[med-svn] r10823 - in trunk/packages/ncbi-blast+/tags: . 2.2.26-3/debian 2.2.26-3/debian/patches
Aaron M. Ucko
ucko at alioth.debian.org
Fri May 11 03:48:48 UTC 2012
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 <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/2.2.26-3/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 <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/2.2.26-3/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 <osallou at debian.org>,
- Andreas Tille <tille at debian.org>
-DM-Upload-Allowed: yes
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ncbi-blast+/trunk/
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast+/trunk/
-
-Package: ncbi-blast+
-Architecture: any
-Enhances: t-coffee
-Depends: ${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 <osallou at debian.org>, Andreas Tille <tille at debian.org>
+DM-Upload-Allowed: yes
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ncbi-blast+/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast+/trunk/
+
+Package: ncbi-blast+
+Architecture: any
+Enhances: t-coffee
+Depends: ncbi-data, python, ${misc:Depends}, ${perl:Depends}, ${shlibs:Depends}
+Multi-Arch: foreign
+Description: next generation suite of BLAST sequence search tools
+ The Basic Local Alignment Search Tool (BLAST) is the most widely
+ used sequence similarity tool. There are versions of BLAST that
+ compare protein queries to protein databases, nucleotide queries
+ to nucleotide databases, as well as versions that translate nucleotide
+ queries or databases in all six frames and compare to protein databases
+ or queries.
+ PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting
+ with a protein query, and then uses that PSSM to perform further searches.
+ It is also possible to compare a protein or nucleotide query to a
+ database of PSSM’s.
+ The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as
+ a network service.
+
+Package: ncbi-blast+-legacy
+Architecture: all
+Depends: ncbi-blast+, ${misc:Depends}
+Multi-Arch: foreign
+Description: NCBI Blast legacy call script
+ This package adds some fake scripts to call NCBI+ programs
+ with the NCBI blast command line. It makes use of the
+ legacy_blast script in ncbi-blast+ package.
+ .
+ To use those scripts, /usr/share/ncbi-blast+/bin must be added
+ to the PATH.
Copied: trunk/packages/ncbi-blast+/tags/2.2.26-3/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 <ucko at 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 <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)
+
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
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