[Bug 876714] Re: Sync ncbi-blast+ 2.2.25-6 (universe) from Debian unstable (main)

[Julian Taylor]

** Attachment added: "buildlog"
   https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/876714/+attachment/2554668/+files/ncbi-blast%2B_2.2.25-6.log.gz

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Title:
  Sync ncbi-blast+ 2.2.25-6 (universe) from Debian unstable (main)

Status in “ncbi-blast+” package in Ubuntu:
  New

Bug description:
  Please sync ncbi-blast+ 2.2.25-6 (universe) from Debian unstable
  (main)

  Explanation of the Ubuntu delta and why it can be dropped:
    * debian/rules: disable --as-needed build (LP: #803185)
      almost all private libs are underlinked, fixing them is not worth the
      effort
  this issue has been fixed in the debian package and it now builds

  Changelog entries since current precise version 2.2.25-3ubuntu1:

  ncbi-blast+ (2.2.25-6) unstable; urgency=low

     * debian/control:
       Luca Capello <luca at pca.it>, 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 <olivier.sallou at irisa.fr>  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 <ucko at debian.org>  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 <ucko at debian.org>  Sun, 28 Aug 2011 18:45:19 -0400

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