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.
|