for using data in the INSDC Sequence Read Archives
and Java.
Package: libncbi-vdb-dev
-Architecture: amd64 i386 x32
+Architecture: amd64 arm64 i386 x32
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -73,7 +73,7 @@ Description: libraries for using data in the INSDC Sequence Read Archives (devel
This is the development package.
Package: libkdf5-2
-Architecture: amd64 i386 x32
+Architecture: amd64 arm64 i386 x32
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -90,7 +90,7 @@ Description: hdf5 access to data in the INSDC Sequence Read Archives
to the Hierarchical Data Format 5 (HDF5).
Package: libkdf5-dev
-Architecture: amd64 i386 x32
+Architecture: amd64 arm64 i386 x32
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -109,7 +109,7 @@ Description: hdf5 access to data in the INSDC Sequence Read Archives (devel)
This is the development package.
Package: libncbi-wvdb2
-Architecture: amd64 i386 x32
+Architecture: amd64 arm64 i386 x32
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
@@ -124,7 +124,7 @@ Description: virtual layer update modul of ncbi-vdb library
This library is part of the ncbi-vdb package.
Package: libncbi-wvdb-dev
-Architecture: amd64 i386 x32
+Architecture: amd64 arm64 i386 x32
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -142,7 +142,7 @@ Description: virtual layer update modul of ncbi-vdb library (devel)
This is the development package.
Package: libvdb-sqlite2
-Architecture: amd64 i386 x32
+Architecture: amd64 arm64 i386 x32
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
@@ -158,7 +158,7 @@ Description: sqlite modul of ncbi-vdb library
interface.
Package: libvdb-sqlite-dev
-Architecture: amd64 i386 x32
+Architecture: amd64 arm64 i386 x32
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
=====================================
debian/patches/add_-msse2.patch
=====================================
@@ -1,17 +1,18 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 31 Aug 2016 07:55:11 +0200
+Last-Update: Sat, 20 Nov 2021 22:47:22 -0500
Bug-Debian: https://bugs.debian.org/836128
-Description: Add -msse2 to libs/search
+Description: Add -msse2 to libs/search on 32-bit x86
-Index: ncbi-vdb/libs/search/Makefile
-===================================================================
---- ncbi-vdb.orig/libs/search/Makefile
-+++ ncbi-vdb/libs/search/Makefile
-@@ -39,6 +39,8 @@ OBJFILES = \
+--- a/libs/search/Makefile
++++ b/libs/search/Makefile
+@@ -39,6 +39,11 @@ OBJFILES = \
include $(TOP)/build/Makefile.env
-+CFLAGS += -msse2
++MARCH := $(shell uname -m)
++ifneq ($(filter i%86, $(MARCH)),)
++ CFLAGS += -msse2
++endif
+
#-------------------------------------------------------------------------------
# outer targets
=====================================
debian/rules
=====================================
@@ -13,12 +13,12 @@ CPU := $(shell dpkg-architecture -qDEB_BUILD_GNU_CPU)
MULTIARCH := $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
# since build-results are not ending up in the proper dir its saver to use "*" instead of "$(CPU)"
SODIR := $(DEB_SOURCE)/$(DEB_SOURCE)/$(OS)/gcc
-VDB_ARCH := $(word 1, $(subst -, ,$(DEB_HOST_MULTIARCH)))
+# VDB_ARCH := $(word 1, $(subst -, ,$(DEB_HOST_MULTIARCH)))
+VDB_ARCH := *
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/
+DSLMFLAGS := --commit --multiarch --devunversioned --exclude-la
# See debian/patches/fix-linking
# export DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs -Wl,--as-needed
@@ -48,7 +48,7 @@ override_dh_auto_configure:
sed -i 's?HDF5_INCDIR = /usr/include?&/hdf5/serial?' build/Makefile.config*
override_dh_auto_build:
- dh_auto_build --no-parallel
+ 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 \
find . \( -name "*.so" -o -name "*.a" \) -exec strings \{\} \; | tee | grep vdb_mbedtls ; \
@@ -60,7 +60,7 @@ override_dh_auto_build:
override_dh_auto_test:
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 || true
+ dh_auto_test -- NO_VDB3=1 || true
else
echo "Skip testing which takes a long time"
endif
@@ -69,7 +69,7 @@ override_dh_prep:
dh_prep -Xdebian/tmp
override_dh_auto_install:
- dh_auto_install
+ dh_auto_install -- NO_VDB3=1
find $(LIBINSTALLDIR) -name "*-static.a" -delete
# upstream installs versioned *.a libs - we only want a single version
for slib in $(LIBINSTALLDIR)/*.a ; do \
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/ncbi/ncbi-vdb/releases .*/@ANY_VERSION@@ARCHIVE_EXT@
+ https://github.com/ncbi/ncbi-vdb/tags .*/@ANY_VERSION@@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/307f40a49dcee51c99069adf07e8c800d0868243...182e49d87c8912f3311376f0455ce968ce8a9a40
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/307f40a49dcee51c99069adf07e8c800d0868243...182e49d87c8912f3311376f0455ce968ce8a9a40
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