[med-svn] [Git][med-team/ncbi-tools6][master] ncbi-tools6 6.1.20170106+dfsg2-4: Drop libpcre3-dev (#1077825).
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6 Commits: 395473f5 by Aaron M. Ucko at 2024-09-08T22:50:20-04:00 ncbi-tools6 6.1.20170106+dfsg2-4: Drop libpcre3-dev (#1077825). * debian/control: Drop B-D on obsolete libpcre3-dev. * make/makedemo.unx: Comment out upstream PCRE3 demos and tests, which were the only things that needed it and weren't getting installed anyway. - - - - - 4 changed files: - debian/changelog - debian/control - debian/patches/debian-changes - make/makedemo.unx Changes: = debian/changelog = @@ -1,3 +1,13 @@ +ncbi-tools6 (6.1.20170106+dfsg2-4) unstable; urgency=medium + + * debian/control: Drop B-D on obsolete libpcre3-dev. +(Closes: #1078825.) + * make/makedemo.unx: Comment out upstream PCRE3 demos and tests, which +were the only things that needed it and weren't getting installed +anyway. + + -- Aaron M. Ucko Sun, 08 Sep 2024 22:50:02 -0400 + ncbi-tools6 (6.1.20170106+dfsg2-3) unstable; urgency=medium * Fix compilation under GCC 14. (Closes: #1075307.) = debian/control = @@ -9,7 +9,6 @@ Build-Depends-Arch: csh | c-shell, libglu1-mesa-dev | libglu-dev, libgnutls28-dev | gnutls-dev, libmotif-dev, -libpcre3-dev, libpng-dev, libxmu-dev Build-Depends-Indep: icoutils, = debian/patches/debian-changes = @@ -711,6 +711,28 @@ Combined patches from git. # # $Id: makedemo.unx,v 6.96 2016/08/31 19:05:26 ucko Exp $ # +@@ -100,8 +100,8 @@ EXE1 = testcore makeset \ + entrcmd errhdr cdscan findspl \ + ncbisort fa2htgs .WAIT testval \ + vecscreen gil2bin \ +- asn2xml debruijn asn2idx sortbyquote subfuse \ +- test_regexp demo_regexp demo_regexp_grep ++ asn2xml debruijn asn2idx sortbyquote subfuse ++# test_regexp demo_regexp demo_regexp_grep + # fastacmd formatdb formatrpsdb blastall blastpgp seedtop makemat copymat + # impala megablast blastclust rpsblast + +@@ -111,8 +111,8 @@ SRC1 = testcore.c makeset.c \ + entrcmd.c errhdr.c cdscan.c findspl.c \ + ncbisort.c fa2htgs.c testval.c \ + vecscreen.c gil2bin.c blastclust.c rpsblast.c \ +- asn2xml.c debruijn.c asn2idx.c sortbyquote.c subfuse.c \ +- pcretest.c pcredemo.c pcregrep.c ++ asn2xml.c debruijn.c asn2idx.c sortbyquote.c subfuse.c ++# pcretest.c pcredemo.c pcregrep.c + # fastacmd.c formatdb.c formatrpsdb.c blastall.c blastpgp.c seedtop.c + # makemat.c copymat.c impala.c megablast.c blastclust.c rpsblast.c + @@ -228,7 +228,8 @@ cdscan : cdscan.c # findspl = make/makedemo.unx = @@ -100,8 +100,8 @@ EXE1 = testcore makeset \ entrcmd errhdr cdscan findspl \ ncbisort fa2htgs .WAIT testval \ vecscreen gil2bin \ - asn2xml debruijn asn2idx sortbyquote subfuse \ - test_regexp demo_regexp demo_regexp_grep + asn2xml debruijn asn2idx sortbyquote subfuse +# test_regexp demo_regexp demo_regexp_grep # fastacmd formatdb formatrpsdb blastall blastpgp seedtop makemat copymat # impala megablast blastclust rpsblast @@ -111,8 +111,8 @@ SRC1 = testcore.c makeset.c \ entrcmd.c errhdr.c cdscan.c findspl.c \ ncbisort.c fa2htgs.c testval.c \ vecscreen.c gil2bin.c blastclust.c rpsblast.c \ - asn2xml.c debruijn.c asn2idx.c sortbyquote.c subfuse.c \ - pcretest.c pcredemo.c pcregrep.c + asn2xml.c debruijn.c asn2idx.c sortbyquote.c subfuse.c +# pcretest.c pcredemo.c pcregrep.c # fastacmd.c formatdb.c formatrpsdb.c blastall.c blastpgp.c seedtop.c # makemat.c copymat.c impala.c megablast.c blastclust.c rpsblast.c View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/commit/395473f56ca1e389cab296ce7ad92933b4dfa1d9 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/commit/395473f56ca1e389cab296ce7ad92933b4dfa1d9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6] Pushed new tag debian/6.1.20170106+dfsg2-4
Aaron M. Ucko pushed new tag debian/6.1.20170106+dfsg2-4 at Debian Med / ncbi-tools6 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/tree/debian/6.1.20170106+dfsg2-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag debian/2.16.0+ds-6
Aaron M. Ucko pushed new tag debian/2.16.0+ds-6 at Debian Med / ncbi-blastplus -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/debian/2.16.0+ds-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus][master] 4 commits: Start work on ncbi-blast+ 2.16.0+ds-6 (yet more arch tuneups).
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus
Commits:
d00524e8 by Aaron M. Ucko at 2024-08-06T21:35:42-04:00
Start work on ncbi-blast+ 2.16.0+ds-6 (yet more arch tuneups).
- - - - -
aba12722 by Aaron M. Ucko at 2024-08-06T21:44:20-04:00
Reinstate big-endian builds, with default blastdb_version 4.
* debian/control: Reinstate big-endian builds, which can be salvaged
adequately well.
* debian/patches/big_endian_workaround (new): On big-endian
architectures, roll makeblastdb's and makeprofiledb's default
blastdb_version back to 4 pending a proper fix. Some things,
including in particular q2-feature-classifier, will still explicitly
request version 5, but everything else should be OK. (See #107.)
- - - - -
56f72ef1 by Aaron M. Ucko at 2024-08-06T21:44:53-04:00
debian/rules: Try disabling optimization altogether on sh4.
- - - - -
5f9892c6 by Aaron M. Ucko at 2024-08-06T21:45:10-04:00
Finalize ncbi-blast+ 2.16.0+ds-6 for unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/big_endian_workaround
- debian/patches/series
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,16 @@
+ncbi-blast+ (2.16.0+ds-6) unstable; urgency=medium
+
+ * debian/control: Reinstate big-endian builds, which can be salvaged
+adequately well.
+ * debian/patches/big_endian_workaround (new): On big-endian
+architectures, roll makeblastdb's and makeprofiledb's default
+blastdb_version back to 4 pending a proper fix. Some things,
+including in particular q2-feature-classifier, will still explicitly
+request version 5, but everything else should be OK. (See #107.)
+ * debian/rules: Try disabling optimization altogether on sh4.
+
+ -- Aaron M. Ucko Tue, 06 Aug 2024 21:45:09 -0400
+
ncbi-blast+ (2.16.0+ds-5) unstable; urgency=medium
* debian/control: Forbid builds for big-endian architectures, at least
=
debian/control
=
@@ -6,7 +6,6 @@ Uploaders: Olivier Sallou ,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- architecture-is-little-endian,
autoconf2.69
Build-Depends-Arch: libboost-test-dev,
libbz2-dev,
=
debian/patches/big_endian_workaround
=
@@ -0,0 +1,34 @@
+--- a/c++/src/app/blastdb/makeblastdb.cpp
b/c++/src/app/blastdb/makeblastdb.cpp
+@@ -293,7 +293,13 @@ void CMakeBlastDBApp::Init()
+ arg_desc->AddDefaultKey("blastdb_version", "version",
+ "Version of BLAST database to be created",
+ CArgDescriptions::eInteger,
+-
NStr::NumericToString(static_cast(eBDB_Version5)));
++ NStr::NumericToString(static_cast
++#ifdef WORDS_BIGENDIAN
++ (eBDB_Version4)
++#else
++ (eBDB_Version5)
++#endif
++ ));
+ arg_desc->SetConstraint("blastdb_version",
+ new CArgAllow_Integers(eBDB_Version4,
eBDB_Version5));
+ arg_desc->AddDefaultKey("max_file_sz", "number_of_bytes",
+--- a/c++/src/app/blastdb/makeprofiledb.cpp
b/c++/src/app/blastdb/makeprofiledb.cpp
+@@ -420,7 +420,13 @@ void CMakeProfileDBApp::x_SetupArgDescri
+ arg_desc->AddDefaultKey("blastdb_version", "version",
+ "Version of BLAST database to be created",
+ CArgDescriptions::eInteger,
+-
NStr::NumericToString(static_cast(eBDB_Version5)));
++ NStr::NumericToString(static_cast
++#ifdef WORDS_BIGENDIAN
++ (eBDB_Version4)
++#else
++ (eBDB_Version5)
++#endif
++ ));
+ arg_desc->SetConstraint("blastdb_version",
+ new CArgAllow_Integers(eBDB_Version4,
eBDB_Version5));
+
=
debian/patches/series
=
@@ -20,3 +20,4 @@ support_gcc10
run_perl_directly
tune_lmdb_defaults
2to3
+big_endian_workaround
=
debian/rules
=
@@ -54,10 +54,13 @@ endif
include /usr/share/dpkg/buildflags.mk
-ifneq (,$(filter mips% sh4,$(DEB_HOST_ARCH)))
+ifneq (,$(filter mips%,$(DEB_HOST_ARCH)))
CXXFLAGS := $(CXXFLAGS:-O%=-O)
DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O
endif
+ifeq (sh4,$(DEB_HOST_ARCH))
+DEB_CONFIGURE_COMMON_FLAGS += --without-optimization
+endif
export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE
View it on GitLab:
https://salsa.debian.org/med-te
[med-svn] [Git][med-team/ncbi-blastplus][master] 5 commits: Start work on ncbi-blast+ 2.16.0+ds5 (more arch tuneups).
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus Commits: 43e1771a by Aaron M. Ucko at 2024-08-04T15:52:26-04:00 Start work on ncbi-blast+ 2.16.0+ds5 (more arch tuneups). - - - - - 32585817 by Aaron M. Ucko at 2024-08-04T15:58:14-04:00 d/control: Forbid builds for big-endian archs, at least for now. They nominally succeed, but two dependent autopkgtests (for cct and kleborate) have started failing on s390x, and there's no evidence that other BE architectures fare any better. (See #107.) - - - - - 55470f19 by Aaron M. Ucko at 2024-08-04T16:00:50-04:00 debian/rules: Try building with -fsection-anchors on alpha ... in hopes of satisfying the GOT size limit there too. - - - - - 17b63f36 by Aaron M. Ucko at 2024-08-04T16:04:02-04:00 Extend -O1 cap to sh4, which still encountered VM exhaustion. - - - - - 66da03ab by Aaron M. Ucko at 2024-08-04T16:04:33-04:00 Finalize ncbi-blast+ 2.16.0+ds-5 for unstable. - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes: = debian/changelog = @@ -1,3 +1,16 @@ +ncbi-blast+ (2.16.0+ds-5) unstable; urgency=medium + + * debian/control: Forbid builds for big-endian architectures, at least +for now. They nominally succeed, but two dependent autopkgtests (for +cct and kleborate) have started failing on s390x, and there's no +evidence that other BE architectures fare any better. (See #107.) + * debian/rules: +- Try building with -fsection-anchors on alpha in hopes of satisfying + the GOT size limit there too. +- Extend -O1 cap to sh4, which still encountered VM exhaustion. + + -- Aaron M. Ucko Sun, 04 Aug 2024 16:04:32 -0400 + ncbi-blast+ (2.16.0+ds-4) unstable; urgency=medium * debian/rules: = debian/control = @@ -6,6 +6,7 @@ Uploaders: Olivier Sallou , Section: science Priority: optional Build-Depends: debhelper-compat (= 13), + architecture-is-little-endian, autoconf2.69 Build-Depends-Arch: libboost-test-dev, libbz2-dev, = debian/rules = @@ -38,6 +38,10 @@ ifeq ($(DEB_HOST_ARCH_BITS),32) endif endif +ifeq (alpha,$(DEB_HOST_ARCH)) + export DEB_CFLAGS_MAINT_APPEND += -fsection-anchors + export DEB_CXXFLAGS_MAINT_APPEND += -fsection-anchors +endif ifeq (hppa,$(DEB_HOST_ARCH)) export DEB_CFLAGS_MAINT_APPEND += -ffunction-sections export DEB_CXXFLAGS_MAINT_APPEND += -ffunction-sections @@ -50,7 +54,7 @@ endif include /usr/share/dpkg/buildflags.mk -ifneq (,$(findstring mips,$(DEB_HOST_ARCH))) +ifneq (,$(filter mips% sh4,$(DEB_HOST_ARCH))) CXXFLAGS := $(CXXFLAGS:-O%=-O) DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O endif View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/52c39a81773b4fd6326a51d10183dbb44e296ae1...66da03abfe7a40c0dd64c70ca3339a8f179f0225 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/52c39a81773b4fd6326a51d10183dbb44e296ae1...66da03abfe7a40c0dd64c70ca3339a8f179f0225 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag debian/2.16.0+ds-5
Aaron M. Ucko pushed new tag debian/2.16.0+ds-5 at Debian Med / ncbi-blastplus -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/debian/2.16.0+ds-5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus][master] 5 commits: Start ncbi-blast+ 2.16.0+ds-4 for more arch-specific tuneups.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus Commits: 993f4083 by Aaron M. Ucko at 2024-07-27T22:25:36-04:00 Start ncbi-blast+ 2.16.0+ds-4 for more arch-specific tuneups. - - - - - 8b91d14e by Aaron M. Ucko at 2024-07-27T22:28:38-04:00 debian/rules: Move architecture.mk inclusion to the very top ... for the sake of hypothetical builds bypassing dpkg-buildpackage. - - - - - 4c228421 by Aaron M. Ucko at 2024-07-27T22:35:02-04:00 Compile with -ffunction-sections on hppa and -mxgot on mips* ... (mips64el in practice) due to having outgrown default settings. - - - - - f38fd07d by Aaron M. Ucko at 2024-07-27T22:37:56-04:00 Disable parallel building on sh4 ... in hopes of avoiding buildd virtual memory exhaustion. - - - - - 52c39a81 by Aaron M. Ucko at 2024-07-27T22:38:53-04:00 Finalize ncbi-blast+ 2.16.0+ds-4 for unstable. - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,15 @@ +ncbi-blast+ (2.16.0+ds-4) unstable; urgency=medium + + * debian/rules: +- Move architecture.mk inclusion to the very top for the sake of + hypothetical builds bypassing dpkg-buildpackage. +- Compile with -ffunction-sections on hppa and -mxgot on mips* + (mips64el in practice) due to having outgrown default settings. +- Disable parallel building on sh4 in hopes of avoiding buildd virtual + memory exhaustion. + + -- Aaron M. Ucko Sat, 27 Jul 2024 22:38:52 -0400 + ncbi-blast+ (2.16.0+ds-3) unstable; urgency=medium * debian/rules: Fix typo (missing parenthesis). = debian/rules = @@ -1,6 +1,8 @@ #!/usr/bin/make -f # -*- makefile -*- +include /usr/share/dpkg/architecture.mk + # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 @@ -8,7 +10,9 @@ export HOME=$(CURDIR)/fakehome NUMJOBS=1 ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) + ifneq (sh4,$(DEB_BUILD_ARCH)) NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) + endif endif DEB_CONFIGURE_COMMON_FLAGS=--without-autodep --without-makefile-auto-update \ @@ -34,7 +38,16 @@ ifeq ($(DEB_HOST_ARCH_BITS),32) endif endif -include /usr/share/dpkg/architecture.mk +ifeq (hppa,$(DEB_HOST_ARCH)) + export DEB_CFLAGS_MAINT_APPEND += -ffunction-sections + export DEB_CXXFLAGS_MAINT_APPEND += -ffunction-sections +endif +# Down to mips64el in practice, but easy enough to generalize +ifneq (,$(findstring mips,$(DEB_HOST_ARCH))) + export DEB_CFLAGS_MAINT_APPEND += -mxgot + export DEB_CXXFLAGS_MAINT_APPEND += -mxgot +endif + include /usr/share/dpkg/buildflags.mk ifneq (,$(findstring mips,$(DEB_HOST_ARCH))) View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/21d06e91516f3e6ff59bd39576cb41f3ae486df5...52c39a81773b4fd6326a51d10183dbb44e296ae1 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/21d06e91516f3e6ff59bd39576cb41f3ae486df5...52c39a81773b4fd6326a51d10183dbb44e296ae1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag debian/2.16.0+ds-4
Aaron M. Ucko pushed new tag debian/2.16.0+ds-4 at Debian Med / ncbi-blastplus -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/debian/2.16.0+ds-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag debian/2.16.0+ds-3
Aaron M. Ucko pushed new tag debian/2.16.0+ds-3 at Debian Med / ncbi-blastplus -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/debian/2.16.0+ds-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus][master] ncbi-blast+ 2.16.0+ds-3: d/rules typo fix (missing parenthesis).
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus Commits: 21d06e91 by Aaron M. Ucko at 2024-07-26T15:37:28-04:00 ncbi-blast+ 2.16.0+ds-3: d/rules typo fix (missing parenthesis). - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,9 @@ +ncbi-blast+ (2.16.0+ds-3) unstable; urgency=medium + + * debian/rules: Fix typo (missing parenthesis). + + -- Aaron M. Ucko Fri, 26 Jul 2024 15:37:28 -0400 + ncbi-blast+ (2.16.0+ds-2) unstable; urgency=medium * debian/patches/hurd_fixes: Extend to ncbi_localip.c, which otherwise = debian/rules = @@ -29,7 +29,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie reproducible=-timeless export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic ifeq ($(DEB_HOST_ARCH_BITS),32) - ifeq (,$(filter armhf %i386 x32,$(DEB_HOST_ARCH)) + ifeq (,$(filter armhf %i386 x32,$(DEB_HOST_ARCH))) export LIBS=-latomic endif endif View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/21d06e91516f3e6ff59bd39576cb41f3ae486df5 -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/commit/21d06e91516f3e6ff59bd39576cb41f3ae486df5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag debian/2.16.0+ds-2
Aaron M. Ucko pushed new tag debian/2.16.0+ds-2 at Debian Med / ncbi-blastplus -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/debian/2.16.0+ds-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus][master] 4 commits: Start work on ncbi-blast+ 2.16.0+ds-2 to fix FTBFS on some archs.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus Commits: accc7d00 by Aaron M. Ucko at 2024-07-26T14:28:02-04:00 Start work on ncbi-blast+ 2.16.0+ds-2 to fix FTBFS on some archs. - - - - - 14aea822 by Aaron M. Ucko at 2024-07-26T14:43:38-04:00 debian/rules: Link with -latomic on most 32-bit architectures ... excepting only x86 and armhf, which succeed as is. - - - - - c0f41780 by Aaron M. Ucko at 2024-07-26T14:54:31-04:00 debian/patches/hurd_fixes: Extend to ncbi_localip.c. It otherwise accommodates PATH_MAX's absence only under Windows. - - - - - 31d0b479 by Aaron M. Ucko at 2024-07-26T14:54:56-04:00 Finalize ncbi-blast+ 2.16.0+ds-2 for unstable. - - - - - 3 changed files: - debian/changelog - debian/patches/hurd_fixes - debian/rules Changes: = debian/changelog = @@ -1,3 +1,12 @@ +ncbi-blast+ (2.16.0+ds-2) unstable; urgency=medium + + * debian/patches/hurd_fixes: Extend to ncbi_localip.c, which otherwise +accommodates PATH_MAX's absence only under Windows. + * debian/rules: Link with -latomic on most 32-bit architectures +(excepting only x86 and armhf, which succeed as is). + + -- Aaron M. Ucko Fri, 26 Jul 2024 14:54:55 -0400 + ncbi-blast+ (2.16.0+ds-1) unstable; urgency=medium * New upstream release, which should be (more than) new enough for = debian/patches/hurd_fixes = @@ -40,3 +40,14 @@ Last-Update: 2020-09-19 # define PATH_MAX 512 // will actually use less than 32 chars #endif // NCBI_OS_MSWIN && !PATH_MAX +--- a/c++/src/connect/ncbi_localip.c b/c++/src/connect/ncbi_localip.c +@@ -67,7 +67,7 @@ + # define INADDR_LOOPBACK 0x7F01 + #endif /*!INADDR_LOOPBACK*/ + +-#if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX) ++#if /* defined(NCBI_OS_MSWIN) && */ !defined(PATH_MAX) + # ifdef _MAX_PATH + #define PATH_MAX _MAX_PATH + #else = debian/rules = @@ -28,6 +28,12 @@ DEB_CONFIGURE_EXTRA_FLAGS += --without-strip --with-symbols export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie reproducible=-timeless export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic +ifeq ($(DEB_HOST_ARCH_BITS),32) + ifeq (,$(filter armhf %i386 x32,$(DEB_HOST_ARCH)) +export LIBS=-latomic + endif +endif + include /usr/share/dpkg/architecture.mk include /usr/share/dpkg/buildflags.mk View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/1411bc81806aad716ae2e204821a73378587bf88...31d0b4795bf0f8056948bd455ef1bae5915a85c5 -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/1411bc81806aad716ae2e204821a73378587bf88...31d0b4795bf0f8056948bd455ef1bae5915a85c5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag debian/2.16.0+ds-1
Aaron M. Ucko pushed new tag debian/2.16.0+ds-1 at Debian Med / ncbi-blastplus -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/debian/2.16.0+ds-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus][master] 19 commits: New upstream version 2.15.0+ds
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus Commits: 67807fe0 by Aaron M. Ucko at 2024-07-17T21:22:59-04:00 New upstream version 2.15.0+ds - - - - - fbfbf2ee by Aaron M. Ucko at 2024-07-17T21:28:39-04:00 Merge tag 'upstream/2.15.0+ds' (#1074316). Upstream version 2.15.0(+ds) should be (more than) new enough for recent q2-feature-classifier, which merely needs at least 2.13. - - - - - abe67c72 by Aaron M. Ucko at 2024-07-17T21:39:29-04:00 d/patches: Update for new release (2.15.0[+ds]), mostly formally. - - - - - c492f265 by Aaron M. Ucko at 2024-07-22T23:20:45-04:00 BDA on libnghttp2-dev, libsqlite3-dev, and libuv1-dev, newly needed. - - - - - 135c5cbd by Aaron M. Ucko at 2024-07-22T23:29:52-04:00 Move debian/patches/system_mbedtls_only up and extend it. * debian/patches/series: Move system_mbedtls_only up in conjunction with incorporating part of an upstream patch needed by support_mbedtls3. * debian/patches/system_mbedtls: Extend to cover ncbi_mbedtls.c (as in https://github.com/ncbi/ncbi-cxx-toolkit-public/commit/f9c7297dd1) and Makefile.xxconnect2.lib. - - - - - a3d3e495 by Aaron M. Ucko at 2024-07-22T23:30:47-04:00 d/p/support_mbedtls3 (new): Support Mbed TLS 3.x (#1075867). Don't specifically require it, though. - - - - - f9d97278 by Aaron M. Ucko at 2024-07-22T23:30:56-04:00 Regenerate configure and config.h.in with Autoconf 2.69. To that end, add a B-D on autoconf2.69. - - - - - bdc3fc7f by Aaron M. Ucko at 2024-07-22T23:31:22-04:00 Make it possible to build against PCRE2, and do so (#891197). * debian/control: Build against libpcre2-dev. * debian/patches/allow_pcre2 (new): Allow use of PCRE2. * debian/rules: Build against PCRE2. - - - - - 8f6aa0b1 by Aaron M. Ucko at 2024-07-22T23:31:32-04:00 Refresh patches after prepending allow_pcre2 and support_mbedtls3. - - - - - ad520e4e by Aaron M. Ucko at 2024-07-22T23:31:32-04:00 debian/rules: Add --without-strip, disable reproducible=timeless. Tune flags: Add --without-strip to make --with-symbols effective; switch off warnings from __DATE__/__TIME__ usage, since dpkg-buildpackage's SOURCE_DATE_EPOCH injection should suffice. - - - - - e016e597 by Aaron M. Ucko at 2024-07-22T23:32:00-04:00 debian/patches/series: Comment out reprobuild (overkill). I'm all for reproducibility, but the package already automatically builds with flags that make __FILE__ relative, and many of its uses are in header-defined macros that intend to pick up their callers' paths. - - - - - a1513d3e by Aaron M. Ucko at 2024-07-22T23:32:03-04:00 debian/rules: Extend generated-sources cleanup to objtools/eutils. Not entirely straightforward due to input format variation. - - - - - 6bdc2344 by Aaron M. Ucko at 2024-07-22T23:32:03-04:00 debian/source/lintian-overrides: No more rapidjson10 (just ...11). - - - - - a9e68c34 by Aaron M. Ucko at 2024-07-25T20:00:49-04:00 Stop relying on 2to3 at build time. * debian/control: Stop building against 2to3, which may not be around much longer. * debian/patches/allow_pcre2 (new): Allow use of PCRE2. * debian/rules: Drop build-time 2to3 invocation in favor of debian/patches/2to3. - - - - - e69e9a2f by Aaron M. Ucko at 2024-07-25T20:02:52-04:00 New upstream version 2.16.0+ds - - - - - e5d75ace by Aaron M. Ucko at 2024-07-25T20:40:28-04:00 Merge tag 'upstream/2.16.0+ds' Upstream version 2.16.0(+ds). - - - - - 4678cd3f by Aaron M. Ucko at 2024-07-25T20:41:04-04:00 routine-update: Standards-Version: 4.7.0 - - - - - 19a32770 by Aaron M. Ucko at 2024-07-25T20:41:15-04:00 Update patches again for 2.16.0(+ds). - - - - - 1411bc81 by Aaron M. Ucko at 2024-07-25T20:41:31-04:00 Finalize ncbi-blast+ 2.16.0+ds-1 for unstable. - - - - - 30 changed files: - c++/compilers/cygwin/build.sh - c++/compilers/unix/GCC.sh - c++/compilers/unix/ICC.sh - c++/compilers/unix/Xcode.sh - − c++/compilers/vs2017/Makefile.WinMain.app.msvc - − c++/compilers/vs2017/Makefile.wxWidgets.app.msvc - − c++/compilers/vs2017/build.sh - − c++/compilers/vs2017/build_exec.bat - − c++/compilers/vs2017/build_util.sh - − c++/compilers/vs2017/check.sh - − c++/compilers/vs2017/configure.bat - − c++/compilers/vs2017/datatool.bat - − c++/compilers/vs2017/dll/build/UtilityProjects/_CONFIGURE_.vcxproj - − c++/compilers/vs2017/dll/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj - − c++/compilers/vs2017/dll/build/UtilityProjects/configure._ - − c++/compilers/vs2017/dll/build/UtilityProjects/configure_dialog._ - − c++/compilers/vs2017/dll/build/all.bat - − c++/compilers/vs2017/dll/build/all_gbench.bat - − c++/compilers/vs2017/dll/build/all_gui.bat - − c++/compilers/vs2017/dll/build/all_ncbi.bat - − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/_CONFIGURE_.vcxproj - − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj - − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/configure._ - − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/configure_dialog._ - − c++/compilers/vs2017/dll/build/gbe
[med-svn] [Git][med-team/ncbi-blastplus][upstream] 2 commits: New upstream version 2.15.0+ds
Aaron M. Ucko pushed to branch upstream at Debian Med / ncbi-blastplus Commits: 67807fe0 by Aaron M. Ucko at 2024-07-17T21:22:59-04:00 New upstream version 2.15.0+ds - - - - - e69e9a2f by Aaron M. Ucko at 2024-07-25T20:02:52-04:00 New upstream version 2.16.0+ds - - - - - 30 changed files: - c++/compilers/cygwin/build.sh - c++/compilers/unix/GCC.sh - c++/compilers/unix/ICC.sh - c++/compilers/unix/Xcode.sh - − c++/compilers/vs2017/Makefile.WinMain.app.msvc - − c++/compilers/vs2017/Makefile.wxWidgets.app.msvc - − c++/compilers/vs2017/build.sh - − c++/compilers/vs2017/build_exec.bat - − c++/compilers/vs2017/build_util.sh - − c++/compilers/vs2017/check.sh - − c++/compilers/vs2017/configure.bat - − c++/compilers/vs2017/datatool.bat - − c++/compilers/vs2017/dll/build/UtilityProjects/_CONFIGURE_.vcxproj - − c++/compilers/vs2017/dll/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj - − c++/compilers/vs2017/dll/build/UtilityProjects/configure._ - − c++/compilers/vs2017/dll/build/UtilityProjects/configure_dialog._ - − c++/compilers/vs2017/dll/build/all.bat - − c++/compilers/vs2017/dll/build/all_gbench.bat - − c++/compilers/vs2017/dll/build/all_gui.bat - − c++/compilers/vs2017/dll/build/all_ncbi.bat - − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/_CONFIGURE_.vcxproj - − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj - − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/configure._ - − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/configure_dialog._ - − c++/compilers/vs2017/dll/build/gbench/configure_prebuild.bat - − c++/compilers/vs2017/dll/build/gbench/gbench_install/gbench-install.vcxproj - − c++/compilers/vs2017/dll/build/gbench/ncbi_gbench.sln - − c++/compilers/vs2017/dll/build/gui/UtilityProjects/_CONFIGURE_.vcxproj - − c++/compilers/vs2017/dll/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj - − c++/compilers/vs2017/dll/build/gui/UtilityProjects/configure._ The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/12379a63cc5affadbbcd17e292a8cb410c81dd91...e69e9a2f4c6f482245434666ca15379112a6cdfe -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/12379a63cc5affadbbcd17e292a8cb410c81dd91...e69e9a2f4c6f482245434666ca15379112a6cdfe You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag upstream/2.16.0+ds
Aaron M. Ucko pushed new tag upstream/2.16.0+ds at Debian Med / ncbi-blastplus -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/upstream/2.16.0+ds You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag upstream/2.15.0+ds
Aaron M. Ucko pushed new tag upstream/2.15.0+ds at Debian Med / ncbi-blastplus -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/upstream/2.15.0+ds You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6] Pushed new tag debian/6.1.20170106+dfsg2-3
Aaron M. Ucko pushed new tag debian/6.1.20170106+dfsg2-3 at Debian Med / ncbi-tools6 -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/tree/debian/6.1.20170106+dfsg2-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.9+dfsg-3
Aaron M. Ucko pushed new tag debian/3.0.9+dfsg-3 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.9+dfsg-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.3+dfsg-7
Aaron M. Ucko pushed new tag debian/3.0.3+dfsg-7 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.3+dfsg-7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new branch debian/mbedtls-2
Aaron M. Ucko pushed new branch debian/mbedtls-2 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/mbedtls-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.9+dfsg-2
Aaron M. Ucko pushed new tag debian/3.0.9+dfsg-2 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.9+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] sra-sdk 3.0.9+dfsg-2: Add fix_arm64_build.patch.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: 2b50228c by Aaron M. Ucko at 2024-04-12T19:32:52-04:00 sra-sdk 3.0.9+dfsg-2: Add fix_arm64_build.patch. Fix arm64 builds by tweaking BitMagic to treat __aarch64__ like __arm64__. - - - - - 3 changed files: - debian/changelog - + debian/patches/fix_arm64_build.patch - debian/patches/series Changes: = debian/changelog = @@ -1,3 +1,10 @@ +sra-sdk (3.0.9+dfsg-2) experimental; urgency=medium + + * debian/patches/fix_arm64_build.patch (new): Fix arm64 builds by +tweaking BitMagic to treat __aarch64__ like __arm64__. + + -- Aaron M. Ucko Fri, 12 Apr 2024 19:32:51 -0400 + sra-sdk (3.0.9+dfsg-1) experimental; urgency=medium [ Andreas Tille ] = debian/patches/fix_arm64_build.patch = @@ -0,0 +1,49 @@ +Index: b/libs/inc/bm/bmsse2.h +=== +--- a/libs/inc/bm/bmsse2.h b/libs/inc/bm/bmsse2.h +@@ -22,7 +22,7 @@ For more information please visit: http + \brief Compute functions for SSE2 SIMD instruction set (internal) + */ + +-#if !defined(__arm64__) && !defined(__arm__) ++#if !defined(__aarch64__) && !defined(__arm64__) && !defined(__arm__) + #ifndef BMWASMSIMDOPT + #include + #endif +Index: b/libs/inc/bm/bmutil.h +=== +--- a/libs/inc/bm/bmutil.h b/libs/inc/bm/bmutil.h +@@ -26,7 +26,7 @@ For more information please visit: http + #include "bmdef.h" + #include "bmconst.h" + +-#if defined(__arm64__) || defined(__arm__) ++#if defined(__aarch64__) || defined(__arm64__) || defined(__arm__) + //#include "sse2neon.h" + #else + #if defined(_M_AMD64) || defined(_M_X64) +@@ -611,7 +611,7 @@ unsigned word_bitcount64(bm::id64_t x) B + return _mm_popcnt_u32(x >> 32) + _mm_popcnt_u32((unsigned)x); + #endif + #else +-#if defined(BM_USE_GCC_BUILD) || defined(__arm64__) ++#if defined(BM_USE_GCC_BUILD) || defined(__aarch64__) || defined(__arm64__) + return (unsigned)__builtin_popcountll(x); + #else + #if (defined(__arm__)) // 32-bit +Index: b/libs/inc/bm/encoding.h +=== +--- a/libs/inc/bm/encoding.h b/libs/inc/bm/encoding.h +@@ -1810,7 +1810,8 @@ unsigned bit_in::gamma() BMNOE + continue; + } + unsigned first_bit_idx = +-#if defined(BM_x86) && (defined(__GNUG__) || defined(_MSC_VER)) && !(defined(__arm64__) || defined(__arm__)) ++#if defined(BM_x86) && (defined(__GNUG__) || defined(_MSC_VER)) && \ ++!defined(__aarch64__) || (defined(__arm64__) || defined(__arm__)) + bm::bsf_asm32(acc); + #else + bm::bit_scan_fwd(acc); = debian/patches/series = @@ -38,3 +38,4 @@ prefer_dynamic_libraries.patch fix_ngs-c++-underlinkage.patch use_c_locale_for_comma.patch no_sse4.2.patch +fix_arm64_build.patch View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/2b50228c25c245cc6672411284719fd6b739bcba -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/2b50228c25c245cc6672411284719fd6b739bcba You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.9+dfsg-1
Aaron M. Ucko pushed new tag debian/3.0.9+dfsg-1 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.9+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] 2 commits: routine-update: Standards-Version: 4.7.0
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: e816b301 by Aaron M. Ucko at 2024-04-12T18:01:03-04:00 routine-update: Standards-Version: 4.7.0 - - - - - 3c24d355 by Aaron M. Ucko at 2024-04-12T18:02:50-04:00 Finalize sra-sdk 3.0.9+dfsg-1 for experimental. - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = @@ -1,4 +1,4 @@ -sra-sdk (3.0.9+dfsg-1) UNRELEASED; urgency=medium +sra-sdk (3.0.9+dfsg-1) experimental; urgency=medium [ Andreas Tille ] * New upstream version @@ -21,8 +21,9 @@ sra-sdk (3.0.9+dfsg-1) UNRELEASED; urgency=medium using job 5576517. * debian/sra-toolkit.links: Drop; its only entry has dangled since vdb-get retired (in upstream version 3.0.1). (Closes: #1040391.) + * Standards-Version: 4.7.0 (routine-update) - -- Aaron M. Ucko Fri, 12 Apr 2024 17:15:20 -0400 + -- Aaron M. Ucko Fri, 12 Apr 2024 18:02:49 -0400 sra-sdk (3.0.3+dfsg-6) unstable; urgency=high = debian/control = @@ -25,7 +25,7 @@ Build-Depends: debhelper-compat (= 13), default-jdk, flex, bison -Standards-Version: 4.6.2 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/sra-sdk Vcs-Git: https://salsa.debian.org/med-team/sra-sdk.git Homepage: https://github.com/ncbi/sra-tools/ View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/0d5b0dc49ee2b611296c7e1015a52f9bd91c042e...3c24d355a2123f8435454bf6d85df213b9f45fea -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/0d5b0dc49ee2b611296c7e1015a52f9bd91c042e...3c24d355a2123f8435454bf6d85df213b9f45fea You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] label_online_tests.patch: Fix a paste-o in the latest change.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
0d5b0dc4 by Aaron M. Ucko at 2024-04-12T17:29:10-04:00
label_online_tests.patch: Fix a paste-o in the latest change.
- - - - -
1 changed file:
- debian/patches/label_online_tests.patch
Changes:
=
debian/patches/label_online_tests.patch
=
@@ -1,5 +1,5 @@
Author: Aaron M. Ucko
-Last-Update: 2024-04-12 17:15;20
+Last-Update: 2024-04-12 17:29;10
Description: Label tests "online" to have an easy option to run/ignore them
properly
--- a/ngs/ngs-sdk/examples/CMakeLists.txt
@@ -374,7 +374,7 @@ Description: Label tests "online" to have an easy option to
run/ignore them prop
+PROPERTIES LABELS online )
add_test ( NAME SraSearch-3.05-single-run-default-WGS WORKING_DIRECTORY
${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
${SRA_SEARCH} 3.05-single-run-default-WGS
--sort --args "AGCTAGCTA ALAI01" )
-+ set_tests_properties( SlowTest_SraSearch-3.05-single-run-default-WGS
++ set_tests_properties( SraSearch-3.05-single-run-default-WGS
+PROPERTIES LABELS online )
add_test ( NAME SlowTest_SraSearch-3.1-single-run-fgrep-standard
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMAND runtestcase.sh
${SRA_SEARCH} 3.1-single-run-fgrep-standard
--args "AGCTAGCTAGCT -T 1 -a FgrepStandard SRR01" )
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/0d5b0dc49ee2b611296c7e1015a52f9bd91c042e
--
View it on GitLab:
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[med-svn] [Git][med-team/sra-sdk][master] debian/salsa-ci.yml: Correct aptly line to specify experimental.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: 4b9c6e38 by Aaron M. Ucko at 2024-04-11T21:02:11-04:00 debian/salsa-ci.yml: Correct aptly line to specify experimental. - - - - - 1 changed file: - debian/salsa-ci.yml Changes: = debian/salsa-ci.yml = @@ -9,5 +9,5 @@ variables: RELEASE: 'experimental' before_script: - - echo "deb [trusted=yes] https://salsa.debian.org/med-team/ncbi-vdb/-/jobs/5576517/artifacts/raw/aptly unstable main" | tee /etc/apt/sources.list.d/pkga.list + - echo "deb [trusted=yes] https://salsa.debian.org/med-team/ncbi-vdb/-/jobs/5576517/artifacts/raw/aptly experimental main" | tee /etc/apt/sources.list.d/pkga.list - apt-get update View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/4b9c6e38094251e1ff1af75472f19d97a467d124 -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/4b9c6e38094251e1ff1af75472f19d97a467d124 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] 4 commits: d/control: Tighten libncbi-vdb-dev requirement to (>= 3.0.9+dfsg~)
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: 1e03fff7 by Aaron M. Ucko at 2024-04-11T20:12:29-04:00 d/control: Tighten libncbi-vdb-dev requirement to (>= 3.0.9+dfsg~) ... per upstream expectations; this stack has to stay in experimental as long as mbed TLS 3 does, calling for explicit hints. - - - - - 1facc476 by Aaron M. Ucko at 2024-04-11T20:19:08-04:00 debian/control: Drop explicit B-D on python3-distutils (#1065961) ... currently redundant with dh-python (which depends on it via python3-setuptools) and found unnecessary regardless in Ubuntu. - - - - - 6a672f8e by Aaron M. Ucko at 2024-04-11T20:38:23-04:00 debian/sra-toolkit.links: Drop (#1040391). Its only entry has dangled since vdb-get retired (in upstream version 3.0.1). - - - - - 678791c9 by Aaron M. Ucko at 2024-04-11T20:45:46-04:00 debian/salsa-ci.yml: Try to ensure availability of experimental VDB ... both by setting RELEASE to experimental and by reinstating aptly, now using job 5576517. - - - - - 4 changed files: - debian/changelog - debian/control - debian/salsa-ci.yml - − debian/sra-toolkit.links Changes: = debian/changelog = @@ -1,8 +1,23 @@ sra-sdk (3.0.9+dfsg-1) UNRELEASED; urgency=medium + [ Andreas Tille ] * New upstream version - -- Andreas Tille Sat, 09 Dec 2023 18:49:51 +0100 + [ Aaron M. Ucko ] + * debian/control: +- Tighten libncbi-vdb-dev requirement to (>= 3.0.9+dfsg~) per + upstream expectations; this stack has to stay in experimental as + long as mbed TLS 3 does, calling for explicit hints. +- Drop explicit B-D on python3-distutils, currently redundant with + dh-python (which depends on it via python3-setuptools) and found + unnecessary regardless in Ubuntu. (Closes: #1065961.) + * debian/salsa-ci.yml: Try to ensure availability of experimental VDB, +both by setting RELEASE to experimental and by reinstating aptly, now +using job 5576517. + * debian/sra-toolkit.links: Drop; its only entry has dangled since +vdb-get retired (in upstream version 3.0.1). (Closes: #1040391.) + + -- Aaron M. Ucko Thu, 11 Apr 2024 20:42:53 -0400 sra-sdk (3.0.3+dfsg-6) unstable; urgency=high = debian/control = @@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13), d-shlibs, dh-python, javahelper, - libncbi-vdb-dev (>= 3.0.1+dfsg~), + libncbi-vdb-dev (>= 3.0.9+dfsg~), libfuse-dev, libhdf5-dev, libmagic-dev, @@ -22,7 +22,6 @@ Build-Depends: debhelper-compat (= 13), markdown | libtext-markdown-perl | discount , maven-repo-helper, python3-all, - python3-distutils, default-jdk, flex, bison = debian/salsa-ci.yml = @@ -6,3 +6,8 @@ include: variables: # Does not build on i386 SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1 + RELEASE: 'experimental' + +before_script: + - echo "deb [trusted=yes] https://salsa.debian.org/med-team/ncbi-vdb/-/jobs/5576517/artifacts/raw/aptly unstable main" | tee /etc/apt/sources.list.d/pkga.list + - apt-get update = debian/sra-toolkit.links deleted = @@ -1 +0,0 @@ -usr/bin/vdb-get/usr/lib/debian-med/bin/kget View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/cc4a934048e04ad5b99109d2cfb47cc8f799b809...678791c9de54670333731c45b988b32a3ea0854c -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/cc4a934048e04ad5b99109d2cfb47cc8f799b809...678791c9de54670333731c45b988b32a3ea0854c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb] Pushed new tag debian/3.0.9+dfsg-1
Aaron M. Ucko pushed new tag debian/3.0.9+dfsg-1 at Debian Med / ncbi-vdb -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/tree/debian/3.0.9+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb][master] 4 commits: Add debian/patches/system_mbedtls_3.patch.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb
Commits:
a6a4a594 by Aaron M. Ucko at 2024-04-11T17:33:48-04:00
Add debian/patches/system_mbedtls_3.patch.
Reinstate test for system mbed TLS, tweaking it to accept (and
moreover require) 3.x.
- - - - -
5dc35d4a by Aaron M. Ucko at 2024-04-11T17:36:08-04:00
Version libmbedtls-dev B-D to (>= 3) [experimental]
Match recent versions' usage.
- - - - -
5c48af82 by Aaron M. Ucko at 2024-04-11T17:38:28-04:00
Reenable aptly per the need to target experimental again for now.
- - - - -
495b52bf by Aaron M. Ucko at 2024-04-11T17:40:20-04:00
routine-update: Ready to upload to experimental
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/system_mbedtls_3.patch
- debian/salsa-ci.yml
Changes:
=
debian/changelog
=
@@ -1,10 +1,17 @@
-ncbi-vdb (3.0.9+dfsg-1) UNRELEASED; urgency=medium
+ncbi-vdb (3.0.9+dfsg-1) experimental; urgency=medium
+ [ Andreas Tille ]
* New upstream version
- TODO: Wait for mbedtls 3.x
-see https://lists.debian.org/debian-med/2023/12/msg00029.html
- -- Andreas Tille Sun, 10 Dec 2023 10:49:48 +0100
+ [ Aaron M. Ucko ]
+ * debian/control: Version libmbedtls-dev B-D to (>= 3), so far available
+only in experimental, to match recent versions' usage.
+ * debian/patches/system_mbedtls_3.patch (new): Reinstate test for system
+mbed TLS, tweaking it to accept (and moreover require) 3.x.
+ * debian/salsa-ci.yml: Reenable aptly per the need to target
+experimental again for now.
+
+ -- Aaron M. Ucko Thu, 11 Apr 2024 17:40:20 -0400
ncbi-vdb (3.0.2+dfsg-2) unstable; urgency=medium
=
debian/control
=
@@ -10,7 +10,7 @@ Build-Depends-Arch: cmake,
libbz2-dev,
libxml2-dev,
libmagic-dev,
-libmbedtls-dev,
+libmbedtls-dev (>= 3),
zlib1g-dev,
libzstd-dev,
flex,
=
debian/patches/series
=
@@ -6,3 +6,4 @@ soversion.patch
libsam-extract_shared.patch
detect_BITS.patch
fix_x32.patch
+system_mbedtls_3.patch
=
debian/patches/system_mbedtls_3.patch
=
@@ -0,0 +1,23 @@
+Index: b/build/common.cmake
+===
+--- a/build/common.cmake
b/build/common.cmake
+@@ -225,8 +225,7 @@ function( AddExecutableTest test_name so
+ endfunction()
+
+ include(CheckIncludeFileCXX)
+-#check_include_file_cxx(mbedtls/md.h HAVE_MBEDTLS_H)
+-set(HAVE_MBEDTLS_H 0) # TODO: disabling system mbedtls since it may be
outdated
++check_include_file_cxx(mbedtls/md.h HAVE_MBEDTLS_H)
+ set( MBEDTLS_LIBS mbedx509 mbedtls mbedcrypto ) # need to link against
mbedtls in any case: system or local mbedtls
+ set(CMAKE_REQUIRED_LIBRARIES ${MBEDTLS_LIBS})
+ if ( HAVE_MBEDTLS_H )
+@@ -239,7 +238,7 @@ int main(int argc, char *argv[]) {
+ mbedtls_md_context_t ctx;
+ mbedtls_md_type_t md_type = MBEDTLS_MD_SHA256;
+ mbedtls_md_init(&ctx);
+- printf(\"test p: %p\", ctx.md_ctx);
++ printf(\"test p: %p\", mbedtls_md_info_from_ctx(&ctx));
+ }
+ " HAVE_MBEDTLS_F)
+ else()
=
debian/salsa-ci.yml
=
@@ -2,3 +2,5 @@
include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
-
https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+variables:
+ SALSA_CI_DISABLE_APTLY: 0
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-vdb/-/compare/4322984b6e9a886b7cfffc3513c0ed300da2f4f9...495b52bfc25edf7250906cdc3bac5576c66c7f6d
--
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-vdb/-/compare/4322984b6e9a886b7cfffc3513c0ed300da2f4f9...495b52bfc25edf7250906cdc3bac5576c66c7f6d
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[med-svn] [Git][med-team/ncbi-tools6] Pushed new tag debian/6.1.20170106+dfsg2-2
Aaron M. Ucko pushed new tag debian/6.1.20170106+dfsg2-2 at Debian Med / ncbi-tools6 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/tree/debian/6.1.20170106+dfsg2-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6] Pushed new tag debian/6.1.20170106+dfsg2-1
Aaron M. Ucko pushed new tag debian/6.1.20170106+dfsg2-1 at Debian Med / ncbi-tools6 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/tree/debian/6.1.20170106+dfsg2-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6][master] 6 commits: ncbi-tools6 6.1.20170106+dfsg1-10.1: final time64 NMU (#1064245).
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6
Commits:
4e093c7e by Steve Langasek at 2024-03-01T08:33:40-05:00
ncbi-tools6 6.1.20170106+dfsg1-10.1: final time64 NMU (#1064245).
- - - - -
2c420c00 by Aaron M. Ucko at 2024-03-01T08:44:21-05:00
Start ncbi-tools6 6.1.20170106+dfsg2-1, with final time64 changes.
- - - - -
0c7c5445 by Aaron M. Ucko at 2024-03-01T08:50:54-05:00
Merge final time64 changes (debian/6.1.20170106+dfsg1-10.1+final).
ncbi-tools6 6.1.20170106+dfsg1-10.1: final time64 NMU (#1064245).
The previous two uploads used 6.1.20170106+dfsg1-10.1~exp2 as their
basis. Adjust ...-1~exp1's changelog entry accordingly, dropping the
Closes: annotation and the note about properly handling multi-library
.symbols files.
- - - - -
a255aeb1 by Aaron M. Ucko at 2024-03-01T08:57:14-05:00
debian/rules: Don't explicitly opt into time64 anywhere.
The final version of the NMU added a suitable versioned B-D on
dpkg-dev, and the explicit logic (formally?) overshot on hurd-i386 and
any even less official i386 architectures. (RIP kfreebsd-i386.)
- - - - -
d303abbf by Aaron M. Ucko at 2024-03-01T08:59:05-05:00
Trim redundant versioned build dependencies on dpkg-dev.
A single mention in B-D should suffice.
- - - - -
d7cce688 by Aaron M. Ucko at 2024-03-01T08:59:46-05:00
Finalize ncbi-tools6 6.1.20170106+dfsg2-1 for unstable.
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,18 @@
+ncbi-tools6 (6.1.20170106+dfsg2-1) unstable; urgency=medium
+
+ * Incorporate final time64 changes; the previous two uploads used
+6.1.20170106+dfsg1-10.1~exp2 as their basis. Adjust ...-1~exp1's
+changelog entry accordingly, dropping the Closes: annotation and the
+note about properly handling multi-library .symbols files.
+ * debian/control: Trim redundant versioned build dependencies on
+dpkg-dev; a single mention in B-D should suffice.
+ * debian/rules: Don't explicitly opt into time64 anywhere. The final
+version of the NMU added a suitable versioned B-D on dpkg-dev, and the
+explicit logic (formally?) overshot on hurd-i386 and any even less
+official i386 architectures. (RIP kfreebsd-i386.)
+
+ -- Aaron M. Ucko Fri, 01 Mar 2024 08:59:45 -0500
+
ncbi-tools6 (6.1.20170106+dfsg2-1~exp2) experimental; urgency=medium
* debian/rules: Explicitly opt back out of the time64 ABI on i386.
@@ -9,11 +24,9 @@ ncbi-tools6 (6.1.20170106+dfsg2-1~exp1) experimental;
urgency=medium
* New tarball, with the webdesign subtree dropped; at least some of its
content was generated but supplied without corresponding sources and
inputs, and nothing from there was getting packaged anyway.
- * Merge initial (NMU-ed) time64 changes. (Closes: #1064245.)
+ * Merge initial (NMU-ed) time64 changes.
* debian/{.gitignore,libncbi6t64.doc-base,*.lintian-overrides,*.symbols}:
-Correct stray references to old library package names. NB: The
-initial .symbols changes missed the fact that each library package
-contained multiple libraries (not worth splitting up), and these
+Correct stray references to old library package names. NB: These
lintian-overrides tuneups drop post-colon package names altogether.
* debian/copyright (Files-Excluded):
- Drop spurious leading ncbi/.
@@ -23,12 +36,12 @@ ncbi-tools6 (6.1.20170106+dfsg2-1~exp1) experimental;
urgency=medium
-- Aaron M. Ucko Sun, 18 Feb 2024 21:10:49 -0500
-ncbi-tools6 (6.1.20170106+dfsg1-10.1) experimental; urgency=medium
+ncbi-tools6 (6.1.20170106+dfsg1-10.1) unstable; urgency=medium
* Non-maintainer upload.
- * Rename libraries for 64-bit time_t transition.
+ * Rename libraries for 64-bit time_t transition. Closes: #1064245
- -- Steve Langasek Sun, 18 Feb 2024 23:06:02 +
+ -- Steve Langasek Fri, 01 Mar 2024 10:43:06 +
ncbi-tools6 (6.1.20170106+dfsg1-10) unstable; urgency=medium
=
debian/control
=
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team
Section: libdevel
Priority: optional
-Build-Depends: debhelper-compat (= 13)
+Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13)
Build-Depends-Arch: csh | c-shell,
libglu1-mesa-dev | libglu-dev,
libgnutls28-dev | gnutls-dev,
=
debian/rules
=
@@ -29,9 +29,6 @@ THREAD_OBJ = ncbithr.o
NETENTREZVERSION = 2.02c2ASN1SPEC6
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-ifneq ($(DEB_HOST_ARCH),i386)
- DEB_BUILD_MAINT_OPTIONS += abi=+time64
-endif
CFLAGS := $(shell dpkg-buildflags --get CFLAGS) -Wall \
$(shell dpkg-buildflags --get CPPFLAGS)
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-tools6/-/compare/c34ff0c8cd61d4fad3ba24c22d4a3846712a59e1..
[med-svn] [Git][med-team/ncbi-tools6] Pushed new tag debian/6.1.20170106+dfsg1-10.1+final
Aaron M. Ucko pushed new tag debian/6.1.20170106+dfsg1-10.1+final at Debian Med / ncbi-tools6 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/tree/debian/6.1.20170106+dfsg1-10.1+final You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6][master] ncbi-tools6 6.1.20170106+dfsg2-1~exp2: No time64 for i386.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6 Commits: c34ff0c8 by Aaron M. Ucko at 2024-02-26T21:38:37-05:00 ncbi-tools6 6.1.20170106+dfsg2-1~exp2: No time64 for i386. debian/rules: Explicitly opt back out of the time64 ABI on i386. - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,9 @@ +ncbi-tools6 (6.1.20170106+dfsg2-1~exp2) experimental; urgency=medium + + * debian/rules: Explicitly opt back out of the time64 ABI on i386. + + -- Aaron M. Ucko Mon, 26 Feb 2024 21:38:36 -0500 + ncbi-tools6 (6.1.20170106+dfsg2-1~exp1) experimental; urgency=medium * New tarball, with the webdesign subtree dropped; at least some of its = debian/rules = @@ -28,7 +28,10 @@ MT_OTHERLIBS = -lpthread THREAD_OBJ = ncbithr.o NETENTREZVERSION = 2.02c2ASN1SPEC6 -export DEB_BUILD_MAINT_OPTIONS=hardening=+all abi=+time64 +export DEB_BUILD_MAINT_OPTIONS = hardening=+all +ifneq ($(DEB_HOST_ARCH),i386) + DEB_BUILD_MAINT_OPTIONS += abi=+time64 +endif CFLAGS := $(shell dpkg-buildflags --get CFLAGS) -Wall \ $(shell dpkg-buildflags --get CPPFLAGS) View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/commit/c34ff0c8cd61d4fad3ba24c22d4a3846712a59e1 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/commit/c34ff0c8cd61d4fad3ba24c22d4a3846712a59e1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6] Pushed new tag debian/6.1.20170106+dfsg2-1_exp2
Aaron M. Ucko pushed new tag debian/6.1.20170106+dfsg2-1_exp2 at Debian Med / ncbi-tools6 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/tree/debian/6.1.20170106+dfsg2-1_exp2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6][pristine-tar] pristine-tar data for ncbi-tools6_6.1.20170106+dfsg2.orig.tar.xz
Aaron M. Ucko pushed to branch pristine-tar at Debian Med / ncbi-tools6 Commits: 914cd531 by Aaron M. Ucko at 2024-02-18T19:30:37-05:00 pristine-tar data for ncbi-tools6_6.1.20170106+dfsg2.orig.tar.xz - - - - - 2 changed files: - + ncbi-tools6_6.1.20170106+dfsg2.orig.tar.xz.delta - + ncbi-tools6_6.1.20170106+dfsg2.orig.tar.xz.id Changes: = ncbi-tools6_6.1.20170106+dfsg2.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-tools6_6.1.20170106+dfsg2.orig.tar.xz.delta differ = ncbi-tools6_6.1.20170106+dfsg2.orig.tar.xz.id = @@ -0,0 +1 @@ +95393501b1f2135f5687718ce9d3185351814566 View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/commit/914cd531f45671249d8de3878a958c2db011397a -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/commit/914cd531f45671249d8de3878a958c2db011397a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6][master] 9 commits: ncbi-tools6 6.1.20170106+dfsg1-10.1: time64 NMU (#1064245).
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6
Commits:
84f54801 by Steve Langasek at 2024-02-18T19:27:03-05:00
ncbi-tools6 6.1.20170106+dfsg1-10.1: time64 NMU (#1064245).
- - - - -
46d92b0d by Aaron M. Ucko at 2024-02-18T19:29:00-05:00
New upstream version 6.1.20170106+dfsg2
- - - - -
2602dc6f by Aaron M. Ucko at 2024-02-18T21:09:15-05:00
Merge tag 'upstream/6.1.20170106+dfsg2', now dropping webdesign.
At least some of its content was generated but supplied without
corresponding sources and inputs, and nothing from there was getting
packaged anyway.
- - - - -
b04e17a8 by Aaron M. Ucko at 2024-02-18T21:09:15-05:00
debian/copyright (Files-Excluded): Drop spurious leading ncbi/.
- - - - -
24510624 by Aaron M. Ucko at 2024-02-18T21:09:15-05:00
debian/{copyright,watch}: Go to dfsg2, dropping webdesign.
- - - - -
fb5308f6 by Aaron M. Ucko at 2024-02-18T21:09:15-05:00
Acknowledge time64 NMU. (Closes: #1064245.)
- - - - -
508ce5cd by Aaron M. Ucko at 2024-02-18T21:09:15-05:00
debian/rules: Explicitly enable the time64 ABI for now.
- - - - -
3fc3b388 by Aaron M. Ucko at 2024-02-18T21:09:15-05:00
Correct stray references to old library package names.
... in d/{.gitignore,libncbi6t64.doc-base,*.lintian-overrides,*.symbols}.
NB: The initial .symbols changes missed the fact that each library
package contained multiple libraries (not worth splitting up), and these
lintian-overrides tuneups drop post-colon package names altogether.
- - - - -
783945a0 by Aaron M. Ucko at 2024-02-18T21:10:50-05:00
Finalize ncbi-tools6 6.1.20170106+dfsg2-1~exp1.
- - - - -
28 changed files:
- debian/.gitignore
- debian/changelog
- debian/control
- debian/copyright
- debian/libncbi6.doc-base → debian/libncbi6t64.doc-base
- debian/libncbi6.docs → debian/libncbi6t64.docs
- debian/libncbi6.examples → debian/libncbi6t64.examples
- debian/libncbi6.install → debian/libncbi6t64.install
- + debian/libncbi6t64.lintian-overrides
- debian/libncbi6.symbols → debian/libncbi6t64.symbols
- − debian/libvibrant6b.lintian-overrides
- debian/libvibrant6b.install → debian/libvibrant6t64.install
- + debian/libvibrant6t64.lintian-overrides
- debian/libvibrant6b.symbols → debian/libvibrant6t64.symbols
- debian/patches/debian-changes
- debian/rules
- debian/watch
- − webdesign/designs/cubby/filters/ClinicalTrials.html
- − webdesign/designs/cubby/filters/ClinicalTrials_files/GoUp1.gif
- − webdesign/designs/cubby/filters/ClinicalTrials_files/GoUp2.gif
- − webdesign/designs/cubby/filters/ClinicalTrials_files/bkgd.gif
- − webdesign/designs/cubby/filters/ClinicalTrials_files/cubby.jfif
- − webdesign/designs/cubby/filters/ClinicalTrials_files/filters.css
- − webdesign/designs/cubby/filters/ClinicalTrials_files/left.GIF
- − webdesign/designs/cubby/filters/ClinicalTrials_files/ncbi_test.css
- − webdesign/designs/cubby/filters/ClinicalTrials_files/new.gif
- − webdesign/designs/cubby/filters/ClinicalTrials_files/query.js
- − webdesign/designs/cubby/filters/ClinicalTrials_files/transparent.gif
The diff was not included because it is too large.
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-tools6/-/compare/0872cc8190e7087fc9bad8645d4b6d0818f8a179...783945a086261acfaf70bf548b1a8003f18f344c
--
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-tools6/-/compare/0872cc8190e7087fc9bad8645d4b6d0818f8a179...783945a086261acfaf70bf548b1a8003f18f344c
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[med-svn] [Git][med-team/ncbi-tools6] Pushed new tag debian/6.1.20170106+dfsg2-1_exp1
Aaron M. Ucko pushed new tag debian/6.1.20170106+dfsg2-1_exp1 at Debian Med / ncbi-tools6 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/tree/debian/6.1.20170106+dfsg2-1_exp1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6] Pushed new tag debian/6.1.20170106+dfsg1-10.1
Aaron M. Ucko pushed new tag debian/6.1.20170106+dfsg1-10.1 at Debian Med / ncbi-tools6 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/tree/debian/6.1.20170106+dfsg1-10.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-tools6][upstream] New upstream version 6.1.20170106+dfsg2
Aaron M. Ucko pushed to branch upstream at Debian Med / ncbi-tools6 Commits: 46d92b0d by Aaron M. Ucko at 2024-02-18T19:29:00-05:00 New upstream version 6.1.20170106+dfsg2 - - - - - 11 changed files: - − webdesign/designs/cubby/filters/ClinicalTrials.html - − webdesign/designs/cubby/filters/ClinicalTrials_files/GoUp1.gif - − webdesign/designs/cubby/filters/ClinicalTrials_files/GoUp2.gif - − webdesign/designs/cubby/filters/ClinicalTrials_files/bkgd.gif - − webdesign/designs/cubby/filters/ClinicalTrials_files/cubby.jfif - − webdesign/designs/cubby/filters/ClinicalTrials_files/filters.css - − webdesign/designs/cubby/filters/ClinicalTrials_files/left.GIF - − webdesign/designs/cubby/filters/ClinicalTrials_files/ncbi_test.css - − webdesign/designs/cubby/filters/ClinicalTrials_files/new.gif - − webdesign/designs/cubby/filters/ClinicalTrials_files/query.js - − webdesign/designs/cubby/filters/ClinicalTrials_files/transparent.gif The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/commit/46d92b0d2fae3931c3c93ec6238576631d44d5e9 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/commit/46d92b0d2fae3931c3c93ec6238576631d44d5e9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct][master] 4 commits: Start work on ncbi-entrez-direct 19.2.20230331+dfsg-3, for #1054198.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct Commits: 286cfd30 by Aaron M. Ucko at 2023-10-18T21:13:59-04:00 Start work on ncbi-entrez-direct 19.2.20230331+dfsg-3, for #1054198. - - - - - 9785167c by Aaron M. Ucko at 2023-10-18T21:33:14-04:00 Explicitly build-depend on golang-golang-x-net-dev (#1054198). AFAICT, it had been coming in as an indirect dependency of golang-github-gin-gonic-gin-dev, most immediately via golang-golang-x-crypto-dev, which recently dropped its dependency to break a cycle. - - - - - 1b692889 by Aaron M. Ucko at 2023-10-18T21:33:25-04:00 .gitignore: Drop "saved" again, slightly belatedly. - - - - - 1845bd9a by Aaron M. Ucko at 2023-10-18T21:34:23-04:00 Finalize ncbi-entrez-direct 19.2.20230331+dfsg-3 for unstable. - - - - - 4 changed files: - .gitignore - debian/changelog - debian/control - debian/patches/debian-changes Changes: = .gitignore = @@ -2,4 +2,3 @@ bin go-build obj-*/ -saved = debian/changelog = @@ -1,3 +1,14 @@ +ncbi-entrez-direct (19.2.20230331+dfsg-3) unstable; urgency=medium + + * .gitignore: Drop "saved" again, slightly belatedly. + * debian/control: Explicitly build-depend on golang-golang-x-net-dev. +AFAICT, it had been coming in as an indirect dependency of +golang-github-gin-gonic-gin-dev, most immediately via +golang-golang-x-crypto-dev, which recently dropped its dependency to +break a cycle. (Closes: #1054198.) + + -- Aaron M. Ucko Wed, 18 Oct 2023 21:34:22 -0400 + ncbi-entrez-direct (19.2.20230331+dfsg-2) unstable; urgency=medium * debian/rules: Formally build cmd/*.go as main/*.go, adjusting DH_GOPKG = debian/control = @@ -15,6 +15,7 @@ Build-Depends: debhelper-compat (= 13), golang-github-klauspost-pgzip-dev, golang-github-rainycape-unidecode-dev, golang-github-shirou-gopsutil-dev, + golang-golang-x-net-dev, golang-golang-x-text-dev, python3 Standards-Version: 4.6.2 = debian/patches/debian-changes = @@ -58,9 +58,8 @@ Last-Update: 2020-02-03 --- /dev/null +++ ncbi-entrez-direct-12.0.20190816+ds/.gitignore -@@ -0,0 +1,5 @@ +@@ -0,0 +1,4 @@ +.pc +bin +go-build +obj-*/ -+saved View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/191db126151a3310a8204eb2a1ad32c9cb7cdc3e...1845bd9aafe987fae9686c818e78be07885e7210 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/191db126151a3310a8204eb2a1ad32c9cb7cdc3e...1845bd9aafe987fae9686c818e78be07885e7210 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct] Pushed new tag debian/19.2.20230331+dfsg-3
Aaron M. Ucko pushed new tag debian/19.2.20230331+dfsg-3 at Debian Med / ncbi-entrez-direct -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/tree/debian/19.2.20230331+dfsg-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct][master] ncbi-entrez-direct 19.2.20230331+dfsg-2: Build cmd/*.go as main/*.go
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct
Commits:
191db126 by Aaron M. Ucko at 2023-09-16T22:36:02-04:00
ncbi-entrez-direct 19.2.20230331+dfsg-2: Build cmd/*.go as main/*.go
* debian/rules: Formally build cmd/*.go as main/*.go, adjusting DH_GOPKG
accordingly. This approach both avoids an FTBFS with Go 1.21 (under
which cmd tries to pick up e.g. cmd/compile) and facilitates bypassing
upstream's cmd/go.{mod,sum} without moving them aside. (In
retrospect, Built-Using was already missing third-party packages.)
* Reupload to unstable.
- - - - -
2 changed files:
- debian/changelog
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,14 @@
+ncbi-entrez-direct (19.2.20230331+dfsg-2) unstable; urgency=medium
+
+ * debian/rules: Formally build cmd/*.go as main/*.go, adjusting DH_GOPKG
+accordingly. This approach both avoids an FTBFS with Go 1.21 (under
+which cmd tries to pick up e.g. cmd/compile) and facilitates bypassing
+upstream's cmd/go.{mod,sum} without moving them aside. (In
+retrospect, Built-Using was already missing third-party packages.)
+ * Reupload to unstable.
+
+ -- Aaron M. Ucko Sat, 16 Sep 2023 22:36:01 -0400
+
ncbi-entrez-direct (19.2.20230331+dfsg-1) experimental; urgency=medium
* New upstream point release, still to experimental.
=
debian/rules
=
@@ -11,7 +11,7 @@ export CGO_CXXFLAGS = $(CXXFLAGS) # probably irrelevant
export CGO_FFLAGS = $(FFLAGS) # even more so
export CGO_LDFLAGS = $(LDFLAGS)
-export DH_GOPKG = cmd
+export DH_GOPKG = main
%:
dh $@ --with=golang,python3
@@ -130,11 +130,12 @@ endif
$(BIN_GO_APPS): bin/%: cmd/%.go $(GOLIBS)
# Always use gccgo? The resulting binary would be much smaller, but
# pull in a large shared library with few other reverse dependencies.
- go build -v -gccgoflags '$(CFLAGS) $(LDFLAGS)' -o $@ cmd/$*.go
+ go build -v -gccgoflags '$(CFLAGS) $(LDFLAGS)' -o $@ \
+ $(GOPATH)/src/$(DH_GOPKG)/$*.go
override_dh_auto_configure:
- mkdir -p saved
- -mv cmd/go.mod cmd/go.sum saved/
+ mkdir -p $(GOPATH)/src/$(DH_GOPKG)
+ ln -sv $(CURDIR)/cmd/*.go $(GOPATH)/src/$(DH_GOPKG)
override_dh_auto_build: $(WRAPPERS) $(BIN_PERL_SCRIPTS) \
$(BIN_ECOMMON_SCRIPTS) $(BIN_OTHER_SCRIPTS) \
@@ -164,4 +165,3 @@ override_dh_installexamples:
override_dh_auto_clean:
dh_auto_clean
rm -rf bin debian/edirect.py $(GOCACHE) $(GOPATH)
- if [ -d saved ]; then mv saved/* cmd && rmdir saved; fi
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/191db126151a3310a8204eb2a1ad32c9cb7cdc3e
--
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https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/191db126151a3310a8204eb2a1ad32c9cb7cdc3e
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[med-svn] [Git][med-team/ncbi-entrez-direct] Pushed new tag debian/19.2.20230331+dfsg-2
Aaron M. Ucko pushed new tag debian/19.2.20230331+dfsg-2 at Debian Med / ncbi-entrez-direct -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/tree/debian/19.2.20230331+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-blastplus][master] 8 commits: Start work on ncbi-blast2+ 2.12.0+ds-4 to downgrade #891197.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus Commits: ad472d06 by Aaron M. Ucko at 2023-09-04T22:32:21-04:00 Start work on ncbi-blast2+ 2.12.0+ds-4 to downgrade #891197. - - - - - d41ab8a0 by Aaron M. Ucko at 2023-09-04T22:32:48-04:00 debian/control: Drop build dependency on libpcre3-dev (#891197). PCRE2 support isn't ready yet, but there's a convenience copy of classic PCRE that will suffice for now. (Partly addresses #891197.) - - - - - f6feb225 by Aaron M. Ucko at 2023-09-04T22:35:34-04:00 debian/source/lintian-overrides: Accommodate bracketed paths. - - - - - d7eeaa54 by Aaron M. Ucko at 2023-09-04T22:36:10-04:00 routine-update: Standards-Version: 4.6.2 - - - - - b6a87ef6 by Aaron M. Ucko at 2023-09-04T22:36:14-04:00 routine-update: Remove trailing whitespace in debian/changelog - - - - - 9a9542de by Aaron M. Ucko at 2023-09-04T22:39:41-04:00 Refer to common license file for Apache-2.0. Changes-By: lintian-brush Fixes: lintian: copyright-does-not-refer-to-common-license-file See-also: https://lintian.debian.org/tags/copyright-does-not-refer-to-common-license-file.html Fixes: lintian: copyright-not-using-common-license-for-apache2 See-also: https://lintian.debian.org/tags/copyright-not-using-common-license-for-apache2.html - - - - - 2dec42c5 by Aaron M. Ucko at 2023-09-04T22:39:43-04:00 Avoid explicitly specifying -Wl,--as-needed linker flag. Changes-By: lintian-brush Fixes: lintian: debian-rules-uses-as-needed-linker-flag See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html - - - - - 77519dae by Aaron M. Ucko at 2023-09-04T22:40:43-04:00 Finalize ncbi-blast+ 2.12.0+ds-4 for unstable. - - - - - 5 changed files: - debian/changelog - debian/control - debian/copyright - debian/rules - debian/source/lintian-overrides Changes: = debian/changelog = @@ -1,7 +1,20 @@ +ncbi-blast+ (2.12.0+ds-4) unstable; urgency=medium + + * debian/control: Drop build dependency on libpcre3-dev; PCRE2 support +isn't ready yet, but there's a convenience copy of classic PCRE that +will suffice for now. (Partly addresses #891197.) + * debian/source/lintian-overrides: Accommodate bracketed paths. + * Standards-Version: 4.6.2 (routine-update) + * Remove trailing whitespace in debian/changelog (routine-update) + * Refer to common license file for Apache-2.0. + * Avoid explicitly specifying -Wl,--as-needed linker flag. + + -- Aaron M. Ucko Mon, 04 Sep 2023 22:40:42 -0400 + ncbi-blast+ (2.12.0+ds-3) unstable; urgency=medium * d/patches/optin_usage_report change usage reports sending over -internet strategy to optin (disabled by default unless specified) +internet strategy to optin (disabled by default unless specified) (Closes # 1005279). -- Olivier Sallou Thu, 10 Feb 2022 12:17:56 + @@ -11,7 +24,7 @@ ncbi-blast+ (2.12.0+ds-2) unstable; urgency=medium * Clean up spurious release-status comment from 2.12.0+ds-1. * debian/patches/system_mbedtls_only: Patch out use of local mbed TLS headers, which formally rename all symbols. - + -- Aaron M. Ucko Wed, 01 Dec 2021 23:36:32 -0500 ncbi-blast+ (2.12.0+ds-1) unstable; urgency=medium = debian/control = @@ -13,11 +13,10 @@ Build-Depends-Arch: 2to3, libgnutls28-dev, liblmdb-dev, libmbedtls-dev, -libpcre3-dev, time, zlib1g-dev, procps -Standards-Version: 4.6.0 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ = debian/copyright = @@ -40,6 +40,9 @@ License: Apache-2.0 WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. + . + On Debian systems, the full text of the Apache License, Version 2.0 can be + found in the file `/usr/share/common-licenses/Apache-2.0'. Files: c++/src/html/ncbi_menu.js c++/src/html/ncbi_menu_dnd.js = debian/rules = @@ -26,8 +26,6 @@ DEB_CONFIGURE_EXTRA_FLAGS += --with-symbols #export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic -# Kept for the sake of backports, which can't rely on GCC 9+. -export DEB_LDFLAGS_MAINT_APPEND=-Wl,--as-needed include /usr/share/dpkg/architecture.mk include /usr/share/dpkg/buildflags.mk = debian/source/lintian-overrides ==
[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag debian/2.12.0+ds-4
Aaron M. Ucko pushed new tag debian/2.12.0+ds-4 at Debian Med / ncbi-blastplus -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/tree/debian/2.12.0+ds-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.3+dfsg-6_deb12u1
Aaron M. Ucko pushed new tag debian/3.0.3+dfsg-6_deb12u1 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.3+dfsg-6_deb12u1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new branch debian/bookworm
Aaron M. Ucko pushed new branch debian/bookworm at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/bookworm You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.3+dfsg-6
Aaron M. Ucko pushed new tag debian/3.0.3+dfsg-6 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.3+dfsg-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] sra-sdk 3.0.3+dfsg-6: Fully expand libngs-java.links.in (#1039621).
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
40334dd5 by Aaron M. Ucko at 2023-06-27T22:14:42-04:00
sra-sdk 3.0.3+dfsg-6: Fully expand libngs-java.links.in (#1039621).
Account for its use of DEB_HOST_MULTIARCH, with accidentally different
delimiters in source and destination paths. (Closes: #1039621.)
- - - - -
2 changed files:
- debian/changelog
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+sra-sdk (3.0.3+dfsg-6) unstable; urgency=high
+
+ * debian/rules: Expand $(DEB_HOST_MULTIARCH) in libngs-java.links.in.
+(Closes: #1039621.)
+
+ -- Aaron M. Ucko Tue, 27 Jun 2023 22:14:41 -0400
+
sra-sdk (3.0.3+dfsg-5) unstable; urgency=medium
* Limit libngs-java to those architectures where libs are available
=
debian/rules
=
@@ -152,7 +152,10 @@ override_dh_prep:
execute_before_dh_link:
# Putting the upstream version number (without the dfsg part) at the
end of
# symlink source in the -jni package.
- sed 's/\(#STRIPPED_UPSTREAM_VERSION#\)/\1$(DEB_VERSION_UPSTREAM)/;
s/#STRIPPED_UPSTREAM_VERSION#\(.*\)+dfsg[0-9]*/\1/' debian/libngs-jni.links.in
> debian/libngs-jni.links
+ sed -e 's/\(#STRIPPED_UPSTREAM_VERSION#\)/\1$(DEB_VERSION_UPSTREAM)/' \
+ -e 's/#STRIPPED_UPSTREAM_VERSION#\(.*\)+dfsg[0-9]*/\1/' \
+ -e 's/\$$[({]DEB_HOST_MULTIARCH[)}]/$(DEB_HOST_MULTIARCH)/g' \
+ debian/libngs-jni.links.in > debian/libngs-jni.links
# require network, not automatically run
# use it when the pom file must be re-downloaded from maven repo
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/40334dd5d3d5de2b4801fbcc8dfef1a93811db07
--
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/40334dd5d3d5de2b4801fbcc8dfef1a93811db07
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[med-svn] [Git][med-team/ncbi-entrez-direct] Pushed new tag upstream/19.2.20230331+dfsg
Aaron M. Ucko pushed new tag upstream/19.2.20230331+dfsg at Debian Med / ncbi-entrez-direct -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/tree/upstream/19.2.20230331+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct] Pushed new tag debian/19.2.20230331+dfsg-1
Aaron M. Ucko pushed new tag debian/19.2.20230331+dfsg-1 at Debian Med / ncbi-entrez-direct -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/tree/debian/19.2.20230331+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct][pristine-tar] pristine-tar data for ncbi-entrez-direct_19.2.20230331+dfsg.orig.tar.xz
Aaron M. Ucko pushed to branch pristine-tar at Debian Med / ncbi-entrez-direct Commits: 35df025c by Aaron M. Ucko at 2023-03-31T17:34:26-04:00 pristine-tar data for ncbi-entrez-direct_19.2.20230331+dfsg.orig.tar.xz - - - - - 2 changed files: - + ncbi-entrez-direct_19.2.20230331+dfsg.orig.tar.xz.delta - + ncbi-entrez-direct_19.2.20230331+dfsg.orig.tar.xz.id Changes: = ncbi-entrez-direct_19.2.20230331+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-entrez-direct_19.2.20230331+dfsg.orig.tar.xz.delta differ = ncbi-entrez-direct_19.2.20230331+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +a91ee56c47acaea00f6c786a2be1ed1184993710 View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/35df025cea078aa9f9dd387347093ec966bf43ce -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/35df025cea078aa9f9dd387347093ec966bf43ce You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct][pristine-tar] 6 commits: pristine-tar data for ncbi-entrez-direct_19.0.20230314+dfsg.orig.tar.xz
Aaron M. Ucko pushed to branch pristine-tar at Debian Med / ncbi-entrez-direct Commits: 9a912291 by Aaron M. Ucko at 2023-03-15T21:42:15-04:00 pristine-tar data for ncbi-entrez-direct_19.0.20230314+dfsg.orig.tar.xz - - - - - 9c6099f5 by Aaron M. Ucko at 2023-03-22T21:35:32-04:00 pristine-tar data for ncbi-entrez-direct_19.1.20230316+dfsg.orig.tar.xz - - - - - 14e8151d by Aaron M. Ucko at 2023-03-22T21:36:50-04:00 pristine-tar data for ncbi-entrez-direct_19.1.20230317+dfsg.orig.tar.xz - - - - - ea0d29dc by Aaron M. Ucko at 2023-03-29T22:01:59-04:00 pristine-tar data for ncbi-entrez-direct_19.2.20230323+dfsg.orig.tar.xz - - - - - 30d36dc2 by Aaron M. Ucko at 2023-03-29T22:03:48-04:00 pristine-tar data for ncbi-entrez-direct_19.2.20230324+dfsg.orig.tar.xz - - - - - 89d954ff by Aaron M. Ucko at 2023-03-30T23:04:12-04:00 pristine-tar data for ncbi-entrez-direct_19.2.20230330+dfsg.orig.tar.xz - - - - - 12 changed files: - + ncbi-entrez-direct_19.0.20230314+dfsg.orig.tar.xz.delta - + ncbi-entrez-direct_19.0.20230314+dfsg.orig.tar.xz.id - + ncbi-entrez-direct_19.1.20230316+dfsg.orig.tar.xz.delta - + ncbi-entrez-direct_19.1.20230316+dfsg.orig.tar.xz.id - + ncbi-entrez-direct_19.1.20230317+dfsg.orig.tar.xz.delta - + ncbi-entrez-direct_19.1.20230317+dfsg.orig.tar.xz.id - + ncbi-entrez-direct_19.2.20230323+dfsg.orig.tar.xz.delta - + ncbi-entrez-direct_19.2.20230323+dfsg.orig.tar.xz.id - + ncbi-entrez-direct_19.2.20230324+dfsg.orig.tar.xz.delta - + ncbi-entrez-direct_19.2.20230324+dfsg.orig.tar.xz.id - + ncbi-entrez-direct_19.2.20230330+dfsg.orig.tar.xz.delta - + ncbi-entrez-direct_19.2.20230330+dfsg.orig.tar.xz.id Changes: = ncbi-entrez-direct_19.0.20230314+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-entrez-direct_19.0.20230314+dfsg.orig.tar.xz.delta differ = ncbi-entrez-direct_19.0.20230314+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +32ed5b9cdd9dc0c76d86f3c6bc6ea602f8345ca0 = ncbi-entrez-direct_19.1.20230316+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-entrez-direct_19.1.20230316+dfsg.orig.tar.xz.delta differ = ncbi-entrez-direct_19.1.20230316+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +67e95467dd5ed270369a3ba9d57886219fc485e1 = ncbi-entrez-direct_19.1.20230317+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-entrez-direct_19.1.20230317+dfsg.orig.tar.xz.delta differ = ncbi-entrez-direct_19.1.20230317+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +5894c1bd19d2183eaf204fa14713c447e32b3390 = ncbi-entrez-direct_19.2.20230323+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-entrez-direct_19.2.20230323+dfsg.orig.tar.xz.delta differ = ncbi-entrez-direct_19.2.20230323+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +e876ed53733be6b398aa5ffb1180538e778aeaa3 = ncbi-entrez-direct_19.2.20230324+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-entrez-direct_19.2.20230324+dfsg.orig.tar.xz.delta differ = ncbi-entrez-direct_19.2.20230324+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +52c84c8d073401afa6ba571fc5cfabadd352655b = ncbi-entrez-direct_19.2.20230330+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-entrez-direct_19.2.20230330+dfsg.orig.tar.xz.delta differ = ncbi-entrez-direct_19.2.20230330+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +295f3d81bdf5575a0b5efc841d0b2b2b953693ac View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/285a03aefa80cc585673f8a79ddba78de5823269...89d954ff6bcec5b6e1e027ab8188aade356f32ee -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/285a03aefa80cc585673f8a79ddba78de5823269...89d954ff6bcec5b6e1e027ab8188aade356f32ee You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct][master] Go ahead with ncbi-entrez-direct 19.0.20230216+dfsg-2 for unstable.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct Commits: 5d5d21b1 by Aaron M. Ucko at 2023-03-01T18:12:44-05:00 Go ahead with ncbi-entrez-direct 19.0.20230216+dfsg-2 for unstable. Don't read too much into the version number difference -- upstream has a low threshold for bumping the second component, and has been keeping it to a single digit. Also, many of the code changes are refactoring and similar formalities, and as previously noted this is a specialized leaf package. - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,3 +1,13 @@ +ncbi-entrez-direct (19.0.20230216+dfsg-2) unstable; urgency=medium + + * Upload to unstable. (Don't read too much into the version number +difference -- upstream has a low threshold for bumping the second +component, and has been keeping it to a single digit. Also, many of +the code changes are refactoring and similar formalities, and as +previously noted this is a specialized leaf package.) + + -- Aaron M. Ucko Wed, 01 Mar 2023 18:11:52 -0500 + ncbi-entrez-direct (19.0.20230216+dfsg-1) experimental; urgency=medium * New upstream release; uploading to experimental, at least for now. View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/5d5d21b1b14cc1693cd768554c83675f61fa6f8b -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/5d5d21b1b14cc1693cd768554c83675f61fa6f8b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct] Pushed new tag debian/19.0.20230216+dfsg-2
Aaron M. Ucko pushed new tag debian/19.0.20230216+dfsg-2 at Debian Med / ncbi-entrez-direct -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/tree/debian/19.0.20230216+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct][upstream] 45 commits: New upstream version 16.7.20220301+dfsg
Aaron M. Ucko pushed to branch upstream at Debian Med / ncbi-entrez-direct Commits: 7edd60bd by Aaron M. Ucko at 2023-02-14T21:42:40-05:00 New upstream version 16.7.20220301+dfsg - - - - - 3b59a997 by Aaron M. Ucko at 2023-02-14T22:52:50-05:00 New upstream version 16.7.20220309+dfsg - - - - - 4f19907b by Aaron M. Ucko at 2023-02-16T17:15:04-05:00 New upstream version 16.8.20220314+dfsg - - - - - 82372aab by Aaron M. Ucko at 2023-02-16T17:16:24-05:00 New upstream version 16.8.20220329+dfsg - - - - - 397e3b0f by Aaron M. Ucko at 2023-02-16T22:58:51-05:00 New upstream version 16.9.20220406+dfsg - - - - - dddeb2a2 by Aaron M. Ucko at 2023-02-18T20:42:32-05:00 New upstream version 16.9.20220413+dfsg - - - - - 3ef7c930 by Aaron M. Ucko at 2023-02-18T21:48:43-05:00 New upstream version 17.0.20220418+dfsg - - - - - 7ca3daa1 by Aaron M. Ucko at 2023-02-18T22:06:51-05:00 New upstream version 17.0.20220513+dfsg - - - - - 71358c9d by Aaron M. Ucko at 2023-02-20T11:30:02-05:00 New upstream version 17.1.20220516+dfsg - - - - - 70981b5b by Aaron M. Ucko at 2023-02-20T11:32:09-05:00 New upstream version 17.1.20220527+dfsg - - - - - c5d5496f by Aaron M. Ucko at 2023-02-20T12:08:56-05:00 New upstream version 17.2.20220610+dfsg - - - - - ce7b8092 by Aaron M. Ucko at 2023-02-20T12:24:48-05:00 New upstream version 17.2.20220624+dfsg - - - - - 422d553d by Aaron M. Ucko at 2023-02-20T14:06:57-05:00 New upstream version 17.3.20220629+dfsg - - - - - e26f7acd by Aaron M. Ucko at 2023-02-20T16:11:29-05:00 New upstream version 17.3.20220713+dfsg - - - - - 25cbed1a by Aaron M. Ucko at 2023-02-20T16:25:53-05:00 New upstream version 17.4.20220718+dfsg - - - - - dec81591 by Aaron M. Ucko at 2023-02-20T16:27:24-05:00 New upstream version 17.4.20220729+dfsg - - - - - bdedf1e6 by Aaron M. Ucko at 2023-02-20T19:42:20-05:00 New upstream version 17.5.20220801+dfsg - - - - - fba70974 by Aaron M. Ucko at 2023-02-20T19:56:16-05:00 New upstream version 17.5.20220812+dfsg - - - - - ae07c1c0 by Aaron M. Ucko at 2023-02-20T21:49:47-05:00 New upstream version 17.6.20220815+dfsg - - - - - 1d9d500e by Aaron M. Ucko at 2023-02-20T22:16:15-05:00 New upstream version 17.6.20220819+dfsg - - - - - 220e252a by Aaron M. Ucko at 2023-02-20T22:19:07-05:00 New upstream version 17.7.20220829+dfsg - - - - - f51693a4 by Aaron M. Ucko at 2023-02-20T22:21:13-05:00 New upstream version 17.7.20220830+dfsg - - - - - a115e121 by Aaron M. Ucko at 2023-02-20T22:22:05-05:00 New upstream version 17.8.20220906+dfsg - - - - - a3d008bb by Aaron M. Ucko at 2023-02-20T22:24:02-05:00 New upstream version 17.8.20220907+dfsg - - - - - f8ab37aa by Aaron M. Ucko at 2023-02-20T22:32:20-05:00 New upstream version 17.9.20220919+dfsg - - - - - e1d033a9 by Aaron M. Ucko at 2023-02-21T20:33:02-05:00 New upstream version 17.9.20221004+dfsg - - - - - 8b6b7ffe by Aaron M. Ucko at 2023-02-21T21:08:22-05:00 New upstream version 18.0.20221011+dfsg - - - - - 70d41eca by Aaron M. Ucko at 2023-02-21T21:38:25-05:00 New upstream version 18.0.20221018+dfsg - - - - - 935be45f by Aaron M. Ucko at 2023-02-21T21:39:55-05:00 New upstream version 18.1.20221021+dfsg - - - - - 169824a3 by Aaron M. Ucko at 2023-02-21T21:41:15-05:00 New upstream version 18.1.20221109+dfsg - - - - - 97034129 by Aaron M. Ucko at 2023-02-21T22:09:35-05:00 New upstream version 18.2.20221114+dfsg - - - - - 255d15e8 by Aaron M. Ucko at 2023-02-21T22:28:56-05:00 New upstream version 18.2.20221128+dfsg - - - - - 5adda0c4 by Aaron M. Ucko at 2023-02-22T20:43:22-05:00 New upstream version 18.3.20221202+dfsg - - - - - f8cfc120 by Aaron M. Ucko at 2023-02-22T20:46:49-05:00 New upstream version 18.4.20221205+dfsg - - - - - 6da6d2e9 by Aaron M. Ucko at 2023-02-22T20:47:46-05:00 New upstream version 18.4.20221207+dfsg - - - - - 3374a019 by Aaron M. Ucko at 2023-02-22T20:48:34-05:00 New upstream version 18.5.20221212+dfsg - - - - - 5cab0884 by Aaron M. Ucko at 2023-02-22T20:49:57-05:00 New upstream version 18.6.20221219+dfsg - - - - - f713e34b by Aaron M. Ucko at 2023-02-22T21:53:27-05:00 New upstream version 18.6.20221222+dfsg - - - - - bfc42aff by Aaron M. Ucko at 2023-02-22T22:19:04-05:00 New upstream version 18.7.20230103+dfsg - - - - - b09d5a5f by Aaron M. Ucko at 2023-02-26T15:38:24-05:00 New upstream version 18.7.20230125+dfsg - - - - - 0471d8b0 by Aaron M. Ucko at 2023-02-26T15:48:41-05:00 New upstream version 18.8.20230126+dfsg - - - - - 1f67be80 by Aaron M. Ucko at 2023-02-26T15:50:22-05:00 New upstream version 18.8.20230203+dfsg - - - - - 32507332 by Aaron M. Ucko at 2023-02-26T15:53:55-05:00 New upstream version 18.9.20230210+dfsg - - - - - ff81b217 by Aaron M. Ucko at 2023-02-26T15:56:53-05:00 New upstream version 18.9.20230216+dfsg - - - - - e0137fd0 by Aaron M. Ucko at 2023-02-26T16:04:08-05:00 New upstream version 19.0.20230216+dfsg - - - - - 9 changed files: - README - + archive-pmc - archive-pubmed - + asn2ref - + cit2pmid - cmd/build.sh - + cmd/edict.go - cmd/go.mod - cmd/go.sum The diff was not included because it is
[med-svn] [Git][med-team/ncbi-entrez-direct][pristine-tar] 45 commits: pristine-tar data for ncbi-entrez-direct_16.7.20220301+dfsg.orig.tar.xz
Aaron M. Ucko pushed to branch pristine-tar at Debian Med / ncbi-entrez-direct Commits: d3ef1046 by Aaron M. Ucko at 2023-02-14T21:42:44-05:00 pristine-tar data for ncbi-entrez-direct_16.7.20220301+dfsg.orig.tar.xz - - - - - 9b392818 by Aaron M. Ucko at 2023-02-14T22:52:52-05:00 pristine-tar data for ncbi-entrez-direct_16.7.20220309+dfsg.orig.tar.xz - - - - - 9a815a46 by Aaron M. Ucko at 2023-02-16T17:15:05-05:00 pristine-tar data for ncbi-entrez-direct_16.8.20220314+dfsg.orig.tar.xz - - - - - 0842423d by Aaron M. Ucko at 2023-02-16T17:16:25-05:00 pristine-tar data for ncbi-entrez-direct_16.8.20220329+dfsg.orig.tar.xz - - - - - f6334941 by Aaron M. Ucko at 2023-02-16T22:58:53-05:00 pristine-tar data for ncbi-entrez-direct_16.9.20220406+dfsg.orig.tar.xz - - - - - 2f713a93 by Aaron M. Ucko at 2023-02-18T20:42:34-05:00 pristine-tar data for ncbi-entrez-direct_16.9.20220413+dfsg.orig.tar.xz - - - - - 0542ecae by Aaron M. Ucko at 2023-02-18T21:48:49-05:00 pristine-tar data for ncbi-entrez-direct_17.0.20220418+dfsg.orig.tar.xz - - - - - a2ef1ef7 by Aaron M. Ucko at 2023-02-18T22:06:56-05:00 pristine-tar data for ncbi-entrez-direct_17.0.20220513+dfsg.orig.tar.xz - - - - - 10aac7ed by Aaron M. Ucko at 2023-02-20T11:30:08-05:00 pristine-tar data for ncbi-entrez-direct_17.1.20220516+dfsg.orig.tar.xz - - - - - 28099520 by Aaron M. Ucko at 2023-02-20T11:32:10-05:00 pristine-tar data for ncbi-entrez-direct_17.1.20220527+dfsg.orig.tar.xz - - - - - f3a9850a by Aaron M. Ucko at 2023-02-20T12:09:00-05:00 pristine-tar data for ncbi-entrez-direct_17.2.20220610+dfsg.orig.tar.xz - - - - - a744ce1b by Aaron M. Ucko at 2023-02-20T12:24:53-05:00 pristine-tar data for ncbi-entrez-direct_17.2.20220624+dfsg.orig.tar.xz - - - - - 7a0461c1 by Aaron M. Ucko at 2023-02-20T14:07:01-05:00 pristine-tar data for ncbi-entrez-direct_17.3.20220629+dfsg.orig.tar.xz - - - - - c4f43067 by Aaron M. Ucko at 2023-02-20T16:11:33-05:00 pristine-tar data for ncbi-entrez-direct_17.3.20220713+dfsg.orig.tar.xz - - - - - 3f045802 by Aaron M. Ucko at 2023-02-20T16:25:55-05:00 pristine-tar data for ncbi-entrez-direct_17.4.20220718+dfsg.orig.tar.xz - - - - - 49cd0522 by Aaron M. Ucko at 2023-02-20T16:27:25-05:00 pristine-tar data for ncbi-entrez-direct_17.4.20220729+dfsg.orig.tar.xz - - - - - 8ec3c35a by Aaron M. Ucko at 2023-02-20T19:42:24-05:00 pristine-tar data for ncbi-entrez-direct_17.5.20220801+dfsg.orig.tar.xz - - - - - 854f1e27 by Aaron M. Ucko at 2023-02-20T19:56:17-05:00 pristine-tar data for ncbi-entrez-direct_17.5.20220812+dfsg.orig.tar.xz - - - - - af8a53bb by Aaron M. Ucko at 2023-02-20T21:50:36-05:00 pristine-tar data for ncbi-entrez-direct_17.6.20220815+dfsg.orig.tar.xz - - - - - 9b44b1c4 by Aaron M. Ucko at 2023-02-20T22:16:20-05:00 pristine-tar data for ncbi-entrez-direct_17.6.20220819+dfsg.orig.tar.xz - - - - - 9b38a363 by Aaron M. Ucko at 2023-02-20T22:19:08-05:00 pristine-tar data for ncbi-entrez-direct_17.7.20220829+dfsg.orig.tar.xz - - - - - e9d85b76 by Aaron M. Ucko at 2023-02-20T22:21:14-05:00 pristine-tar data for ncbi-entrez-direct_17.7.20220830+dfsg.orig.tar.xz - - - - - c08cf1f6 by Aaron M. Ucko at 2023-02-20T22:22:06-05:00 pristine-tar data for ncbi-entrez-direct_17.8.20220906+dfsg.orig.tar.xz - - - - - 066d6181 by Aaron M. Ucko at 2023-02-20T22:24:03-05:00 pristine-tar data for ncbi-entrez-direct_17.8.20220907+dfsg.orig.tar.xz - - - - - 6a4dd4d6 by Aaron M. Ucko at 2023-02-20T22:32:22-05:00 pristine-tar data for ncbi-entrez-direct_17.9.20220919+dfsg.orig.tar.xz - - - - - c975b2a9 by Aaron M. Ucko at 2023-02-21T20:33:05-05:00 pristine-tar data for ncbi-entrez-direct_17.9.20221004+dfsg.orig.tar.xz - - - - - df6910dc by Aaron M. Ucko at 2023-02-21T21:08:23-05:00 pristine-tar data for ncbi-entrez-direct_18.0.20221011+dfsg.orig.tar.xz - - - - - 64a271f0 by Aaron M. Ucko at 2023-02-21T21:38:26-05:00 pristine-tar data for ncbi-entrez-direct_18.0.20221018+dfsg.orig.tar.xz - - - - - c0fbf3a1 by Aaron M. Ucko at 2023-02-21T21:39:56-05:00 pristine-tar data for ncbi-entrez-direct_18.1.20221021+dfsg.orig.tar.xz - - - - - 195e286b by Aaron M. Ucko at 2023-02-21T21:41:16-05:00 pristine-tar data for ncbi-entrez-direct_18.1.20221109+dfsg.orig.tar.xz - - - - - e5c89514 by Aaron M. Ucko at 2023-02-21T22:09:36-05:00 pristine-tar data for ncbi-entrez-direct_18.2.20221114+dfsg.orig.tar.xz - - - - - d26132cd by Aaron M. Ucko at 2023-02-21T22:28:57-05:00 pristine-tar data for ncbi-entrez-direct_18.2.20221128+dfsg.orig.tar.xz - - - - - 8c4e2426 by Aaron M. Ucko at 2023-02-22T20:43:25-05:00 pristine-tar data for ncbi-entrez-direct_18.3.20221202+dfsg.orig.tar.xz - - - - - 5ef22c78 by Aaron M. Ucko at 2023-02-22T20:46:50-05:00 pristine-tar data for ncbi-entrez-direct_18.4.20221205+dfsg.orig.tar.xz - - - - - b8b64a35 by Aaron M. Ucko at 2023-02-22T20:47:47-05:00 pristine-tar data for ncbi-entrez-direct_18.4.20221207+dfsg.orig.tar.xz - - - - - f6a5f92d by Aaron M. Ucko at 2023-02-22T20:48:35-05:00 pristine-tar data for
[med-svn] [Git][med-team/ncbi-entrez-direct][master] 126 commits: New upstream version 16.7.20220301+dfsg
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct Commits: 7edd60bd by Aaron M. Ucko at 2023-02-14T21:42:40-05:00 New upstream version 16.7.20220301+dfsg - - - - - cf61d79b by Aaron M. Ucko at 2023-02-14T22:50:57-05:00 Merge tag 'upstream/16.7.20220301+dfsg' Upstream version 16.7.20220301(+dfsg). - - - - - 3b59a997 by Aaron M. Ucko at 2023-02-14T22:52:50-05:00 New upstream version 16.7.20220309+dfsg - - - - - 51209681 by Aaron M. Ucko at 2023-02-15T22:59:58-05:00 debian/man: Update for new release (16.7.20220301[+dfsg]). * ref2pmid.1: Defer to transmute.1 now that -r2p appears in its help text. * transmute.1: Document -r2p, equivalent to ref2pmid, complete with suboptions (Data Conversion). - - - - - 01fab70a by Aaron M. Ucko at 2023-02-15T23:01:26-05:00 Merge tag 'upstream/16.7.20220309+dfsg' Upstream version 16.7.20220309(+dfsg). - - - - - 4f19907b by Aaron M. Ucko at 2023-02-16T17:15:04-05:00 New upstream version 16.8.20220314+dfsg - - - - - 7cac1e44 by Aaron M. Ucko at 2023-02-16T17:15:38-05:00 Merge tag 'upstream/16.8.20220314+dfsg' Upstream version 16.8.20220314(+dfsg). - - - - - 82372aab by Aaron M. Ucko at 2023-02-16T17:16:24-05:00 New upstream version 16.8.20220329+dfsg - - - - - 7ef1aea8 by Aaron M. Ucko at 2023-02-16T17:16:43-05:00 Merge tag 'upstream/16.8.20220329+dfsg' Upstream version 16.8.20220329(+dfsg). - - - - - db028b0c by Aaron M. Ucko at 2023-02-16T22:56:35-05:00 debian/man: Update for new release (16.8.20220329[+dfsg]). * archive-pubmed.1: Note additional baseline functionality and new (-)(e2)invert / (-)(e2)index option. * download-ncbi-data.1: Note new taxnames mode. * Somewhat belatedly add SEE ALSO links between the above. - - - - - 397e3b0f by Aaron M. Ucko at 2023-02-16T22:58:51-05:00 New upstream version 16.9.20220406+dfsg - - - - - 6a4c9dc9 by Aaron M. Ucko at 2023-02-16T22:59:27-05:00 Merge tag 'upstream/16.9.20220406+dfsg' Upstream version 16.9.20220406(+dfsg). - - - - - 6365737a by Aaron M. Ucko at 2023-02-18T20:37:48-05:00 Account for new use of github.com/klauspost/pgzip. * debian/control: Add a B-D on golang-github-klauspost-pgzip-dev. * debian/rules: Account for use of github.com/klauspost/pgzip and its dependency github.com/klauspost/compress. - - - - - dc92aed1 by Aaron M. Ucko at 2023-02-18T20:40:54-05:00 debian/man: Update for new release (16.9.20220406[+dfsg]). * archive-pubmed.1: Rework new options; they're now (-)daily and (-)index, with different semantics. * Belatedly add SEE ALSO references between archive-pubmed and xtract. - - - - - dddeb2a2 by Aaron M. Ucko at 2023-02-18T20:42:32-05:00 New upstream version 16.9.20220413+dfsg - - - - - ecb86ecf by Aaron M. Ucko at 2023-02-18T20:43:10-05:00 Merge tag 'upstream/16.9.20220413+dfsg' Upstream version 16.9.20220413(+dfsg). - - - - - 233f0726 by Aaron M. Ucko at 2023-02-18T21:29:18-05:00 debian/install: Install new nhance.sh helper to /usr/lib/n-e-d. - - - - - 9a13a279 by Aaron M. Ucko at 2023-02-18T21:41:16-05:00 debian/man: Update for new release (16.9.20220413[+dfsg]). * nquire.1: Note return of -pubchem, albeit with a different expansion (now just https://pubchem.ncbi.nlm.nih.gov) * rchive.1: Add -e2index (now that it's native), -e2invert, -e2delete, and -e2join (Local Record Index). * xtract.1: Keep -e2index for now, but belatedly mark its argument as optional. - - - - - 3ef7c930 by Aaron M. Ucko at 2023-02-18T21:48:43-05:00 New upstream version 17.0.20220418+dfsg - - - - - 59007503 by Aaron M. Ucko at 2023-02-18T21:49:37-05:00 Merge tag 'upstream/17.0.20220418+dfsg' Upstream version 17.0.20220418(+dfsg). - - - - - 948e376f by Aaron M. Ucko at 2023-02-18T21:52:37-05:00 debian/man: Update for new release (17.0.20220418[+dfsg]). * archive-pubmed.1: Note additional download of GeneRIFs. * xtract.1: Add -stemmed (Entrez Indexing). - - - - - 7ca3daa1 by Aaron M. Ucko at 2023-02-18T22:06:51-05:00 New upstream version 17.0.20220513+dfsg - - - - - f7ae402d by Aaron M. Ucko at 2023-02-18T22:08:15-05:00 Merge tag 'upstream/17.0.20220513+dfsg' Upstream version 17.0.20220513(+dfsg). - - - - - bc486add by Aaron M. Ucko at 2023-02-18T23:01:13-05:00 debian/rules: Install new as-is script cit2pmid. - - - - - 1633746c by Aaron M. Ucko at 2023-02-18T23:07:11-05:00 debian/man: Update for new release (17.0.20220513[+dfsg]). * archive-pubmed.1: Add (-)reindex (alias for [-]index), (-)clean, and (-)clear. * cit2pmid.1: New. * efilter.1: Drop Biosystems Filters (-kind, -pathway). * phrase-search.1: Belatedly drop mention of old entrez-phrase-search. * pm-prepare.1: Requires two directories now (master and working). * pm-stash.1: Optional invert directory. * rchive.1: Add -padz (Local Record Cache). * Update SEE ALSO accordingly. - - - - - 71358c9d by Aaron M. Ucko at 2023-02-20T11:30:02-05:00 New upstream version 17.1.20220516+dfsg - - - - - ead77dd5 by Aaron M. Ucko at 2023-02-20T11:31:12-05:00 Merge tag 'upstream/17.1.20220516+dfsg' Upstream version 17.1.2
[med-svn] [Git][med-team/ncbi-entrez-direct] Pushed new tag debian/16.6.20220228+dfsg-2
Aaron M. Ucko pushed new tag debian/16.6.20220228+dfsg-2 at Debian Med / ncbi-entrez-direct -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/tree/debian/16.6.20220228+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct][master] ncbi-entrez-direct 16.6.20220228+dfsg-2: test w/libxml-simple-perl.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct Commits: a0a67170 by Aaron M. Ucko at 2023-02-14T07:47:26-05:00 ncbi-entrez-direct 16.6.20220228+dfsg-2: test w/libxml-simple-perl. debian/tests/control: Depend on libxml-simple-perl for the private script behind transmute -x2j. - - - - - 2 changed files: - debian/changelog - debian/tests/control Changes: = debian/changelog = @@ -1,3 +1,10 @@ +ncbi-entrez-direct (16.6.20220228+dfsg-2) unstable; urgency=medium + + * debian/tests/control: Depend on libxml-simple-perl for the private +script behind transmute -x2j. + + -- Aaron M. Ucko Tue, 14 Feb 2023 07:47:26 -0500 + ncbi-entrez-direct (16.6.20220228+dfsg-1) unstable; urgency=medium * New(er) upstream release. (Still carefully catching up, but this is = debian/tests/control = @@ -1,3 +1,3 @@ Tests: run-unit-test -Depends: @ +Depends: @, libxml-simple-perl Restrictions: allow-stderr View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/a0a67170a726a9095c24d0eca101f4413d737519 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/a0a67170a726a9095c24d0eca101f4413d737519 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-entrez-direct][pristine-tar] 39 commits: pristine-tar data for ncbi-entrez-direct_14.7.20210306+dfsg.orig.tar.xz
Aaron M. Ucko pushed to branch pristine-tar at Debian Med / ncbi-entrez-direct Commits: 547be379 by Aaron M. Ucko at 2022-01-17T15:36:22-05:00 pristine-tar data for ncbi-entrez-direct_14.7.20210306+dfsg.orig.tar.xz - - - - - 2b2f6181 by Aaron M. Ucko at 2022-01-17T19:56:41-05:00 pristine-tar data for ncbi-entrez-direct_14.7.20210317+dfsg.orig.tar.xz - - - - - f81cab4d by Aaron M. Ucko at 2023-01-23T20:16:08-05:00 pristine-tar data for ncbi-entrez-direct_14.8.20210324+dfsg.orig.tar.xz - - - - - 601a0e49 by Aaron M. Ucko at 2023-01-23T20:22:27-05:00 pristine-tar data for ncbi-entrez-direct_14.8.20210413+dfsg.orig.tar.xz - - - - - a9e998ea by Aaron M. Ucko at 2023-01-23T20:56:10-05:00 pristine-tar data for ncbi-entrez-direct_14.9.20210414+dfsg.orig.tar.xz - - - - - aade81e2 by Aaron M. Ucko at 2023-01-23T20:57:36-05:00 pristine-tar data for ncbi-entrez-direct_14.9.20210426+dfsg.orig.tar.xz - - - - - 58456946 by Aaron M. Ucko at 2023-01-24T20:37:03-05:00 pristine-tar data for ncbi-entrez-direct_15.0.20210428+dfsg.orig.tar.xz - - - - - ccaaa87a by Aaron M. Ucko at 2023-01-26T19:46:26-05:00 pristine-tar data for ncbi-entrez-direct_15.0.20210517+dfsg.orig.tar.xz - - - - - 79407156 by Aaron M. Ucko at 2023-01-27T18:08:31-05:00 pristine-tar data for ncbi-entrez-direct_15.1.20210519+dfsg.orig.tar.xz - - - - - fa24dcf9 by Aaron M. Ucko at 2023-01-30T20:22:52-05:00 pristine-tar data for ncbi-entrez-direct_15.1.20210525+dfsg.orig.tar.xz - - - - - 2cad5bc5 by Aaron M. Ucko at 2023-01-30T21:07:20-05:00 pristine-tar data for ncbi-entrez-direct_15.2.20210601+dfsg.orig.tar.xz - - - - - 9bdc3962 by Aaron M. Ucko at 2023-01-30T21:36:28-05:00 pristine-tar data for ncbi-entrez-direct_15.2.20210615+dfsg.orig.tar.xz - - - - - bbd45665 by Aaron M. Ucko at 2023-01-30T22:35:17-05:00 pristine-tar data for ncbi-entrez-direct_15.3.20210617+dfsg.orig.tar.xz - - - - - 9920b835 by Aaron M. Ucko at 2023-01-30T22:44:02-05:00 pristine-tar data for ncbi-entrez-direct_15.3.20210707+dfsg.orig.tar.xz - - - - - 35a24037 by Aaron M. Ucko at 2023-01-31T22:29:03-05:00 pristine-tar data for ncbi-entrez-direct_15.4.20210715+dfsg.orig.tar.xz - - - - - 760714d0 by Aaron M. Ucko at 2023-01-31T22:32:55-05:00 pristine-tar data for ncbi-entrez-direct_15.4.20210802+dfsg.orig.tar.xz - - - - - 2fb98072 by Aaron M. Ucko at 2023-02-01T22:55:01-05:00 pristine-tar data for ncbi-entrez-direct_15.5.20210806+dfsg.orig.tar.xz - - - - - 97a975c1 by Aaron M. Ucko at 2023-02-01T23:28:50-05:00 pristine-tar data for ncbi-entrez-direct_15.5.20210827+dfsg.orig.tar.xz - - - - - 67bed06a by Aaron M. Ucko at 2023-02-03T10:27:13-05:00 pristine-tar data for ncbi-entrez-direct_15.6.20210831+dfsg.orig.tar.xz - - - - - 734833ea by Aaron M. Ucko at 2023-02-03T10:42:03-05:00 pristine-tar data for ncbi-entrez-direct_15.6.20210908+dfsg.orig.tar.xz - - - - - 6566ed86 by Aaron M. Ucko at 2023-02-03T14:32:03-05:00 pristine-tar data for ncbi-entrez-direct_15.7.20210909+dfsg.orig.tar.xz - - - - - d0be692f by Aaron M. Ucko at 2023-02-03T14:39:36-05:00 pristine-tar data for ncbi-entrez-direct_15.7.20210914+dfsg.orig.tar.xz - - - - - 2b0e5e5a by Aaron M. Ucko at 2023-02-03T17:18:21-05:00 pristine-tar data for ncbi-entrez-direct_15.8.20210915+dfsg.orig.tar.xz - - - - - e47b3fb2 by Aaron M. Ucko at 2023-02-03T17:30:14-05:00 pristine-tar data for ncbi-entrez-direct_15.8.20210923+dfsg.orig.tar.xz - - - - - 7f9f9efa by Aaron M. Ucko at 2023-02-05T14:33:31-05:00 pristine-tar data for ncbi-entrez-direct_15.9.20210924+dfsg.orig.tar.xz - - - - - 14a33305 by Aaron M. Ucko at 2023-02-05T16:47:22-05:00 pristine-tar data for ncbi-entrez-direct_15.9.20210929+dfsg.orig.tar.xz - - - - - 1241d65b by Aaron M. Ucko at 2023-02-05T18:30:50-05:00 pristine-tar data for ncbi-entrez-direct_16.0.20211001+dfsg.orig.tar.xz - - - - - 1fb531ba by Aaron M. Ucko at 2023-02-05T18:44:22-05:00 pristine-tar data for ncbi-entrez-direct_16.0.20211004+dfsg.orig.tar.xz - - - - - 2035be43 by Aaron M. Ucko at 2023-02-05T18:53:11-05:00 pristine-tar data for ncbi-entrez-direct_16.1.20211012+dfsg.orig.tar.xz - - - - - 52bd369f by Aaron M. Ucko at 2023-02-06T22:17:28-05:00 pristine-tar data for ncbi-entrez-direct_16.1.20211020+dfsg.orig.tar.xz - - - - - 72146518 by Aaron M. Ucko at 2023-02-07T21:29:15-05:00 pristine-tar data for ncbi-entrez-direct_16.2.20211022+dfsg.orig.tar.xz - - - - - 47a19ea6 by Aaron M. Ucko at 2023-02-07T21:35:36-05:00 pristine-tar data for ncbi-entrez-direct_16.2.20211103+dfsg.orig.tar.xz - - - - - f64762e3 by Aaron M. Ucko at 2023-02-07T22:56:10-05:00 pristine-tar data for ncbi-entrez-direct_16.3.20211215+dfsg.orig.tar.xz - - - - - 66116a72 by Aaron M. Ucko at 2023-02-08T21:26:52-05:00 pristine-tar data for ncbi-entrez-direct_16.4.20211217+dfsg.orig.tar.xz - - - - - 0b3574fd by Aaron M. Ucko at 2023-02-08T21:28:36-05:00 pristine-tar data for ncbi-entrez-direct_16.4.20211222+dfsg.orig.tar.xz - - - - - a2f21beb by Aaron M. Ucko at 2023-02-08T22:21:54-05:00 pristine-tar data for
[med-svn] [Git][med-team/ncbi-entrez-direct][upstream] 39 commits: New upstream version 14.7.20210306+dfsg
Aaron M. Ucko pushed to branch upstream at Debian Med / ncbi-entrez-direct Commits: 80fd4329 by Aaron M. Ucko at 2022-01-17T15:36:22-05:00 New upstream version 14.7.20210306+dfsg - - - - - 1c3b39b2 by Aaron M. Ucko at 2022-01-17T19:56:40-05:00 New upstream version 14.7.20210317+dfsg - - - - - 157b9786 by Aaron M. Ucko at 2023-01-23T20:16:02-05:00 New upstream version 14.8.20210324+dfsg - - - - - 6ac53edf by Aaron M. Ucko at 2023-01-23T20:22:22-05:00 New upstream version 14.8.20210413+dfsg - - - - - 2825701b by Aaron M. Ucko at 2023-01-23T20:56:07-05:00 New upstream version 14.9.20210414+dfsg - - - - - b6f2cabf by Aaron M. Ucko at 2023-01-23T20:57:36-05:00 New upstream version 14.9.20210426+dfsg - - - - - 781e4a40 by Aaron M. Ucko at 2023-01-24T20:36:59-05:00 New upstream version 15.0.20210428+dfsg - - - - - 7189238e by Aaron M. Ucko at 2023-01-26T19:46:24-05:00 New upstream version 15.0.20210517+dfsg - - - - - 06013334 by Aaron M. Ucko at 2023-01-27T18:08:30-05:00 New upstream version 15.1.20210519+dfsg - - - - - 081c90db by Aaron M. Ucko at 2023-01-30T20:22:48-05:00 New upstream version 15.1.20210525+dfsg - - - - - be558636 by Aaron M. Ucko at 2023-01-30T21:07:19-05:00 New upstream version 15.2.20210601+dfsg - - - - - d2c807a2 by Aaron M. Ucko at 2023-01-30T21:36:27-05:00 New upstream version 15.2.20210615+dfsg - - - - - a1ee6c9f by Aaron M. Ucko at 2023-01-30T22:35:15-05:00 New upstream version 15.3.20210617+dfsg - - - - - 6f845428 by Aaron M. Ucko at 2023-01-30T22:44:02-05:00 New upstream version 15.3.20210707+dfsg - - - - - cdc07f33 by Aaron M. Ucko at 2023-01-31T22:29:01-05:00 New upstream version 15.4.20210715+dfsg - - - - - 7b240f55 by Aaron M. Ucko at 2023-01-31T22:32:55-05:00 New upstream version 15.4.20210802+dfsg - - - - - c1994a0c by Aaron M. Ucko at 2023-02-01T22:54:58-05:00 New upstream version 15.5.20210806+dfsg - - - - - 6177c749 by Aaron M. Ucko at 2023-02-01T23:28:49-05:00 New upstream version 15.5.20210827+dfsg - - - - - 5d2dc8e4 by Aaron M. Ucko at 2023-02-03T10:27:11-05:00 New upstream version 15.6.20210831+dfsg - - - - - b74e3f37 by Aaron M. Ucko at 2023-02-03T10:42:03-05:00 New upstream version 15.6.20210908+dfsg - - - - - 367531f3 by Aaron M. Ucko at 2023-02-03T14:32:01-05:00 New upstream version 15.7.20210909+dfsg - - - - - 49c58f7c by Aaron M. Ucko at 2023-02-03T14:39:35-05:00 New upstream version 15.7.20210914+dfsg - - - - - c55a7f5b by Aaron M. Ucko at 2023-02-03T17:18:21-05:00 New upstream version 15.8.20210915+dfsg - - - - - a7cd8583 by Aaron M. Ucko at 2023-02-03T17:30:13-05:00 New upstream version 15.8.20210923+dfsg - - - - - 7ff17579 by Aaron M. Ucko at 2023-02-05T14:33:30-05:00 New upstream version 15.9.20210924+dfsg - - - - - a818c5bb by Aaron M. Ucko at 2023-02-05T16:47:21-05:00 New upstream version 15.9.20210929+dfsg - - - - - ed504d41 by Aaron M. Ucko at 2023-02-05T18:30:49-05:00 New upstream version 16.0.20211001+dfsg - - - - - b1eb2ebc by Aaron M. Ucko at 2023-02-05T18:44:21-05:00 New upstream version 16.0.20211004+dfsg - - - - - 0b3e191f by Aaron M. Ucko at 2023-02-05T18:53:10-05:00 New upstream version 16.1.20211012+dfsg - - - - - 16bea89a by Aaron M. Ucko at 2023-02-06T22:17:27-05:00 New upstream version 16.1.20211020+dfsg - - - - - 9a096e33 by Aaron M. Ucko at 2023-02-07T21:29:10-05:00 New upstream version 16.2.20211022+dfsg - - - - - feb250a8 by Aaron M. Ucko at 2023-02-07T21:35:35-05:00 New upstream version 16.2.20211103+dfsg - - - - - 244cee56 by Aaron M. Ucko at 2023-02-07T22:56:09-05:00 New upstream version 16.3.20211215+dfsg - - - - - abc75b54 by Aaron M. Ucko at 2023-02-08T21:26:48-05:00 New upstream version 16.4.20211217+dfsg - - - - - f10d5a66 by Aaron M. Ucko at 2023-02-08T21:28:36-05:00 New upstream version 16.4.20211222+dfsg - - - - - 7e49c039 by Aaron M. Ucko at 2023-02-08T22:21:52-05:00 New upstream version 16.5.20220103+dfsg - - - - - 3a7e8f73 by Aaron M. Ucko at 2023-02-08T22:24:06-05:00 New upstream version 16.5.20220114+dfsg - - - - - bc8a7dd9 by Aaron M. Ucko at 2023-02-08T22:41:15-05:00 New upstream version 16.6.20220208+dfsg - - - - - 35277b19 by Aaron M. Ucko at 2023-02-11T23:28:52-05:00 New upstream version 16.6.20220228+dfsg - - - - - 19 changed files: - README - accn-at-a-time - align-columns - amino-acid-composition - archive-pubmed - + asn2xml - − asp-cp - − asp-ls - between-two-genes - + blst2tkns - − bt-context.txt - − bt-link - − bt-load - − bt-save - − bt-srch - − build.sh - + cmd/build.sh - + cmd/go.mod - + cmd/go.sum The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/509e0c274178abf9d5c16abde65bf7b08d9352cd...35277b19441a93b82408e67900d826d19744d756 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/509e0c274178abf9d5c16abde65bf7b08d9352cd...35277b19441a93b82408e67900d826d19744d756 You're receiving this email because of your account on salsa.debian.org. ___
[med-svn] [Git][med-team/htsjdk][master] htsjdk 3.0.4+dfsg-2: Restrict autopkgtest to amd64 and arm64.
Aaron M. Ucko pushed to branch master at Debian Med / htsjdk Commits: 98fddc59 by Aaron M. Ucko at 2023-01-23T22:16:15-05:00 htsjdk 3.0.4+dfsg-2: Restrict autopkgtest to amd64 and arm64. sra-sdk subsumed ngs-sdk and supports only those two architectures. Urgency high to avoid delaying its migration. - - - - - 2 changed files: - debian/changelog - debian/tests/control Changes: = debian/changelog = @@ -1,3 +1,11 @@ +htsjdk (3.0.4+dfsg-2) unstable; urgency=high + + * Team upload. + * debian/tests/control: Restrict all tests to architectures supported by +sra-sdk, which subsumed ngs-sdk: amd64 and arm64. + + -- Aaron M. Ucko Mon, 23 Jan 2023 22:16:14 -0500 + htsjdk (3.0.4+dfsg-1) unstable; urgency=medium * New upstream version 3.0.4+dfsg = debian/tests/control = @@ -1,30 +1,36 @@ Tests: beagle-run-sample-analysis Depends: beagle, beagle-doc -Architecture: !armhf +Architecture: amd64 arm64 Tests: chromhmm-run-sample-analysis Depends: chromhmm, chromhmm-example +Architecture: amd64 arm64 Tests: drop-seq-run-unit-test Depends: drop-seq-tools, drop-seq-testdata, samtools +Architecture: amd64 arm64 Restrictions: allow-stderr, skip-not-installable Tests: fastqc-run-unit-test Depends: fastqc, unzip +Architecture: amd64 arm64 Restrictions: allow-stderr Tests: jalview-run-unit-test Depends: jalview +Architecture: amd64 arm64 Restrictions: allow-stderr Test-Command: java -cp /usr/share/java/igv.jar org.broad.igv.tools.IgvTools index src/test/resources/htsjdk/samtools/example.bam Depends: igv +Architecture: amd64 arm64 Tests: picard-tools-run-unit-test Depends: picard-tools +Architecture: amd64 arm64 Restrictions: allow-stderr, skip-not-installable Tests: pilon-run-unit-test Depends: pilon -Architecture: amd64 arm64 ppc64el s390x +Architecture: amd64 arm64 Restrictions: allow-stderr View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/98fddc5949e96a26c4a13ace7e10a3ee32a5480f -- View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/98fddc5949e96a26c4a13ace7e10a3ee32a5480f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/htsjdk] Pushed new tag debian/3.0.4+dfsg-2
Aaron M. Ucko pushed new tag debian/3.0.4+dfsg-2 at Debian Med / htsjdk -- View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/tree/debian/3.0.4+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.3+dfsg-4
Aaron M. Ucko pushed new tag debian/3.0.3+dfsg-4 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.3+dfsg-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] sra-sdk 3.0.3+dfsg-4: -fsigned-char to fix arm64 FTBFS.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: 4a2246e9 by Aaron M. Ucko at 2023-01-22T17:04:23-05:00 sra-sdk 3.0.3+dfsg-4: -fsigned-char to fix arm64 FTBFS. debian/rules: Explicitly build with signed characters (-fsigned-char). On arm64, where char is normally unsigned, two tests otherwise fail because messages reporting certain characters' numeric values formally differ from expectations. - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,12 @@ +sra-sdk (3.0.3+dfsg-4) unstable; urgency=medium + + * debian/rules: Explicitly build with signed characters (-fsigned-char). +On arm64, where char is normally unsigned, two tests otherwise fail +because messages reporting certain characters' numeric values formally +differ from expectations. + + -- Aaron M. Ucko Sun, 22 Jan 2023 17:04:21 -0500 + sra-sdk (3.0.3+dfsg-3) unstable; urgency=medium * debian/copyright: Account for a second(!) version of BitMagic under = debian/rules = @@ -6,6 +6,9 @@ DEBIAN_GUID = 806b5c3b-0088-4732-8359-51630950d723 # +pie breaks the build export DEB_BUILD_MAINT_OPTIONS = hardening=+all +export DEB_CFLAGS_MAINT_APPEND = -fsigned-char +export DEB_CXXFLAGS_MAINT_APPEND = -fsigned-char + pkg := sra-toolkit include /usr/share/dpkg/architecture.mk View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/4a2246e923dff0b1dc93bbacdc55b37613849b17 -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/4a2246e923dff0b1dc93bbacdc55b37613849b17 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-igblast][master] debian/igblast.install: Install correct build output.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-igblast Commits: 3544c545 by Aaron M. Ucko at 2023-01-22T13:39:14-05:00 debian/igblast.install: Install correct build output. - - - - - 2 changed files: - debian/changelog - debian/igblast.install Changes: = debian/changelog = @@ -12,6 +12,7 @@ ncbi-igblast (1.20.0-1) UNRELEASED; urgency=medium 4-6. [ Aaron M. Ucko ] + * debian/igblast.install: Install correct build output. * debian/patches/avoid-gcc-crash.patch (new): Work around a consistent internal compiler error whose fix may run into the toolchain freeze: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=108137 @@ -20,7 +21,7 @@ ncbi-igblast (1.20.0-1) UNRELEASED; urgency=medium - Enable optimization unless DEB_BUILD_OPTIONS contains noopt. - Copy-hack clean logic from ncbi-blast+. - -- Aaron M. Ucko Fri, 20 Jan 2023 17:20:22 -0500 + -- Aaron M. Ucko Sun, 22 Jan 2023 13:39:13 -0500 ncbi-igblast (1.19.0-1) unstable; urgency=medium = debian/igblast.install = @@ -1,7 +1,3 @@ -c++/GCC*-Release*/bin usr/lib/ncbi-igblast/ -c++/GCC*-Release*/inc usr/lib/ncbi-igblast/ -c++/GCC*-Release*/lib usr/lib/ncbi-igblast/ -c++/GCC*-Release*/status usr/lib/ncbi-igblast/ - +c++/GCC*/bin/igblast* usr/bin c++/src/app/igblast/edit_imgt_file.pl usr/bin c++/src/app/igblast/internal_data/*usr/share/ncbi/igblast View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/commit/3544c545c3932daf3404e73396fd7e27fc24f8a8 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/commit/3544c545c3932daf3404e73396fd7e27fc24f8a8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/skesa][master] 4 commits: Start work on skesa 2.4.0-6.
Aaron M. Ucko pushed to branch master at Debian Med / skesa Commits: 01c51326 by Aaron M. Ucko at 2023-01-22T13:32:27-05:00 Start work on skesa 2.4.0-6. - - - - - 16344bf4 by Aaron M. Ucko at 2023-01-22T13:33:17-05:00 debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2. It's a baseline violation on x86, and entirely unavailable elsewhere. - - - - - fcf90e16 by Aaron M. Ucko at 2023-01-22T13:34:04-05:00 d/patches/hardening.patch: Reinstate use of dpkg-supplied CFLAGS. The addition accidentally got lost in the course of updating use_debian_packaged_ngs-sdk.patch. - - - - - c9036203 by Aaron M. Ucko at 2023-01-22T13:35:16-05:00 Finalize skesa 2.4.0-6 for unstable. - - - - - 4 changed files: - debian/changelog - debian/patches/hardening.patch - + debian/patches/no_sse4.2.patch - debian/patches/series Changes: = debian/changelog = @@ -1,3 +1,13 @@ +skesa (2.4.0-6) unstable; urgency=medium + + * debian/patches/hardening.patch: Reinstate use of dpkg-supplied CFLAGS. +The addition accidentally got lost in the course of updating +use_debian_packaged_ngs-sdk.patch. + * debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2. It's a +baseline violation on x86, and entirely unavailable elsewhere. + + -- Aaron M. Ucko Sun, 22 Jan 2023 13:35:16 -0500 + skesa (2.4.0-5) unstable; urgency=medium [ Andreas Tille ] = debian/patches/hardening.patch = @@ -6,8 +6,12 @@ Index: b/Makefile === --- a/Makefile +++ b/Makefile -@@ -43,7 +43,7 @@ CC = c++ -std=c++11 -fdiagnostics-color= - CFLAGS = -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \ +@@ -40,10 +40,10 @@ NGS_INCL := -I $(NGS_PATH)/include + NGS_LIB := -L $(NGS_PATH)/lib64 + + CC = c++ -std=c++11 -fdiagnostics-color=never +-CFLAGS = -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \ ++CFLAGS += -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \ -fomit-frame-pointer -msse4.2 $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL) -LIBS = -lngs-c++ -lncbi-vdb -lzstd \ = debian/patches/no_sse4.2.patch = @@ -0,0 +1,13 @@ +Index: b/Makefile +=== +--- a/Makefile b/Makefile +@@ -41,7 +41,7 @@ NGS_LIB := -L $(NGS_PATH)/lib64 + + CC = c++ -std=c++11 -fdiagnostics-color=never + CFLAGS += -Wall -Wno-format-y2k -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \ +- -fomit-frame-pointer -msse4.2 $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL) ++ -fomit-frame-pointer $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL) + + LIBS += -lngs-c++ -lncbi-vdb -lzstd \ +$(BOOST_LIB) \ = debian/patches/series = @@ -1,3 +1,4 @@ use_debian_packaged_ngs-sdk.patch hardening.patch link_boost_dynamically.patch +no_sse4.2.patch View it on GitLab: https://salsa.debian.org/med-team/skesa/-/compare/5208d7218d3c5043c6950f140981271f4bcc6467...c903620376731d46db778c6bdb693873aea6a0cb -- View it on GitLab: https://salsa.debian.org/med-team/skesa/-/compare/5208d7218d3c5043c6950f140981271f4bcc6467...c903620376731d46db778c6bdb693873aea6a0cb You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/skesa] Pushed new tag debian/2.4.0-6
Aaron M. Ucko pushed new tag debian/2.4.0-6 at Debian Med / skesa -- View it on GitLab: https://salsa.debian.org/med-team/skesa/-/tree/debian/2.4.0-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] 5 commits: Start work on sra-sdk 3.0.3+dfsg-3.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
9f5e1645 by Aaron M. Ucko at 2023-01-22T13:13:19-05:00
Start work on sra-sdk 3.0.3+dfsg-3.
- - - - -
84d6d236 by Aaron M. Ucko at 2023-01-22T13:15:28-05:00
d/patches/use_c_locale_for_comma (new): Stick with the C locale.
en_US.UTF-8 isn't necessarily available, particularly on the buildds,
and C is perfectly sufficient to ensure recognition of comma as a
thousands separator. (Recent versions of glibc supply a middle-ground
C.utf8, but even that looks like overkill at the moment.)
- - - - -
dcb99276 by Aaron M. Ucko at 2023-01-22T13:16:48-05:00
debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2.
It's a baseline violation on x86, and entirely unavailable elsewhere.
- - - - -
8da20705 by Aaron M. Ucko at 2023-01-22T13:22:02-05:00
debian/copyright: Account for bam-loader's BitMagic from 2022.
Account for a second(!) version of BitMagic under
tools/loaders/bam-loader, with copyright running through 2022.
- - - - -
4148a38e by Aaron M. Ucko at 2023-01-22T13:26:17-05:00
Finalize sra-sdk 3.0.3+dfsg-3 for unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/copyright
- + debian/patches/no_sse4.2.patch
- debian/patches/series
- + debian/patches/use_c_locale_for_comma.patch
Changes:
=
debian/changelog
=
@@ -1,3 +1,17 @@
+sra-sdk (3.0.3+dfsg-3) unstable; urgency=medium
+
+ * debian/copyright: Account for a second(!) version of BitMagic under
+tools/loaders/bam-loader, with copyright running through 2022.
+ * debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2. It's a
+baseline violation on x86, and entirely unavailable elsewhere.
+ * debian/patches/use_c_locale_for_comma (new): Stick with the C locale.
+en_US.UTF-8 isn't necessarily available, particularly on the buildds,
+and C is perfectly sufficient to ensure recognition of comma as a
+thousands separator. (Recent versions of glibc supply a middle-ground
+C.utf8, but even that looks like overkill at the moment.)
+
+ -- Aaron M. Ucko Sun, 22 Jan 2023 13:26:16 -0500
+
sra-sdk (3.0.3+dfsg-2) unstable; urgency=medium
* Upload to unstable.
=
debian/copyright
=
@@ -103,8 +103,8 @@ License: BSD-3-clause-CLI11
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Files: tools/loaders/sharq/bm/*
-Copyright: 2002-2021 Anatoliy Kuznetsov (anatoliy_kuznetsov at yahoo.com)
+Files: tools/loaders/*/bm/*
+Copyright: 2002-2022 Anatoliy Kuznetsov (anatoliy_kuznetsov at yahoo.com)
License: Apache-2
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
=
debian/patches/no_sse4.2.patch
=
@@ -0,0 +1,49 @@
+Index: b/test/loaders/sharq/CMakeLists.txt
+===
+--- a/test/loaders/sharq/CMakeLists.txt
b/test/loaders/sharq/CMakeLists.txt
+@@ -31,7 +31,7 @@ if( SINGLE_CONFIG )
+ if ( ZLIB_FOUND AND BZip2_FOUND AND Threads_FOUND )
+
+ set(CMAKE_CXX_STANDARD 17)
+-add_definitions(-msse4.2 -DBMSSE42OPT)
++# add_definitions(-msse4.2 -DBMSSE42OPT)
+
+ # assume tools/sharq built libre2
+ set(LOCAL_BUILD_DIR ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+Index: b/tools/loaders/bam-loader/CMakeLists.txt
+===
+--- a/tools/loaders/bam-loader/CMakeLists.txt
b/tools/loaders/bam-loader/CMakeLists.txt
+@@ -58,9 +58,9 @@ if( NOT WIN32)
+
+ GenerateExecutableWithDefs( bam-load "${SRC}" ""
"${CMAKE_SOURCE_DIR}/libs/inc"
"loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE}" )
+ target_compile_features(bam-load PUBLIC cxx_std_17)
+-if (COMPILER_OPTION_SSE42_SUPPORTED)
+-target_compile_options( bam-load PUBLIC -msse4.2 -DBMSSE42OPT)
+-endif()
++#if (COMPILER_OPTION_SSE42_SUPPORTED)
++#target_compile_options( bam-load PUBLIC -msse4.2 -DBMSSE42OPT)
++#endif()
+ target_include_directories( bam-load PRIVATE
${CMAKE_SOURCE_DIR}/libs/inc)
+ target_link_libraries( bam-load loader OpenSSL::SSL
${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_WRITE} -lz )
+
+Index: b/tools/loaders/sharq/CMakeLists.txt
+===
+--- a/tools/loaders/sharq/CMakeLists.txt
b/tools/loaders/sharq/CMakeLists.txt
+@@ -52,10 +52,10 @@ if ( ZLIB_FOUND AND BZip2_FOUND AND Thre
+ #set(CMAKE_VERBOSE_MAKEFILE ON)
+ set(CMAKE_CXX_STANDARD 17)
+
+-#specific to BitMagic
+-if (COMPILER_OPTION_SSE42_SUPPORTED)
+-add_definitions(-msse4.2 -DBMSSE42OPT)
+-endif()
++##specific to BitMagic
++#if (COMPILER_OPT
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.3+dfsg-3
Aaron M. Ucko pushed new tag debian/3.0.3+dfsg-3 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.3+dfsg-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/skesa] Pushed new tag debian/2.4.0-5
Aaron M. Ucko pushed new tag debian/2.4.0-5 at Debian Med / skesa -- View it on GitLab: https://salsa.debian.org/med-team/skesa/-/tree/debian/2.4.0-5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.3+dfsg-2
Aaron M. Ucko pushed new tag debian/3.0.3+dfsg-2 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.3+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb][master] 3 commits: Start work on ncbi-vdb 3.0.2+dfsg-2.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb Commits: 0c5cb3d2 by Aaron M. Ucko at 2023-01-20T17:37:45-05:00 Start work on ncbi-vdb 3.0.2+dfsg-2. - - - - - 7567b9e6 by Aaron M. Ucko at 2023-01-20T17:38:35-05:00 debian/salsa-ci.yml: Stop reenabling aptly, no longer needed. - - - - - e28c99ce by Aaron M. Ucko at 2023-01-20T17:43:13-05:00 Finalize ncbi-vdb 3.0.2+dfsg-2, back to unstable. - - - - - 2 changed files: - debian/changelog - debian/salsa-ci.yml Changes: = debian/changelog = @@ -1,3 +1,10 @@ +ncbi-vdb (3.0.2+dfsg-2) unstable; urgency=medium + + * Upload to unstable. + * debian/salsa-ci.yml: Stop reenabling aptly, no longer needed. + + -- Aaron M. Ucko Fri, 20 Jan 2023 17:43:12 -0500 + ncbi-vdb (3.0.2+dfsg-1) experimental; urgency=medium * New upstream release. = debian/salsa-ci.yml = @@ -2,5 +2,3 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml -variables: - SALSA_CI_DISABLE_APTLY: 0 View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/01fdd8463d3baf3b68a25cf4f40077b7cba3d1cf...e28c99ceab326bdd916a866b5393c15b048b034e -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/01fdd8463d3baf3b68a25cf4f40077b7cba3d1cf...e28c99ceab326bdd916a866b5393c15b048b034e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb] Pushed new tag debian/3.0.2+dfsg-2
Aaron M. Ucko pushed new tag debian/3.0.2+dfsg-2 at Debian Med / ncbi-vdb -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/tree/debian/3.0.2+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-igblast][master] debian/rules: Fix ifeq syntax.
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-igblast Commits: 8932193a by Aaron M. Ucko at 2023-01-20T17:30:48-05:00 debian/rules: Fix ifeq syntax. - - - - - 1 changed file: - debian/rules Changes: = debian/rules = @@ -3,7 +3,7 @@ %: dh $@ --sourcedirectory=c++ -ifeq(,$(filter noopt,$(DEB_BUILD_OPTIONS))) +ifeq "" "$(filter noopt,$(DEB_BUILD_OPTIONS))" WITH_OPTIM=--with-optimization endif View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/commit/8932193af1cf759393bab4163209fb1a875a8480 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/commit/8932193af1cf759393bab4163209fb1a875a8480 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-igblast][master] 4 commits: avoid-gcc-crash.patch (new): Work around a consistent ICE
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-igblast
Commits:
7f9c4ebe by Aaron M. Ucko at 2023-01-20T17:06:42-05:00
avoid-gcc-crash.patch (new): Work around a consistent ICE
... whose fix may run into the toolchain freeze:
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=108137
- - - - -
cdaf8ca5 by Aaron M. Ucko at 2023-01-20T17:12:49-05:00
debian/rules: Add possibly relevant subtrees to VDB_INCLUDE.
- - - - -
3ea3684a by Aaron M. Ucko at 2023-01-20T17:14:51-05:00
Enable optimization unless DEB_BUILD_OPTIONS contains noopt.
- - - - -
5dbd0ce5 by Aaron M. Ucko at 2023-01-20T17:20:23-05:00
debian/rules: Copy-hack clean logic from ncbi-blast+.
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/avoid-gcc-crash.patch
- + debian/patches/series
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,5 +1,6 @@
ncbi-igblast (1.20.0-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Team upload.
* Fix lintian-overrides
* Recommends: ncbi-blast+
@@ -10,7 +11,16 @@ ncbi-igblast (1.20.0-1) UNRELEASED; urgency=medium
* Update lintian override info format in d/source/lintian-overrides on line
4-6.
- -- Andreas Tille Sat, 30 Jul 2022 09:29:11 +0200
+ [ Aaron M. Ucko ]
+ * debian/patches/avoid-gcc-crash.patch (new): Work around a consistent
+internal compiler error whose fix may run into the toolchain freeze:
+https://gcc.gnu.org/bugzilla/show_bug.cgi?id=108137
+ * debian/rules:
+- Add possibly relevant subtrees to VDB_INCLUDE.
+- Enable optimization unless DEB_BUILD_OPTIONS contains noopt.
+- Copy-hack clean logic from ncbi-blast+.
+
+ -- Aaron M. Ucko Fri, 20 Jan 2023 17:20:22 -0500
ncbi-igblast (1.19.0-1) unstable; urgency=medium
=
debian/patches/avoid-gcc-crash.patch
=
@@ -0,0 +1,18 @@
+Index: b/c++/src/connect/ncbi_socket.c
+===
+--- a/c++/src/connect/ncbi_socket.c
b/c++/src/connect/ncbi_socket.c
+@@ -6037,11 +6037,12 @@ static EIO_Status s_SendMsg(SOCK
+
+ if (!x_host || !x_port) {
+ SOCK_HostPortToString(x_host, x_port, w, sizeof(w)/2);
++const char* missing = x_port ? "host" : &"host:port"[x_host ? 5 : 0];
+ CORE_LOGF_X(89, eLOG_Error,
+ ("%s[DSOCK::SendMsg] "
+ " Address \"%s\" incomplete, missing %s",
+ s_ID(sock, w + sizeof(w)/2), w,
+- x_port ? "host" : &"host:port"[x_host ? 5 : 0]));
++ missing));
+ return eIO_Unknown;
+ }
+ if (s_ApproveHook) {
=
debian/patches/series
=
@@ -0,0 +1 @@
+avoid-gcc-crash.patch
=
debian/rules
=
@@ -3,11 +3,19 @@
%:
dh $@ --sourcedirectory=c++
+ifeq(,$(filter noopt,$(DEB_BUILD_OPTIONS)))
+ WITH_OPTIM=--with-optimization
+endif
+
+VDB_SUBTREES=os/$(DEB_HOST_ARCH_OS) os/unix cc/gcc/$(DEB_HOST_GNU_CPU) cc/gcc
+VDB_INC=-I/usr/include/ncbi-vdb
+VDB_INCLUDE=$(VDB_INC) $(VDB_SUBTREES:%=$(VDB_INC)/%)
+
override_dh_auto_configure:
cd c++ && yes | \
./configure.orig --prefix=/usr \
- --with-openmp \
- --with-vdb=/usr VDB_INCLUDE=-I/usr/include/ncbi-vdb \
+ --with-openmp $(WITH_OPTIM) \
+ --with-vdb=/usr VDB_INCLUDE="$(VDB_INCLUDE)" \
--without-runpath \
--with-flat-makefile
@@ -22,5 +30,20 @@ override_dh_auto_install:
override_dh_clean:
# cleans *.orig files, which it should not
- rm -fr ./c++/GCC1020-ReleaseDLL64
dh_clean -X*.orig
+ #Tricky - for each module directory there may be several module files
+ #or there may be none but then there is still a module named after the
+ #directory. Clean everything!
+ -for x in c++/src/objects/* ; do \
+ (cd "$$x" && ( \
+ mods="`echo *.module`" ; \
+ [ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \
+ for mod in $$mods ; do \
+ ../../../GCC*/build/new_module.sh $$mod \
+ purge_sources ; \
+ done ) ; \
+ ) ; \
+ done
+ rm -rf c++/compilers/dll c++/config.log c++/Makefile c++/GCC*
+ rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module
+ rm -f c++/include/common/ncbi_revision.h
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-igblast/-/compare/f1b140f84d26166d4fa75eb072276a3a118f092d...5dbd0ce570f921053441fb3c14d1274d8a827049
--
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-igblast/-/compare/f1b140f84d26166d4fa75eb072276a3a118f092d...5dbd0ce570f921053441fb3c14d1274d8a827049
You're receiving this email because of your account on salsa.debian
[med-svn] [Git][med-team/sra-sdk][master] salsa-ci.yml: Add quoting to preclude colon misinterpretation.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: 3aac5e63 by Aaron M. Ucko at 2023-01-19T21:21:54-05:00 salsa-ci.yml: Add quoting to preclude colon misinterpretation. - - - - - 1 changed file: - debian/salsa-ci.yml Changes: = debian/salsa-ci.yml = @@ -3,9 +3,9 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml before_script: - - echo "Package: ncbi-vdb-data" | tee/etc/apt/preferences.d/exp-data - - echo "Pin: release a=experimental" | tee -a /etc/apt/preferences.d/exp-data - - echo "Pin-Priority: 999" | tee -a /etc/apt/preferences.d/exp-data + - 'echo "Package: ncbi-vdb-data" | tee /etc/apt/preferences.d/exp-data' + - 'echo "Pin: release a=experimental" | tee -a /etc/apt/preferences.d/exp-data' + - 'echo "Pin-Priority: 999" | tee -a /etc/apt/preferences.d/exp-data' - apt-get update variables: RELEASE: 'experimental' View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/3aac5e632a5641ffca698d6df5d799e1b053469d -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/3aac5e632a5641ffca698d6df5d799e1b053469d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] salsa-ci.yml: Rework before_script to avoid invalid YAML.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: ffa0d09d by Aaron M. Ucko at 2023-01-19T20:28:15-05:00 salsa-ci.yml: Rework before_script to avoid invalid YAML. - - - - - 1 changed file: - debian/salsa-ci.yml Changes: = debian/salsa-ci.yml = @@ -3,7 +3,9 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml before_script: - - printf "Package: ncbi-vdb-data\nPin: release a=experimental\nPin-Priority: 999\n" | tee /etc/apt/preferences.d/exp-data + - echo "Package: ncbi-vdb-data" | tee/etc/apt/preferences.d/exp-data + - echo "Pin: release a=experimental" | tee -a /etc/apt/preferences.d/exp-data + - echo "Pin-Priority: 999" | tee -a /etc/apt/preferences.d/exp-data - apt-get update variables: RELEASE: 'experimental' View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/ffa0d09da3077d3141dfd8e02afcbeda85590011 -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/ffa0d09da3077d3141dfd8e02afcbeda85590011 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] New salsa-ci taming approach: before_script setting a pin.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
b32b243c by Aaron M. Ucko at 2023-01-19T20:24:07-05:00
New salsa-ci taming approach: before_script setting a pin.
* debian/control: Drop useless explicit dependency on ncbi-vdb-data 3.
* debian/salsa-ci.yml: Reinstate a before_script to favor experimental
ncbi-vdb-data (by pinning a higher preference on it).
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/salsa-ci.yml
Changes:
=
debian/changelog
=
@@ -1,15 +1,17 @@
sra-sdk (3.0.3+dfsg-2) UNRELEASED; urgency=medium
* NOT RELEASED YET.
- * debian/control: Replace vestigial versioned dependency on
-libncbi-wvdb2 with a temporary one on ncbi-vdb-data 3.x.
+ * debian/control: Drop vestigial versioned dependency on libncbi-wvdb2.
* debian/patches/prefer_dynamic_libraries.patch: Comment out upstream
logic that favored static linkage.
- * debian/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE
-variable rather than a before_script. The new approach is simpler,
-and with any luck will apply to autopkgtest and/or piuparts.
-
- -- Aaron M. Ucko Thu, 19 Jan 2023 19:54:20 -0500
+ * debian/salsa-ci.yml:
+- Pull in experimental ncbi-vdb via a RELEASE variable rather than a
+ before_script. The new approach is simpler, and with any luck will
+ apply to autopkgtest and/or piuparts.
+- Reinstate a before_script to favor experimental ncbi-vdb-data (by
+ pinning a higher preference on it).
+
+ -- Aaron M. Ucko Thu, 19 Jan 2023 20:24:06 -0500
sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium
=
debian/control
=
@@ -35,7 +35,6 @@ Rules-Requires-Root: no
Package: sra-toolkit
Architecture: any
Depends: ${shlibs:Depends},
- ncbi-vdb-data (>= 3~),
${misc:Depends}
Recommends: med-config
Description: utilities for the NCBI Sequence Read Archive
=
debian/salsa-ci.yml
=
@@ -2,5 +2,8 @@
include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
-
https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+before_script:
+ - printf "Package: ncbi-vdb-data\nPin: release a=experimental\nPin-Priority:
999\n" | tee /etc/apt/preferences.d/exp-data
+ - apt-get update
variables:
RELEASE: 'experimental'
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/b32b243c7dcba4b517eecc988556b5f0189d3741
--
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[med-svn] [Git][med-team/sra-sdk][master] Switch sra-toolkit's explicit versioned dependency.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
2ffd2137 by Aaron M. Ucko at 2023-01-19T19:54:21-05:00
Switch sra-toolkit's explicit versioned dependency.
Replace vestigial versioned dependency on libncbi-wvdb2 with a
temporary one on ncbi-vdb-data 3.x.
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -1,13 +1,15 @@
sra-sdk (3.0.3+dfsg-2) UNRELEASED; urgency=medium
* NOT RELEASED YET.
+ * debian/control: Replace vestigial versioned dependency on
+libncbi-wvdb2 with a temporary one on ncbi-vdb-data 3.x.
* debian/patches/prefer_dynamic_libraries.patch: Comment out upstream
logic that favored static linkage.
* debian/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE
variable rather than a before_script. The new approach is simpler,
and with any luck will apply to autopkgtest and/or piuparts.
- -- Aaron M. Ucko Thu, 19 Jan 2023 19:13:24 -0500
+ -- Aaron M. Ucko Thu, 19 Jan 2023 19:54:20 -0500
sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium
=
debian/control
=
@@ -35,7 +35,7 @@ Rules-Requires-Root: no
Package: sra-toolkit
Architecture: any
Depends: ${shlibs:Depends},
- libncbi-wvdb2 (>= 2.10.6+dfsg-3~),
+ ncbi-vdb-data (>= 3~),
${misc:Depends}
Recommends: med-config
Description: utilities for the NCBI Sequence Read Archive
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/2ffd213775c13eeda47d3a978439d52c36d1dfbf
--
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/commit/2ffd213775c13eeda47d3a978439d52c36d1dfbf
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[med-svn] [Git][med-team/sra-sdk][master] d/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE variable
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk Commits: 2e94098c by Aaron M. Ucko at 2023-01-19T19:13:25-05:00 d/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE variable ... rather than a before_script. The new approach is simpler, and with any luck will apply to autopkgtest and/or piuparts. - - - - - 2 changed files: - debian/changelog - debian/salsa-ci.yml Changes: = debian/changelog = @@ -3,8 +3,11 @@ sra-sdk (3.0.3+dfsg-2) UNRELEASED; urgency=medium * NOT RELEASED YET. * debian/patches/prefer_dynamic_libraries.patch: Comment out upstream logic that favored static linkage. + * debian/salsa-ci.yml: Pull in experimental ncbi-vdb via a RELEASE +variable rather than a before_script. The new approach is simpler, +and with any luck will apply to autopkgtest and/or piuparts. - -- Aaron M. Ucko Wed, 18 Jan 2023 22:47:03 -0500 + -- Aaron M. Ucko Thu, 19 Jan 2023 19:13:24 -0500 sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium = debian/salsa-ci.yml = @@ -2,6 +2,5 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml -before_script: - - echo "deb [trusted=yes] https://salsa.debian.org/med-team/ncbi-vdb/-/jobs/3711898/artifacts/raw/aptly unstable main" | tee /etc/apt/sources.list.d/pkga.list - - apt-get update +variables: + RELEASE: 'experimental' View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/2e94098c86fe8ad3b736adfa6273a3bfb9301d2a -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/2e94098c86fe8ad3b736adfa6273a3bfb9301d2a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] 2 commits: Start work towards sra-sdk 3.0.3+dfsg-2.
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
f29c518d by Aaron M. Ucko at 2023-01-18T22:42:03-05:00
Start work towards sra-sdk 3.0.3+dfsg-2.
- - - - -
5ab5aa8b by Aaron M. Ucko at 2023-01-18T22:47:05-05:00
Add debian/patches/prefer_dynamic_libraries.patch.
Comment out upstream logic that favored static linkage.
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/prefer_dynamic_libraries.patch
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+sra-sdk (3.0.3+dfsg-2) UNRELEASED; urgency=medium
+
+ * NOT RELEASED YET.
+ * debian/patches/prefer_dynamic_libraries.patch: Comment out upstream
+logic that favored static linkage.
+
+ -- Aaron M. Ucko Wed, 18 Jan 2023 22:47:03 -0500
+
sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium
[ Andreas Tille ]
=
debian/patches/prefer_dynamic_libraries.patch
=
@@ -0,0 +1,28 @@
+--- a/build/env.cmake
b/build/env.cmake
+@@ -523,9 +523,9 @@ endfunction()
+ #
+ function(MakeLinksExe target install_via_driver)
+
+-if ( "GNU" STREQUAL "${CMAKE_C_COMPILER_ID}" )
+-target_link_options( ${target} PRIVATE -static-libgcc
-static-libstdc++ )
+-endif()
++# if ( "GNU" STREQUAL "${CMAKE_C_COMPILER_ID}" )
++# target_link_options( ${target} PRIVATE -static-libgcc
-static-libstdc++ )
++# endif()
+
+ # creates dependency loops
+ # if ( install_via_driver )
+--- a/tools/loaders/sharq/CMakeLists.txt
b/tools/loaders/sharq/CMakeLists.txt
+@@ -42,8 +42,8 @@ if( SINGLE_CONFIG )
+ cmake_minimum_required(VERSION 3.16)
+ project(sharq)
+
+-# prefer static linkage
+-set(CMAKE_FIND_LIBRARY_SUFFIXES .a .so .dylib)
++## prefer static linkage
++#set(CMAKE_FIND_LIBRARY_SUFFIXES .a .so .dylib)
+ find_package(ZLIB)
+ find_package(BZip2)
+ find_package (Threads)
=
debian/patches/series
=
@@ -34,3 +34,4 @@ use_soversions.patch
# use_stock_magic.patch
label_online_tests.patch
# reflect_code_donations.patch
+prefer_dynamic_libraries.patch
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/compare/d0f29526aa51a0d4949349d5f8f8c8c31a361af2...5ab5aa8bd70c090d025a5f4d5b55d78a993ba8a6
--
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/compare/d0f29526aa51a0d4949349d5f8f8c8c31a361af2...5ab5aa8bd70c090d025a5f4d5b55d78a993ba8a6
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[med-svn] [Git][med-team/sra-sdk][upstream] 2 commits: New upstream version 3.0.2+dfsg
Aaron M. Ucko pushed to branch upstream at Debian Med / sra-sdk Commits: 1400bb48 by Aaron M. Ucko at 2022-12-27T12:30:32-05:00 New upstream version 3.0.2+dfsg - - - - - 8fa7e4f1 by Aaron M. Ucko at 2023-01-15T20:38:17-05:00 New upstream version 3.0.3+dfsg - - - - - 24 changed files: - CHANGES.md - CMakeLists.txt - − Makefile.old - README-blastn - README.md - build/.gitignore - − build/Makefile.cc - − build/Makefile.clang - − build/Makefile.deb - build/Makefile.env - − build/Makefile.env.old - − build/Makefile.gcc - − build/Makefile.icc - − build/Makefile.install - − build/Makefile.linux - − build/Makefile.rpm - − build/Makefile.rules - − build/Makefile.scm - − build/Makefile.shell - − build/Makefile.targets - − build/Makefile.tools - build/Makefile.vers - − build/Xcode/asm-trace/asm-trace.xcodeproj/project.pbxproj - − build/Xcode/old-toolkit/.gitignore The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/728c74654b532dcad244c504be12c5445a0d2b8b...8fa7e4f18c6b877e01b14ec426981bb152d9b753 -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/728c74654b532dcad244c504be12c5445a0d2b8b...8fa7e4f18c6b877e01b14ec426981bb152d9b753 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag upstream/3.0.3+dfsg
Aaron M. Ucko pushed new tag upstream/3.0.3+dfsg at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/upstream/3.0.3+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag upstream/3.0.2+dfsg
Aaron M. Ucko pushed new tag upstream/3.0.2+dfsg at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/upstream/3.0.2+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/3.0.3+dfsg-1
Aaron M. Ucko pushed new tag debian/3.0.3+dfsg-1 at Debian Med / sra-sdk -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/tree/debian/3.0.3+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sra-sdk][master] 15 commits: New upstream version 3.0.2+dfsg
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
1400bb48 by Aaron M. Ucko at 2022-12-27T12:30:32-05:00
New upstream version 3.0.2+dfsg
- - - - -
27090bec by Aaron M. Ucko at 2022-12-27T15:21:05-05:00
Merge tag 'upstream/3.0.2+dfsg'
Upstream version 3.0.2(+dfsg).
- - - - -
8fa7e4f1 by Aaron M. Ucko at 2023-01-15T20:38:17-05:00
New upstream version 3.0.3+dfsg
- - - - -
a7dcc0e7 by Aaron M. Ucko at 2023-01-15T20:41:21-05:00
Merge tag 'upstream/3.0.3+dfsg'
Upstream version 3.0.3(+dfsg).
- - - - -
52dee6ae by Aaron M. Ucko at 2023-01-15T20:56:15-05:00
debian/patches: Update for 3.0.3 (3.0.1+, really).
In particular, account for layout changes and better support for using
system libraries.
- - - - -
6ca5347a by Aaron M. Ucko at 2023-01-15T21:56:40-05:00
d/rules: Correctly accommodate multiple supported Python versions.
I'd insufficiently adapted ncbi-ngs's relevant logic.
- - - - -
d3f15196 by Aaron M. Ucko at 2023-01-18T21:47:52-05:00
d/rules: Account for layout changes and CMAKE_INSTALL_LIBDIR support
... with the latter yielding multiarch paths.
- - - - -
679ca4be by Aaron M. Ucko at 2023-01-18T21:48:18-05:00
debian/{control,salsa-ci.yml}: Build against libncbi-vdb-dev 3.0.1+.
- - - - -
4be6d160 by Aaron M. Ucko at 2023-01-18T21:48:18-05:00
debian/copyright: Update for 3.0.3 (3.0.1+, really).
Account for layout changes as of 3.0.1 and drop references to content
removed upstream, both in Files-Excluded and in special cases.
- - - - -
32f271b0 by Aaron M. Ucko at 2023-01-18T21:48:19-05:00
.gitignore: Unhardcode architecture name in build tree (obj-*).
- - - - -
fab5f257 by Aaron M. Ucko at 2023-01-18T21:48:19-05:00
Ignore build results under ngs/ngs-python (dist, ngs.egg-info).
- - - - -
2107510c by Aaron M. Ucko at 2023-01-18T21:48:30-05:00
debian/rules: Clean up newly generated files under ngs/ngs-python.
- - - - -
473e7662 by Aaron M. Ucko at 2023-01-18T21:48:32-05:00
debian/{rules,sra-toolkit.install}: +/usr/lib/sra-toolkit (#1025278)
Move sratools and *-orig to a new /usr/lib/sra-toolkit directory;
repoint symlinks accordingly.
- - - - -
4752653e by Aaron M. Ucko at 2023-01-18T21:48:32-05:00
routine-update: Standards-Version: 4.6.2
- - - - -
d0f29526 by Aaron M. Ucko at 2023-01-18T21:48:32-05:00
Finalize sra-sdk 3.0.3+dfsg-1, still targeting experimental
(necessarily, until ncbi-vdb 3 hits unstable).
- - - - -
25 changed files:
- .gitignore
- CHANGES.md
- CMakeLists.txt
- − Makefile.old
- README-blastn
- README.md
- build/.gitignore
- − build/Makefile.cc
- − build/Makefile.clang
- − build/Makefile.deb
- build/Makefile.env
- − build/Makefile.env.old
- − build/Makefile.gcc
- − build/Makefile.icc
- − build/Makefile.install
- − build/Makefile.linux
- − build/Makefile.rpm
- − build/Makefile.rules
- − build/Makefile.scm
- − build/Makefile.shell
- − build/Makefile.targets
- − build/Makefile.tools
- build/Makefile.vers
- − build/Xcode/asm-trace/asm-trace.xcodeproj/project.pbxproj
- − build/Xcode/old-toolkit/.gitignore
The diff was not included because it is too large.
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/compare/28357c83c7254f8ff883f3fdeb505dd427c4833c...d0f29526aa51a0d4949349d5f8f8c8c31a361af2
--
View it on GitLab:
https://salsa.debian.org/med-team/sra-sdk/-/compare/28357c83c7254f8ff883f3fdeb505dd427c4833c...d0f29526aa51a0d4949349d5f8f8c8c31a361af2
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[med-svn] [Git][med-team/sra-sdk][pristine-tar] 2 commits: pristine-tar data for sra-sdk_3.0.2+dfsg.orig.tar.xz
Aaron M. Ucko pushed to branch pristine-tar at Debian Med / sra-sdk Commits: 0a7b4c59 by Aaron M. Ucko at 2022-12-27T12:31:56-05:00 pristine-tar data for sra-sdk_3.0.2+dfsg.orig.tar.xz - - - - - 7f72be26 by Aaron M. Ucko at 2023-01-15T20:39:38-05:00 pristine-tar data for sra-sdk_3.0.3+dfsg.orig.tar.xz - - - - - 4 changed files: - + sra-sdk_3.0.2+dfsg.orig.tar.xz.delta - + sra-sdk_3.0.2+dfsg.orig.tar.xz.id - + sra-sdk_3.0.3+dfsg.orig.tar.xz.delta - + sra-sdk_3.0.3+dfsg.orig.tar.xz.id Changes: = sra-sdk_3.0.2+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/sra-sdk_3.0.2+dfsg.orig.tar.xz.delta differ = sra-sdk_3.0.2+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +0ba77591d7984914b77db60f09d6c65452f5d80e = sra-sdk_3.0.3+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/sra-sdk_3.0.3+dfsg.orig.tar.xz.delta differ = sra-sdk_3.0.3+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +1773d8fa7d2af3ebf808e9893e53a0cc439c6627 View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/0ed818872d6c3981fcd6f4d169460298dcfcbbca...7f72be26ee0dbbf9c8d6585450b30ec0f42bf6db -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/0ed818872d6c3981fcd6f4d169460298dcfcbbca...7f72be26ee0dbbf9c8d6585450b30ec0f42bf6db You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb] Pushed new tag debian/3.0.2+dfsg-1
Aaron M. Ucko pushed new tag debian/3.0.2+dfsg-1 at Debian Med / ncbi-vdb -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/tree/debian/3.0.2+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb][master] 2 commits: routine-update: Standards-Version: 4.6.2
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb Commits: a7296f4d by Aaron M. Ucko at 2022-12-27T11:52:37-05:00 routine-update: Standards-Version: 4.6.2 - - - - - 01fdd846 by Aaron M. Ucko at 2022-12-27T12:01:45-05:00 Finalize ncbi-vdb 3.0.2+dfsg-1 (still targeting experimental for now). - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = @@ -1,6 +1,6 @@ -ncbi-vdb (3.0.2+dfsg-1) UNRELEASED; urgency=medium +ncbi-vdb (3.0.2+dfsg-1) experimental; urgency=medium - * New upstream release. (NOT RELEASED YET.) + * New upstream release. * debian/control: Drop libkdf5-* and corresponding libhdf5-dev build-dep. * debian/copyright: Drop references to content removed upstream, both in Files-Excluded and in special cases. @@ -13,8 +13,9 @@ ncbi-vdb (3.0.2+dfsg-1) UNRELEASED; urgency=medium - Dropping several static libraries (which had been installed on principle). - Dropping libkdf5. + * Standards-Version: 4.6.2 (routine-update) - -- Aaron M. Ucko Sat, 17 Dec 2022 23:17:00 -0500 + -- Aaron M. Ucko Tue, 27 Dec 2022 12:01:29 -0500 ncbi-vdb (3.0.0+dfsg2-4) experimental; urgency=medium = debian/control = @@ -19,7 +19,7 @@ Build-Depends-Arch: cmake, doxygen, graphviz, chrpath -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-vdb Vcs-Git: https://salsa.debian.org/med-team/ncbi-vdb.git Homepage: https://github.com/ncbi/ncbi-vdb View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/eaa562b0b0d3e664d8a3af46464c6c7245688486...01fdd8463d3baf3b68a25cf4f40077b7cba3d1cf -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/eaa562b0b0d3e664d8a3af46464c6c7245688486...01fdd8463d3baf3b68a25cf4f40077b7cba3d1cf You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb][master] 2 commits: New upstream version 3.0.2+dfsg
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb
Commits:
d0768652 by Aaron M. Ucko at 2022-12-17T23:16:44-05:00
New upstream version 3.0.2+dfsg
- - - - -
eaa562b0 by Aaron M. Ucko at 2022-12-17T23:20:09-05:00
Merge tag 'upstream/3.0.2+dfsg'
Upstream version 3.0.2(+dfsg).
- - - - -
8 changed files:
- CHANGES.md
- build/Makefile.vers
- debian/changelog
- interfaces/klib/vdb_release_version.h
- libs/blast/blast-mgr.c
- libs/kdb/libkdb.vers.h
- libs/ncbi-vdb/libncbi-vdb.vers
- libs/vdb/libvdb.vers.h
Changes:
=
CHANGES.md
=
@@ -1,6 +1,12 @@
# NCBI External Developer Release:
+## NCBI VDB 3.0.2
+**December 12, 2022**
+
+ **ncbi-vdb**: changed version to match that of _sra-tools_
+
+
## NCBI VDB 3.0.1
**November 15, 2022**
=
build/Makefile.vers
=
@@ -23,4 +23,4 @@
# ===
# NCBI-VDB and library version
-VERSION = 3.0.1
+VERSION = 3.0.2
=
debian/changelog
=
@@ -1,18 +1,20 @@
-ncbi-vdb (3.0.1+dfsg-1) UNRELEASED; urgency=medium
+ncbi-vdb (3.0.2+dfsg-1) UNRELEASED; urgency=medium
* New upstream release. (NOT RELEASED YET.)
* debian/control: Drop libkdf5-* and corresponding libhdf5-dev build-dep.
* debian/copyright: Drop references to content removed upstream, both in
Files-Excluded and in special cases.
- * debian/patches: Refresh for 3.0.1(+dfsg); many of our changes can go
-away now that upstream supports using system mbed TLS.
+ * debian/patches: Refresh for 3.0.{1,2}(+dfsg); many of our changes can go
+away now that upstream supports using system mbed TLS. (The only
+difference between 3.0.1 and 3.0.2 is a formal version bump to sync
+with sra-tools 3.0.2.)
* debian/rules: Account for upstream library installation changes:
- Honoring CMAKE_INSTALL_LIBDIR (which specifies multiarch paths).
- Dropping several static libraries (which had been installed on
principle).
- Dropping libkdf5.
- -- Aaron M. Ucko Sat, 17 Dec 2022 23:06:23 -0500
+ -- Aaron M. Ucko Sat, 17 Dec 2022 23:17:00 -0500
ncbi-vdb (3.0.0+dfsg2-4) experimental; urgency=medium
=
interfaces/klib/vdb_release_version.h
=
@@ -26,6 +26,6 @@
*
==
*/
-#define VDB_RELEASE_VERSION 0x0301
+#define VDB_RELEASE_VERSION 0x0302
#endif /* _h_klib_vdb_release_version_ */
=
libs/blast/blast-mgr.c
=
@@ -50,7 +50,7 @@
#include /* fprintf */
#include /* memset */
-#define TOOLKIT "sratoolkit3_0_1"
+#define TOOLKIT "sratoolkit3_0_2"
/**/
=
libs/kdb/libkdb.vers.h
=
@@ -24,4 +24,4 @@
*
*/
-#define LIBKDB_VERS 0x0207002F
+#define LIBKDB_VERS 0x02070030
=
libs/ncbi-vdb/libncbi-vdb.vers
=
@@ -1 +1 @@
-3.0.1
+3.0.2
=
libs/vdb/libvdb.vers.h
=
@@ -24,4 +24,4 @@
*
*/
-#define LIBVDB_VERS 0x0207002F
+#define LIBVDB_VERS 0x02070030
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-vdb/-/compare/003b98b4e1c4f4a8fb4963557edb848e81bd9f5c...eaa562b0b0d3e664d8a3af46464c6c7245688486
--
View it on GitLab:
https://salsa.debian.org/med-team/ncbi-vdb/-/compare/003b98b4e1c4f4a8fb4963557edb848e81bd9f5c...eaa562b0b0d3e664d8a3af46464c6c7245688486
You're receiving this email because of your account on salsa.debian.org.
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[med-svn] [Git][med-team/ncbi-vdb][upstream] New upstream version 3.0.2+dfsg
Aaron M. Ucko pushed to branch upstream at Debian Med / ncbi-vdb Commits: d0768652 by Aaron M. Ucko at 2022-12-17T23:16:44-05:00 New upstream version 3.0.2+dfsg - - - - - 7 changed files: - CHANGES.md - build/Makefile.vers - interfaces/klib/vdb_release_version.h - libs/blast/blast-mgr.c - libs/kdb/libkdb.vers.h - libs/ncbi-vdb/libncbi-vdb.vers - libs/vdb/libvdb.vers.h Changes: = CHANGES.md = @@ -1,6 +1,12 @@ # NCBI External Developer Release: +## NCBI VDB 3.0.2 +**December 12, 2022** + + **ncbi-vdb**: changed version to match that of _sra-tools_ + + ## NCBI VDB 3.0.1 **November 15, 2022** = build/Makefile.vers = @@ -23,4 +23,4 @@ # === # NCBI-VDB and library version -VERSION = 3.0.1 +VERSION = 3.0.2 = interfaces/klib/vdb_release_version.h = @@ -26,6 +26,6 @@ * == */ -#define VDB_RELEASE_VERSION 0x0301 +#define VDB_RELEASE_VERSION 0x0302 #endif /* _h_klib_vdb_release_version_ */ = libs/blast/blast-mgr.c = @@ -50,7 +50,7 @@ #include /* fprintf */ #include /* memset */ -#define TOOLKIT "sratoolkit3_0_1" +#define TOOLKIT "sratoolkit3_0_2" /**/ = libs/kdb/libkdb.vers.h = @@ -24,4 +24,4 @@ * */ -#define LIBKDB_VERS 0x0207002F +#define LIBKDB_VERS 0x02070030 = libs/ncbi-vdb/libncbi-vdb.vers = @@ -1 +1 @@ -3.0.1 +3.0.2 = libs/vdb/libvdb.vers.h = @@ -24,4 +24,4 @@ * */ -#define LIBVDB_VERS 0x0207002F +#define LIBVDB_VERS 0x02070030 View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/commit/d0768652c84d0c99a11ef087ab8bcad49db17552 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/commit/d0768652c84d0c99a11ef087ab8bcad49db17552 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb] Pushed new tag upstream/3.0.2+dfsg
Aaron M. Ucko pushed new tag upstream/3.0.2+dfsg at Debian Med / ncbi-vdb -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/tree/upstream/3.0.2+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb][pristine-tar] pristine-tar data for ncbi-vdb_3.0.2+dfsg.orig.tar.xz
Aaron M. Ucko pushed to branch pristine-tar at Debian Med / ncbi-vdb Commits: dbeb5bd6 by Aaron M. Ucko at 2022-12-17T23:17:00-05:00 pristine-tar data for ncbi-vdb_3.0.2+dfsg.orig.tar.xz - - - - - 2 changed files: - + ncbi-vdb_3.0.2+dfsg.orig.tar.xz.delta - + ncbi-vdb_3.0.2+dfsg.orig.tar.xz.id Changes: = ncbi-vdb_3.0.2+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-vdb_3.0.2+dfsg.orig.tar.xz.delta differ = ncbi-vdb_3.0.2+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +c72f84a4e7b7441d83eba6922ddc765693bd470a View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/commit/dbeb5bd6ba7a20546f9e629701e586a7190a70a5 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/commit/dbeb5bd6ba7a20546f9e629701e586a7190a70a5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb][pristine-tar] pristine-tar data for ncbi-vdb_3.0.1+dfsg.orig.tar.xz
Aaron M. Ucko pushed to branch pristine-tar at Debian Med / ncbi-vdb Commits: 06f37715 by Aaron M. Ucko at 2022-11-27T11:07:01-05:00 pristine-tar data for ncbi-vdb_3.0.1+dfsg.orig.tar.xz - - - - - 2 changed files: - + ncbi-vdb_3.0.1+dfsg.orig.tar.xz.delta - + ncbi-vdb_3.0.1+dfsg.orig.tar.xz.id Changes: = ncbi-vdb_3.0.1+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/ncbi-vdb_3.0.1+dfsg.orig.tar.xz.delta differ = ncbi-vdb_3.0.1+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +549d6c150535d2a241c3c2c0fa52aa6e54c74851 View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/commit/06f377153bd4df5d8bf1f552560036fafc2e9df1 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/commit/06f377153bd4df5d8bf1f552560036fafc2e9df1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb][master] 6 commits: New upstream version 3.0.1+dfsg
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-vdb Commits: 873a5c14 by Aaron M. Ucko at 2022-11-27T11:06:45-05:00 New upstream version 3.0.1+dfsg - - - - - 2d193f72 by Aaron M. Ucko at 2022-11-27T11:10:19-05:00 Merge tag 'upstream/3.0.1+dfsg' Upstream version 3.0.1(+dfsg). - - - - - 871a6951 by Aaron M. Ucko at 2022-11-27T15:37:26-05:00 debian/patches: Refresh for 3.0.1. Many of our changes can go away now that upstream supports using system mbed TLS. - - - - - 6afaa7fd by Aaron M. Ucko at 2022-11-27T15:44:23-05:00 debian/rules: Account for upstream library installation changes. * Honoring CMAKE_INSTALL_LIBDIR (which specifies multiarch paths). * Dropping several static libraries (which had been installed on principle). * Dropping libkdf5. - - - - - e465ff9a by Aaron M. Ucko at 2022-11-27T15:47:28-05:00 d/control: Drop libkdf5-* and corresponding libhdf5-dev build-dep. - - - - - 003b98b4 by Aaron M. Ucko at 2022-12-17T23:06:24-05:00 debian/copyright: Drop references to content removed upstream ... both in Files-Excluded and in special cases. - - - - - 21 changed files: - .gitignore - CHANGES.md - CMakeLists.txt - README.md - build/.gitignore - − build/Makefile.cc - − build/Makefile.clang - build/Makefile.env - − build/Makefile.gcc - − build/Makefile.icc - − build/Makefile.install - − build/Makefile.linux - − build/Makefile.rules - − build/Makefile.scm - − build/Makefile.targets - build/Makefile.vers - − build/abspath.sh - − build/cc.sh - build/common.cmake - − build/cp.sh - build/env.cmake The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/5bae53b142d647d7ef37bbb090228915466cf229...003b98b4e1c4f4a8fb4963557edb848e81bd9f5c -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/compare/5bae53b142d647d7ef37bbb090228915466cf229...003b98b4e1c4f4a8fb4963557edb848e81bd9f5c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ncbi-vdb] Pushed new tag upstream/3.0.1+dfsg
Aaron M. Ucko pushed new tag upstream/3.0.1+dfsg at Debian Med / ncbi-vdb -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-vdb/-/tree/upstream/3.0.1+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
