Package: ncbi-blast+ / 2.8.1-1

Metadata

Package Version Patches format
ncbi-blast+ 2.8.1-1 3.0 (quilt)

Patch series

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

c++/src/build-system/new_module.sh.in | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 enable clean
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/ncbi_socket_cxx.cpp | 2 1 + 1 - 0 !
3 files changed, 3 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/api/Makefile.xblast.lib | 4 2 + 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 | 2 2 + 0 - 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 | 2 1 + 1 - 0 !
c++/src/build-system/library_relations.txt | 2 1 + 1 - 0 !
c++/src/cgi/Makefile.cgi.lib | 2 2 + 0 - 0 !
c++/src/connect/Makefile.xconnect.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/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/blastxml2/Makefile.blastxml2.lib | 2 2 + 0 - 0 !
c++/src/objects/entrez2/Makefile.entrez2.lib | 1 1 + 0 - 0 !
c++/src/objects/entrez2/Makefile.entrez2cli.lib | 2 1 + 1 - 0 !
c++/src/objects/gbseq/Makefile.gbseq.lib | 1 1 + 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/medlars/Makefile.medlars.lib | 1 1 + 0 - 0 !
c++/src/objects/medline/Makefile.medline.lib | 2 1 + 1 - 0 !
c++/src/objects/mla/Makefile.mla.lib | 1 1 + 0 - 0 !
c++/src/objects/mla/Makefile.mlacli.lib | 2 2 + 0 - 0 !
c++/src/objects/pub/Makefile.pub.lib | 2 1 + 1 - 0 !
c++/src/objects/pubmed/Makefile.pubmed.lib | 1 1 + 0 - 0 !
c++/src/objects/scoremat/Makefile.scoremat.lib | 2 1 + 1 - 0 !
c++/src/objects/seq/Makefile.seq.lib | 2 1 + 1 - 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 1 + 1 - 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/objects/taxon1/Makefile.taxon1.lib | 1 1 + 0 - 0 !
c++/src/objects/taxon3/Makefile.taxon3.lib | 1 1 + 0 - 0 !
c++/src/objects/valerr/Makefile.valerr.lib | 1 1 + 0 - 0 !
c++/src/objects/valid/Makefile.valid.lib | 2 2 + 0 - 0 !
c++/src/objects/variation/Makefile.variation.lib | 1 1 + 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 | 1 1 + 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 | 1 1 + 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/cleanup/Makefile.cleanup.lib | 3 1 + 2 - 0 !
c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 2 1 + 1 - 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/format/Makefile.xformat.lib | 2 2 + 0 - 0 !
c++/src/objtools/readers/Makefile.xobjread.lib | 3 1 + 2 - 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 !
c++/src/util/xregexp/Makefile.xregexp_template_tester.lib | 2 2 + 0 - 0 !
71 files changed, 120 insertions(+), 23 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/build-system/library_relations.txt: Change xblast's
   relationship to blast from includes to needs, accordingly.
 * src/algo/blast/Makefile.blast_macros.mk: Add blast to BLAST_LIBS.
 * 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.
use_pie_for_apps | (download)

c++/src/build-system/Makefile.app.in | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 build executables with -fpie, not -fpic

* -fPIC is only useful for shared libraries; substitute -fPIE (along
   with -pie at link time) when building executables.

skip_services_unit_test | (download)

c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 test require internet connection
Last-Updated: 2013-06-01

fix_configure | (download)

c++/configure.orig | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 debian build is not done in configure directory,
 need to update way to get relative configure.orig script
support_x32 | (download)

c++/include/corelib/impl/ncbi_atomic_defs.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---
suppress_gnutls_version_check | (download)

c++/src/connect/ncbi_gnutls.c | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

---
optionally_keep_sequence | (download)

c++/src/algo/blast/api/search_strategy.cpp | 7 6 + 1 - 0 !
1 file changed, 6 insertions(+), 1 deletion(-)

---
fix_unit_tests | (download)

c++/src/algo/blast/Makefile.blast_macros.mk | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 unit_test need blast lib to compile
system_mbedtls_only | (download)

c++/src/connect/Makefile.connssl.lib | 4 3 + 1 - 0 !
1 file changed, 3 insertions(+), 1 deletion(-)

---