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