Author: ucko Date: 2012-05-11 03:48:48 +0000 (Fri, 11 May 2012) New Revision: 10823
Added: trunk/packages/ncbi-blast+/tags/2.2.26-3/ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/changelog trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/control trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/fix_gcc47_errors trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/series trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/use_pie_for_apps trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/rules Removed: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/changelog trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/control trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/series trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/rules Log: [svn-buildpackage] Tagging ncbi-blast+ 2.2.26-3 Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/changelog =================================================================== --- trunk/packages/ncbi-blast+/trunk/debian/changelog 2012-05-10 10:20:56 UTC (rev 10814) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/changelog 2012-05-11 03:48:48 UTC (rev 10823) @@ -1,113 +0,0 @@ -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 <osal...@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 <osal...@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 <ti...@debian.org> Wed, 21 Dec 2011 15:47:04 +0100 - -ncbi-blast+ (2.2.25-6) unstable; urgency=low - - * debian/control: - Luca Capello <l...@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.sal...@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 <u...@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 <u...@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 <u...@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 <u...@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.sal...@irisa.fr> Wed, 08 Jun 2011 00:15:15 +0200 Copied: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/changelog (from rev 10822, trunk/packages/ncbi-blast+/trunk/debian/changelog) =================================================================== --- trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/changelog (rev 0) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/changelog 2012-05-11 03:48:48 UTC (rev 10823) @@ -0,0 +1,133 @@ +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 <u...@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 <osal...@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 <osal...@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 <ti...@debian.org> Wed, 21 Dec 2011 15:47:04 +0100 + +ncbi-blast+ (2.2.25-6) unstable; urgency=low + + * debian/control: + Luca Capello <l...@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.sal...@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 <u...@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 <u...@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 <u...@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 <u...@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.sal...@irisa.fr> Wed, 08 Jun 2011 00:15:15 +0200 Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/control =================================================================== --- trunk/packages/ncbi-blast+/trunk/debian/control 2012-05-10 10:20:56 UTC (rev 10814) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/control 2012-05-11 03:48:48 UTC (rev 10823) @@ -1,43 +0,0 @@ -Source: ncbi-blast+ -Section: science -Priority: optional -Build-Depends: debhelper (>= 7.0.50~), autotools-dev (>= 20100122), libbz2-dev, libpcre3-dev, zlib1g-dev, libboost-test-dev, quilt (>= 0.46-7~), time, libc0.3-dev (>= 2.13-9~) [hurd-i386] -Standards-Version: 3.9.3 -Uploaders: Olivier Sallou <osal...@debian.org>, - Andreas Tille <ti...@debian.org> -DM-Upload-Allowed: yes -Maintainer: Debian Med Packaging Team <debian-med-packag...@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: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, python, ncbi-data -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/2.2.26-3/debian/control (from rev 10820, trunk/packages/ncbi-blast+/trunk/debian/control) =================================================================== --- trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/control (rev 0) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/control 2012-05-11 03:48:48 UTC (rev 10823) @@ -0,0 +1,51 @@ +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 <osal...@debian.org>, Andreas Tille <ti...@debian.org> +DM-Upload-Allowed: yes +Maintainer: Debian Med Packaging Team <debian-med-packag...@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/2.2.26-3/debian/patches/fix_gcc47_errors (from rev 10818, trunk/packages/ncbi-blast+/trunk/debian/patches/fix_gcc47_errors) =================================================================== --- trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/fix_gcc47_errors (rev 0) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/fix_gcc47_errors 2012-05-11 03:48:48 UTC (rev 10823) @@ -0,0 +1,320 @@ +Subject: fix various GCC 4.7 compilation errors and warnings + + * 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. + +Author: Aaron M. Ucko <u...@debian.org> +Last-Update: 2012-04-13 +--- a/c++/include/connect/ncbi_conn_stream.hpp ++++ b/c++/include/connect/ncbi_conn_stream.hpp +@@ -259,7 +259,7 @@ + class CConn_IOStreamSetReadTimeout : protected CConn_IOStreamSetTimeout + { + public: +- CConn_IOStreamSetTimeout::GetTimeout; ++ using CConn_IOStreamSetTimeout::GetTimeout; + + protected: + CConn_IOStreamSetReadTimeout(const STimeout* timeout) +@@ -289,7 +289,7 @@ + class CConn_IOStreamSetWriteTimeout : protected CConn_IOStreamSetTimeout + { + public: +- CConn_IOStreamSetTimeout::GetTimeout; ++ using CConn_IOStreamSetTimeout::GetTimeout; + + protected: + CConn_IOStreamSetWriteTimeout(const STimeout* timeout) +--- a/c++/include/corelib/ncbiexpt.hpp ++++ b/c++/include/corelib/ncbiexpt.hpp +@@ -852,7 +852,7 @@ + exception_class(const exception_class& other) \ + : base_class(other) \ + { \ +- x_Assign(other); \ ++ this->x_Assign(other); \ + } \ + public: \ + virtual ~exception_class(void) throw() {} \ +@@ -1172,7 +1172,7 @@ + : TBase( other) + { + m_Errno = other.m_Errno; +- x_Assign(other); ++ this->x_Assign(other); + } + + /// Destructor. +--- a/c++/include/corelib/ncbimisc.hpp ++++ b/c++/include/corelib/ncbimisc.hpp +@@ -39,6 +39,7 @@ + #ifdef HAVE_SYS_TYPES_H + # include <sys/types.h> + #endif ++#include <cstdlib> + #ifdef NCBI_COMPILER_ICC + // Preemptively pull in <cctype>, which breaks if we've already + // repointed is* at NCBI_is*. +--- a/c++/include/corelib/ncbistl.hpp ++++ b/c++/include/corelib/ncbistl.hpp +@@ -37,6 +37,7 @@ + + #include <common/ncbi_export.h> + ++#include <algorithm> + + // Get rid of some warnings in MSVC++ + #if (_MSC_VER >= 1200) +--- a/c++/include/corelib/ncbistr.hpp ++++ b/c++/include/corelib/ncbistr.hpp +@@ -3039,7 +3039,7 @@ + : TBase(other) + { + m_Pos = other.m_Pos; +- x_Assign(other); ++ this->x_Assign(other); + } + + /// Destructor. +--- a/c++/include/serial/impl/stltypes.hpp ++++ b/c++/include/serial/impl/stltypes.hpp +@@ -412,6 +412,7 @@ + typedef StlIterator TStlIterator; + typedef TypeInfoIterator TTypeInfoIterator; + typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr; ++ typedef CStlClassInfoFunctions<Container> CParent; + + static TStlIterator& It(TTypeInfoIterator& iter) + { +@@ -437,7 +438,8 @@ + } + static bool InitIterator(TTypeInfoIterator& iter) + { +- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin(); ++ TStlIterator stl_iter ++ = CParent::Get(iter.GetContainerPtr()).begin(); + if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) { + void* data = &iter.m_IteratorData; + new (data) TStlIterator(stl_iter); +@@ -445,7 +447,7 @@ + else { + iter.m_IteratorData = new TStlIterator(stl_iter); + } +- return stl_iter != Get(iter.GetContainerPtr()).end(); ++ return stl_iter != CParent::Get(iter.GetContainerPtr()).end(); + } + static void ReleaseIterator(TTypeInfoIterator& iter) + { +@@ -466,7 +468,7 @@ + + static bool NextElement(TTypeInfoIterator& iter) + { +- return ++It(iter) != Get(iter.GetContainerPtr()).end(); ++ return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end(); + } + static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter) + { +@@ -503,7 +505,7 @@ + + static bool EraseElement(TTypeInfoIterator& iter) + { +- TStlIterator& it = It(iter); ++ TStlIterator& it = CParent::It(iter); + Container* c = static_cast<Container*>(iter.GetContainerPtr()); + it = c->erase(it); + return it != c->end(); +@@ -511,7 +513,7 @@ + static void EraseAllElements(TTypeInfoIterator& iter) + { + Container* c = static_cast<Container*>(iter.GetContainerPtr()); +- c->erase(It(iter), c->end()); ++ c->erase(CParent::It(iter), c->end()); + } + + static void SetIteratorFunctions(CStlOneArgTemplate* info) +@@ -542,7 +544,7 @@ + } + static bool EraseElement(TTypeInfoIterator& iter) + { +- TStlIterator& it = It(iter); ++ TStlIterator& it = CParent::It(iter); + Container* c = static_cast<Container*>(iter.GetContainerPtr()); + TStlIterator erase = it++; + c->erase(erase); +@@ -551,7 +553,7 @@ + static void EraseAllElements(TTypeInfoIterator& iter) + { + Container* c = static_cast<Container*>(iter.GetContainerPtr()); +- c->erase(It(iter), c->end()); ++ c->erase(CParent::It(iter), c->end()); + } + + static void SetIteratorFunctions(CStlOneArgTemplate* info) +--- a/c++/include/serial/iterator.hpp ++++ b/c++/include/serial/iterator.hpp +@@ -520,13 +520,13 @@ + CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo) + : m_NeedType(needType) + { +- Init(beginInfo); ++ this->Init(beginInfo); + } + CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo, + const string& filter) + : m_NeedType(needType) + { +- Init(beginInfo, filter); ++ this->Init(beginInfo, filter); + } + + virtual bool CanSelect(const CConstObjectInfo& object) +--- a/c++/include/util/bitset/bmfunc.h ++++ b/c++/include/util/bitset/bmfunc.h +@@ -39,6 +39,13 @@ + namespace bm + { + ++bm::id_t bit_block_any_range(const bm::word_t* block, ++ bm::word_t left, ++ bm::word_t right); ++ ++bm::id_t bit_block_calc_count_range(const bm::word_t* block, ++ bm::word_t left, ++ bm::word_t right); + + /*! + @brief Structure with statistical information about bitset's memory +--- a/c++/include/util/bitset/bmserial.h ++++ b/c++/include/util/bitset/bmserial.h +@@ -1381,7 +1381,7 @@ + case set_block_arrgap: + case set_block_arrgap_egamma: + { +- unsigned arr_len = read_id_list(dec, btype, this->id_array_); ++ unsigned arr_len = this->read_id_list(dec, btype, this->id_array_); + gap_len = gap_set_array(gap_temp_block_, this->id_array_, arr_len); + break; + } +@@ -1390,7 +1390,7 @@ + (sizeof(gap_word_t) == 2 ? dec.get_16() : dec.get_32()); + case set_block_arrgap_egamma_inv: + case set_block_arrgap_inv: +- gap_len = read_gap_block(dec, btype, gap_temp_block_, gap_head); ++ gap_len = this->read_gap_block(dec, btype, gap_temp_block_, gap_head); + break; + default: + BM_ASSERT(0); +--- a/c++/include/util/linkedset.hpp ++++ b/c++/include/util/linkedset.hpp +@@ -268,10 +268,10 @@ + pair<iterator, bool> ins = m_Container.insert(value); + if ( ins.second ) { + if ( ins.first == begin() ) +- insertToStart(*ins.first); ++ this->insertToStart(*ins.first); + else { + iterator prev = ins.first; +- insertAfter(*--prev, *ins.first); ++ this->insertAfter(*--prev, *ins.first); + } + } + return ins; +@@ -280,10 +280,10 @@ + void erase(iterator iter) + { + if ( iter == begin() ) +- removeFromStart(*iter); ++ this->removeFromStart(*iter); + else { + iterator prev = iter; +- removeAfter(*--prev, *iter); ++ this->removeAfter(*--prev, *iter); + } + m_Container.erase(iter); + } +@@ -422,10 +422,10 @@ + { + iterator iter = m_Container.insert(value); + if ( iter == begin() ) +- insertToStart(get(iter)); ++ this->insertToStart(get(iter)); + else { + iterator prev = iter; +- insertAfter(get(--prev), get(iter)); ++ this->insertAfter(get(--prev), get(iter)); + } + return iter; + } +@@ -433,10 +433,10 @@ + void erase(iterator iter) + { + if ( iter == begin() ) +- removeFromStart(get(iter)); ++ this->removeFromStart(get(iter)); + else { + iterator prev = iter; +- removeAfter(get(--prev), get(iter)); ++ this->removeAfter(get(--prev), get(iter)); + } + m_Container.erase(iter); + } +--- a/c++/include/util/rangemap.hpp ++++ b/c++/include/util/rangemap.hpp +@@ -578,7 +578,7 @@ + // get level + + // insert element +- TSelectMapI selectIter = insertLevel(selectKey); ++ TSelectMapI selectIter = this->insertLevel(selectKey); + pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value); + + pair<iterator, bool> ret; +@@ -640,7 +640,7 @@ + // insert element + iterator ret; + ret.m_Range = range_type::GetWhole(); +- ret.m_SelectIter = insertLevel(selectKey); ++ ret.m_SelectIter = this->insertLevel(selectKey); + ret.m_SelectIterEnd = this->m_SelectMap.end(); + ret.m_LevelIter = ret.m_SelectIter->second.insert(value); + return ret; +--- a/c++/src/serial/stdtypes.cpp ++++ b/c++/src/serial/stdtypes.cpp +@@ -720,7 +720,7 @@ + if ( IsSigned() ) { + // signed -> unsigned + // check for negative value +- if ( IsNegative(value) ) ++ if ( CParent::IsNegative(value) ) + ThrowIntegerOverflow(); + } + if ( sizeof(value) > sizeof(result) ) { +@@ -751,7 +751,7 @@ + // unsigned -> signed + if ( sizeof(value) == sizeof(result) ) { + // same size - check for sign change only +- if ( IsNegative(result) ) ++ if ( CParent::IsNegative(result) ) + ThrowIntegerOverflow(); + } + } +@@ -786,7 +786,7 @@ + if ( IsSigned() ) { + // signed -> unsigned + // check for negative value +- if ( IsNegative(value) ) ++ if ( CParent::IsNegative(value) ) + ThrowIntegerOverflow(); + } + if ( sizeof(value) > sizeof(result) ) { +@@ -817,7 +817,7 @@ + // unsigned -> signed + if ( sizeof(value) == sizeof(result) ) { + // same size - check for sign change only +- if ( IsNegative(result) ) ++ if ( CParent::IsNegative(result) ) + ThrowIntegerOverflow(); + } + } Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/series =================================================================== --- trunk/packages/ncbi-blast+/trunk/debian/patches/series 2012-05-10 10:20:56 UTC (rev 10814) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/series 2012-05-11 03:48:48 UTC (rev 10823) @@ -1,5 +0,0 @@ -hurd_fixes -legacy_rename_rpsblast -fix_lib_deps -no_multiarch_rpath -wrong_path_to_touch.patch Copied: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/series (from rev 10820, trunk/packages/ncbi-blast+/trunk/debian/patches/series) =================================================================== --- trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/series (rev 0) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/series 2012-05-11 03:48:48 UTC (rev 10823) @@ -0,0 +1,7 @@ +hurd_fixes +legacy_rename_rpsblast +fix_lib_deps +no_multiarch_rpath +wrong_path_to_touch.patch +fix_gcc47_errors +use_pie_for_apps Copied: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/use_pie_for_apps (from rev 10820, trunk/packages/ncbi-blast+/trunk/debian/patches/use_pie_for_apps) =================================================================== --- trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/use_pie_for_apps (rev 0) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/patches/use_pie_for_apps 2012-05-11 03:48:48 UTC (rev 10823) @@ -0,0 +1,20 @@ +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 <u...@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) + Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/rules =================================================================== --- trunk/packages/ncbi-blast+/trunk/debian/rules 2012-05-10 10:20:56 UTC (rev 10814) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/rules 2012-05-11 03:48:48 UTC (rev 10823) @@ -1,74 +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 LDFLAGS='-Wl,--as-needed -Wl,--enable-new-dtags' -proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/ - -# XXX - not quite right, as we get -DNDEBUG vs. -D_DEBUG -ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS))) -DEB_CONFIGURE_EXTRA_FLAGS += --without-debug -else -DEB_CONFIGURE_EXTRA_FLAGS += --with-optimization -endif - -DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH) -ifneq (,$(findstring mips,$(DEB_HOST_ARCH))) -DEB_CONFIGURE_EXTRA_FLAGS += CXXFLAGS=-O FAST_CXXFLAGS=-O -endif - -export 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/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 \ - (cd `dirname $$x` && ../../../BUILD/build/new_module.sh \ - `basename $$x .files`.module purge_sources); \ - done - rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile - rm -f c++/src/objects/blastxml/blastxml.module - -%: - dh $@ -Dc++ --with autotools_dev --with quilt - -get-orig-source: - . debian/get-orig-source Copied: trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/rules (from rev 10821, trunk/packages/ncbi-blast+/trunk/debian/rules) =================================================================== --- trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/rules (rev 0) +++ trunk/packages/ncbi-blast+/tags/2.2.26-3/debian/rules 2012-05-11 03:48:48 UTC (rev 10823) @@ -0,0 +1,82 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \ + --without-makefile-auto-update --with-flat-makefile --without-caution \ + --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ \ + --with-build-root=BUILD --without-debug +proj=algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/ + +ifneq (,$(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/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 \ + (cd `dirname $$x` && ../../../BUILD/build/new_module.sh \ + `basename $$x .files`.module purge_sources); \ + 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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit