ncbi-tools6 (6.1.20170106+dfsg2-5) unstable; urgency=medium * debian/tests/control: Unconditionally skip network-based tests. They rely on NCBI's ID1 service, which is slated to retire. -- Aaron M. Ucko Wed, 06 Nov 2024 22:08:28 -0500 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.) - algo/blast/api/hspfilter_queue.c: Cast ersatz virtual function implementation pointers as appropriate. - api/asn2ff{2,4}.c, corelib/ncbimain.c, demo/trna2tbl.c, tools/{ncbisort,pattern1}.c, vibrant/vibmain.c: Stop relying on implicit int. (In the case of ncbisort.c, take the opportunity to comment out an occurrence of the deprecated keyword "register.") - desktop/seqpanel.c: Correct fputs argument order (accidentally left unswapped when substituting it for printf years ago). * Standards-Version: 4.7.0 (routine-update) * Rely on pre-initialized dpkg-architecture variables (routine-update) -- Aaron M. Ucko Wed, 24 Jul 2024 21:56:34 -0400 ncbi-tools6 (6.1.20170106+dfsg2-2) unstable; urgency=medium * Don't rely on any implicit function declarations. (Closes: #1066356.) - api/asn2gnb2.c: Correct the first(!) to for PrintDate. - api/salutil.c: + for AlnMgr2IndexSingleChildSeqAlign. - vibrant/shim3d.h: Add a prototype for Nlm_SetOGLContext and supporting forward declarations. (Some name clashes preclude reliably including X headers from here.) * debian/control: Apply routine-update. - List fields in its preferred order. - Wrap lists to hold one item per line. - Standards-Version: 4.6.2 (no changes needed). - Drop ncbi-cn3d's Breaks/Replaces on ancient ncbi-tools-x11. -- Aaron M. Ucko Tue, 19 Mar 2024 23:21:24 -0400 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. -- 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 content was generated but supplied without corresponding sources and inputs, and nothing from there was getting packaged anyway. * Merge initial (NMU-ed) time64 changes. * debian/{.gitignore,libncbi6t64.doc-base,*.lintian-overrides,*.symbols}: 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/. - Add webdesign. * debian/rules: Explicitly enable the time64 ABI for now. * debian/watch: Update for bump to +dfsg2. -- Aaron M. Ucko Sun, 18 Feb 2024 21:10:49 -0500 ncbi-tools6 (6.1.20170106+dfsg1-10.1) unstable; urgency=medium * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. Closes: #1064245 -- Steve Langasek Fri, 01 Mar 2024 10:43:06 +0000 ncbi-tools6 (6.1.20170106+dfsg1-10) unstable; urgency=medium * debian/.ncbirc: Help igblast find the auxiliary data it will ship. * debian/source/lintian-overrides: Ignore spurious source-is-missing for unwrapped text in readme.html files under network/wwwblast (but not for webdesign/designs/cubby/filters/ClinicalTrials.html, where it's more legitimate -- that file is a dump of HTML generated on an old web server). * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Reorder sequence of d/control fields by cme (routine-update) * Remove trailing whitespace in debian/copyright (routine-update) * Add salsa-ci file (routine-update) -- Aaron M. Ucko Fri, 02 Sep 2022 16:28:02 -0400 ncbi-tools6 (6.1.20170106+dfsg1-9) unstable; urgency=medium [ Andreas Tille ] * debian/upstream/metadata: Fix typo. [ Aaron M. Ucko ] * Trim trailing whitespace. * debian/copyright: - Use spaces rather than tabs to start continuation lines. - Clean up spurious trailing content on Files: lines. (Several somehow wound up with trailing colons, and one had a parenthesized comment, which the spec doesn't allow.) - Correct the spelling of "downloaded." * Use secure URIs in Homepage field and debian/watch. * Bump debhelper from old 11 to 12. * Set debhelper-compat version in Build-Depends. * Move development files usable with libvibgif.so.6 to libncbi6-dev from libvibrant6-dev; set Breaks/Replaces accordingly. (The runtime library has long been in libncbi6, since it adds no extra dependencies.) * debian/*.symbols: Use Build-Depends-Package, missed earlier. * debian/ncbi-cn3d.{postinst,prerm}: Supply -e via set, per best practice. * Update Lintian overrides: drop overrides associated with former .menu files, and go ahead and override custom-compression-in-debian-rules for the ncbi-rrna-data binary package, which is architecture-independent and benefits from tuning. * debian/rules: Use pkg-info.mk rather than raw dpkg-parsechangelog. -- Aaron M. Ucko Mon, 12 Oct 2020 22:08:56 -0400 ncbi-tools6 (6.1.20170106+dfsg1-8) unstable; urgency=medium [ Steffen Moeller ] * d/u/metadata: yamllint. [ Andreas Tille ] * Remove duplicate which breaks UDD import. [ Aaron M. Ucko ] * debian/control: Standards-Version: 4.5.0 (already compliant). * debian/ncbi-data.links (new): Establish /etc/.ncbirc (as notably consulted by ncbi-blast+) as a symlink to /etc/ncbi/.ncbirc (which this source package's binaries consult). (LP: #1860109.) -- Aaron M. Ucko Sun, 16 Feb 2020 22:09:14 -0500 ncbi-tools6 (6.1.20170106+dfsg1-7) unstable; urgency=medium * debian/control: Broaden ncbi-cn3d Breaks/Replaces on ncbi-tools-x11 to (<= 6.1.20170106+dfsg1-5~) per delayed split. (Closes: #940210.) -- Aaron M. Ucko Sat, 14 Sep 2019 20:53:39 -0400 ncbi-tools6 (6.1.20170106+dfsg1-6) unstable; urgency=medium * Reupload to unstable, having cleared NEW. -- Aaron M. Ucko Thu, 12 Sep 2019 21:42:48 -0400 ncbi-tools6 (6.1.20170106+dfsg1-5) experimental; urgency=medium * Split Cn3D(-3.0) out into a new ncbi-cn3d binary package; update debian/upstream/metadata accordingly. (Originally done in 6.1.20170106-7, but reverted in 6.1.20170106+dfsg1-1 to avoid holding up DFSG fixes.) * Give ncbi-cn3d a binary-specific version, missed earlier. * Upload to experimental to clear NEW. -- Aaron M. Ucko Sat, 07 Sep 2019 22:07:41 -0400 ncbi-tools6 (6.1.20170106+dfsg1-4) unstable; urgency=medium * debian/NEWS: Rename from ncbi-data.NEWS to work around apt-listchanges bug #383803; bump version to ensure visibility. -- Aaron M. Ucko Mon, 26 Aug 2019 21:54:59 -0400 ncbi-tools6 (6.1.20170106+dfsg1-3) unstable; urgency=medium * debian/ncbi-data.NEWS: Note UniVec removal, which turned out to have a bigger impact than anticipated. * debian/tests/run-unit-test: Explicitly point vecscreen at UniVec_Core. (Closes: #935424.) -- Aaron M. Ucko Sun, 25 Aug 2019 21:03:24 -0400 ncbi-tools6 (6.1.20170106+dfsg1-2) unstable; urgency=medium * debian/test/run-unit-test: Substitute UniVec_Core for UniVec (removed in -1 per license considerations). -- Aaron M. Ucko Sun, 11 Aug 2019 21:59:19 -0400 ncbi-tools6 (6.1.20170106+dfsg1-1) unstable; urgency=medium [Andreas Tille] * debian/upstream/metadata: Fix DOI syntax (shouldn't be a full URL). [Aaron M. Ucko] * Belatedly repackage without data/UniVec.*, some portions of which turned out to be non-free (with copyright held by Invitrogen Corporation, which requires a license for commercial use thereof.) * debian/copyright: - Cover previously overlooked third-party code (all DFSG-free). - Update authors and dates for debian/*. - Set Files-Excluded to reflect repackaging. * debian/rules: Introduce NCBI_VERSION_SHLIB, with +dfsg1 stripped off. * debian/watch: Reflect usage of +dfsg1. * make/makeshlb.unx: NCBI_VERSION -> NCBI_VERSION_SHLIB. * Temporarily revert ncbi-cn3d splitout to expedite the above fixes. -- Aaron M. Ucko Mon, 29 Jul 2019 22:12:41 -0400 ncbi-tools6 (6.1.20170106-7) unstable; urgency=medium [ Steffen Möller ] * debian/upstream/metadata: Add metadata for Cn3D. [ Aaron M. Ucko ] * Split Cn3D(-3.0) out into a new ncbi-cn3d binary package; update debian/upstream/metadata accordingly. * debian/upstream/metadata: Quote title because it contains a colon. -- Aaron M. Ucko Sun, 24 Feb 2019 16:35:37 -0500 ncbi-tools6 (6.1.20170106-6) unstable; urgency=medium * debian/rules: Find indirectly needed libraries via -rpath-link rather than LD_LIBRARY_PATH; the -rpath-link approach is generally saner, and in particular has a decent shot at fully fixing cross-building. -- Aaron M. Ucko Thu, 27 Dec 2018 22:39:09 -0500 ncbi-tools6 (6.1.20170106-5) unstable; urgency=medium [ Andreas Tille ] * Improve cross building: Don't force the build architecture compiler (Thanks for the patch to Helmut Grohne) Closes: #908353 * cme fix dpkg-control [ Aaron M. Ucko ] * debian/control: libvibrant6b Recommends: sensible-utils (no longer guaranteed present, per #871260). * Standards-Version: 4.3.0 (already compliant). -- Aaron M. Ucko Mon, 24 Dec 2018 23:40:58 -0500 ncbi-tools6 (6.1.20170106-4) unstable; urgency=medium * debian/compat: Advance to Debhelper 11. * debian/control: - Mark *-data reshuffling with Breaks, not just Replaces. (Closes: #902364.) - Build-Depends: Advance to debhelper (>= 11~). * debian/copyright: Fix years (packaging through 2018, upstream through 2017). -- Aaron M. Ucko Mon, 25 Jun 2018 21:36:10 -0400 ncbi-tools6 (6.1.20170106-3) unstable; urgency=medium [ Liubov Chuprikova ] * Added autopkgtest for ncbi-tools-bin. Closes: #879619 [ Aaron M. Ucko ] * debian/{*.gif,ncbi2.css}: Add local copies of NCBI resources used by HTML docs. * debian/control: - Repoint Vcs-* at salsa.debian.org. - Standards-Version: 4.1.4 (already compliant). - Rules-Requires-Root: no (confirmed safe). * debian/{libncbi6,ncbi-tools-x11}.docs: Install resources from debian/ as needed. * debian/source/format: Set to 3.0 (quilt) to accommodate binary test data. * debian/source/include-binaries: List debian/tests/test-data/nc0305.aso.gz and (individually) debian/*.gif. * debian/source/options: single-debian-patch (tracking changes purely with git for now). * debian/source/patch-header: "Combined patches from git." * demo/{findspl,taxblast_main}.c: Call SOCK_SetupSSL (accidentally missed earlier). * doc/{dispatcher,firewall}.html: Patch to use (newly supplied) local resources, addressing a generic privacy breach caught by Lintian. * make/make{demo,net}.unx: Link findspl and taxblast against $(LIBTLS) and $(GNUTLS_LIBS). -- Aaron M. Ucko Sun, 24 Jun 2018 12:06:15 -0400 ncbi-tools6 (6.1.20170106-2) unstable; urgency=medium * debian/control: Correctly version ncbi-tools-bin's Breaks/Replaces on blast2 over taxblast move. (Closes: #854329.) -- Aaron M. Ucko Sun, 05 Feb 2017 21:40:38 -0500 ncbi-tools6 (6.1.20170106-1) unstable; urgency=medium * New upstream release (after all). * debian/*.symbols: Update accordingly. * doc/man/cleanasn.1: Update accordingly. * debian/copyright: Update years. -- Aaron M. Ucko Mon, 09 Jan 2017 22:35:15 -0500 ncbi-tools6 (6.1.20160908-2) unstable; urgency=medium * Stop building the transitional blast2 package (taken over by ncbi-blast+) and retire its remaining vestiges (the bibliograpy and autopkgtest setup). * connect/ncbi_util.c: Fix a FTBFS on hurd-i386 by conditionally using a more appropriate header for PAGE_SIZE (). * Reinstate taxblast (now part of ncbi-tools-bin, and correctly documented as a postprocessing tool), accidentally dropped with the rest of blast2. -- Aaron M. Ucko Tue, 06 Dec 2016 18:37:19 -0500 ncbi-tools6 (6.1.20160908-1) unstable; urgency=medium [ Andreas Tille ] * (Final) new upstream release, incorporating most Debian changes, adding HTTPS support, and desupporting legacy BLAST. (Closes: #846477, #821075.) * cme fix dpkg-control * drop -dbg packages since these will be created automatically * Fixed watch file (thanks to Eriberto ) * DEP5 [ Aaron M. Ucko ] * Reinstate direct upstream changes lost in merge. * Ensure that apps that could potentially hit the network can use HTTPS. (Don't bother with anything that only supports the old Entrez1 service.) * Allow Entrez2 over HTTPS by switching to the Entrez2s service, making HTTPS connections by default, and allowing HTTPS POST redirections from raw IP addresses (which NCBI's certificates don't cover). * Let GCC take care of setting __DATE__ and __TIME__ per SOURCE_DATE_EPOCH. * api/sqnutil3.c: Substitute strcpy for sprintf with no extra arguments, which our hardening flags disallow. * connect/ncbi_gnutls.c: Suppress strict version check. * debian/*.symbols: Update for new release. * debian/{blast2.*,control,rules}, make/makedemo.unx: Turn blast2 into an architecture-independent transitional package for ncbi-blast+-legacy. (Retire blastcl3, which is obsolete.) * debian/{compat,control}: Advance to Debhelper compat level 10. * debian/control: Drop unversioned B-D-I on dpkg-dev left behind by cme. * debian/{control,rules}: - Build against GNU TLS. - Retune ncbi-data/ncbi-rrna-data split. * debian/libncbi6(-dev).install, make/makeshlib.unx: Account for new libconnssl library. * debian/rules: - Drop override_dh_strip-arch target now that -dbg packages are gone. - Fix typo in name of override_dh_makeshlibs-arch target from #806084. * debian/{rules,.gitignore}: Stop generating legacy menu files for non-interactive tools (already retired in favor of XDG desktop files for true graphical applications). * debian/rules, make/make{demo,net}.unx: Substitute -Wl,--as-needed for manual linkage cleanups. * demo/tbl2asn.c: Complain about date only if failing for other reasons. (Closes: #821075.) * doc/man/blastcl3.1: Fix a stray reference to retired programs. -- Aaron M. Ucko Sun, 04 Dec 2016 21:33:55 -0500 ncbi-tools6 (6.1.20120620-12) unstable; urgency=medium * Team upload. * Autopkgtest added. -- Canberk Koç Sat, 20 Aug 2016 10:20:38 +0300 ncbi-tools6 (6.1.20120620-11) unstable; urgency=medium * Team upload. * Add support for SOURCE_DATE_EPOCH, making packages building BLAST indexes reproducible (Closes: #834139) -- Sascha Steinbiss Fri, 12 Aug 2016 20:29:37 +0000 ncbi-tools6 (6.1.20120620-10) unstable; urgency=medium * debian/rules: chmod +x private scripts in the targets that use them. (Doing so in override_dh_auto_build-arch broke indep-only builds.) -- Aaron M. Ucko Thu, 10 Dec 2015 01:19:59 -0500 ncbi-tools6 (6.1.20120620-9) unstable; urgency=medium * debian/control: Split most of Build-Depends into Build-Depends-Arch. * debian/makemenu: Elide menu entries, and potentially entire menu files, when .desktop(.in) files cover the same apps. (See #741573.) * debian/rules: - Fix and streamline builds covering only the architecture-independent (*-data) packages. (Closes: #806084.) - Arrange to define BUILD_{DATE,TIME} based on the last changelog entry. - clean: chmod -x private scripts, for compatibility with dgit. * debian/sbtedit.desktop.in: Add a menu entry for sbtedit, accidentally missed earlier. * {demo,sequin}/*.c: Favor BUILD_{DATE,TIME} over __DATE__ and __TIME__ for the sake of reproducibility. * doc/man/sbtedit.1: Fix some minor typos. -- Aaron M. Ucko Wed, 09 Dec 2015 23:52:45 -0500 ncbi-tools6 (6.1.20120620-8) unstable; urgency=low [ Aaron M. Ucko ] * corelib/ncbimisc.c (MergeStringArray): Ensure all return paths explicitly return a value, as Clang reasonably requires. * debian/control: Formally update Standards-Version (3.9.6) and Vcs-Browser. [ James McCoy ] * Move debian/upstream to debian/upstream/metadata -- Aaron M. Ucko Wed, 08 Oct 2014 22:26:33 -0400 ncbi-tools6 (6.1.20120620-7) unstable; urgency=low * debian/rules: Use find -perm /..., not deprecated +.... (Closes: #724777.) * debian/.gitignore: Belatedly update for switch to libvibrant6b. -- Aaron M. Ucko Tue, 01 Oct 2013 10:58:03 -0400 ncbi-tools6 (6.1.20120620-6) unstable; urgency=low * debian/installman: Eliminate for $var qw(...) syntax that broke with Perl 5.18. (Closes: #722913.) -- Aaron M. Ucko Sat, 14 Sep 2013 23:16:12 -0400 ncbi-tools6 (6.1.20120620-5) unstable; urgency=low * demo/makeset.c: If unable to open an input ASN.1 file, report an error and exit rather than trying to work with a NULL pointer and crashing. (Thanks to Alexandre Rebert and the Mayhem Team at Carnegie Mellon University's Cylab for revealing this possibility.) * debian/control: Modernize libvibrant6b-dbg's short description. -- Aaron M. Ucko Thu, 27 Jun 2013 22:23:19 -0400 ncbi-tools6 (6.1.20120620-4) unstable; urgency=low * Rename libvibrant6(-dbg) to libvibrant6b(-dbg), as the release team doesn't condone ever reusing binary package names. * blast2: Conflict with unofficial ncbi-blast packages. (LP: #658240.) * Rebuild in a clean environment. (Closes: #714070.) -- Aaron M. Ucko Tue, 25 Jun 2013 22:00:52 -0400 ncbi-tools6 (6.1.20120620-3) unstable; urgency=low * Migrate from Lesstif to Motif, which is (finally!) free these days. - Substitute libmotif-dev for liblesstif-dev in Build-Depends and libvibrant6-dev's Depends. - Rename libvibrant6a(-dbg) back to libvibrant6(-dbg). * Standards-Version: 3.9.4. (Already compliant.) -- Aaron M. Ucko Tue, 28 May 2013 22:26:01 -0400 ncbi-tools6 (6.1.20120620-2) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Strings containing ': ' need to be quoted. -- Aaron M. Ucko Sun, 24 Jun 2012 22:54:29 -0400 ncbi-tools6 (6.1.20120620-1) unstable; urgency=low * New upstream release, just in time for Wheezy. * debian/*.symbols: update accordingly. * api/txalign.c: turn one more sprintf into a (nominally safer) snprintf. * make/makenet.unx: link asnmacro against libblastapi now that it actually needs to. * debian/*-dev.install: make sure to install all headers collectively. * doc/man/*.1: update for new release. * debian/ncbi-tools-bin.examples: new, covering scripts from demo/. -- Aaron M. Ucko Sun, 24 Jun 2012 22:15:27 -0400 ncbi-tools6 (6.1.20110713-6) unstable; urgency=low * debian/rules: Tweak -fPIC -> -fPIE substitution to accommodate platforms (kFreeBSD, and some Linux architectures) lacking PIE support. -- Aaron M. Ucko Fri, 01 Jun 2012 21:02:58 -0400 ncbi-tools6 (6.1.20110713-5) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Added citation information [ Aaron M. Ucko ] * debian/control: - Build-Depends-Indep: dpkg-dev (>= 1.16.2~) for dpkg-deb -Sextreme. - Repoint Vcs-* at anonscm.debian.org (vs. git.debian.org). * debian/rules: - Enable full hardening flags, contriving to substitute -fPIC for -fPIE as necessary. - Build ncbi-rrna-data with -Sextreme rather than hacking XZ_OPT. * make/makeshlb.unx: Honor externally supplied (hardening) LDFLAGS. -- Aaron M. Ucko Fri, 01 Jun 2012 18:36:37 -0400 ncbi-tools6 (6.1.20110713-4) unstable; urgency=low * debian/control: - Give ncbi-rrna-data a pre-dependency on dpkg (>= 1.15.6) for xz support. - Wrap and sort (build) dependencies. - Drop specific build dependency on libpng12-dev, even as a preferred libpng-dev provider. (Closes: #662442.) - Require debhelper (>= 9), which has been final for some time. - Standards-Version: 3.9.3. (No changes needed.) * debian/{libncbi6,ncbi-tools-bin}.install: sort as well. -- Aaron M. Ucko Thu, 08 Mar 2012 19:14:20 -0500 ncbi-tools6 (6.1.20110713-3) unstable; urgency=low * debian/{libncbi6-dev,ncbi-tools-bin}.install: move /usr/bin/asntool and /usr/bin/errhdr from libncbi6-dev to ncbi-tools-bin so that the former can properly be Multi-Arch: same. (Closes: #646970.) * debian/libncbi6-dev.NEWS.debian: note the above move. * debian/control: adjust descriptions and relationships accordingly. * debian/{libncbi6-dev,ncbi-tools-bin}.lintian-overrides: update accordingly. * debian/rules: - Don't try to give libncbi6-dev manpages or menu entries. - Compress the giant ncbi-rrna-data package with xz -7e (the sweet spot). -- Aaron M. Ucko Sun, 30 Oct 2011 20:52:57 -0400 ncbi-tools6 (6.1.20110713-2) unstable; urgency=low * api/alignmgr2.c, api/pgppop.c, api/txalign.c, desktop/seqpanel.c, tools/spidey.c: avoid calling printf and the like with non-constant strings, as caught by -Werror=format-security. (Closes: #643444.) -- Aaron M. Ucko Sat, 01 Oct 2011 22:08:13 -0400 ncbi-tools6 (6.1.20110713-1) unstable; urgency=low * New upstream release. * debian/*.symbols: update accordingly. * make/makeshlb.unx: link libcn3dOGL.so against -lm for sqrt. * doc/man/*.1: update for new release. * debian/rules: - (VIB): add asnmacro, as upstream takes care to publish binaries thereof. - Retire obsolete multiarch-unaware checks for libpthread. - Fully modernize Debhelper usage; in particular, transition to overrides. * debian/compat: advance to 9 per rules modernization. * debian/ncbi-tools-bin.install: add asnmacro. * make/makenet.unx: link asnmacro only against libraries it directly needs. * doc/man/asnmacro.1: give asnmacro a man page. * doc/man/Psequin.1: list it in SEE ALSO. * network/id1arch/idfetch.c: revert redundant change (from #295110). * Convert to multiarch. - debian/rules: Install libraries (and ncbithr.o) to multiarch directories. - debian/lib*.install: match multiarch library paths. - debian/control: + Build-Depends: debhelper (>= 8.1.3~), implying a recent dpkg-dev. + Set Multi-Arch: as appropriate across the board, and specify Pre-Depends: ${misc:Pre-Depends} for runtime libraries. * debian/*.lintian-overrides: drop leading slashes for Lintian 2.5.x. * debian/control: Standards-Version: 3.9.2 (already compliant). -- Aaron M. Ucko Mon, 05 Sep 2011 18:55:02 -0400 ncbi-tools6 (6.1.20100808-3) unstable; urgency=low * vibrant/shim3d.c: support libpng 1.5+, per Nobuhiro Iwamatsu's most helpful patch. (Closes: #636006.) -- Aaron M. Ucko Sat, 30 Jul 2011 11:51:21 -0400 ncbi-tools6 (6.1.20100808-2) unstable; urgency=low * Reupload to unstable following the release of Debian 6.0 (squeeze). -- Aaron M. Ucko Sun, 13 Feb 2011 15:07:22 -0500 ncbi-tools6 (6.1.20100808-1) experimental; urgency=low * New upstream release; the upgrade to BLAST 2.2.24 (from 2.2.21) should address a formatdb regression. (LP: #586219.) * Uploading to experimental because squeeze is frozen. * debian/rules (install-indep-stamp): adapt to new ncbilogo.ico contents. * debian/lib{ncbi6,vibrant6a}.symbols: update for latest release. * doc/man/*.1: update for latest release. [plus the cleanups backported to unstable in 6.1.20090809-2] -- Aaron M. Ucko Fri, 03 Sep 2010 17:43:17 -0400 ncbi-tools6 (6.1.20090809-2) unstable; urgency=low * debian/rules - Clean up compilation settings; in particular, use dpkg-buildflags rather than relying on dpkg-buildpackage to have set CFLAGS appropriately. - (clean): restore expected empty directories if necessary, for compatibility with VCSes (notably git) that don't track them. - (VIB): add asndisc, as upstream takes care to publish binaries thereof. * debian/ncbi-tools6.install: likewise add asndisc. * (debian/).gitignore: Ignore content generated during build. * make/makenet.unx: don't link asndisc against extraneous libraries. * doc/man/asndisc.1: throw together a man page for asndisc. * doc/man/cleanasn.1: fix SEE ALSO formatting. * debian/control: - bump dpkg-dev build-dep to >= 1.15.7 for dpkg-buildflags. - Standards-Version: 3.9.1 (already compliant). - note switch to git-mediated Debian-Med team maintenance. -- Aaron M. Ucko Wed, 13 Oct 2010 20:23:37 -0400 ncbi-tools6 (6.1.20090809-1) unstable; urgency=low * New upstream release. * debian/libncbi6.symbols: update accordingly. * debian/control: clean up obsolete or redundant relationship declarations. -- Aaron M. Ucko Tue, 11 Aug 2009 22:03:47 -0400 ncbi-tools6 (6.1.20090719-1) unstable; urgency=low * New upstream release. * debian/lib{ncbi6,vibrant6a}.symbols: update accordingly. * doc/man/*.1: update accordingly as well. * debian/control: declare compliance with Policy 3.8.2 (no changes needed). -- Aaron M. Ucko Sat, 01 Aug 2009 21:19:49 -0400 ncbi-tools6 (6.1.20090301-1) unstable; urgency=low * New upstream release; uploading to unstable now that lenny is out. * debian/lib{ncbi6,vibrant6a}.symbols: update accordingly. * doc/man/*.1: update accordingly as well. * debian/control: place lib*-dbg in the new debug section, per the current override file. * debian/control: declare compliance with Policy 3.8.1 (no changes needed). * api/aliread.c: merge in fix (from 6.1.20080302-4) to undefined use of sprintf caught by Kees Cook's scan. * debian/watch: belatedly update regex to recognize releases like the previous one ([6.1.]20081116a). -- Aaron M. Ucko Thu, 19 Mar 2009 10:17:26 -0400 ncbi-tools6 (6.1.20081116a-2) experimental; urgency=low * debian/control: per Lintian's advice, depend on ${misc:Depends} across the board, in case Debhelper ever populates it. * debian/{control,rules}: split newly added large BLAST databases into a new ncbi-rrna-data package to keep ncbi-data to a reasonable size. -- Aaron M. Ucko Wed, 17 Dec 2008 19:45:48 -0500 ncbi-tools6 (6.1.20081116a-1) experimental; urgency=low * New upstream release. * debian/lib{ncbi6,vibrant6a}.symbols: update accordingly. * debian/rules: resync VIB with makedis.csh, adding the new app taxblast. * debian/{blast2,ncbi-tools-bin}.install: add the new apps taxblast and subfuse, respectively. * debian/libncbi6-dev.install: add the new headers ace{read,rdapi}.h. * debian/ncbi-tools-x11.{postinst,prerm}: run update-alternatives without an explicit path, per Lintian. * debian/rules (clean): drop stray references to CDBS's debian/stamp-*. * make/make{demo,net}.unx: link asn2gb, debruijn, subfuse, and taxblast correctly. * doc/fwd_check.sh: use mktemp rather than predictable names (formally CVE-2008-5149). * doc/man/*.1: update for latest release; document new apps. -- Aaron M. Ucko Sat, 13 Dec 2008 18:25:17 -0500 ncbi-tools6 (6.1.20080302-4) unstable; urgency=medium * doc/fwd_check.sh: use mktemp rather than predictable names (formally CVE-2008-5149). * api/aliread.c: fix undefined use of sprintf caught by Kees Cook's scan. -- Aaron M. Ucko Sun, 28 Dec 2008 20:31:00 -0500 ncbi-tools6 (6.1.20080302-3) unstable; urgency=high * tools/readdb.c: enable madvise()-based code on all glibc (hence all Debian) systems, not just Linux. (Closes: #490437.) -- Aaron M. Ucko Mon, 14 Jul 2008 19:43:15 -0400 ncbi-tools6 (6.1.20080302-2) unstable; urgency=low * Migrate from CDBS to Debhelper 7 (along with dpkg-dev >= 1.14.17), replacing some files with equivalent symlinks. * debian/makemenu: stop generating obsolete linda overrides. * Declare compliance with Policy 3.8.0. (No changes needed.) -- Aaron M. Ucko Wed, 11 Jun 2008 19:08:50 -0400 ncbi-tools6 (6.1.20080302-1) unstable; urgency=low * New upstream release * debian/lib{ncbi6,vibrant6a}.symbols: update and clean up. * debian/lib{ncbi,vibrant}6-dev.install: ship new headers. * debian/ncbi-tools-bin.docs, doc/man/tbl2asn.1: belatedly ship tbl2asn.txt, and restore tbl2asn.1's reference thereto. * doc/man/*.1: correct usage of ' and -. * doc/man/{blast,cleanasn,nps2gps,tbl2asn}.1: resync with help output. * debian/control: tighten dependencies between binary packages. * debian/{control,rules}: require cdbs 0.4.51; drop workaround for #462130. * debian/{control,rules,*.override}: rename Lintian overrides to $pkg.lintian-overrides and employ dh_lintian from debhelper (>= 6.0.7) in lieu of custom logic. * debian/*.doc-base*: modernize (and correct) section assignments per doc-base 0.8.10: science -> Science/Biology, net -> System/Administration. * debian/makemenu: drop obsolete Encoding key from generated .desktop files. -- Aaron M. Ucko Wed, 19 Mar 2008 19:42:00 -0400 ncbi-tools6 (6.1.20070822-5) unstable; urgency=low * debian/{control,rules}, make/make{all,demo,net}.unx: adjust makefiles for compatibility with GNU Make 3.81, and switch back from pmake. * debian/{compat,control,rules}: advance to Debhelper 6, with a temporary workaround for CDBS bug #462130. * debian/lib{ncbi6,vibrant6a}.symbols: new, to allow looser reverse dependencies. * debian/watch: move unsupported downloadurlmangle option to a comment so that uscan actually works. * debian/control: clean up crufty relations, assuming a build environment of at least etch (stable) and an installation environment of at least sarge (oldstable). -- Aaron M. Ucko Wed, 30 Jan 2008 21:56:22 -0500 ncbi-tools6 (6.1.20070822-4) unstable; urgency=low * debian/control: enable ${shlibs:Depends} for libncbi6-dev, which contains a couple of utilities in addition to its other contents. * make/make{demo,net,shlb}.unx: ensure that every shipped executable and shared library links against everything it uses directly and nothing else, per dpkg-shlibdeps's new warnings. * debian/watch: reformat, as the old version didn't actually have the desired semantics (which uscan doesn't actually support AFAICT :-/). * doc/man/tbl2asn.1: drop obsolete reference to tbl2asn.txt. * debian/control: give blast2 its own Homepage field. * debian/libncbi6.dirs: dropped, not actually pointful. * debian/{installman,ncbi-tools-x11.links}: make symlinks automatically. * debian/control: declare compliance with Policy 3.7.3. -- Aaron M. Ucko Fri, 18 Jan 2008 19:43:04 -0500 ncbi-tools6 (6.1.20070822-3) unstable; urgency=low * debian/control: fix typo (ncbi-tools-data for ncbi-data) that left ncbi-tools-x11 uninstallable. :-/ -- Aaron M. Ucko Tue, 30 Oct 2007 19:14:18 -0400 ncbi-tools6 (6.1.20070822-2) unstable; urgency=low * debian/control: set Homepage. * debian/{control,makemenu,rules,*.desktop.in}: supply XDG desktop entries and icons for inherently graphical apps. (Closes: #448031.) * debian/{man.unused,old-blast-man,shlibs.local}: remove (obsolete cruft; shlibs.local contained only comments anyway.) -- Aaron M. Ucko Fri, 26 Oct 2007 19:27:01 -0400 ncbi-tools6 (6.1.20070822-1) unstable; urgency=low * New upstream release. * vibrant/vib{main,wndws.c}: restore sane behavior in key corner cases (no Nlm_Main, no DISPLAY). * debian/{control,rules}: ncbilogo.ico now contains multiple variants; use icotool from icoutils to extract the right one to convert. * debian/libncbi6-dev.install: handle two new "unclaimed" headers. * debian/ncbi-tools-bin.install: drop getfeat (dead), entrcmd (obsolete). * debian/ncbi-tools-x11.install: drop netentcf (dead), Nentrez (obsolete). * debian/ncbi-tools-x11.links: repoint entrez at entrez2 (vs. Nentrez). * debian/rules: stop building Nentrez; update list of built but unwanted executables. * debian/makemenu: fix section assignments per menu policy 2.1.35. * Update man pages. -- Aaron M. Ucko Mon, 08 Oct 2007 16:42:46 -0400 ncbi-tools6 (6.1.20061015-2) unstable; urgency=low * debian/installman: don't append .gz to *.htm(l) files' paths, as dh_compress (rightly) excludes them by default. (Closes: #412651.) * debian/makemenu: correct vibrate's package requirement to libvibrant6a (closes: #429955, #429956); generate appropriate linda overrides (for command-not-exist), another "problem" with the setup. * debian/libvibrant6a.override (new): suppress lintian warnings about the package name not precisely matching any SONAME. -- Aaron M. Ucko Fri, 29 Jun 2007 13:29:17 -0400 ncbi-tools6 (6.1.20061015-1) unstable; urgency=low * New upstream release. * Don't bother linking against indirectly used system libraries. * Update man pages. -- Aaron M. Ucko Sun, 22 Oct 2006 19:32:02 -0400 ncbi-tools6 (6.1.20060507-3) unstable; urgency=low * Drop transitional packages, which are now entirely redundant thanks to the binNMU of clustalx for i386 earlier this June. (Closes: #322059.) * Migrate to lesstif2, renaming libvibrant6(-dbg) to libvibrant6a(-dbg) to avoid any possibility of version skew. [Lesstif lacks versioned symbols, though admittedly so does Vibrant.] (Closes: #374233.) * Make debian/stamp-setup a dependency of common-configure-indep as well as common-configure-arch so that building via an immediate call to "fakeroot debian/rules binary" works properly, per #373971. * Explicitly build depend on modular versions of *all* relevant X libraries, per the other issue in #373971 (and to ensure that the arm autobuilder's failure mode *really* can't recur). -- Aaron M. Ucko Sat, 24 Jun 2006 09:28:43 -0400 ncbi-tools6 (6.1.20060507-2) unstable; urgency=low * Version the build-dependency on libxmu-dev to (>= 1:1) to ensure that we *can* actually drop -I/usr/X11R6/include and -L/usr/X11R6/lib, avoiding the failure mode observed on the arm autobuilder. * Further increase cdbs's minimum required version to the brand new 0.4.40, which automatically sets DEB_DBG_PACKAGE_* appropriately. -- Aaron M. Ucko Mon, 29 May 2006 20:42:28 -0400 ncbi-tools6 (6.1.20060507-1) unstable; urgency=low * New upstream release (issued on May 26, but from older sources). * Drop obsolete -I/usr/X11R6/include and -L/usr/X11R6/lib flags. * Rework inter-package relationships with the help of dpkg-dev 1.13.19. * Migrate remaining shared library support files (including vibrate) to ncbi-data, as they're conveniently all architecture-independent. * Add cleanasn (new) to the list of applications to build, and give it a man page. * Update existing man pages. * Increase the cdbs requirement to 0.4.39-0.1, and drop workarounds for (some?) older versions. * Switch to debhelper compatibility level 5, with its reworked -dbg package handling. * Standards-Version: 3.7.2. -- Aaron M. Ucko Mon, 29 May 2006 16:50:27 -0400 ncbi-tools6 (6.1.20060301-1) unstable; urgency=low * New (relatively, anyway ;-P) upstream release. * (Build-)depend directly on libgl(u)1-mesa-dev by default (but keep the alternate [build-]dependencies on virtual packages, of course). * Add insdseqget to the list of applications to build. * Stop installing wwwblast.h, which is private to code we don't even build. * Update man pages (and add one for insdseqget, forked from gbseqget's). -- Aaron M. Ucko Sun, 16 Apr 2006 12:52:44 -0400 ncbi-tools6 (6.1.20051206-1) unstable; urgency=low * New upstream release. * Temporarily switch to pmake (added to Build-Depends) for upstream's makefiles, as GNU make 3.81.b4 gets mysteriously confused when trying to build from them (but, oddly, only when invoked from debian/rules). * Add "new" blastall_old executable to the blast2 package. * Reshuffle documents slightly, and make sure to register all top-level HTML documents with doc-base. * Loosen libncbi6's dependency on ncbi-data to accommodate binary-only NMUs. -- Aaron M. Ucko Thu, 12 Jan 2006 18:50:27 -0500 ncbi-tools6 (6.1.20050828-1) unstable; urgency=low * New upstream release - Adds two new programs: sbtedit (in ncbi-tools-x11) and trna2sap (in ncbi-tools-bin). * Drop obsolete alternative (build-)dependencies on ancient versions of xlibs-dev, and silly build-dependency on libglu1-xorg | libglu1c2, and resync libvibrant-dev's dependencies properly. * Add man pages for the new programs, and clean up and update others as needed. -- Aaron M. Ucko Fri, 4 Nov 2005 16:41:18 -0500 ncbi-tools6 (6.1.20050605-2) unstable; urgency=low * Adjust default libglu-dev to libglu1-xorg-dev to avoid confusing the autobuilders. -- Aaron M. Ucko Fri, 15 Jul 2005 23:37:06 -0400 ncbi-tools6 (6.1.20050605-1) unstable; urgency=low * New upstream release. * Enable asn2asn via VIB rather than unnecessarily modifying makedemo.unx, and add (and document) nps2gps and trna2tbl along the way. * Make sure to build with libglu1c2 for the C++ transition. * Don't set DEB_DH_SHLIBDEPS_ARGS; it's not necessary with current versions of dpkg and cdbs, and -L isn't actually additive anyway. * Bump standards-version to 3.6.2 (no changes needed). -- Aaron M. Ucko Fri, 15 Jul 2005 19:03:40 -0400 ncbi-tools6 (6.1.20050429-1) unstable; urgency=low * New upstream release. * Add and document asn2all, asn2fsa, asnval, and gene2xml, even though makedis.csh still omits them. * Make Nentrez and Psequin available under the saner names entrez and sequin. * Tweak debian/rules to better handle "draft" builds from subversion. -- Aaron M. Ucko Tue, 17 May 2005 17:43:14 -0400 ncbi-tools6 (6.1.20041020-3) unstable; urgency=low * Fix FTBFS under GCC 4.0 caused by inconsistent use of "static" on functions. (Closes: #295110.) * Add a watch file, now that we can. (Upstream's layout needs version=3.) -- Aaron M. Ucko Sun, 27 Mar 2005 12:00:15 -0500 ncbi-tools6 (6.1.20041020-2) unstable; urgency=low * Add spidey to ncbi-tools-bin by Steffen Moeller's request, and incorporate some documentation he supplied for it. (Closes: #291895.) -- Aaron M. Ucko Tue, 25 Jan 2005 18:16:49 -0500 ncbi-tools6 (6.1.20041020-1) unstable; urgency=low * New upstream release; debian/* resynched as necessary. - Fixes Vibrant invisible text bug! * Take advantage of menu 2.1.8's support for multiple required packages. -- Aaron M. Ucko Mon, 1 Nov 2004 20:07:56 -0500 ncbi-tools6 (6.1.20040616-1) unstable; urgency=low * New upstream release. * debian/blast2.docs: adjusted for new arrangement (a separate source-tree directory full of HTML files). * debian/{control,lib*-dbg.install,rules}: switch to new-style -dbg packages containing just the stripped-out symbols. * debian/{installman,ncbi-tools-bin.install,rules}: upstream has dropped f(asta)merge. -- Aaron M. Ucko Sat, 26 Jun 2004 00:18:09 -0400 ncbi-tools6 (6.1.20040505-1) unstable; urgency=low * New upstream release. * debian/rules: - set BLAST_VERSION from demo/.BLAST_VERSION rather than parsing tools/blastdef.h. -- Aaron M. Ucko Sat, 15 May 2004 17:49:45 -0400 ncbi-tools6 (6.1.20040204-3) unstable; urgency=low * Update X-related (build-)dependencies per the changes in 4.3. * Reunite the Vibrant packages, with libvibrant.so.6 and libncbicn3d.so.6 always pointing at the OpenGL-enabled versions, now that xlibmesa-gl merely suggests the heavyweight packages containing acceleration modules. * As such, tighten shlibdeps for libvibrant6 to avoid possible trouble. -- Aaron M. Ucko Wed, 10 Mar 2004 18:48:26 -0500 ncbi-tools6 (6.1.20040204-2) unstable; urgency=low * debian/{libncbi6-dev,rules}: account for new include subdirectories. -- Aaron M. Ucko Sun, 8 Feb 2004 22:42:12 -0500 ncbi-tools6 (6.1.20040204-1) unstable; urgency=low * New upstream release. * debian/copyright: expand public domain notice to full length. * debian/*.install: install newly added files. * debian/rules: - supply appropriate -L args to dh_shlibdeps (accidentally lost when converting to CDBS). - various minor cleanups. * demo/debruijn.c: fix fencepost error. * desktop/bspview.c, vibrant/netscape.c: launch sensible-browser rather than netscape. * doc/man/blast.1: document new blast2 executable. * doc/man/debruijn.1: new, based on help output. * make/makeshlb.unx: add dependency info for libblast(api). -- Aaron M. Ucko Fri, 6 Feb 2004 22:03:25 -0500 ncbi-tools6 (6.1.20031028-1) unstable; urgency=low * New upstream release. * debian/blast2.docs: follow README.* -> *.txt renaming. * debian/libncbi6-dev.install: add new headers scoremat.h and wwwblast.h. * debian/installman: new; factored out of debian/rules, and enhanced to look in doc/man before debian/man and tweak pages as needed. * debian/instdoc: removed (not used since conversion to CDBS). * debian/man/*: remove pages now committed upstream. * debian/{ncbi-tools-bin.files,rules}: remove cdscan (obsolete). * debian/rules: run new debian/installman script. * debian/vibrant/vibwndws.c: add a weak declaration of Nlm_Main (and code to complain if it's not satisfied) here too. -- Aaron M. Ucko Mon, 10 Nov 2003 22:51:03 -0500 ncbi-tools6 (6.1.20030421-6) unstable; urgency=low * debian/control: Fix libncbi6-dbg to depend directly on libncbi6 rather than on the transitional ncbi-tools6 package. * debian/{control,lib*-dbg.install,rules}: While I'm at it, move unstripped libraries from /usr/lib/ncbi-tools-dbg to /usr/lib/debug. -- Aaron M. Ucko Fri, 17 Oct 2003 23:24:32 -0400 ncbi-tools6 (6.1.20030421-5) unstable; urgency=low * debian/control: - Downgrade oldlibs packages (ncbi-tools6 and vibrant6) to priority extra, per override. - Bump CDBS build-dependency to >= 0.4.12. - Drop redundant entries from build-depends-indep. * debian/libncbi6.doc-base: Actually supply the documentation directory's current name. (Closes: #215398.) * debian/rules: Take advantage of CDBS 0.4.12's support for -dbg packages. * corelib/ncbimain.c: Use an __attribute__((weak)) declaration for Nlm_Main rather than a dummy implementation + #pragma weak. * vibrant/shim3d.c: Likewise for Cn3D_GetCurrentOGLData. -- Aaron M. Ucko Sun, 12 Oct 2003 11:18:21 -0400 ncbi-tools6 (6.1.20030421-4) unstable; urgency=low * debian/rules: compile with -mieee on Alpha to fix platform-specific FPEs. (Closes: #127224). * doc/README.bls: updated to latest upstream version (which includes the missing release notes for 2.2.6). -- Aaron M. Ucko Tue, 2 Sep 2003 11:13:09 -0400 ncbi-tools6 (6.1.20030421-3) unstable; urgency=low * debian/control: - Bump Standards-Version to 3.6.1 (no changes needed). - blast2, ncbi-tools-bin: Suggest libvibrant6 rather than vibrant6. - libvibrant6-gl{,-dev}, ncbi-tools-x11: lower priority to extra due to conflicts with libvibrant6-nogl, which is optional. -- Aaron M. Ucko Fri, 22 Aug 2003 20:21:56 -0400 ncbi-tools6 (6.1.20030421-2) unstable; urgency=low * The "overdue cleanup" release. * general (debian/*, make/makeshlb.unx): - Rename library packages to start with "lib"; ncbi-tools6 and vibrant6 are now dummy forwarding packages. - Move libvibgif.so.6 to libncbi6, since it's independent of X. - Split GL and non-GL variants of libvibrant and libncbicn3d into separate packages. - Standardize on the network version of the Entrez 1 access library (libncbiNacc), if only for the sake of other libraries that need any of the three variants; the CDROM-only version's not so useful nowadays, and the combo version seems to misfire without the CDs. Note that all three remain available in static form. - Handle the circular relationship between libncbiNacc and libnetentr by linking the PIC version of libnetentr.a into libncbiNacc.so and making libnetentr.so.6 merely another link to libncbiNacc.so.6. (Kludge.) - Set up proper shared library dependencies, now that it is possible to do so uniquely. - Now compliant with Policy 3.6.0. * connect/ncbi_http_connector.c: Don't half-close sockets after sending headers, as we can't always successfully read from them afterwards (due to broken firewalls?). * debian/rules: - Switch to CDBS, despite upstream's funky build system. - Stop imposing the obsolete menu icon color restriction. -- Aaron M. Ucko Mon, 28 Jul 2003 20:11:26 -0400 ncbi-tools6 (6.1.20030421-1) unstable; urgency=low * New upstream release. * api/aliread.c: avoid char vs. EOF comparisons. * debian/{blast2,ncbi-tools6-dev}.docs: package new upstream docs. * debian/control: - Change section to devel. - Bump standards version to 3.5.9 (already compliant). - Change preferred libpng-dev to libpng12-dev (12-0-dev went away). * debian/man/Psequin.1: sequin seems to take options after all; (very roughly) document them. * debian/man/{asn2gb,blast,fastacmd,gbseqget,gil2bin,tbl2asn}.1: - Update to reflect current help output. * debian/rules: add bl2seq to VIB so we still actually build it. * demo/gil2bin.c: #include for GetGisFromFile prototype. -- Aaron M. Ucko Sun, 27 Apr 2003 12:41:48 -0400 ncbi-tools6 (6.1.20021213-5) unstable; urgency=low * debian/control: Build-Conflict on xlibmesa-glu-dev (<< 4.2.1-6), and drop corresponding workarounds. (See #178310 and #178374.) -- Aaron M. Ucko Tue, 25 Feb 2003 23:44:39 -0500 ncbi-tools6 (6.1.20021213-4) unstable; urgency=low * Oops, add a dependency on xlibmesa-gl-dev|libgl-dev because xlibmesa-glu-dev doesn't seem to depend on it.... * Likewise for xlibmesa3-glu | libglu1, due to #178310. * Still no (intentional) changes in actual content relative to 6.1.20021213-2. -- Aaron M. Ucko Fri, 24 Jan 2003 22:07:51 -0500 ncbi-tools6 (6.1.20021213-3) unstable; urgency=low * Update OpenGL deps to xlibmesa-glu-dev|libglu-dev. * Hack debian/rules to give blast2 a more meaningful version number. * Finally rename *.files to *.install and change dh_movefiles -a to dh_install -a --autodest --list-missing --sourcedir=debian/tmp. (Drop ncbi-data.files in favor of installing directly into debian/ncbi-data.) * Add lintian overrides for menu-icon-missing warnings. -- Aaron M. Ucko Fri, 24 Jan 2003 14:43:59 -0500 ncbi-tools6 (6.1.20021213-2) unstable; urgency=low * Address char-signedness issues. (Closes: #177392) -- Aaron M. Ucko Tue, 21 Jan 2003 21:04:50 -0500 ncbi-tools6 (6.1.20021213-1) unstable; urgency=low * New upstream release. (Man pages updated.) * Change preferred libpng-dev to libpng12-0-dev rather than libpng3-dev (which is a dummy package these days). * Abandon plans for switching to lesstif2, as Vibrant seems to work better with lesstif1. -- Aaron M. Ucko Tue, 17 Dec 2002 22:34:26 -0500 ncbi-tools6 (6.1.20021119-1) unstable; urgency=low * New upstream release. (Man pages updated accordingly.) * Update for policy 3.5.8: move menu entries to Apps/Science per #162812. * Indicate options in man pages with \- rather than - per #159872. * Move icons from /usr/X11R6/include/X11/pixmaps to /usr/share/pixmaps. -- Aaron M. Ucko Thu, 21 Nov 2002 09:05:38 -0500 ncbi-tools6 (6.1.20020828-2) unstable; urgency=low * Try to use madvise only if MADV_NORMAL is actually defined. -- Aaron M. Ucko Thu, 5 Sep 2002 10:49:01 -0400 ncbi-tools6 (6.1.20020828-1) unstable; urgency=low * New upstream release. * Update man pages based on current help output. * Go to standards version 3.5.7 (support "noopt" rather than "debug" in DEB_BUILD_OPTIONS). * Strictly speaking, the ABI changes should necessitate a new soname, but no external Debian packages seem to use the affected interfaces, so I'll be lazy. You may need to rebuild any local binaries you have. (Conflict with old versions of our binary packages, though.) -- Aaron M. Ucko Wed, 4 Sep 2002 20:30:31 -0400 ncbi-tools6 (6.1.20020426-5) unstable; urgency=low * Add a second hyphen before (no-)whole-archive to fix the ARM build. -- Aaron M. Ucko Mon, 26 Aug 2002 18:41:08 -0400 ncbi-tools6 (6.1.20020426-4) unstable; urgency=low * Partially migrate to debhelper v4. * Pave the way for C++ toolkit packages (in progress): - Provide a weak default definition of Nlm_Main so that our shared libncbi doesn't bite applications which supply their own main(). - Rename Cn3D to Cn3D-3.0 and register it as an alternative for Cn3D. * Move to libpng3 (only affects applications). * Rename fmerge to fastamerge to resolve conflict with fhist. (Closes: #155791) -- Aaron M. Ucko Fri, 23 Aug 2002 22:34:17 -0400 ncbi-tools6 (6.1.20020426-3) unstable; urgency=low * Remove getseq (which isn't terribly useful) to resolve conflict with hmmer. (Closes: #147793) -- Aaron M. Ucko Thu, 23 May 2002 21:20:47 -0400 ncbi-tools6 (6.1.20020426-2) unstable; urgency=low * Enable large-file support; please let me know if this turns out to break anything. (Closes: #144531) * Don't build ncbithr.o or link against -lpthread unless that library actually exists; should help on non-Linux ports. -- Aaron M. Ucko Thu, 9 May 2002 19:26:35 -0400 ncbi-tools6 (6.1.20020426-1) unstable; urgency=low * New upstream release; apparently fixes formatdb segfault on PowerPC (closes: #144783). * Some existing interfaces have changed, but not enough to justify bumping the soname; if binaries built against older revisions of the toolkit no longer work, try rebuilding them. (I don't believe this affects any other Debian packages.) * Updated man pages based on current help output. * Patched both versions (regular and Vibrant) of common argument- processing code to honor "--help" (closes: #144785). -- Aaron M. Ucko Sun, 28 Apr 2002 18:30:43 -0400 ncbi-tools6 (6.1.20011220a-2) unstable; urgency=low * Whoops, ncbi-data should replace pre-split versions of ncbi-tools6. -- Aaron M. Ucko Thu, 4 Apr 2002 22:13:09 -0500 ncbi-tools6 (6.1.20011220a-1) unstable; urgency=low * New upstream release, mostly appears to address some megablast issues. * Deal with some 64-bit-cleanliness issues. * Partially fix Cn3D lossage in #127224. (It still crashes, but later.) * Fix copymat lossage with trailing spaces and improve its error messages (closes: #138933). * Split architecture-independent files into new ncbi-data package. * Fix path to libXm.so.1 in vibrate. -- Aaron M. Ucko Sun, 31 Mar 2002 10:33:49 -0500 ncbi-tools6 (6.1.20011220-2) unstable; urgency=low * Update manpages based on current help output. * Fix typo in description (ASN1 -> ASN.1). * Use $(CC) rather than gcc in makeshlb.unx. * Build asn2asn. -- Aaron M. Ucko Fri, 28 Dec 2001 13:48:20 -0500 ncbi-tools6 (6.1.20011220-1) unstable; urgency=low * New upstream release (Closes: #126625). * Bug #31724 is probably fixed by now, and too vague to do much of anything with anyway. (Closes: #31724; please supply useful details if reopening.) * Tweak rules so that the shlibs dependency is always (>= [latest.upstream.version]-1). -- Aaron M. Ucko Thu, 27 Dec 2001 21:08:17 -0500 ncbi-tools6 (6.1.20010709-9) unstable; urgency=low * Menu seems to be broken on some architectures, so drop build dependency and add a copy of cmap.xpm to debian/. * Slightly rework treatment of icons in debian/rules. * Change "c-shell" to "tcsh|c-shell" in build-deps to address buildd warnings. * Add lintian overrides for new menu file. -- Aaron M. Ucko Thu, 20 Dec 2001 11:47:53 -0500 ncbi-tools6 (6.1.20010709-8) unstable; urgency=low * Change priority of debugging libraries to extra, per the override file. * Add menu file for ncbi-tools6-dev (asntool) and menu icons. * Add build-depends on ImageMagick and menu for icon creation. * Clean up internal script for creating menu files. -- Aaron M. Ucko Tue, 18 Dec 2001 21:12:41 -0500 ncbi-tools6 (6.1.20010709-7) unstable; urgency=low * Change section of debugging libraries from libs to devel. -- Aaron M. Ucko Sun, 18 Nov 2001 20:36:31 -0500 ncbi-tools6 (6.1.20010709-6) unstable; urgency=low * Introduce debugging libraries. (Closes: #38354). -- Aaron M. Ucko Mon, 12 Nov 2001 12:08:44 -0500 ncbi-tools6 (6.1.20010709-5) unstable; urgency=low * Sigh, the change in -4 intended to fix arm broke it instead; revert to __arm__. Where'd I put that paper bag? ;-) * Allow #cpu(...) and #machine(...) for all platforms. * Downgrade "unknown platform" to a warning; the code mostly doesn't care which PROC_XXX macro, if any, gets defined (and when it does, may read too much from it; see below). * Fix uses of PROC_XXX not to assume that MIPS -> IRIX or HPPA -> HP/UX. * Use appropriate sysconf to get processor count. -- Aaron M. Ucko Tue, 16 Oct 2001 13:26:49 -0400 ncbi-tools6 (6.1.20010709-4) unstable; urgency=low * Also fix test for m68k. Why can't the macros be more consistent? * Check everything else against the GCC sources and find that __arm__ should be arm. * That should be all of these; apologies for the inconvenience. -- Aaron M. Ucko Sat, 13 Oct 2001 14:50:03 -0400 ncbi-tools6 (6.1.20010709-3) unstable; urgency=low * Fix test for powerpc in ncbilcl.lnx. (Check for two likely definitions to be extra safe. ;-)) -- Aaron M. Ucko Fri, 12 Oct 2001 10:50:39 -0400 ncbi-tools6 (6.1.20010709-2) unstable; urgency=low * Fix problems caught by autobuilders: * Rewrite clean rule to avoid mkdir. (Closes: #115103) * Add build-dependency on c-shell (ugh) for ln-if-absent. * * Whoops, my previous sweep missed two (old, minor) bugs on ncbi-tools6-dev: * 31724: I suspect I can close this by now, but don't have a whole lot of information to go on; could somebody on an Alpha investigate? * 38354: Debugging libraries would be a good idea, but I'm holding off until autobuilds succeed because adding more binary packages introduces ftpmaster wait. * * Keep shlib requirement at >= 6.1.20010709-1, because this version doesn't change anything relevant. * Add HTTP URL for HTML SDK docs. * Optimize out blast.REAL build. -- Aaron M. Ucko Wed, 10 Oct 2001 18:42:44 -0400 ncbi-tools6 (6.1.20010709-1) unstable; urgency=low * New upstream version; adds more apps, and includes newer BLAST (2.2.1 rather than 2.0.9). (Closes: #33451, #37966, #37967, #47369, #101168) * Repackaged largely from scratch, acknowledging the convoluted nature of the upstream build system. * Put ncbi-tools6 and vibrant6 in section "libs", where they belong, rather than "devel" (already correct in override file). * Used the same form of my name in the control file and the changelog so that katie doesn't think I'm making NMUs. * Acknowledged my own last "NMU" (Closes: #100247, #103550, #104365) * Enabled thread support for appropriate applications. (Closes: #35216) * Added automatic fallback to /etc/ncbi if NCBI not set in the environment; did away with no-longer-necessary wrappers. * New binary packages for apps: ncbi-tools-bin and ncbi-tools-x11. * Moved data to /usr/share/ncbi/data, since it's architecture-independent. * Closes all existing bugs. Let's see how long that lasts... and no fair filing silly reports just to thwart me. ;-) * Dropped text version of old SDK docs in favor of pointer to online HTML version. * Don't link against Vibrant unnecessarily; instead, provide a wrapper script (vibrate) with the same net effect. * Added menu entries (using vibrate for apps it benefits). * Added Lintian overrides to deal with cross-package menu entries. * Registered with doc-base. * Clean by Lintian 1.20.15, modulo the aforementioned overrides. -- Aaron M. Ucko Sat, 6 Oct 2001 10:51:36 -0400 ncbi-tools6 (6.0.2-3) unstable; urgency=low * Adopted. (Closes: #100247) * Acknowledge previous NMUs. (Closes: #103550, #104365) * Stop installing /usr/share/doc/ncbi-tools6/NCBI/fa2htgs/updateHtgsDoc; it was causing a Lintian error (executable file under /usr/share/doc) and not useful as-is anyway (referring to paths only valid on NCBI systems). * Honor DEB_BUILD_OPTIONS, and build without -g by default. * Above change should suffice to bump standards version to 3.5.6. Yay! * Now clean by Lintian 1.20.14.1. -- Aaron M. Ucko Thu, 6 Sep 2001 11:05:49 -0400 ncbi-tools6 (6.0.2-2.2) unstable; urgency=low * NMU * The previous maintainer has resigned. Setting maintainer to Debian QA Group . * debian/ncbi-tools6-dev.README.debian: add final newline to shut diff up * debian/control: tidied up package descriptions * debian/rules: use dh_shlibdeps -l instead of LD_LIBRARY_PATH * debian/{shlibs,vibrant6.shlibs}: while we're at it, why don't we have some shlibs files to go with these shared library packages, like they taught us in freshman year at Debian University * Thanks to the above two fixes... (Closes: #104365) -- Dr. Branden Robinson Sat, 11 Aug 2001 20:57:17 -0500 ncbi-tools6 (6.0.2-2.1) unstable; urgency=low * Non-maintainer upload. * va_arg promotes shorts to ints. This is flagged as an error by gcc >= 2.96. Closes: #103550 -- LaMont Jones Mon, 9 Jul 2001 21:39:34 -0600 ncbi-tools6 (6.0.2-2) unstable; urgency=low * Adopted by new maintainer; closes: #92794, #92796, #92798, #48176 * Corrected typo in manpage for formatdb; closes: #38483 * Removed self-conflict of vibrant-dev; closes: #49712 * Changed the double installation of the copyright file by ncbi-tools6 and ncbi-tools6-dev into the same doc directory (and added a README.Debian in /usr/share/doc/ncbi-tools6-dev); closes: #51122, #77541, #56643 * Added the installation of README.blast. * Updated to newer standards version and added Build-Depends. * Added debhelper token to vibrant6.preinst to fix lintian warning. * Moved blast2 from section misc to science, because it is a tool that is exclusively useful for molecular biologists. -- Dr. Guenter Bechly Fri, 13 Apr 2001 15:12:10 +0200 ncbi-tools6 (6.0.2-1.1) unstable; urgency=low * NMU. * Recompiled against lesstif1. Closes: #48176 -- Adam Heath Mon, 25 Oct 1999 07:05:49 -0500 ncbi-tools6 (6.0.2-1) unstable; urgency=low * New upstream release (includes Blast 2.0.8). Addresses #33451 but does not solve it completely. * Manual page. Closes #30227 * Add the vibrant package * Proper symlinks in -dev packages. Closes #31619 -- Stephane Bortzmeyer Mon, 15 Feb 1999 12:55:01 +0100 ncbi-tools6 (6.0.1-1) unstable; urgency=low * New upstream release * Add the blast package -- Stephane Bortzmeyer Thu, 12 Nov 1998 15:55:02 +0100 ncbi-tools6 (6.0-3) frozen; urgency=low * Changes in the dependencies in control. Closes #28610 * Change in rules: the source package was broken and uncompilable. Closes #28978 -- Stephane Bortzmeyer Wed, 28 Oct 1998 09:16:49 +0100 ncbi-tools6 (6.0-2) unstable; urgency=low * Various lintian warnings suppressed * Not all files are copied in /usr/lib/ncbi/data, to save space -- Stephane Bortzmeyer Mon, 26 Oct 1998 15:59:25 +0100 ncbi-tools6 (6.0-1) unstable; urgency=low * Initial Release. First public release. -- Stephane Bortzmeyer Tue, 22 Sep 1998 17:23:12 +0200