Package: ncbi-blast+ / 2.2.26-3

Metadata

Package Version Patches format
ncbi-blast+ 2.2.26-3 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
hurd_fixes | (download)

c++/src/build-system/configure | 2 1 + 1 - 0 !
c++/src/build-system/configure.ac | 2 1 + 1 - 0 !
c++/src/connect/ext/ncbi_localnet.c | 2 2 + 0 - 0 !
c++/src/connect/ncbi_socket_cxx.cpp | 2 1 + 1 - 0 !
4 files changed, 5 insertions(+), 3 deletions(-)

 fix portability issues that led to hurd build failures

* src/build-system/configure(.ac):
  - Reflect the Hurd's support for -Wl,rpath,... .
* src/connect/ncbi_socket_cxx.cpp, src/connect/ext/ncbi_localnet.c:
  cope with missing PATH_MAX everywhere, not just under Windows.

legacy_rename_rpsblast | (download)

c++/src/app/blast/legacy_blast.pl | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 rename binary as blast+ for package coherency.
Last-Updated: 2011-10-03

fix_lib_deps | (download)

c++/src/algo/blast/Makefile.blast_macros.mk | 2 1 + 1 - 0 !
c++/src/algo/blast/api/Makefile.xblast.lib | 7 5 + 2 - 0 !
c++/src/algo/blast/blastinput/Makefile.blastinput.lib | 4 3 + 1 - 0 !
c++/src/algo/blast/core/Makefile.blast.lib | 1 1 + 0 - 0 !
c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib | 2 2 + 0 - 0 !
c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app | 2 1 + 1 - 0 !
c++/src/algo/blast/format/Makefile.xblastformat.lib | 3 2 + 1 - 0 !
c++/src/algo/dustmask/Makefile.xalgodustmask.lib | 2 2 + 0 - 0 !
c++/src/algo/segmask/Makefile.xalgosegmask.lib | 2 2 + 0 - 0 !
c++/src/algo/winmask/Makefile.xalgowinmask.lib | 1 1 + 0 - 0 !
c++/src/cgi/Makefile.cgi.lib | 2 2 + 0 - 0 !
c++/src/connect/Makefile.xconnect.lib | 2 2 + 0 - 0 !
c++/src/connect/ext/Makefile.xconnext.lib | 2 2 + 0 - 0 !
c++/src/corelib/Makefile.test_boost.lib | 2 2 + 0 - 0 !
c++/src/corelib/Makefile.test_mt.lib | 2 2 + 0 - 0 !
c++/src/html/Makefile.html.lib | 2 2 + 0 - 0 !
c++/src/objects/biblio/Makefile.biblio.lib | 2 2 + 0 - 0 !
c++/src/objects/blast/Makefile.blast.lib | 2 2 + 0 - 0 !
c++/src/objects/blast/Makefile.xnetblastcli.lib | 2 2 + 0 - 0 !
c++/src/objects/blastdb/Makefile.blastdb.lib | 2 2 + 0 - 0 !
c++/src/objects/blastxml/Makefile.blastxml.lib | 2 2 + 0 - 0 !
c++/src/objects/entrez2/Makefile.entrez2.lib | 2 2 + 0 - 0 !
c++/src/objects/entrez2/Makefile.entrez2cli.lib | 2 2 + 0 - 0 !
c++/src/objects/general/Makefile.general.lib | 2 2 + 0 - 0 !
c++/src/objects/genomecoll/Makefile.genome_collection.lib | 2 2 + 0 - 0 !
c++/src/objects/id1/Makefile.id1.lib | 2 2 + 0 - 0 !
c++/src/objects/id2/Makefile.id2.lib | 2 2 + 0 - 0 !
c++/src/objects/medline/Makefile.medline.lib | 2 2 + 0 - 0 !
c++/src/objects/pub/Makefile.pub.lib | 2 2 + 0 - 0 !
c++/src/objects/scoremat/Makefile.scoremat.lib | 2 2 + 0 - 0 !
c++/src/objects/seq/Makefile.seq.lib | 2 2 + 0 - 0 !
c++/src/objects/seqcode/Makefile.seqcode.lib | 2 2 + 0 - 0 !
c++/src/objects/seqedit/Makefile.seqedit.lib | 3 2 + 1 - 0 !
c++/src/objects/seqset/Makefile.seqset.lib | 2 2 + 0 - 0 !
c++/src/objects/seqsplit/Makefile.seqsplit.lib | 2 2 + 0 - 0 !
c++/src/objects/submit/Makefile.submit.lib | 2 2 + 0 - 0 !
c++/src/objmgr/split/Makefile.id2_split.lib | 2 1 + 1 - 0 !
c++/src/objmgr/util/Makefile.util.lib | 2 2 + 0 - 0 !
c++/src/objtools/align_format/Makefile.align_format.lib | 4 4 + 0 - 0 !
c++/src/objtools/alnmgr/Makefile.alnmgr.lib | 2 2 + 0 - 0 !
c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 1 1 + 0 - 0 !
c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib | 2 2 + 0 - 0 !
c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 2 + 0 - 0 !
c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib | 3 3 + 0 - 0 !
c++/src/objtools/blast/services/Makefile.blast_services.lib | 2 2 + 0 - 0 !
c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 2 2 + 0 - 0 !
c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib | 2 2 + 0 - 0 !
c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib | 3 3 + 0 - 0 !
c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 3 3 + 0 - 0 !
c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib | 2 2 + 0 - 0 !
c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib | 2 2 + 0 - 0 !
c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 5 4 + 1 - 0 !
c++/src/objtools/readers/Makefile.xobjread.lib | 2 1 + 1 - 0 !
c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib | 2 1 + 1 - 0 !
c++/src/objtools/simple/Makefile.xobjsimple.lib | 2 2 + 0 - 0 !
c++/src/serial/Makefile.serial.lib | 2 2 + 0 - 0 !
c++/src/util/Makefile.util.lib | 1 1 + 0 - 0 !
c++/src/util/compress/api/Makefile.compress.lib | 2 1 + 1 - 0 !
c++/src/util/sequtil/Makefile.sequtil.lib | 2 2 + 0 - 0 !
c++/src/util/xregexp/Makefile.xregexp.lib | 2 1 + 1 - 0 !
60 files changed, 120 insertions(+), 13 deletions(-)

 ensure that all libraries link against all direct dependencies

 * src/**/Makefile.*.lib: set DLL_(D)LIB correctly.  Break the dependency
   loop between libxblast and libxalgoblastdbindex by having the former
   provide only the C++ BLAST API, leaving the C core only in libblast.
 * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
   rather than libconnect for consistency with libblast, which uses the
   former to keep the aforementioned cycle-breaking from causing
   inconsistency elsewhere.

Debian-Bug: 633567.
no_multiarch_rpath | (download)

c++/src/build-system/configure | 2 1 + 1 - 0 !
c++/src/build-system/configure.ac | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 avoid redundant rpath entries on multiarch systems

 * src/build-system/configure(.ac): when ensuring that executables
   will be able to find libstdc++, don't add rpath entries that files
   under /etc/ld.so.conf.d already specify, even if they don't resemble
   traditional single-architecture or biarch locations.

Debian-Bug: 633567.
wrong_path_to_touch.patch | (download)

c++/src/build-system/Makefile.meta.in | 2 1 + 1 - 0 !
c++/src/build-system/Makefile.mk.in | 2 1 + 1 - 0 !
c++/src/build-system/NEWS | 2 2 + 0 - 0 !
c++/src/build-system/configure | 43 42 + 1 - 0 !
c++/src/build-system/configure.ac | 1 1 + 0 - 0 !
5 files changed, 47 insertions(+), 3 deletions(-)

 upstream makes use of a hard path that 
does not match on hurd systems. Patch comes from upstream
 and will be included in next release
fix_gcc47_errors | (download)

c++/include/connect/ncbi_conn_stream.hpp | 4 2 + 2 - 0 !
c++/include/corelib/ncbiexpt.hpp | 4 2 + 2 - 0 !
c++/include/corelib/ncbimisc.hpp | 1 1 + 0 - 0 !
c++/include/corelib/ncbistl.hpp | 1 1 + 0 - 0 !
c++/include/corelib/ncbistr.hpp | 2 1 + 1 - 0 !
c++/include/serial/impl/stltypes.hpp | 16 9 + 7 - 0 !
c++/include/serial/iterator.hpp | 4 2 + 2 - 0 !
c++/include/util/bitset/bmfunc.h | 7 7 + 0 - 0 !
c++/include/util/bitset/bmserial.h | 4 2 + 2 - 0 !
c++/include/util/linkedset.hpp | 16 8 + 8 - 0 !
c++/include/util/rangemap.hpp | 4 2 + 2 - 0 !
c++/src/serial/stdtypes.cpp | 8 4 + 4 - 0 !
12 files changed, 41 insertions(+), 30 deletions(-)

 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.

use_pie_for_apps | (download)

c++/src/build-system/Makefile.app.in | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 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.