[med-svn] r13803 - in trunk/packages/ncbi-blast+/tags: . 2.2.28-2/debian 2.2.28-2/debian/patches
Aaron M. Ucko
ucko at alioth.debian.org
Mon Jun 3 03:34:24 UTC 2013
Author: ucko
Date: 2013-06-03 03:34:20 +0000 (Mon, 03 Jun 2013)
New Revision: 13803
Added:
trunk/packages/ncbi-blast+/tags/2.2.28-2/
trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/control
trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/patches/use_pie_for_apps
trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/rules
Removed:
trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/control
trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/patches/use_pie_for_apps
trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/rules
Log:
[svn-buildpackage] Tagging ncbi-blast+ 2.2.28-2
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2013-06-02 14:02:48 UTC (rev 13798)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/changelog 2013-06-03 03:34:20 UTC (rev 13803)
@@ -1,161 +0,0 @@
-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
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/changelog (from rev 13802, trunk/packages/ncbi-blast+/trunk/debian/changelog)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/changelog (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/changelog 2013-06-03 03:34:20 UTC (rev 13803)
@@ -0,0 +1,171 @@
+ncbi-blast+ (2.2.28-2) unstable; urgency=low
+
+ * debian/patches/use_pie_for_apps: Explicitly build all executables with
+ -fPIE -pie, to avoid giving project_tree_builder a partial PIE
+ treatment that now fails on mips and mipsel. (Closes: #710807.)
+ * debian/rules: Retire redundant APP_LDFLAGS override.
+ * Standards-Version: 3.9.4. (Already compliant.)
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 02 Jun 2013 23:00:44 -0400
+
+ncbi-blast+ (2.2.28-1) unstable; urgency=low
+
+ * New upstream release
+ - Thanks to Tim Booth for package update help.
+
+ -- Olivier Sallou <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/2.2.28-2/debian/control
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/control 2013-06-02 14:02:48 UTC (rev 13798)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/control 2013-06-03 03:34:20 UTC (rev 13803)
@@ -1,50 +0,0 @@
-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/2.2.28-2/debian/control (from rev 13801, trunk/packages/ncbi-blast+/trunk/debian/control)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/control (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/control 2013-06-03 03:34:20 UTC (rev 13803)
@@ -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: 3.9.4
+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.
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/patches/use_pie_for_apps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/use_pie_for_apps 2013-06-02 14:02:48 UTC (rev 13798)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/patches/use_pie_for_apps 2013-06-03 03:34:20 UTC (rev 13803)
@@ -1,20 +0,0 @@
-Subject: build executables with -fPIE, not -fPIC
-
-* -fPIC is only useful for shared libraries; substitute -fPIE (to be
- accompanied by appropriate APP_LDFLAGS) when building executables.
-
-Author: Aaron M. Ucko <ucko at debian.org>
-Last-Update: 2012-05-10
---- a/c++/src/build-system/Makefile.app.in
-+++ b/c++/src/build-system/Makefile.app.in
-@@ -24,8 +24,8 @@
-
- ### C/C++ source file compilation (and maybe auto-dependencies) build rules
-
--CXXFLAGS_ALL = @f_compile@ $(CXXFLAGS) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
--CFLAGS_ALL = @f_compile@ $(CFLAGS) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
-+CXXFLAGS_ALL = @f_compile@ $(CXXFLAGS:-fPIC=-fPIE) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
-+CFLAGS_ALL = @f_compile@ $(CFLAGS:-fPIC=-fPIE) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
- SOURCES = @UNIX_SRC@ $(SRC)
- include $(builddir)/Makefile.$(Rules)
-
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/patches/use_pie_for_apps (from rev 13800, trunk/packages/ncbi-blast+/trunk/debian/patches/use_pie_for_apps)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/patches/use_pie_for_apps (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/patches/use_pie_for_apps 2013-06-03 03:34:20 UTC (rev 13803)
@@ -0,0 +1,29 @@
+Subject: build executables with -fPIE, not -fPIC
+
+* -fPIC is only useful for shared libraries; substitute -fPIE (along
+ with -pie at link time) when building executables.
+
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2012-05-10
+--- a/c++/src/build-system/Makefile.app.in
++++ b/c++/src/build-system/Makefile.app.in
+@@ -24,8 +24,8 @@ default_rule: all
+
+ ### C/C++ source file compilation (and maybe auto-dependencies) build rules
+
+-CXXFLAGS_ALL = @f_compile@ $(CXXFLAGS) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
+-CFLAGS_ALL = @f_compile@ $(CFLAGS) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
++CXXFLAGS_ALL = @f_compile@ $(CXXFLAGS:-fPIC=-fPIE) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
++CFLAGS_ALL = @f_compile@ $(CFLAGS:-fPIC=-fPIE) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
+ SOURCES = @UNIX_SRC@ $(SRC)
+ include $(builddir)/Makefile.$(Rules)
+
+@@ -72,7 +72,7 @@ rebuild-libs:
+
+ $(XAPP): $(XOBJ) $(XLIBDEP)
+ @-$(RM) .$(XAPP).stamp
+- $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
++ $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
+ $(STRIP) $(XAPP)
+ $(POST_LINK) $(XAPP)
+ ifneq "$(BINCOPY)" "@:"
Deleted: trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/rules
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/rules 2013-06-02 14:02:48 UTC (rev 13798)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/rules 2013-06-03 03:34:20 UTC (rev 13803)
@@ -1,98 +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
-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 $@ -Dc++ --with autotools_dev --with quilt
-
-get-orig-source:
- . debian/get-orig-source
Copied: trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/rules (from rev 13800, trunk/packages/ncbi-blast+/trunk/debian/rules)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/rules (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.28-2/debian/rules 2013-06-03 03:34:20 UTC (rev 13803)
@@ -0,0 +1,97 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \
+ --without-makefile-auto-update --with-flat-makefile --without-caution \
+ --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ \
+ --with-build-root=BUILD --without-debug
+proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/
+
+ifneq (,$(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)"
+
+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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