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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 24 Sep 2012 09:28:29 +0200 - -ncbi-blast+ (2.2.27-1) unstable; urgency=low - - * New upstream release - - -- Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 21 Dec 2011 15:47:04 +0100 - -ncbi-blast+ (2.2.25-6) unstable; urgency=low - - * debian/control: - Luca Capello <[email protected]>, 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 08 Jun 2011 21:42:52 -0400 - -ncbi-blast+ (2.2.25-1) unstable; urgency=low - - * Initial release (Closes: #624394) - - -- Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 24 Sep 2012 09:28:29 +0200 + +ncbi-blast+ (2.2.27-1) unstable; urgency=low + + * New upstream release + + -- Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 21 Dec 2011 15:47:04 +0100 + +ncbi-blast+ (2.2.25-6) unstable; urgency=low + + * debian/control: + Luca Capello <[email protected]>, 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 08 Jun 2011 21:42:52 -0400 + +ncbi-blast+ (2.2.25-1) unstable; urgency=low + + * Initial release (Closes: #624394) + + -- Olivier Sallou <[email protected]> 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 <[email protected]>, Andreas Tille <[email protected]> -Maintainer: Debian Med Packaging Team <[email protected]> -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 <[email protected]>, Andreas Tille <[email protected]> +Maintainer: Debian Med Packaging Team <[email protected]> +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 <[email protected]> -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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
