[med-svn] [ncbi-blast+] branch master created (now 236e9a9)
Andreas Tille
tille at debian.org
Tue Apr 12 11:17:47 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository ncbi-blast+.
at 236e9a9 Re-add debian/ dir
This branch includes the following new commits:
new e662ab8 Seed of a package of blast+
new 32393f1 add ncbi-blast-plus debian packaging stuff
new 5c2551b update upstream get scripts
new 396bad9 update doc
new 47a796c changelog modify dir name
new c73f4c5 changelog modify dir name
new dacfeed update comments
new cf0048f update homepage, limit projects make
new 8f8bdb7 set svn stuff
new d220368 force test binaries removal
new 88ca18a a libs not generated anymore, skip move
new e245824 remove dev, update rpath issues
new 8a9371a remote some rpath references, change compil options
new e1ea04e wrong package name
new 712a1dc add dependency to avoid internal use
new 3a131dc add perl dependency
new 6846f7c boost required by configure
new 010522c fix for pbuilder gcc 4.6 error on prtdiff
new ff90806 gcc46 error patch
new ab47b42 headers update, apply patch from upstream for gcc 4.6
new 8d7e5d1 gcc4.6 does not accept anymore such mutable
new 18166e3 pbuilder requires cpio
new 6238435 Various changes explained in e-mail to list.
new 2bd4aed rename packages to blast+, update copyright for zlib, use libbooost-test instead of all
new 80ed81d add quilt depends
new 0f6e354 add legacy package for blast cmd line compatibility
new ef1e799 move to use/share legacy files
new 76fee29 missing misc depends
new f3cccee Override dh_auto_install in favor of explicitly installing files of interest (executables and shared libraries); supply the requisite ncbi-blast+.dirs.
new 13312e4 Rework configure invocation: + --with-runpath=/usr/lib/ncbi-blast+ (where the libraries will end up) + --with-flat-makefile (making it easier to skip irrelevant projects) + --without-lzo (to avoid picking up an extra dependency in some environments) + --without-autodep and --without-makefile-auto-update for streamlining. + --with-build-root=BUILD for predictable paths * --without-debug -> --with-optimization when DEB_BUILD_OPTIONS contains nostrip. Doing so uncond [...]
new 82ea803 Override dh_auto_build to focus on selected subtrees and their dependencies (as made possible by running configure --with-flat-makefile).
new f526dba Rework override_dh_install; adjust debian/legacy/legacy.sh accordingly. * Don't bother with ${CURDIR}, which just adds noise. * Leave extensions off /usr/bin scripts per Policy 10.4. (Update legacy.sh accordingly, and have it exec legacy_blast for efficiency.) * Clean up tests, demos, and internal build tools, but don't worry about anything that we now arrange not to install in the first place.
new 4a8f5c0 Clean up build and runtime dependencies. * Don't explicitly depend on runtime libraries or related utilities. * Replace libpcre++-dev by libpcre3-dev, which suffices. (NCBI uses its own C++ wrapper.) * Don't build-depend on chrpath or cpio per recent installation changes. * Add a build dependency on time for the test suite. * Depend on ${python:Depends} rather than hard-coding python.
new 54c6c51 Replace the old fix_checks patch (unnecessary when build-depending on time) with a new one (freshly integrated upstream) that allows correct test autodiscovery when unpacked under .../src/... directories.
new 2bad25e Report any test suite errors in more detail but otherwise ignore them, as some tests will likely fail in unnetworked environments (as on some autobuilders).
new f229654 Rework override_dh_clean to clean *all* files produced at build time.
new 77dc1f5 Build with DLL_LDFLAGS=-Wl,--as-needed, addressing some dpkg-shlibdeps warnings.
new 0e0e8b8 Retire postinst and postrm scripts, obsolete as of r6878.
new 8c3ce83 Invoke dh --with autotools_dev to ensure use of fresh config.{guess,sub} files.
new 13b7dea Clean up copyright file. * Remove the stanza for (c++/)scripts/projects/xmlwrapp/*, whose LICENSE file documents material absent from the ncbi-blast+ archive. * Adjust other upstream-related stanzas' Files speifications to prefix c++/ and cover include in addition to src as appropriate.
new 2b8ecea Formal cosmetic cleanups. * debian/control: Drop leading "The" from ncbi-blast+'s short description; use appropriate amounts of whitespace throughout. * debian/patches: Rename lecagy_rename_rpsblast (sic) to legacy_* and fix_gcc46_include_error to fix_gcc46_errors; update series accordingly. * debian/rules: retire long-winded $(SOURCEDIR) and simply pass -Dc++ to dh; drop boilerplate "Sample debian/rules" comment and an extra blank line.
new d539a0e override_dh_auto_configure: respect existing LD_LIBRARY_PATH settings, notably from fakeroot, though best practice remains to use it more selectively (e.g., debuild -rfakeroot).
new 987d2ad rename ncbi-blast-plus ot ncbi-blast+ as per package name
new 1cb456a Update Vcs-* fields per move to ncbi-blast+ and new Alioth setup.
new c9b927e Finalize ncbi-blast+ 2.2.25-1 for upload, updating changelog timestamp.
new 9052690 Start work on ncbi-blast+ 2.2.25-2, which will aim to address several build issues (consolidated into #629656).
new 2df5fe8 debian/rules (override_dh_install): Correctly support building only architecture-dependent packages. (Partially addresses #629656.)
new 3626cd9 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). [Also for #629656.]
new 17e9fa7 debian/rules (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. [Also for #629656.]
new cd1b1e2 debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Limit C++ optimization level to -O (rather than the default -O2) on mips(el), on which g++ otherwise crashes. :-/ [Also for #629656, which should be safe to close now with any luck.]
new d4e894c Correct backwards test in previous revision, which accidentally kept -O2 *only* on mips(el).
new b61877c Finalize ncbi-blast+ 2.2.25-2 for upload to unstable, closing #629656.
new baa0067 Start work on ncbi-blast+ 2.2.25-3, to address remaining build failures (on non-Linux architectures) per #629656.
new 02bf6db 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.)
new b036a3e debian/rules: 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).
new e3f2bd2 Finalize ncbi-blast+ 2.2.25-3 for upload to unstable, hopefully closing #629656 for real.
new 047ac61 Start work on ncbi-blast+ 2.2.25-4, as Hurd builds still fail (#629656).
new b90ea24 debian/patches/support_other_cpus: belatedly add a descriptive header.
new 665c007 debian/patches/hurd_fixes: new; fix hurd-specific issues. (Closes: #629656, this time for sure. ;-)
new d8adde4 Fix one more PATH_MAX assumption, in src/connect/ext/ncbi_localnet.c.
new eb2434d I'm backporting this to Ubuntu LTS. Explicitly specifying newer version of autotools-dev allows me to build this using the PPA system.
new 0a22256 Enhances t-coffee
new 6f1dcc3 d/control: B-D += libc0.3-dev (>= 2.13-9~) [hurd-i386] to avoid #630180; in conjunction with the hurd_fixes patch, finally closes #629656.
new f08342d 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.)
new 4c0b3f4 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.
new 5594d86 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++.)
new 54a65e2 debian/control: Declare both binary packages as Multi-Arch: foreign.
new 9743261 Finalize ncbi-blast+ 2.2.25-4 for upload to unstable.
new 0cba3ab Start work on ncbi-blast+ 2.2.25-5.
new 933bd4b Address ncbi-blast+'s continued failure to build on the Hurd (accidentally broken by the fix for #633567): * 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.
new a5cb66d Finalize ncbi-blast+ 2.2.25-5 for upload to unstable.
new c110eda add comments regarding bug 642991 and add gene_info_reader to package
new 001e121 fix typo
new ceaabb5 add patch info, reduce log size
new 66c4803 Patch for more sensible output of a perl script; Depends python (as needed by a python script); DEP5 fixes
new 02132b8 Patch description
new 92ef219 Added upstream contact
new 95f2065 update for new upstream release
new 42a12dc revert to UNRELEASED, need to update patches for offset/fuzz errors
new ae3711a fix offset/fuzz errors in patch after upstream release update
new c66de8a set back to unstable for upload after patches update
new 63db0c9 change my uploader address, change URL of copyright format
new be254d5 fix upstream bug for Hurd build
new 17c581f revert to UNRELEASE, need more fixes in patch
new a3d66c4 fixed rpath issuer on patch, set back to unstable for upload
new 9258c02 Fix Vcs fields globally in all remaining packages because I'm bored by warnings in logfiles when investigating machine readable files of not yet uploaded packages
new 2c670b2 Start work on ncbi-blast+ 2.2.26-3.
new 5b4cf3c ncbi-blast+: Note Andreas's Vcs-* modernization in debian/changelog.
new e21cdad 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.
new a36aa59 ncbi-blast+: Wrap and sort build dependencies to ease maintenance thereof.
new 1edab70 ncbi-blast+: Enable full hardening flags, introducing a small patch (use_pie_for_apps) to reflect the need to build executables and libraries differently.
new b36970c ncbi-blast+: Use upstream's new --with-symbols flag in nostrip builds.
new 21658ec Finalize ncbi-blast+ 2.2.26-3 for upload to unstable.
new 02d6bfc remove fixed bug patches
new 71c5d50 fix clean target
new 020b2ac update patches for new release
new 0b2bccc set new upstream release 2.2.27
new 365e59c remove fuzzy patch data
new d152d28 add patch for arm/mips FTBS
new 0bcc4d5 rename seedtop to seedtop+ to fix #688684
new 26ef872 add info for sparc buildd errors
new 358320a release to fix conflict with blast2
new 81e494c fix tab issue
new a2e13d8 add patch to series
new 379ea98 new upstream 2.2.28, include updates from T. Booth from Ubuntu to compile this release
new c9c37df remove deprecated parameter
new 86155e7 add headers to patches, prepare for upload
new 6dfbd10 add missing dep
new 9729166 add info on fortify lintian warnings
new 0cf3be5 Start work on ncbi-blast+ 2.2.28-2, to fix mips* FTBFS (#710807).
new e4903d1 * 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.
new cf7d62e Standards-Version: 3.9.4. (Already compliant.)
new fec73d9 Finalize ncbi-blast+ 2.2.28-2 for upload to unstable.
new 64aec12 update patches for new upstream release 2.2.29
new 648fb2a Add patch to fix way to find configure script for Debian build
new 1d00ea8 add missing dep on submit
new a9e92ed prepare new upload 2.2.29
new 5bbd1b5 fix fuzz in patch
new 8baa802 prevent cleanup of configure.orig
new fa187e1 fix include issue with recent compiler
new e045ff3 add patch headers
new 09a8800 Start work on ncbi-blast+ 2.2.29-3, to fix #753190 for real.
new 87e34e9 debian/patches/include_typeinfo: Patch include/corelib/ncbistl.hpp to ensure sufficient coverage; fix typos in patch headers. (Closes: #753190.)
new d861de5 Standards-Version: 3.9.4. (Already compliant.)
new 4d08f0e Finalize ncbi-blast+ 2.2.29-3 for upload to unstable.
new 326d03a prepare new release 2.2.30
new d6310f6 update patch to match new release
new 3cf2838 adapt patches to new release
new e1002a3 adapt patches to new release, add status to changelog
new 53432f7 update patches to fix compilation issues
new 4dee5bb update changes and patch header
new ef835fe changelog: 2.2.30-1 went to experimental.
new 9561f27 Start work on ncbi-blast+ 2.2.30-2, to address GCC 5 FTBFS #778021.
new 1f24df3 d/patches/allow_gcc5 (new): Allow compilation with GCC 5, per upstream. (Closes: #778021.)
new 1ff3087 Finalize ncbi-blast+ 2.2.30-2 for upload to experimental.
new 25eca46 upload to unstable
new d77c734 add changelog entry for unstable upload after experimental
new df0081c Start work on ncbi-blast+ 2.2.30-4, to address #790667 (compilation errors with GCC 5 on platforms such as arm64 on which char is unsigned).
new 564d7eb 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.)
new 4b0cc01 Finalize ncbi-blast+ 2.2.30-4 for upload to unstable.
new 2e7e148 Really finalize ncbi-blast+ 2.2.30-4 for upload to unstable.
new 2dd0c04 prepare new upstream release 2.2.31
new e75a98d upload release 2.2.31
new 08f1d95 fix missing colon causing FTBS on some archs
new e42db0a Drop explicite mentioning of quilt
new 2939d41 There seems to be no change of upstream source any more
new 9b49643 Enable building architecture independent package separately
new 01a97b7 Override false lintian error
new 65d4301 DEP5 fixes
new 37ad202 DEP5 fixes and upload to unstable
new b65bd39 Really enable building architecture independent package separately
new c085268 Save time and do nothing for architecture independent builds
new 03c4257 Imported Upstream version 2.2.31
new 67ada7b Merge tag 'upstream/2.2.31'
new 236e9a9 Re-add debian/ dir
The 155 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
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