[med-svn] r13789 - in trunk/packages/ncbi-blast+/tags: . 2.2.28-1/debian 2.2.28-1/debian/patches
Olivier Sallou
osallou at alioth.debian.org
Sat Jun 1 12:35:10 UTC 2013
Author: osallou
Date: 2013-06-01 12:35:10 +0000 (Sat, 01 Jun 2013)
New Revision: 13789
Added:
trunk/packages/ncbi-blast+/tags/2.2.28-1/
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/README.source
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/compat
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/control
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/enable_clean_after_failed_compile
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/hurd_fixes
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/no_multiarch_rpath
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/series
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/skip_services_unit_test
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/rules
Removed:
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/README.source
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/compat
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/control
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/hurd_fixes
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/no_multiarch_rpath
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/series
trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/rules
Log:
[svn-buildpackage] Tagging ncbi-blast+ 2.2.28-1
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/README.source
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/README.source 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/README.source 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1,8 +0,0 @@
-blast+ for Debian
----------------------
-
-get-orig-source target downloads file via uscan and rearrange the package.
-Patches are required for build.
-
-
-
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/README.source (from rev 13788, trunk/packages/ncbi-blast+/trunk/debian/README.source)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/README.source (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/README.source 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,10 @@
+blast+ for Debian
+---------------------
+
+get-orig-source target downloads file via uscan and rearrange the package.
+Patches are required for build.
+
+Lintian raises hardening no fortify warnings that are false positives.
+
+
+
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/changelog 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1,154 +0,0 @@
-ncbi-blast+ (2.2.27-3) unstable; urgency=low
-
- * debian/series: active patch fix_arm_mips_build (Closes: #688661).
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> Mon, 24 Sep 2012 09:28:29 +0200
-
-ncbi-blast+ (2.2.27-1) unstable; urgency=low
-
- * New upstream release
-
- -- Olivier Sallou <osallou at debian.org> 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 <ucko at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <tille at debian.org> Wed, 21 Dec 2011 15:47:04 +0100
-
-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
-
-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 <ucko at debian.org> 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 <ucko at debian.org> Wed, 08 Jun 2011 21:42:52 -0400
-
-ncbi-blast+ (2.2.25-1) unstable; urgency=low
-
- * Initial release (Closes: #624394)
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 08 Jun 2011 00:15:15 +0200
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/changelog (from rev 13784, trunk/packages/ncbi-blast+/trunk/debian/changelog)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/changelog (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/changelog 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,161 @@
+ncbi-blast+ (2.2.28-1) unstable; urgency=low
+
+ * New upstream release
+ - Thanks to Tim Booth for package update help.
+
+ -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> Mon, 24 Sep 2012 09:28:29 +0200
+
+ncbi-blast+ (2.2.27-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> 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 <ucko at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <tille at debian.org> Wed, 21 Dec 2011 15:47:04 +0100
+
+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
+
+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 <ucko at debian.org> 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 <ucko at debian.org> Wed, 08 Jun 2011 21:42:52 -0400
+
+ncbi-blast+ (2.2.25-1) unstable; urgency=low
+
+ * Initial release (Closes: #624394)
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 08 Jun 2011 00:15:15 +0200
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/compat
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/compat 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/compat 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1 +0,0 @@
-7
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/compat (from rev 13784, trunk/packages/ncbi-blast+/trunk/debian/compat)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/compat (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/compat 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1 @@
+9
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/control
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/control 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/control 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1,51 +0,0 @@
-Source: ncbi-blast+
-Section: science
-Priority: optional
-Build-Depends: autotools-dev (>= 20100122),
- debhelper (>= 7.0.50~),
- dpkg-dev (>= 1.16.1),
- libboost-test-dev,
- libbz2-dev,
- libc0.3-dev (>= 2.13-9~) [hurd-i386],
- libpcre3-dev,
- quilt (>= 0.46-7~),
- time,
- zlib1g-dev
-Standards-Version: 3.9.3
-Uploaders: Olivier Sallou <osallou at debian.org>, Andreas Tille <tille at debian.org>
-DM-Upload-Allowed: yes
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ncbi-blast+/trunk/
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast+/trunk/
-
-Package: ncbi-blast+
-Architecture: any
-Enhances: t-coffee
-Depends: ncbi-data, python, ${misc:Depends}, ${perl:Depends}, ${shlibs:Depends}
-Multi-Arch: foreign
-Description: next generation suite of BLAST sequence search tools
- The Basic Local Alignment Search Tool (BLAST) is the most widely
- used sequence similarity tool. There are versions of BLAST that
- compare protein queries to protein databases, nucleotide queries
- to nucleotide databases, as well as versions that translate nucleotide
- queries or databases in all six frames and compare to protein databases
- or queries.
- PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting
- with a protein query, and then uses that PSSM to perform further searches.
- It is also possible to compare a protein or nucleotide query to a
- database of PSSM’s.
- The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as
- a network service.
-
-Package: ncbi-blast+-legacy
-Architecture: all
-Depends: ncbi-blast+, ${misc:Depends}
-Multi-Arch: foreign
-Description: NCBI Blast legacy call script
- This package adds some fake scripts to call NCBI+ programs
- with the NCBI blast command line. It makes use of the
- legacy_blast script in ncbi-blast+ package.
- .
- To use those scripts, /usr/share/ncbi-blast+/bin must be added
- to the PATH.
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/control (from rev 13787, trunk/packages/ncbi-blast+/trunk/debian/control)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/control (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/control 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,50 @@
+Source: ncbi-blast+
+Section: science
+Priority: optional
+Build-Depends: autotools-dev (>= 20100122),
+ debhelper (>= 9),
+ dpkg-dev (>= 1.16.1),
+ libboost-test-dev,
+ libbz2-dev,
+ libc0.3-dev (>= 2.13-9~) [hurd-i386],
+ libpcre3-dev,
+ quilt,
+ time,
+ zlib1g-dev
+Standards-Version: 3.9.3
+Uploaders: Olivier Sallou <osallou at debian.org>, Andreas Tille <tille at debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ncbi-blast+/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast+/trunk/
+
+Package: ncbi-blast+
+Architecture: any
+Enhances: t-coffee
+Depends: ncbi-data, python, ${misc:Depends}, ${perl:Depends}, ${shlibs:Depends}
+Multi-Arch: foreign
+Description: next generation suite of BLAST sequence search tools
+ The Basic Local Alignment Search Tool (BLAST) is the most widely
+ used sequence similarity tool. There are versions of BLAST that
+ compare protein queries to protein databases, nucleotide queries
+ to nucleotide databases, as well as versions that translate nucleotide
+ queries or databases in all six frames and compare to protein databases
+ or queries.
+ PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting
+ with a protein query, and then uses that PSSM to perform further searches.
+ It is also possible to compare a protein or nucleotide query to a
+ database of PSSM’s.
+ The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as
+ a network service.
+
+Package: ncbi-blast+-legacy
+Architecture: all
+Depends: ncbi-blast+, ${misc:Depends}
+Multi-Arch: foreign
+Description: NCBI Blast legacy call script
+ This package adds some fake scripts to call NCBI+ programs
+ with the NCBI blast command line. It makes use of the
+ legacy_blast script in ncbi-blast+ package.
+ .
+ To use those scripts, /usr/share/ncbi-blast+/bin must be added
+ to the PATH.
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/enable_clean_after_failed_compile (from rev 13786, trunk/packages/ncbi-blast+/trunk/debian/patches/enable_clean_after_failed_compile)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/enable_clean_after_failed_compile (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/enable_clean_after_failed_compile 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,16 @@
+Subject: clean after failure
+Description: Enable clean
+Author: Tim Booth
+Last-Updated: 2013-06-01
+Forwarded: no
+--- a/c++/src/build-system/new_module.sh.in
++++ b/c++/src/build-system/new_module.sh.in
+@@ -178,7 +178,7 @@
+ if test -x "$bindir/datatool"; then
+ datatool=$bindir/datatool
+ COMMON_AddRunpath "$libdir"
+- else
++ elif [ "$1" != "purge_sources" ] ; then
+ echo "Unable to find datatool." >&2
+ exit 2
+ fi
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/fix_lib_deps 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1,593 +0,0 @@
-Subject: ensure that all libraries link against all direct dependencies
-
- * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. 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.
- * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
- rather than libconnect for consistency with libblast, which uses the
- former to keep the aforementioned cycle-breaking from causing
- inconsistency elsewhere.
-
-Debian-Bug: 633567.
-Author: Aaron M. Ucko <ucko at debian.org>
-Last-Update: 2011-08-28
---- a/c++/src/algo/blast/core/Makefile.blast.lib
-+++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -21,5 +21,6 @@
- CFLAGS = $(FAST_CFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = composition_adjustment xconnect tables
-
- WATCHERS = coulouri maning madden camacho
---- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -11,6 +11,8 @@
- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
-+
- ASN_DEP = seqset
-
- WATCHERS = morgulis
---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -7,6 +7,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS)
-
--DLL_LIB = blastxml xhtml xcgi
-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
-+ seq general xser tables xncbi
-
- WATCHERS = jianye zaretska madden camacho fongah2
---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,3 +21,4 @@
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
---- a/c++/src/cgi/Makefile.cgi.lib
-+++ b/c++/src/cgi/Makefile.cgi.lib
-@@ -9,6 +9,8 @@
- user_agent
- LIB = xcgi
-
-+DLL_LIB = xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
-
- WATCHERS = vakatov
---- a/c++/src/html/Makefile.html.lib
-+++ b/c++/src/html/Makefile.html.lib
-@@ -7,4 +7,6 @@
- jsmenu commentdiag indentstream html_exception writer_htmlenc
- LIB = xhtml
-
-+DLL_LIB = xncbi
-+
- WATCHERS = ivanov
---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -2,3 +2,5 @@
-
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-+
-+DLL_LIB = xnetblast xser xconnect xutil xncbi
---- a/c++/src/objtools/align_format/Makefile.align_format.lib
-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -10,6 +10,10 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS)
-
-+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
-+ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
-+ xcgi xhtml tables xncbi
-+
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
- # CFLAGS = $(FAST_CFLAGS)
---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -12,3 +12,5 @@
-
- WATCHERS = todorov dicuccio grichenk
-
-+DLL_LIB = xobjmgr seqset seq xser tables xncbi
-+
---- a/c++/src/objtools/readers/Makefile.xobjread.lib
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -19,5 +19,5 @@
- best_feat_finder source_mod_parser fasta_exception
-
-
--DLL_LIB = creaders
-+DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi
-
---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -11,6 +11,6 @@
- mask_writer_blastdb_maskinfo
-
- ASN_DEP = seqset
--DLL_LIB = seqdb blastdb
-+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
-
- WATCHERS = morgulis camacho
---- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-@@ -7,6 +7,8 @@
-
- ASN_DEP = seqset
-
-+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
-+
- LIB = xobjsimple
- SRC = simple_om
-
---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-@@ -24,6 +24,8 @@
-
- LIB = seqdb
-
-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -5,4 +5,6 @@
-
- ASN_DEP = blastdb seqset
-
-+DLL_LIB = seqdb xobjmgr seqset seq xncbi
-+
- WATCHERS = camacho
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-@@ -3,6 +3,8 @@
- LIB = ncbi_xloader_blastdb_rmt
- SRC = bdbloader_rmt remote_blastdb_adapter
-
-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
-+
- ASN_DEP = blastdb xnetblast
-
- WATCHERS = camacho
---- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-@@ -4,3 +4,5 @@
-
- LIB = gene_info
- SRC = gene_info gene_info_reader file_utils
-+
-+DLL_LIB = xncbi
---- a/c++/src/algo/blast/api/Makefile.xblast.lib
-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,11 +74,14 @@
- deltablast_options \
- deltablast
-
--SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
-+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
-
- LIB = xblast
-
--DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
-+DLL_LIB = xalgoblastdbindex blast composition_adjustment xalgowinmask \
-+ xalgodustmask seqdb xobjread xobjutil xobjmgr \
-+ xnetblastcli xnetblast scoremat seqset seq general \
-+ xser xconnect sequtil tables xutil xncbi
-
- CFLAGS = $(FAST_CFLAGS)
- # Strict gcc flags
---- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -24,7 +24,9 @@
-
- LIB = blastinput
-
--DLL_LIB = xblast $(OBJMGR_LIBS)
-+DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \
-+ ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader seqdb xobjread \
-+ xobjmgr scoremat seqset seq xser xutil xncbi
-
- # should be redundant, given the above :-/
- ASN_DEP = seqset xnetblast
---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-@@ -8,6 +8,8 @@
-
- SRC = symdust
-
-+DLL_LIB = xobjmgr seq xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/connect/Makefile.xconnect.lib
-+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@
- LIB = xconnect
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
-+
- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
-
- WATCHERS = lavr
---- a/c++/src/connect/ext/Makefile.xconnext.lib
-+++ b/c++/src/connect/ext/Makefile.xconnext.lib
-@@ -6,4 +6,6 @@
-
- LIB = xconnext
-
-+DLL_LIB = xconnect xncbi
-+
- WATCHERS = lavr
---- a/c++/src/objects/blast/Makefile.blast.lib
-+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -1,4 +1,6 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
-
-+DLL_LIB = scoremat seqset seq xser xncbi
-+
- WATCHERS = camacho
---- a/c++/src/objects/blastxml/Makefile.blastxml.lib
-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
-@@ -1,2 +1,4 @@
- LIB = blastxml
- SRC = blastxml__ blastxml___
-+
-+DLL_LIB = xser xncbi
---- a/c++/src/objects/entrez2/Makefile.entrez2.lib
-+++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
-@@ -2,3 +2,5 @@
-
- LIB = entrez2
- SRC = entrez2__ entrez2___
-+
-+DLL_LIB = xser xncbi
---- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-@@ -4,3 +4,5 @@
-
- LIB = entrez2cli
- SRC = entrez2_client entrez2_client_
-+
-+DLL_LIB = entrez2 xser xconnect xutil xncbi
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
-@@ -1,2 +1,4 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-+
-+DLL_LIB = seqset seq general xser xncbi
---- a/c++/src/objects/seqedit/Makefile.seqedit.lib
-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
-@@ -1,3 +1,4 @@
- LIB = seqedit
- SRC = seqedit__ seqedit___
--
-+
-+DLL_LIB = seqset seq general xser xncbi
---- a/c++/src/objects/submit/Makefile.submit.lib
-+++ b/c++/src/objects/submit/Makefile.submit.lib
-@@ -1,2 +1,4 @@
- LIB = submit
- SRC = submit__ submit___
-+
-+DLL_LIB = seqset seq biblio general xser xncbi
---- a/c++/src/objmgr/util/Makefile.util.lib
-+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -8,5 +8,7 @@
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
- LIB = xobjutil
-
-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = ucko vasilche
-
---- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-@@ -11,6 +11,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS)
-
-+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
-
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
-@@ -8,6 +8,8 @@
-
- LIB = blast_services
-
-+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,4 +12,7 @@
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
-+ xobjmgr seq xutil xncbi
-+
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -14,4 +14,7 @@
- # Dependencies for shared library
- DLL_LIB =
-
-+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
-+ xser xconnect xcompress xutil xncbi
-+
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-@@ -12,6 +12,8 @@
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-@@ -12,6 +12,8 @@
- # Dependencies for shared library
- DLL_LIB = xconnect ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-@@ -12,6 +12,9 @@
- CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
-
- # Dependencies for shared library (disabled due to problems on Darwin)
--# DLL_LIB = xconnect ncbi_xreader$(DLL)
-+DLL_LIB = xconnect ncbi_xreader$(DLL)
-+
-+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
-+
-
- WATCHERS = vasilche
---- a/c++/src/util/compress/api/Makefile.compress.lib
-+++ b/c++/src/util/compress/api/Makefile.compress.lib
-@@ -6,7 +6,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
-+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
- LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/util/sequtil/Makefile.sequtil.lib
-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
-@@ -3,4 +3,6 @@
- LIB = sequtil
- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
-
-+DLL_LIB = xncbi
-+
- WATCHERS = shomrat
---- a/c++/src/corelib/Makefile.test_boost.lib
-+++ b/c++/src/corelib/Makefile.test_boost.lib
-@@ -3,6 +3,8 @@
- SRC = test_boost
- LIB = test_boost
-
-+DLL_LIB = xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
-
- REQUIRES = Boost.Test.Included
---- a/c++/src/corelib/Makefile.test_mt.lib
-+++ b/c++/src/corelib/Makefile.test_mt.lib
-@@ -3,6 +3,8 @@
- SRC = test_mt
- LIB = test_mt
-
-+DLL_LIB = xncbi
-+
- # REQUIRES = MT
-
- USE_PCH = no
---- a/c++/src/objects/biblio/Makefile.biblio.lib
-+++ b/c++/src/objects/biblio/Makefile.biblio.lib
-@@ -1,2 +1,4 @@
- LIB = biblio
- SRC = biblio__ biblio___ citation_base
-+
-+DLL_LIB = general xser xncbi
---- a/c++/src/objects/blastdb/Makefile.blastdb.lib
-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -1,2 +1,4 @@
- LIB = blastdb
- SRC = blastdb__ blastdb___
-+
-+DLL_LIB = seq xser xncbi
---- a/c++/src/objects/general/Makefile.general.lib
-+++ b/c++/src/objects/general/Makefile.general.lib
-@@ -1,2 +1,4 @@
- LIB = general
- SRC = general__ general___ uoconv
-+
-+DLL_LIB = xser xncbi
---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-@@ -3,4 +3,6 @@
- LIB = genome_collection
- SRC = genome_collection__ genome_collection___
-
-+DLL_LIB = seq general xser xncbi
-+
- WATCHERS = dicuccio
---- a/c++/src/objects/id1/Makefile.id1.lib
-+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -3,4 +3,6 @@
- LIB = id1
- SRC = id1__ id1___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
---- a/c++/src/objects/id2/Makefile.id2.lib
-+++ b/c++/src/objects/id2/Makefile.id2.lib
-@@ -1,4 +1,6 @@
- LIB = id2
- SRC = id2__ id2___
-
-+DLL_LIB = seqsplit seq xser xncbi
-+
- WATCHERS = vasilche
---- a/c++/src/objects/medline/Makefile.medline.lib
-+++ b/c++/src/objects/medline/Makefile.medline.lib
-@@ -1,2 +1,4 @@
- LIB = medline
- SRC = medline__ medline___
-+
-+DLL_LIB = biblio general xser xncbi
---- a/c++/src/objects/pub/Makefile.pub.lib
-+++ b/c++/src/objects/pub/Makefile.pub.lib
-@@ -1,2 +1,4 @@
- LIB = pub
- SRC = pub__ pub___
-+
-+DLL_LIB = medline biblio xser xncbi
---- a/c++/src/objects/seq/Makefile.seq.lib
-+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,4 +12,6 @@
- seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
- seq_loc_from_string seq_loc_reverse_complementer
-
-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = vasilche grichenk
---- a/c++/src/objects/seqcode/Makefile.seqcode.lib
-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
-@@ -1,2 +1,4 @@
- LIB = seqcode
- SRC = seqcode__ seqcode___
-+
-+DLL_LIB = xser xncbi
---- a/c++/src/objects/seqset/Makefile.seqset.lib
-+++ b/c++/src/objects/seqset/Makefile.seqset.lib
-@@ -1,2 +1,4 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
-+
-+DLL_LIB = seq general xser xncbi
---- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-@@ -1,4 +1,6 @@
- LIB = seqsplit
- SRC = seqsplit__ seqsplit___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
---- a/c++/src/serial/Makefile.serial.lib
-+++ b/c++/src/serial/Makefile.serial.lib
-@@ -18,4 +18,6 @@
-
- LIB = xser
-
-+DLL_LIB = xutil xncbi
-+
- WATCHERS = gouriano
---- a/c++/src/util/Makefile.util.lib
-+++ b/c++/src/util/Makefile.util.lib
-@@ -11,6 +11,7 @@
- LIB = xutil
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
- LIBS = $(ORIG_LIBS)
-
- WATCHERS = vakatov
---- a/c++/src/util/xregexp/Makefile.xregexp.lib
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -6,7 +6,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
-
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
- LIBS = $(PCRE_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-@@ -8,6 +8,8 @@
-
- SRC = segmask
-
-+DLL_LIB = blast xobjmgr xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/objmgr/split/Makefile.id2_split.lib
-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,6 +17,6 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(SOBJMGR_LIBS)
-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
-
- WATCHERS = vasilche
---- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@
-
- LIB = writedb
-
-+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
-+ xser sequtil xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
---- a/c++/src/algo/blast/Makefile.blast_macros.mk
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -18,7 +18,7 @@
- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
-
- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
- xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
- xobjread creaders xnetblastcli xnetblast blastdb scoremat tables xalnmgr
- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
---- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-@@ -2,7 +2,7 @@
- SRC = main mkindex_app
-
- LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
-- xobjread creaders xobjutil tables connect $(SOBJMGR_LIBS)
-+ xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
-
- CXXFLAGS = $(FAST_CXXFLAGS)
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/fix_lib_deps (from rev 13784, trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/fix_lib_deps (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/fix_lib_deps 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,594 @@
+Subject: ensure that all libraries link against all direct dependencies
+
+ * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. 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.
+ * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
+ rather than libconnect for consistency with libblast, which uses the
+ former to keep the aforementioned cycle-breaking from causing
+ inconsistency elsewhere.
+
+Debian-Bug: 633567.
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2011-08-28
+--- a/c++/src/algo/blast/core/Makefile.blast.lib
++++ b/c++/src/algo/blast/core/Makefile.blast.lib
+@@ -21,5 +21,6 @@
+ CFLAGS = $(FAST_CFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = composition_adjustment xconnect tables
+
+ WATCHERS = coulouri maning madden camacho
+--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
++++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+@@ -11,6 +11,8 @@
+ CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
++
+ ASN_DEP = seqset
+
+ WATCHERS = morgulis
+--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
++++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
+@@ -7,6 +7,7 @@
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+
+-DLL_LIB = align_format blastxml xhtml xcgi
++DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
++ seq general xser tables xncbi
+
+ WATCHERS = jianye zaretska madden camacho fongah2
+--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
++++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+@@ -21,3 +21,4 @@
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
+--- a/c++/src/cgi/Makefile.cgi.lib
++++ b/c++/src/cgi/Makefile.cgi.lib
+@@ -9,6 +9,8 @@
+ user_agent
+ LIB = xcgi
+
++DLL_LIB = xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+
+ WATCHERS = vakatov
+--- a/c++/src/html/Makefile.html.lib
++++ b/c++/src/html/Makefile.html.lib
+@@ -7,4 +7,6 @@
+ jsmenu commentdiag indentstream html_exception writer_htmlenc
+ LIB = xhtml
+
++DLL_LIB = xncbi
++
+ WATCHERS = ivanov
+--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
++++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
+@@ -2,3 +2,5 @@
+
+ LIB = xnetblastcli
+ SRC = blastclient blastclient_
++
++DLL_LIB = xnetblast xser xconnect xutil xncbi
+--- a/c++/src/objtools/align_format/Makefile.align_format.lib
++++ b/c++/src/objtools/align_format/Makefile.align_format.lib
+@@ -13,6 +13,10 @@
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+
++DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
++ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
++ xcgi xhtml tables xncbi
++
+ ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
+ # CFLAGS = $(FAST_CFLAGS)
+ # CXXFLAGS = $(FAST_CXXFLAGS)
+--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
++++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+@@ -12,3 +12,5 @@
+
+ WATCHERS = todorov dicuccio grichenk
+
++DLL_LIB = xobjmgr seqset seq xser tables xncbi
++
+--- a/c++/src/objtools/readers/Makefile.xobjread.lib
++++ b/c++/src/objtools/readers/Makefile.xobjread.lib
+@@ -19,5 +19,5 @@
+ best_feat_finder source_mod_parser fasta_exception
+
+
+-DLL_LIB = creaders
++DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi
+
+--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
++++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+@@ -12,6 +12,6 @@
+ mask_writer_blastdb_maskinfo
+
+ ASN_DEP = seqset
+-DLL_LIB = seqdb blastdb
++DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
+
+ WATCHERS = morgulis camacho
+--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
++++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
+@@ -7,6 +7,8 @@
+
+ ASN_DEP = seqset
+
++DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
++
+ LIB = xobjsimple
+ SRC = simple_om
+
+--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
++++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+@@ -24,6 +24,8 @@
+
+ LIB = seqdb
+
++DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+@@ -5,4 +5,6 @@
+
+ ASN_DEP = blastdb seqset
+
++DLL_LIB = seqdb xobjmgr seqset seq xncbi
++
+ WATCHERS = camacho
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+@@ -3,6 +3,8 @@
+ LIB = ncbi_xloader_blastdb_rmt
+ SRC = bdbloader_rmt remote_blastdb_adapter
+
++DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
++
+ ASN_DEP = blastdb xnetblast
+
+ WATCHERS = camacho
+--- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
++++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+@@ -4,3 +4,5 @@
+
+ LIB = gene_info
+ SRC = gene_info gene_info_reader file_utils
++
++DLL_LIB = xncbi
+--- a/c++/src/algo/blast/api/Makefile.xblast.lib
++++ b/c++/src/algo/blast/api/Makefile.xblast.lib
+@@ -74,14 +74,15 @@
+ deltablast_options \
+ deltablast
+
+-SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
++SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
+
+ LIB = xblast
+
+ DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \
+ xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \
+ blastdb xnetblastcli xnetblast scoremat xconnect tables \
+- $(SOBJMGR_LIBS)
++ $(SOBJMGR_LIBS) blast seqdb seqset seq general \
++ xser xconnect sequtil tables xutil xncbi
+
+ CFLAGS = $(FAST_CFLAGS)
+ # Strict gcc flags
+--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
++++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+@@ -24,7 +24,9 @@
+
+ LIB = blastinput
+
+-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread $(OBJMGR_LIBS) xutil
++ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
++ $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
++ scoremat seqset seq xser xutil xncbi
+
+ # should be redundant, given the above :-/
+ ASN_DEP = seqset xnetblast
+--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
++++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+@@ -8,6 +8,8 @@
+
+ SRC = symdust
+
++DLL_LIB = xobjmgr seq xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+--- a/c++/src/connect/Makefile.xconnect.lib
++++ b/c++/src/connect/Makefile.xconnect.lib
+@@ -14,6 +14,8 @@
+ LIB = xconnect
+ PROJ_TAG = core
+
++DLL_LIB = xncbi
++
+ LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
+
+ WATCHERS = lavr
+--- a/c++/src/connect/ext/Makefile.xconnext.lib
++++ b/c++/src/connect/ext/Makefile.xconnext.lib
+@@ -6,4 +6,6 @@
+
+ LIB = xconnext
+
++DLL_LIB = xconnect xncbi
++
+ WATCHERS = lavr
+--- a/c++/src/objects/blast/Makefile.blast.lib
++++ b/c++/src/objects/blast/Makefile.blast.lib
+@@ -1,4 +1,6 @@
+ LIB = xnetblast
+ SRC = blast__ blast___ names
+
++DLL_LIB = scoremat seqset seq xser xncbi
++
+ WATCHERS = camacho
+--- a/c++/src/objects/blastxml/Makefile.blastxml.lib
++++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
+@@ -1,2 +1,4 @@
+ LIB = blastxml
+ SRC = blastxml__ blastxml___
++
++DLL_LIB = xser xncbi
+--- a/c++/src/objects/entrez2/Makefile.entrez2.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
+@@ -2,3 +2,5 @@
+
+ LIB = entrez2
+ SRC = entrez2__ entrez2___
++
++DLL_LIB = xser xncbi
+--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+@@ -4,3 +4,5 @@
+
+ LIB = entrez2cli
+ SRC = entrez2_client entrez2_client_
++
++DLL_LIB = entrez2 xser xconnect xutil xncbi
+--- a/c++/src/objects/scoremat/Makefile.scoremat.lib
++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
+@@ -1,2 +1,4 @@
+ LIB = scoremat
+ SRC = scoremat__ scoremat___
++
++DLL_LIB = seqset seq general xser xncbi
+--- a/c++/src/objects/seqedit/Makefile.seqedit.lib
++++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
+@@ -1,3 +1,4 @@
+ LIB = seqedit
+ SRC = seqedit__ seqedit___
+-
++
++DLL_LIB = seqset seq general xser xncbi
+--- a/c++/src/objects/submit/Makefile.submit.lib
++++ b/c++/src/objects/submit/Makefile.submit.lib
+@@ -1,2 +1,4 @@
+ LIB = submit
+ SRC = submit__ submit___
++
++DLL_LIB = seqset seq biblio general xser xncbi
+--- a/c++/src/objmgr/util/Makefile.util.lib
++++ b/c++/src/objmgr/util/Makefile.util.lib
+@@ -8,5 +8,7 @@
+ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
+ LIB = xobjutil
+
++DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
++
+ WATCHERS = ucko vasilche
+
+--- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
++++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+@@ -11,6 +11,7 @@
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+
++DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
+
+ ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
+ # CFLAGS = $(FAST_CFLAGS)
+--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
++++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
+@@ -8,6 +8,8 @@
+
+ LIB = blast_services
+
++DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+@@ -12,4 +12,7 @@
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+
++DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
++ xobjmgr seq xutil xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+@@ -15,4 +15,7 @@
+ DLL_LIB =
+ DLL_DLIB = $(GENBANK_READER_LDEP)
+
++DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
++ xser xconnect xcompress xutil xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
++++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+@@ -12,6 +12,8 @@
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+
++DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+ WATCHERS = vasilche
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+@@ -12,6 +12,8 @@
+ # Dependencies for shared library
+ DLL_LIB = xconnect ncbi_xreader$(DLL)
+
++DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+ WATCHERS = vasilche
+--- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
++++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+@@ -12,6 +12,9 @@
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
+
+ # Dependencies for shared library (disabled due to problems on Darwin)
+-# DLL_LIB = xconnect ncbi_xreader$(DLL)
++DLL_LIB = xconnect ncbi_xreader$(DLL)
++
++DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
++
+
+ WATCHERS = vasilche
+--- a/c++/src/util/compress/api/Makefile.compress.lib
++++ b/c++/src/util/compress/api/Makefile.compress.lib
+@@ -6,7 +6,7 @@
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+-DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
++DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
+ LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS)
+
+ WATCHERS = ivanov
+--- a/c++/src/util/sequtil/Makefile.sequtil.lib
++++ b/c++/src/util/sequtil/Makefile.sequtil.lib
+@@ -3,4 +3,6 @@
+ LIB = sequtil
+ SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
+
++DLL_LIB = xncbi
++
+ WATCHERS = shomrat
+--- a/c++/src/corelib/Makefile.test_boost.lib
++++ b/c++/src/corelib/Makefile.test_boost.lib
+@@ -3,6 +3,8 @@
+ SRC = test_boost
+ LIB = test_boost
+
++DLL_LIB = xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
+
+ REQUIRES = Boost.Test.Included
+--- a/c++/src/corelib/Makefile.test_mt.lib
++++ b/c++/src/corelib/Makefile.test_mt.lib
+@@ -3,6 +3,8 @@
+ SRC = test_mt
+ LIB = test_mt
+
++DLL_LIB = xncbi
++
+ # REQUIRES = MT
+
+ USE_PCH = no
+--- a/c++/src/objects/biblio/Makefile.biblio.lib
++++ b/c++/src/objects/biblio/Makefile.biblio.lib
+@@ -1,2 +1,4 @@
+ LIB = biblio
+ SRC = biblio__ biblio___ citation_base
++
++DLL_LIB = general xser xncbi
+--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
++++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
+@@ -1,2 +1,4 @@
+ LIB = blastdb
+ SRC = blastdb__ blastdb___
++
++DLL_LIB = seq xser xncbi
+--- a/c++/src/objects/general/Makefile.general.lib
++++ b/c++/src/objects/general/Makefile.general.lib
+@@ -1,2 +1,4 @@
+ LIB = general
+ SRC = general__ general___ uoconv
++
++DLL_LIB = xser xncbi
+--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
++++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+@@ -3,4 +3,6 @@
+ LIB = genome_collection
+ SRC = genome_collection__ genome_collection___
+
++DLL_LIB = seq general xser xncbi
++
+ WATCHERS = dicuccio
+--- a/c++/src/objects/id1/Makefile.id1.lib
++++ b/c++/src/objects/id1/Makefile.id1.lib
+@@ -3,4 +3,6 @@
+ LIB = id1
+ SRC = id1__ id1___
+
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/objects/id2/Makefile.id2.lib
++++ b/c++/src/objects/id2/Makefile.id2.lib
+@@ -1,4 +1,6 @@
+ LIB = id2
+ SRC = id2__ id2___
+
++DLL_LIB = seqsplit seq xser xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/objects/medline/Makefile.medline.lib
++++ b/c++/src/objects/medline/Makefile.medline.lib
+@@ -1,2 +1,4 @@
+ LIB = medline
+ SRC = medline__ medline___
++
++DLL_LIB = biblio general xser xncbi
+--- a/c++/src/objects/pub/Makefile.pub.lib
++++ b/c++/src/objects/pub/Makefile.pub.lib
+@@ -1,2 +1,4 @@
+ LIB = pub
+ SRC = pub__ pub___
++
++DLL_LIB = medline biblio xser xncbi
+--- a/c++/src/objects/seq/Makefile.seq.lib
++++ b/c++/src/objects/seq/Makefile.seq.lib
+@@ -12,4 +12,6 @@
+ seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
+ seq_loc_from_string seq_loc_reverse_complementer
+
++DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
++
+ WATCHERS = vasilche grichenk
+--- a/c++/src/objects/seqcode/Makefile.seqcode.lib
++++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
+@@ -1,2 +1,4 @@
+ LIB = seqcode
+ SRC = seqcode__ seqcode___
++
++DLL_LIB = xser xncbi
+--- a/c++/src/objects/seqset/Makefile.seqset.lib
++++ b/c++/src/objects/seqset/Makefile.seqset.lib
+@@ -1,2 +1,4 @@
+ LIB = seqset
+ SRC = seqset__ seqset___ gb_release_file
++
++DLL_LIB = seq general xser xncbi
+--- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
++++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
+@@ -1,4 +1,6 @@
+ LIB = seqsplit
+ SRC = seqsplit__ seqsplit___
+
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/serial/Makefile.serial.lib
++++ b/c++/src/serial/Makefile.serial.lib
+@@ -18,4 +18,6 @@
+
+ LIB = xser
+
++DLL_LIB = xutil xncbi
++
+ WATCHERS = gouriano
+--- a/c++/src/util/Makefile.util.lib
++++ b/c++/src/util/Makefile.util.lib
+@@ -11,6 +11,7 @@
+ LIB = xutil
+ PROJ_TAG = core
+
++DLL_LIB = xncbi
+ LIBS = $(ORIG_LIBS)
+
+ WATCHERS = vakatov
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib
++++ b/c++/src/util/xregexp/Makefile.xregexp.lib
+@@ -6,7 +6,7 @@
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
+
+-DLL_LIB = $(PCRE_LIB)
++DLL_LIB = $(PCRE_LIB) xncbi
+ LIBS = $(PCRE_LIBS)
+
+ WATCHERS = ivanov
+--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
++++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+@@ -8,6 +8,8 @@
+
+ SRC = segmask
+
++DLL_LIB = blast xobjmgr xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+--- a/c++/src/objmgr/split/Makefile.id2_split.lib
++++ b/c++/src/objmgr/split/Makefile.id2_split.lib
+@@ -17,6 +17,6 @@
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+-DLL_LIB = $(SOBJMGR_LIBS)
++DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
+
+ WATCHERS = vasilche
+--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
++++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+@@ -8,6 +8,9 @@
+
+ LIB = writedb
+
++DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
++ xser sequtil xutil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+--- a/c++/src/algo/blast/Makefile.blast_macros.mk
++++ b/c++/src/algo/blast/Makefile.blast_macros.mk
+@@ -18,7 +18,7 @@
+ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
+
+ # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
+-BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
++BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
+ xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
+ xobjread creaders xnetblastcli xnetblast blastdb scoremat tables xalnmgr
+ # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
+--- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
++++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
+@@ -2,7 +2,7 @@
+ SRC = main mkindex_app
+
+ LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
+- xobjread creaders xobjutil tables connect $(SOBJMGR_LIBS)
++ xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS)
+ LIB = $(LIB_:%=%$(STATIC))
+
+ CXXFLAGS = $(FAST_CXXFLAGS)
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/hurd_fixes
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/hurd_fixes 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1,53 +0,0 @@
-Subject: fix portability issues that led to Hurd build failures
-
-* src/build-system/configure(.ac):
- - Reflect the Hurd's support for -Wl,rpath,... .
-* src/connect/ncbi_socket_cxx.cpp, src/connect/ext/ncbi_localnet.c:
- cope with missing PATH_MAX everywhere, not just under Windows.
-
-Author: Aaron M. Ucko <ucko at debian.org>
-Last-Update: 2011-06-10
---- a/c++/src/build-system/configure
-+++ b/c++/src/build-system/configure
-@@ -5817,7 +5817,7 @@
- solaris* )
- CONF_f_runpath="-R"
- ;;
-- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
-+ linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC )
- CONF_f_runpath="-Wl,-rpath,"
- ;;
- linux*:ICC )
---- a/c++/src/build-system/configure.ac
-+++ b/c++/src/build-system/configure.ac
-@@ -1535,7 +1535,7 @@
- solaris* )
- CONF_f_runpath="-R"
- ;;
-- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
-+ linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC )
- CONF_f_runpath="-Wl,-rpath,"
- ;;
- linux*:ICC )
---- a/c++/src/connect/ncbi_socket_cxx.cpp
-+++ b/c++/src/connect/ncbi_socket_cxx.cpp
-@@ -35,7 +35,7 @@
- #include "ncbi_assert.h" // no _ASSERT()s, keep clean from xncbi
- #include <connect/ncbi_socket_unix.hpp>
- #include <limits.h> // for PATH_MAX
--#if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
-+#ifndef PATH_MAX
- # define PATH_MAX 512 // will actually use less than 32 chars
- #endif // NCBI_OS_MSWIN && !PATH_MAX
-
---- a/c++/src/connect/ext/ncbi_localnet.c
-+++ b/c++/src/connect/ext/ncbi_localnet.c
-@@ -64,6 +64,8 @@
-
- #if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
- # define PATH_MAX _MAX_PATH
-+#elif !defined(PATH_MAX)
-+# define PATH_MAX 4096
- #endif /*NCBI_OS_MSWIN && !PATH_MAX*/
-
- #if PATH_MAX < 256
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/hurd_fixes (from rev 13784, trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/hurd_fixes (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/hurd_fixes 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,55 @@
+Subject: fix portability issues that led to Hurd build failures
+
+* src/build-system/configure(.ac):
+ - Reflect the Hurd's support for -Wl,rpath,... .
+* src/connect/ncbi_socket_cxx.cpp, src/connect/ext/ncbi_localnet.c:
+ cope with missing PATH_MAX everywhere, not just under Windows.
+
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2011-06-10
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -5860,7 +5860,7 @@
+ solaris* )
+ CONF_f_runpath="-R"
+ ;;
+- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
++ linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC )
+ CONF_f_runpath="-Wl,-rpath,"
+ ;;
+ linux*:ICC )
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1558,7 +1558,7 @@
+ solaris* )
+ CONF_f_runpath="-R"
+ ;;
+- linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
++ linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC )
+ CONF_f_runpath="-Wl,-rpath,"
+ ;;
+ linux*:ICC )
+--- a/c++/src/connect/ncbi_socket_cxx.cpp
++++ b/c++/src/connect/ncbi_socket_cxx.cpp
+@@ -35,7 +35,7 @@
+ #include "ncbi_assert.h" // no _ASSERT()s, keep clean from xncbi
+ #include <connect/ncbi_socket_unix.hpp>
+ #include <limits.h> // for PATH_MAX
+-#if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
++#ifndef PATH_MAX
+ # define PATH_MAX 512 // will actually use less than 32 chars
+ #endif // NCBI_OS_MSWIN && !PATH_MAX
+
+--- a/c++/src/connect/ext/ncbi_localnet.c
++++ b/c++/src/connect/ext/ncbi_localnet.c
+@@ -62,6 +62,10 @@
+ # endif /*_MAX_PATH*/
+ #endif /*NCBI_OS_MSWIN && !PATH_MAX*/
+
++#if !defined(PATH_MAX)
++# define PATH_MAX 4096
++#endif /*Patch added for Ubuntu build*/
++
+ #if PATH_MAX < 256
+ # define BUFSIZE 256
+ #else
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/no_multiarch_rpath
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/no_multiarch_rpath 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1,32 +0,0 @@
-Subject: avoid redundant rpath entries on multiarch systems
-
- * src/build-system/configure(.ac): when ensuring that executables
- will be able to find libstdc++, don't add rpath entries that files
- under /etc/ld.so.conf.d already specify, even if they don't resemble
- traditional single-architecture or biarch locations.
-
-Debian-Bug: 633567.
-Author: Aaron M. Ucko <ucko at debian.org>
-Last-Update: 2011-08-28
---- a/c++/src/build-system/configure
-+++ b/c++/src/build-system/configure
-@@ -5880,7 +5880,7 @@
- break
- ;;
- /* )
-- found=true
-+ fgrep -qsx $abs_dir /etc/ld.so.conf.d/* || found=true
- break
- ;;
- esac
---- a/c++/src/build-system/configure.ac
-+++ b/c++/src/build-system/configure.ac
-@@ -1597,7 +1597,7 @@
- break
- ;;
- /* )
-- found=true
-+ fgrep -qsx $abs_dir /etc/ld.so.conf.d/* || found=true
- break
- ;;
- esac
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/no_multiarch_rpath (from rev 13784, trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/no_multiarch_rpath (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/no_multiarch_rpath 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,32 @@
+Subject: avoid redundant rpath entries on multiarch systems
+
+ * src/build-system/configure(.ac): when ensuring that executables
+ will be able to find libstdc++, don't add rpath entries that files
+ under /etc/ld.so.conf.d already specify, even if they don't resemble
+ traditional single-architecture or biarch locations.
+
+Debian-Bug: 633567.
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2011-08-28
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -5923,7 +5923,7 @@
+ break
+ ;;
+ /* )
+- found=true
++ fgrep -qsx $abs_dir /etc/ld.so.conf.d/* || found=true
+ break
+ ;;
+ esac
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1620,7 +1620,7 @@
+ break
+ ;;
+ /* )
+- found=true
++ fgrep -qsx $abs_dir /etc/ld.so.conf.d/* || found=true
+ break
+ ;;
+ esac
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/series 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1,6 +0,0 @@
-hurd_fixes
-legacy_rename_rpsblast
-fix_lib_deps
-no_multiarch_rpath
-use_pie_for_apps
-fix_arm_mips_build
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/series (from rev 13784, trunk/packages/ncbi-blast+/trunk/debian/patches/series)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/series (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/series 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,7 @@
+enable_clean_after_failed_compile
+hurd_fixes
+legacy_rename_rpsblast
+fix_lib_deps
+no_multiarch_rpath
+use_pie_for_apps
+skip_services_unit_test
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/skip_services_unit_test (from rev 13786, trunk/packages/ncbi-blast+/trunk/debian/patches/skip_services_unit_test)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/skip_services_unit_test (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/patches/skip_services_unit_test 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,16 @@
+Subject: remove network required test
+Author: Tim Booth
+Forwarded: no
+Description: test require internet connection
+Last-Updated: 2013-06-01
+--- a/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
++++ b/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
+@@ -11,6 +11,7 @@
+
+ LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+
+-CHECK_CMD = blast_services_unit_test
++# This test requires an internet connection, shouldn't be run on a build server
++# CHECK_CMD = blast_services_unit_test
+
+ WATCHERS = madden camacho
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/rules
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/rules 2013-05-31 17:09:58 UTC (rev 13783)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/rules 2013-06-01 12:35:10 UTC (rev 13789)
@@ -1,85 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \
- --without-makefile-auto-update --with-flat-makefile --without-caution \
- --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ \
- --with-build-root=BUILD --without-debug
-proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/
-
-ifneq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
-DEB_CONFIGURE_EXTRA_FLAGS += --with-symbols
-endif
-
-export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
-
-DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
-
-CFLAGS := $(shell dpkg-buildflags --get CFLAGS)
-CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS)
-CXXFLAGS := $(shell dpkg-buildflags --get CXXFLAGS)
-LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -Wl,--as-needed
-
-ifneq (,$(findstring mips,$(DEB_HOST_ARCH)))
-CXXFLAGS := $(CXXFLAGS:-O%=-O)
-DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O
-endif
-
-export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE
-
-llp=LD_LIBRARY_PATH
-override_dh_auto_configure:
- cd c++ && $(llp)=$(CURDIR)/c++/BUILD/lib$${$(llp)+:$$$(llp)} \
- CONFIG_SHELL=/bin/bash ./configure $(DEB_CONFIGURE_EXTRA_FLAGS)
-
-override_dh_auto_build:
- cd c++/BUILD/build && \
- make -f Makefile.flat all_projects="$(proj)" \
- APP_LDFLAGS='-Wl,-E -fPIE -pie'
-
-override_dh_auto_test:
- -dh_auto_test
- -c++/BUILD/build/check.sh concat_err
- -cat c++/BUILD/build/check.sh.out_err
-
-instroot = debian/ncbi-blast+/usr
-leg_bin = debian/ncbi-blast+-legacy/usr/share/ncbi-blast+/bin
-override_dh_auto_install:
- cp c++/BUILD/lib/*.so $(instroot)/lib/ncbi-blast+/
- cp c++/BUILD/bin/* $(instroot)/bin/
-
-override_dh_install:
- # dh_install
- mv $(instroot)/bin/rpsblast $(instroot)/bin/rpsblast+
- mv $(instroot)/bin/seedtop $(instroot)/bin/seedtop+
- mv $(instroot)/bin/legacy_blast.pl $(instroot)/bin/legacy_blast
- mv $(instroot)/bin/update_blastdb.pl $(instroot)/bin/update_blastdb
- mv $(instroot)/bin/windowmasker_2.2.22_adapter.py \
- $(instroot)/bin/windowmasker_2.2.22_adapter
-# Clean up tests, demos, and internal build tools
- rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \
- $(instroot)/bin/datatool \
- $(instroot)/bin/project_tree_builder \
- $(instroot)/lib/ncbi-blast+/libtest_*.so
-
- if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi
-
-override_dh_clean:
- dh_clean
- -for x in c++/src/objects/*/*.files; do \
- if [ -d $$x ]; then \
- (cd `dirname $$x` && ../../../BUILD/build/new_module.sh \
- `basename $$x .files`.module purge_sources); \
- fi \
- done
- rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile
- rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module
-
-%:
- dh $@ -Dc++ --with autotools_dev --with quilt
-
-get-orig-source:
- . debian/get-orig-source
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/rules (from rev 13786, trunk/packages/ncbi-blast+/trunk/debian/rules)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/rules (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-1/debian/rules 2013-06-01 12:35:10 UTC (rev 13789)
@@ -0,0 +1,98 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \
+ --without-makefile-auto-update --with-flat-makefile --without-caution \
+ --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ \
+ --with-build-root=BUILD --without-debug
+proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/
+
+ifneq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+DEB_CONFIGURE_EXTRA_FLAGS += --with-symbols
+endif
+
+#export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
+export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic
+export DEB_LDFLAGS_MAINT_APPEND=-Wl,--as-needed
+
+DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
+
+CFLAGS := $(shell dpkg-buildflags --get CFLAGS)
+CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS)
+CXXFLAGS := $(shell dpkg-buildflags --get CXXFLAGS)
+LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -Wl,--as-needed
+
+ifneq (,$(findstring mips,$(DEB_HOST_ARCH)))
+CXXFLAGS := $(CXXFLAGS:-O%=-O)
+DEB_CONFIGURE_EXTRA_FLAGS += FAST_CXXFLAGS=-O
+endif
+
+export CFLAGS CPPFLAGS CXXFLAGS LDFLAGS MAKE
+
+
+llp=LD_LIBRARY_PATH
+override_dh_auto_configure:
+ cd c++ && $(llp)=$(CURDIR)/c++/BUILD/lib$${$(llp)+:$$$(llp)} \
+ CONFIG_SHELL=/bin/bash ./configure $(DEB_CONFIGURE_EXTRA_FLAGS)
+
+override_dh_auto_build:
+ cd c++/BUILD/build && \
+ make -f Makefile.flat all_projects="$(proj)" \
+ APP_LDFLAGS='-Wl,-E -fPIE -pie'
+
+override_dh_auto_test:
+ -dh_auto_test
+ -c++/BUILD/build/check.sh concat_err
+ -cat c++/BUILD/build/check.sh.out_err
+
+instroot = debian/ncbi-blast+/usr
+leg_bin = debian/ncbi-blast+-legacy/usr/share/ncbi-blast+/bin
+override_dh_auto_install:
+ cp c++/BUILD/lib/*.so $(instroot)/lib/ncbi-blast+/
+ cp c++/BUILD/bin/* $(instroot)/bin/
+
+override_dh_install:
+ # dh_install
+ mv $(instroot)/bin/rpsblast $(instroot)/bin/rpsblast+
+ mv $(instroot)/bin/seedtop $(instroot)/bin/seedtop+
+ mv $(instroot)/bin/legacy_blast.pl $(instroot)/bin/legacy_blast
+ mv $(instroot)/bin/update_blastdb.pl $(instroot)/bin/update_blastdb
+ mv $(instroot)/bin/windowmasker_2.2.22_adapter.py \
+ $(instroot)/bin/windowmasker_2.2.22_adapter
+# Clean up tests, demos, and internal build tools
+ rm -f $(instroot)/bin/*test* $(instroot)/bin/seqdb_demo \
+ $(instroot)/bin/datatool \
+ $(instroot)/bin/project_tree_builder \
+ $(instroot)/lib/ncbi-blast+/libtest_*.so
+
+ if test -d $(leg_bin); then cp debian/legacy/legacy.sh $(leg_bin)/; fi
+
+override_dh_clean:
+ dh_clean
+ #Tricky - for each module directory there may be several module files
+ #or there may be none but then there is still a module named after the
+ #directory. Clean everything!
+ -for x in c++/src/objects/* ; do \
+ (cd "$$x" && ( \
+ mods="`echo *.module`" ; \
+ [ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \
+ for mod in $$mods ; do \
+ ../../../BUILD/build/new_module.sh $$mod purge_sources ; \
+ done ) ; \
+ ) ; \
+ done
+ rm -rf c++/compilers/dll c++/config.log c++/Makefile
+ rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module
+ find -name check_exec.pid -delete
+ rm -rf c++/BUILD
+
+%:
+ dh $@ -Dc++ --with autotools_dev --with quilt
+
+get-orig-source:
+ . debian/get-orig-source
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