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 #1077777.) * 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 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 #1077777.) * 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: - 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). -- 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 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 recent q2-feature-classifier. (Closes: #1074316.) * debian/control: - Build against libnghttp2-dev, libsqlite3-dev, and libuv1-dev, newly needed. - Build against autoconf2.69. - Build against libpcre2-dev, as enabled by debian/patches/allow_pcre2. - Stop building against 2to3, which may not be around much longer. * debian/patches: Update for new release, mostly formally. * debian/patches/2to3 (new): Cache 2to3 diff for windowmasker_2.2.22_adapter. * debian/patches/allow_pcre2 (new): Allow use of PCRE2. * debian/patches/series: - Move system_mbedtls_only up in conjunction with incorporating part of an upstream patch needed by support_mbedtls3. - Comment out reprobuild; 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. * debian/patches/support_mbedtls3 (new): Support (but don't require) Mbed TLS 3.x. (Closes: #1075867.) * 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. * debian/rules: - Regenerate configure and config.h.in with Autoconf 2.69. - Build against PCRE2, as enabled by debian/patches/allow_pcre2. (Closes: #891197.) - 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. - Extend generated-sources cleanup to objtools/eutils (not entirely straightforward due to input format variation). - Drop build-time 2to3 invocation in favor of debian/patches/2to3. * debian/source/lintian-overrides: No more rapidjson10 (just ...11). * Standards-Version: 4.7.0 (routine-update) -- Aaron M. Ucko Thu, 25 Jul 2024 20:07:36 -0400 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) (Closes # 1005279). -- Olivier Sallou Thu, 10 Feb 2022 12:17:56 +0000 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 * New upstream release. * debian/patches: Update accordingly. - fix_lib_deps, fix_unit_tests, spelling: Formally refresh to eliminate fuzz. - fix_x86isms: Retire (fully incorporated upstream.) - run_perl_directly: Formally update to reflect current $Id$ comment. - support_x32: Forward-port. - tune_lmdb_defaults: Keep just the MIPS tuneup; upstream's settings should now be fine elsewhere. * Standards-Version: 4.6.0 (routine-update) * watch file standard 4 (routine-update) * debian/patches/suppress_tls_version_checks (formerly suppress_gnutls_version_check): Suppress the mbed TLS version check too. (Closes: #1000358.) * debian/watch: Correct filenamemangle (wrong syntax for multiple rules, and leading components left unstripped). * debian/source/lintian-overrides: Simplify c++/src/html/ncbi_menu*.js overrides per current Lintian. -- Aaron M. Ucko Wed, 01 Dec 2021 22:27:15 -0500 ncbi-blast+ (2.11.0+ds-1) unstable; urgency=medium [ Steffen Möller ] * Update metadata - fixed indenting. [ Aaron M. Ucko ] * New upstream release. * debian/patches: Update accordingly. - bm-6.4.0: Retire (fully incorporated upstream). - fix_lib_deps: Formally refresh to eliminate fuzz. - run_perl_directly: Formally update to reflect current $Id$ comment. - tune_lmdb_defaults: Port to new setup, conveniently macro-driven. * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) -- Aaron M. Ucko Sun, 31 Jan 2021 21:23:21 -0500 ncbi-blast+ (2.10.1+ds-1) unstable; urgency=medium * Repack without c++/src/build-system/project_tree_builder_gui/bin. Debian builds make no use of this (Java) GUI or supporting third-party jars, and could do without prebuilt binaries even if they did use it. * debian/copyright: - Set Files-Excluded accordingly. - Correct typos for c++/src/html/ncbi_menu*.js; in particular, replace duplicate .../ncbi_menu_dnd.js by .../ncbi_menu_dyn.js. * debian/watch: Set dversionmangle and repacksuffix options accordingly. * debian/source/lintian-overrides: For ncbi_menu*.js, which are editable despite long lines, override source-contains-prebuilt-javascript-object in addition to source-is-missing. -- Aaron M. Ucko Fri, 23 Oct 2020 17:23:46 -0400 ncbi-blast+ (2.10.1-3) unstable; urgency=medium * debian/patches/tune_lmdb_defaults: Scale down slightly more on 32-bit mips* (just mipsel in practice these days). The sizes at this point are 640 MiB there, 750 MB on other 32-bit platforms, and 20 GB on 64-bit platforms. -- Aaron M. Ucko Sun, 04 Oct 2020 21:37:04 -0400 ncbi-blast+ (2.10.1-2) unstable; urgency=medium * debian/patches/bm-6.4.0 (new): Update embedded copy of BitMagic to version 6,4.0 (from 6.0.0), addressing new "inlining failed in call to 'always_inline'" errors on mips*el. (The bmagic package currently has version 6.3.0, slightly predating the necessary fix.) -- Aaron M. Ucko Sun, 20 Sep 2020 21:30:04 -0400 ncbi-blast+ (2.10.1-1) unstable; urgency=medium * New upstream release. - Among other changes, "fix tblastn mt issue". (Closes: #970344.) * debian/patches/fix_x86isms (new): Conditionally stub out CCpuFeatures::InstructionSet::InstructionSet, which compiles only on x86. * debian/patches/{hurd_fixes,run_perl_directly}: Rebase. * debian/patches/{reprobuild,support_x32}: Refresh (had fuzz). * debian/patches/support_gcc10: Drop build-system portions, incorporated upstream as of this release. * debian/patches/tune_lmdb_defaults: Rename from tune_32bit_lmdb_defaults; scale down somewhat even on 64-bit platforms to account for potential use of qemu. (Closes: #969608.) -- Aaron M. Ucko Sat, 19 Sep 2020 22:45:42 -0400 ncbi-blast+ (2.10.0-3) unstable; urgency=medium * debian/patches/tune_32bit_lmdb_defaults: Tweak default map size expressions. - For 64-bit platforms, use an explicit UL suffix on one factor to avoid overflow. - For 32-bit platforms, avoid tying up quite so much address space, since opening a pair of databases is a distinct possibility. - Generally parenthesize expressions per best macro practice. -- Aaron M. Ucko Mon, 07 Sep 2020 21:15:02 -0400 ncbi-blast+ (2.10.0-2) unstable; urgency=high * debian/patches/support_gcc10: Additionally tweak ncbifile.cpp to avoid narrowing errors on some platforms (i386, for one). * debian/patches/tune_32bit_lmdb_defaults (new): Conditionalize default map size to avoid allocation failures on 32-bit platforms. (Closes: #969608.) -- Aaron M. Ucko Sun, 06 Sep 2020 23:07:37 -0400 ncbi-blast+ (2.10.0-1) unstable; urgency=medium * New upstream release. * debian/patches: - Formally refresh. (A few files needed straightforward manual intervention.) - support_gcc10: New, for formal support of GCC 10+. (Closes: #957581.) - run_perl_directly: New, to streamline update_blastdb(.pl)'s #! line. * debian/rules: - override_dh_clean: Clean up new generated artifacts: fakehome/ and c++/include/common/ncbi_revision.h. - override_dh_install-arch: Install new cleanup-blastdb-volumes script without its upstream .py suffix. - Stop directly injecting -Wl,--as-needed into LDFLAGS, but keep DEB_LDFLAGS_MAINT_APPEND for the sake of backports, along with a comment that they can't rely on GCC 9+. * Add salsa-ci file (routine-update) * Wrap long lines in changelog entries: 2.2.25-6. -- Aaron M. Ucko Sun, 26 Apr 2020 19:38:13 -0400 ncbi-blast+ (2.9.0-4) unstable; urgency=high * debian/control: Standards-Version: 4.5.0 (already compliant). * debian/rules: DEB_CONFIGURE_COMMON_FLAGS += --without-sse42. (Closes: #951280.) -- Aaron M. Ucko Sun, 16 Feb 2020 20:16:33 -0500 ncbi-blast+ (2.9.0-3) unstable; urgency=medium * Team upload. * Drop transitional blast2 package. (Closes: #940742). * debian/copyright: refreshed * debhelper-compat 12 * Secure URI in copyright format * Remove trailing whitespace in debian/changelog * Use secure URI in Homepage field. * Move source package lintian overrides to debian/source. * Set upstream metadata fields: Contact, Name. * Remove obsolete fields Name, Contact from debian/upstream/metadata. -- Michael R. Crusoe Thu, 05 Dec 2019 15:42:44 +0100 ncbi-blast+ (2.9.0-2) unstable; urgency=medium * debian/control: Standards-Version: 4.4.1 (already compliant). * debian/copyright: Remove redundant ncbi_menu_*.js stanza. * debian/rules: - Delegate dpkg-{architecture,buildflags} calls to /usr/share/dpkg/{architecture,buildflags}.mk respectively. - Allow for cross-building (Closes: #930240): -- Factor a DEB_CONFIGURE_COMMON_FLAGS macro out of DEB_CONFIGURE_EXTRA_FLAGS for flags that also make sense for native builds of internal helpers. -- Conditionally supply --build=... and --host= to the main (historically, only) configure run per Helmut Grohne's suggestion. (dh_auto_configure would take care of this, but insists on passing a --runstatedir=... flag this configure script doesn't accept.) -- Conditionally add a rule for building native datatool and project_tree_builder binaries (in a parallel build tree established via another configure invocation), make it a dependency of override_dh_auto_configure-arch, and arrange for everything else to use these binaries as needed. -- Honor DEB_BUILD_OPTIONS="... nocheck ...", also per Helmut. -- Rework logic to install (possibly indirect) local library dependencies to use readelf rather than ldd, making as many passes as necessary (four at present, but no hardcoded count). - Install get_species_taxids without the .sh suffix. -- Aaron M. Ucko Sun, 29 Sep 2019 21:57:31 -0400 ncbi-blast+ (2.9.0-1) unstable; urgency=medium * New upstream release -- Olivier Sallou Wed, 11 Sep 2019 07:44:38 +0000 ncbi-blast+ (2.8.1-2) unstable; urgency=medium * Convert windowmasker_2.2.22_adapter to Python 3 via 2to3; update (build-)dependencies accordingly. (Closes: #937121.) -- Aaron M. Ucko Sun, 01 Sep 2019 20:50:43 -0400 ncbi-blast+ (2.8.1-1) unstable; urgency=medium * New upstream release. * debian/compat: Advance to Debhelper 11. * debian/control: - Build-Depend on liblmdb-dev. - Split B-Ds other than Debhelper out to Build-Depends-Arch. - Advance Debhelper requirement to 11~. - Standards-Version: 4.3.0 (already compliant). - Rules-Requires-Root: no. * debian/patches: Formally update for new release. - Retire support_boost_1_67 (already applied upstream). - Update patches that apply with offsets or outright fuzz, or need full-fledged porting. * debian/patches/fix_lib_deps: Link xcleanup against $(OBJEDIT_LIBS). * debian/patches/system_mbedtls_only (new): Omit convenience mbed TLS copy, which is dead weight and yielded a Lintian error. * debian/rules: Also skip (dh_auto)_configure when building only architecture-independent binary packages. -- Aaron M. Ucko Sun, 03 Feb 2019 22:47:45 -0500 ncbi-blast+ (2.7.1-2) unstable; urgency=medium [ David Miguel Susano Pinto ] * d/control: fix Vcs-* links to point to salsa [ Aaron M. Ucko ] * d/control: Standards-Version: 4.2.1 (already compliant). * d/patches/support_boost_1_67: New patch to extend Boost support (used for uninstalled tests) through at least version 1.67, per upstream (https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B) revisions 79910, 79926, 79928, and 79929. (Closes: #916000.) -- Aaron M. Ucko Wed, 12 Dec 2018 22:24:45 -0500 ncbi-blast+ (2.7.1-1) unstable; urgency=medium * New upstream release d/patches: update patch for new release d/control: go to standards 4.1.3 add mbedtls dependency -- Olivier Sallou Sat, 10 Feb 2018 17:35:31 +0000 ncbi-blast+ (2.6.0-1) unstable; urgency=medium * New upstream release -- Olivier Sallou Sun, 15 Jan 2017 17:12:27 +0000 ncbi-blast+ (2.5.0-4) unstable; urgency=medium * New optionally_keep_sequence patch to hang on to sequence data even if -parse_deflines recognized a non-local ID, on the condition that the environment variable BLAST_ALWAYS_KEEP_SEQUENCE (or configuration parameter [BLAST] always_keep_sequence) is set to a "true" value (English-only, case-insensitive true, t, yes, y, or 1). (Closes: #792510.) -- Aaron M. Ucko Wed, 14 Dec 2016 22:46:44 -0500 ncbi-blast+ (2.5.0-3) unstable; urgency=medium * New suppress_gnutls_version_check patch to prevent bailing when the exact compile-time and runtime GNU TLS versions differ; trust dpkg to disallow combinations that are actually incompatible. * debian/rules: If configure fails (as has been happening on alpha), present (BUILD/status/)config.log before bailing. -- Aaron M. Ucko Wed, 07 Dec 2016 21:40:38 -0500 ncbi-blast+ (2.5.0-2) unstable; urgency=medium * debian/patches/fix_lib_deps: Patch Makefile.blast_macros.mk to add blast to BLAST_LIBS to clear up link errors that could otherwise occur. * debian/control: B-D on libgnutls28-dev to enable HTTPS support. * Fully take blast2 over from ncbi-tools6, whose implementation has retired. -- Aaron M. Ucko Mon, 05 Dec 2016 23:16:54 -0500 ncbi-blast+ (2.5.0-1) unstable; urgency=medium * New upstream release -- Olivier Sallou Thu, 01 Dec 2016 14:40:17 +0100 ncbi-blast+ (2.4.0-3) unstable; urgency=medium * debian/rules: - Properly build (but don't install) run_with_lock. (Closes: #833538.) - Comment out nostrip check, which yielded a useless dbgsym package. * Reinstate and refresh the hurd_fixes patch, which mostly still applies. (Closes: #833539.) * Add a new support_x32 patch to avoid picking up wrong inline assembly. (Closes: #833541.) -- Aaron M. Ucko Fri, 05 Aug 2016 19:47:24 -0400 ncbi-blast+ (2.4.0-2) unstable; urgency=medium * Import upstream patch for remaining Boost compatibility issues as debian/patches/support_recent_boost. (Closes: #833451.) * debian/rules: Automatically determine which libraries are needed. (The hand-maintained blacklist was incomplete.) -- Aaron M. Ucko Thu, 04 Aug 2016 23:08:20 -0400 ncbi-blast+ (2.4.0-1) unstable; urgency=medium * New upstream release. * Refresh patches; drop fix_kfreebsd_ftbs.patch (applied upstream). * Import upstream patch to fix Boost version detection (which missed the 2.4.0 release branch) as debian/patches/fix_version_extraction. * fix_lib_deps: List taxon1 in align_format's overridden DLL_LIB, in large part to ensure its headers are generated on time; generally fix remaining cases of underlinkage (several longstanding). * debian/rules: Build --without-downloaded-vdb, to avoid trying to go to Github for code that BLAST+ doesn't even use. (Other parts of the C++ Toolkit do.) * debian/control: Go ahead and add myself to Uploaders. -- Aaron M. Ucko Wed, 03 Aug 2016 21:40:00 -0400 ncbi-blast+ (2.3.0-2) unstable; urgency=medium * Team upload. * Autopkgtest added -- Canberk Koç Tue, 02 Aug 2016 03:32:09 +0300 ncbi-blast+ (2.3.0-1) unstable; urgency=medium * New upstream version * Moved packaging to Git * cme fix dpkg-control * drop get-orig-source target which is simply the usual uscan call -- Andreas Tille Tue, 12 Apr 2016 14:54:08 +0200 ncbi-blast+ (2.2.31-4) unstable; urgency=medium * Really enable building architecture independent package separately Closes: #809120 * Save time and do nothing for architecture independent builds -- Andreas Tille Thu, 07 Jan 2016 18:50:31 +0100 ncbi-blast+ (2.2.31-3) unstable; urgency=medium * Drop explicite mentioning of quilt * Enable building architecture independent package separately Closes: #809120 * Override false lintian error * DEP5 fixes -- Andreas Tille Mon, 28 Dec 2015 12:32:23 +0100 ncbi-blast+ (2.2.31-2) unstable; urgency=medium * Fix a long-standing typo for GNU/kFreeBSD FTBS (Aaron M. Ucko) -- Olivier Sallou Fri, 11 Dec 2015 09:44:43 +0100 ncbi-blast+ (2.2.31-1) unstable; urgency=medium * New upstream release * Allow parallel build (Closes: #798277). Thanks to Aron Xu * GCC break fix (recompile with gcc5, Closes: #793263). -- Olivier Sallou Thu, 10 Dec 2015 13:37:03 +0100 ncbi-blast+ (2.2.30-4) unstable; urgency=medium * d/patches/fix_compilation: Add an upstream patch to include/util/bitset/bmconst.h to fix builds with GCC 5 on platforms such as arm64 on which char is unsigned. (Closes: #790667.) -- Aaron M. Ucko Thu, 02 Jul 2015 16:22:39 -0400 ncbi-blast+ (2.2.30-3) unstable; urgency=medium * Switch to unstable after unfreeze. -- Olivier Sallou Mon, 18 May 2015 14:34:50 +0200 ncbi-blast+ (2.2.30-2) experimental; urgency=medium * d/patches/allow_gcc5 (new): Allow compilation with GCC 5, per upstream. (Closes: #778021.) -- Aaron M. Ucko Mon, 16 Feb 2015 22:38:50 -0500 ncbi-blast+ (2.2.30-1) experimental; urgency=medium * New upstream release * d/control: switch to Standards 3.9.6 fix svn url * d/patches/fix_compilation: fix compilation issue -- Olivier Sallou Fri, 21 Nov 2014 18:21:26 +0100 ncbi-blast+ (2.2.29-3) unstable; urgency=medium * debian/patches/include_typeinfo: Patch include/corelib/ncbistl.hpp to ensure sufficient coverage; fix typos in patch headers. (Closes: #753190.) * Standards-Version: 3.9.4. (Already compliant.) -- Aaron M. Ucko Tue, 01 Jul 2014 18:27:46 -0400 ncbi-blast+ (2.2.29-2) unstable; urgency=medium * d/patches/include_typeinfo (Closes: #753190). -- Olivier Sallou Sat, 07 Jun 2014 11:28:22 +0200 ncbi-blast+ (2.2.29-1) unstable; urgency=medium * New upstream release -- Olivier Sallou Fri, 06 Jun 2014 22:38:40 +0200 ncbi-blast+ (2.2.28-2) unstable; urgency=low * debian/patches/use_pie_for_apps: Explicitly build all executables with -fPIE -pie, to avoid giving project_tree_builder a partial PIE treatment that now fails on mips and mipsel. (Closes: #710807.) * debian/rules: Retire redundant APP_LDFLAGS override. * Standards-Version: 3.9.4. (Already compliant.) -- Aaron M. Ucko Sun, 02 Jun 2013 23:00:44 -0400 ncbi-blast+ (2.2.28-1) unstable; urgency=low * New upstream release - Thanks to Tim Booth for package update help. -- Olivier Sallou Sat, 01 Jun 2013 08:40:51 +0200 ncbi-blast+ (2.2.27-3) unstable; urgency=low * debian/series: active patch fix_arm_mips_build (Closes: #688661). -- Olivier Sallou Fri, 05 Oct 2012 11:03:03 +0200 ncbi-blast+ (2.2.27-2) unstable; urgency=low * debian/patches/fix_arm_mips_build: Fix FTBS on ARM and MIPS (Closes: #688661). * debian/rules: rename seedtop to seedtop+ to avoid blast2 conflict (Closes: #688684). -- Olivier Sallou Mon, 24 Sep 2012 09:28:29 +0200 ncbi-blast+ (2.2.27-1) unstable; urgency=low * New upstream release -- Olivier Sallou Fri, 21 Sep 2012 17:25:41 +0200 ncbi-blast+ (2.2.26-3) unstable; urgency=low [ Aaron M. Ucko ] * debian/patches/fix_gcc47_errors: fix various GCC 4.7 compilation errors and warnings. (Closes: #669679.) - Explicitly qualify more dependent names originating in base templates. - Directly #include headers as needed. - Use modern syntax for making protected base members public. - Add forward declarations as needed. * Wrap and sort build dependencies to ease maintenance thereof. * Enable full hardening flags, introducing a small patch (use_pie_for_apps) to reflect the need to build executables and libraries differently. * Use upstream's new --with-symbols flag in nostrip builds. [ Andreas Tille ] * debian/control: Modernize Vcs-* fields. -- Aaron M. Ucko Thu, 10 May 2012 23:42:49 -0400 ncbi-blast+ (2.2.26-2) unstable; urgency=low * debian/patches/wrong_path_to_touch.patch :Fix upstream FTBFS on the Hurd hardcodes wrong path to touch (Closes: #663244) -- Olivier Sallou Wed, 07 Mar 2012 17:29:23 +0100 ncbi-blast+ (2.2.26-1) unstable; urgency=low [ Olivier Sallou ] * New upstream release * Remove some patches, applied upstream [ Andreas Tille] * debian/copyright: Added Upstream-Contact -- Olivier Sallou Wed, 07 Mar 2012 09:37:10 +0100 ncbi-blast+ (2.2.25-7) unstable; urgency=low * Do not output everything to STDERR in c++/src/app/blast/update_blastdb.pl Closes: #644237 * debian/control: Depends s/${python:Depends}/python/ because the python dependency of /usr/bin/windowmasker_2.2.22_adapter is not detected obviosely * debian/copyright: Indentation fixes to get DEP5 compatibility -- Andreas Tille Wed, 21 Dec 2011 15:47:04 +0100 ncbi-blast+ (2.2.25-6) unstable; urgency=low * debian/control: + Luca Capello , fix reference for legacy_blast (Closes: #642986). + add a new line to separate the actual description from usage instruction in the long Description:. * debian/rules: add gene_info_reader binary in package -- Olivier Sallou Fri, 30 Sep 2011 12:31:05 -0400 ncbi-blast+ (2.2.25-5) unstable; urgency=low * Team upload. * debian/patches/hurd_fixes: further patch configure(.ac) to reflect -Wl,rpath,... support. (Closes: #629656.) * debian/patches/fix_lib_deps: link makembindex and srsearch against libxconnect rather than libconnect for consistency with libblast, which uses the former for consistency with other projects. -- Aaron M. Ucko Mon, 29 Aug 2011 12:31:05 -0400 ncbi-blast+ (2.2.25-4) unstable; urgency=low [ Aaron M. Ucko ] * Team upload. * debian/patches/support_other_cpus: belatedly add a descriptive header. * debian/patches/hurd_fixes: new; fix hurd-specific issues. (In conjunction with the following change, finally closes: #629656.) * debian/control: - Build-Depends += libc0.3-dev (>= 2.13-9~) [hurd-i386] to avoid #630180. - Declare both binary packages as Multi-Arch: foreign. * debian/patches/fix_lib_deps: new; ensure that all libraries link against all direct dependencies. (Break the dependency loop between libxblast and libxalgoblastdbindex by having the former provide only the C++ BLAST API, leaving the C core only in libblast.) (Closes: #633567.) * debian/rules: tweak LDFLAGS, supplying -Wl,--as-needed across the board (as it is now safe to do so) and adding -Wl,--enable-new-dtags to allow LD_LIBRARY_PATH to override the private rpath. * debian/patches/no_multiarch_rpath: new; avoid redundant rpath entries on multiarch systems (courtesy of overzealous logic to ensure executables will be able to find libstdc++.) [ Andreas Tille ] * Enhances: t-coffee (as stated in tasks file) -- Aaron M. Ucko Sun, 28 Aug 2011 18:45:19 -0400 ncbi-blast+ (2.2.25-3) unstable; urgency=low * Team upload. * debian/rules: - Export MAKE to override an internal upstream build script that otherwise incorrectly defaults to gmake on non-Linux architectures. (Really closes: #629656, with any luck.) - Force CONFIG_SHELL=/bin/bash to avoid lossage that can occur with zsh4 masquerading as ksh, which configure otherwise favors (due to complaints from users with broken BASH_ENV scripts that change directories). -- Aaron M. Ucko Thu, 09 Jun 2011 19:25:45 -0400 ncbi-blast+ (2.2.25-2) unstable; urgency=low * Team upload. * Fix several sources of build failures (closes: #629656): - debian/rules (override_dh_install): Correctly support building only architecture-dependent packages. (DEB_CONFIGURE_EXTRA_FLAGS): Add --without-caution to override the upstream build system's reluctance to build shared libraries on the Hurd or kFreeBSD, which it doesn't specifically recognize. Limit C++ optimization level to -O (rather than the default -O2) on mips(el), on which g++ otherwise crashes. :-/ - debian/patches/support_other_cpus (new; committed upstream too): build correctly on architectures that wound up defining NCBI_SLOW_ATOMIC_SWAP (spuriously in the case of powerpc, whose detection the patch fixes as well). -- Aaron M. Ucko Wed, 08 Jun 2011 21:42:52 -0400 ncbi-blast+ (2.2.25-1) unstable; urgency=low * Initial release (Closes: #624394) -- Olivier Sallou Wed, 08 Jun 2011 00:15:15 +0200