From: Aaron M. Ucko Date: Fri, 23 Oct 2020 18:01:18 +0000 (-0400) Subject: Update upstream source from tag 'upstream/2.10.1+ds' X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~91 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=d3605f7d996308a332f73ce3c0af7bf3d1c018d8;p=ncbi-blast%2B.git Update upstream source from tag 'upstream/2.10.1+ds' Update to upstream version '2.10.1+ds'. 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. --- d3605f7d996308a332f73ce3c0af7bf3d1c018d8 diff --cc debian/changelog index 2f487967,00000000..796593e3 mode 100644,000000..100644 --- a/debian/changelog +++ b/debian/changelog @@@ -1,534 -1,0 +1,543 @@@ ++ncbi-blast+ (2.10.1+ds-1) UNRELEASED; urgency=medium ++ ++ * NOT RELEASED YET. ++ * 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. ++ ++ -- Aaron M. Ucko Fri, 23 Oct 2020 14:01:18 -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