[med-svn] [ncbi-blast+] 02/05: fix_lib_deps: Also patch Makefile.blast_macros.mk.
Aaron M. Ucko
ucko at moszumanska.debian.org
Tue Dec 6 04:22:24 UTC 2016
This is an automated email from the git hooks/post-receive script.
ucko pushed a commit to branch master
in repository ncbi-blast+.
commit c0f5a8c1b748e45850cbd9cfc69f642be573dd7a
Author: Aaron M. Ucko <ucko at debian.org>
Date: Mon Dec 5 23:05:55 2016 -0500
fix_lib_deps: Also patch Makefile.blast_macros.mk.
Add blast to BLAST_LIBS to clear up link errors that could otherwise occur.
---
debian/changelog | 4 +-
debian/patches/fix_lib_deps | 144 ++++++++++++++++++++++++--------------------
2 files changed, 81 insertions(+), 67 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 9ba3211..b1815be 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,10 @@
ncbi-blast+ (2.5.0-2) UNRELEASED; urgency=medium
* NOT YET RELEASED.
+ * debian/patches/fix_lib_deps: Patch Makefile.blast_macros.mk to add blast
+ to BLAST_LIBS to clear up link errors that could otherwise occur.
- -- Aaron M. Ucko <ucko at debian.org> Mon, 05 Dec 2016 20:42:34 -0500
+ -- Aaron M. Ucko <ucko at debian.org> Mon, 05 Dec 2016 23:05:54 -0500
ncbi-blast+ (2.5.0-1) unstable; urgency=medium
diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 57cbc8c..6901fcd 100644
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -1,21 +1,22 @@
-Subject: 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/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.
-Author: Aaron M. Ucko <ucko at debian.org>
-Last-Update: 2014-12-02
+Subject: 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.
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2016-12-05
--- a/c++/src/algo/blast/api/Makefile.xblast.lib
+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -76,14 +76,15 @@
+@@ -76,14 +76,15 @@ deltablast \
magicblast_options \
magicblast
@@ -35,7 +36,7 @@ Last-Update: 2014-12-02
CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -26,7 +26,9 @@
+@@ -26,7 +26,9 @@ SRC = $(SRC_CXX)
LIB = blastinput
@@ -48,7 +49,7 @@ Last-Update: 2014-12-02
ASN_DEP = seqset xnetblast
--- a/c++/src/algo/blast/core/Makefile.blast.lib
+++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -23,6 +23,7 @@
+@@ -23,6 +23,7 @@ CFLAGS = $(FAST_CFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
WATCHERS = madden camacho fongah2
@@ -58,7 +59,7 @@ Last-Update: 2014-12-02
composition_adjustment connect tables
--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -11,6 +11,8 @@
+@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
@@ -69,7 +70,7 @@ Last-Update: 2014-12-02
WATCHERS = morgulis
--- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-@@ -2,7 +2,7 @@
+@@ -2,7 +2,7 @@ APP = makembindex
SRC = main mkindex_app
LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
@@ -80,7 +81,7 @@ Last-Update: 2014-12-02
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-@@ -8,6 +8,8 @@
+@@ -8,6 +8,8 @@ LIB = xalgodustmask
SRC = symdust
@@ -91,7 +92,7 @@ Last-Update: 2014-12-02
--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-@@ -8,6 +8,8 @@
+@@ -8,6 +8,8 @@ LIB = xalgosegmask
SRC = segmask
@@ -102,7 +103,7 @@ Last-Update: 2014-12-02
--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,7 +21,7 @@
+@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s
CXXFLAGS = $(FAST_CXXFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
@@ -113,7 +114,7 @@ Last-Update: 2014-12-02
seqmasks_io
--- a/c++/src/build-system/library_relations.txt
+++ b/c++/src/build-system/library_relations.txt
-@@ -1287,7 +1287,7 @@
+@@ -1287,7 +1287,7 @@ xbiosample_util needs $(OBJEDIT_LIBS)
xbiosample_util needs $(XFORMAT_LIBS)
xbiosample_util needs xalnmgr
xbiosample_util needs xmlwrapp
@@ -124,7 +125,7 @@ Last-Update: 2014-12-02
xblast needs xalgowinmask
--- a/c++/src/cgi/Makefile.cgi.lib
+++ b/c++/src/cgi/Makefile.cgi.lib
-@@ -9,6 +9,8 @@
+@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb
user_agent
LIB = xcgi
@@ -135,7 +136,7 @@ Last-Update: 2014-12-02
WATCHERS = vakatov
--- a/c++/src/connect/Makefile.xconnect.lib
+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@
+@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)
LIB = xconnect
PROJ_TAG = core
@@ -168,7 +169,7 @@ Last-Update: 2014-12-02
USE_PCH = no
--- a/c++/src/html/Makefile.html.lib
+++ b/c++/src/html/Makefile.html.lib
-@@ -7,6 +7,8 @@
+@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se
commentdiag indentstream html_exception writer_htmlenc
LIB = xhtml
@@ -179,7 +180,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objects/blast/Makefile.blast.lib
+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -3,6 +3,8 @@
+@@ -3,6 +3,8 @@ SRC = blast__ blast___ names
DLL_LIB = seqset scoremat
@@ -190,7 +191,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -5,6 +5,8 @@
+@@ -5,6 +5,8 @@ SRC = blastdb__ blastdb___
DLL_LIB = xser
@@ -212,7 +213,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objects/id1/Makefile.id1.lib
+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -5,6 +5,8 @@
+@@ -5,6 +5,8 @@ SRC = id1__ id1___
DLL_LIB = seqset
@@ -234,7 +235,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objects/seq/Makefile.seq.lib
+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -14,6 +14,8 @@
+@@ -14,6 +14,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport
DLL_LIB = seqcode pub general xser sequtil
@@ -300,7 +301,7 @@ Last-Update: 2014-12-02
seqset
--- a/c++/src/objmgr/split/Makefile.id2_split.lib
+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,7 +17,7 @@
+@@ -17,7 +17,7 @@ LIB = id2_split
CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
@@ -311,7 +312,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objmgr/util/Makefile.util.lib
+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -11,6 +11,8 @@
+@@ -11,6 +11,8 @@ LIB = xobjutil
DLL_LIB = $(SOBJMGR_LIBS)
@@ -322,7 +323,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/align_format/Makefile.align_format.lib
+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -13,6 +13,10 @@
+@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho
CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
@@ -335,7 +336,7 @@ Last-Update: 2014-12-02
# CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -14,6 +14,7 @@
+@@ -14,6 +14,7 @@ DLL_LIB = tables
WATCHERS = grichenk
@@ -345,7 +346,7 @@ Last-Update: 2014-12-02
tables xobjutil
--- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-@@ -11,6 +11,7 @@
+@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla
CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
@@ -355,7 +356,7 @@ Last-Update: 2014-12-02
# CFLAGS = $(FAST_CFLAGS)
--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-@@ -25,6 +25,8 @@
+@@ -25,6 +25,8 @@ seqdbobj
LIB = seqdb
DLL_LIB = blastdb $(SOBJMGR_LIBS)
@@ -366,7 +367,7 @@ Last-Update: 2014-12-02
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@
+@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum
LIB = writedb
@@ -378,7 +379,7 @@ Last-Update: 2014-12-02
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
-@@ -10,6 +10,8 @@
+@@ -10,6 +10,8 @@ LIB = blast_services
DLL_LIB = xnetblastcli xnetblast
@@ -389,7 +390,7 @@ Last-Update: 2014-12-02
CPPFLAGS = $(ORIG_CPPFLAGS)
--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -9,6 +9,8 @@
+@@ -9,6 +9,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_
ASN_DEP = blastdb seqset
@@ -400,7 +401,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-@@ -7,6 +7,8 @@
+@@ -7,6 +7,8 @@ DLL_LIB = blast_services
CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
@@ -411,7 +412,7 @@ Last-Update: 2014-12-02
WATCHERS = camacho
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,9 @@
+@@ -12,6 +12,9 @@ LIB_OR_DLL = both
# Dependencies for shared library
DLL_LIB = ncbi_xreader$(DLL)
@@ -423,7 +424,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -16,6 +16,9 @@
+@@ -16,6 +16,9 @@ DLL_LIB = $(GENBANK_READER_LDEP)
LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
@@ -435,7 +436,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-@@ -12,6 +12,8 @@
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
# Dependencies for shared library
DLL_LIB = ncbi_xreader$(DLL)
@@ -446,7 +447,7 @@ Last-Update: 2014-12-02
WATCHERS = vasilche
--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-@@ -12,6 +12,8 @@
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
# Dependencies for shared library
DLL_LIB = xconnect ncbi_xreader$(DLL)
@@ -457,7 +458,7 @@ Last-Update: 2014-12-02
WATCHERS = vasilche
--- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-@@ -12,7 +12,10 @@
+@@ -12,7 +12,10 @@ LIB_OR_DLL = both
CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
# Dependencies for shared library (disabled due to problems on Darwin)
@@ -471,7 +472,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -12,7 +12,7 @@
+@@ -12,7 +12,7 @@ mask_writer_seqloc \
mask_writer_blastdb_maskinfo
ASN_DEP = seqset
@@ -482,7 +483,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-@@ -7,6 +7,8 @@
+@@ -7,6 +7,8 @@ WATCHERS = jcherry
ASN_DEP = seqset
@@ -493,7 +494,7 @@ Last-Update: 2014-12-02
--- a/c++/src/serial/Makefile.serial.lib
+++ b/c++/src/serial/Makefile.serial.lib
-@@ -20,6 +20,8 @@
+@@ -20,6 +20,8 @@ LIB = xser
DLL_LIB = xutil
@@ -504,7 +505,7 @@ Last-Update: 2014-12-02
--- a/c++/src/util/Makefile.util.lib
+++ b/c++/src/util/Makefile.util.lib
-@@ -12,6 +12,7 @@
+@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s
LIB = xutil
PROJ_TAG = core
@@ -514,7 +515,7 @@ Last-Update: 2014-12-02
WATCHERS = vakatov
--- a/c++/src/util/compress/api/Makefile.compress.lib
+++ b/c++/src/util/compress/api/Makefile.compress.lib
-@@ -7,7 +7,7 @@
+@@ -7,7 +7,7 @@ LIB = xcompress
CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
@@ -525,7 +526,7 @@ Last-Update: 2014-12-02
WATCHERS = ivanov
--- a/c++/src/util/xregexp/Makefile.xregexp.lib
+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -5,7 +5,7 @@
+@@ -5,7 +5,7 @@ LIB = xregexp
CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
@@ -536,7 +537,7 @@ Last-Update: 2014-12-02
USES_LIBRARIES = \
--- a/c++/src/objtools/readers/Makefile.xobjread.lib
+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -20,8 +20,7 @@
+@@ -20,8 +20,7 @@ SRC = read_util format_guess_ex \
ucscregion_reader \
message_listener line_error
@@ -613,7 +614,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objects/entrez2/Makefile.entrez2.lib
+++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
-@@ -3,6 +3,7 @@
+@@ -3,6 +3,7 @@ WATCHERS = lavr
LIB = entrez2
SRC = entrez2__ entrez2___
@@ -623,7 +624,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-@@ -5,6 +5,7 @@
+@@ -5,6 +5,7 @@ ASN_DEP = entrez2
LIB = entrez2cli
SRC = entrez2_client entrez2_client_
@@ -643,7 +644,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-@@ -6,6 +6,7 @@
+@@ -6,6 +6,7 @@ CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG
LIB = gene_info
SRC = gene_info gene_info_reader file_utils
@@ -673,7 +674,7 @@ Last-Update: 2014-12-02
medlars pub pubmed
--- a/c++/src/objects/mla/Makefile.mlacli.lib
+++ b/c++/src/objects/mla/Makefile.mlacli.lib
-@@ -5,5 +5,7 @@
+@@ -5,5 +5,7 @@ SRC = mla_client mla_client_
DLL_LIB = xconnect
@@ -693,7 +694,7 @@ Last-Update: 2014-12-02
medline
--- a/c++/src/objects/taxon1/Makefile.taxon1.lib
+++ b/c++/src/objects/taxon1/Makefile.taxon1.lib
-@@ -7,6 +7,7 @@
+@@ -7,6 +7,7 @@ DLL_LIB = xconnect
WATCHERS = domrach
@@ -703,7 +704,7 @@ Last-Update: 2014-12-02
$(SEQ_LIBS) pub xconnect
--- a/c++/src/objects/taxon3/Makefile.taxon3.lib
+++ b/c++/src/objects/taxon3/Makefile.taxon3.lib
-@@ -7,6 +7,7 @@
+@@ -7,6 +7,7 @@ DLL_LIB = xconnect
WATCHERS = bollin holmesbr
@@ -713,7 +714,7 @@ Last-Update: 2014-12-02
$(SEQ_LIBS) pub xconnect
--- a/c++/src/objects/valerr/Makefile.valerr.lib
+++ b/c++/src/objects/valerr/Makefile.valerr.lib
-@@ -3,6 +3,7 @@
+@@ -3,6 +3,7 @@ SRC = valerr__ valerr___
ASN_DEP = seqset
@@ -723,7 +724,7 @@ Last-Update: 2014-12-02
xser
--- a/c++/src/objects/valid/Makefile.valid.lib
+++ b/c++/src/objects/valid/Makefile.valid.lib
-@@ -4,5 +4,7 @@
+@@ -4,5 +4,7 @@ SRC = valid__ valid___
ASN_DEP = general
@@ -743,7 +744,7 @@ Last-Update: 2014-12-02
$(SEQ_LIBS) pub
--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -11,6 +11,8 @@
+@@ -11,6 +11,8 @@ DLL_LIB = $(BLAST_LIBS) align_format bla
WATCHERS = jianye zaretska madden camacho fongah2
@@ -754,7 +755,7 @@ Last-Update: 2014-12-02
$(BLAST_LIBS) align_format blastxml blastxml2
--- a/c++/src/objtools/cleanup/Makefile.cleanup.lib
+++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib
-@@ -15,6 +15,7 @@
+@@ -15,6 +15,7 @@ LIB = xcleanup
LIBS = $(PCRE_LIBS)
@@ -764,7 +765,7 @@ Last-Update: 2014-12-02
submit valid xobjutil
--- a/c++/src/objtools/format/Makefile.xformat.lib
+++ b/c++/src/objtools/format/Makefile.xformat.lib
-@@ -22,6 +22,8 @@
+@@ -22,6 +22,8 @@ DLL_LIB = xalnmgr xconnect
WATCHERS = ludwigf dicuccio
@@ -775,7 +776,7 @@ Last-Update: 2014-12-02
gbseq mlacli xalnmgr xcleanup
--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -5,5 +5,7 @@
+@@ -5,5 +5,7 @@ SRC = blastclient blastclient_
DLL_LIB = xconnect
@@ -785,7 +786,7 @@ Last-Update: 2014-12-02
xconnect xnetblast
--- a/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib
+++ b/c++/src/util/xregexp/Makefile.xregexp_template_tester.lib
-@@ -6,6 +6,8 @@
+@@ -6,6 +6,8 @@ LIB = xregexp_template_tester
DLL_LIB = $(PCRE_LIB)
LIBS = $(PCRE_LIBS)
@@ -794,3 +795,14 @@ Last-Update: 2014-12-02
USES_LIBRARIES = \
xregexp $(PCRE_LIB) $(PCRE_LIBS) xncbi
+--- a/c++/src/algo/blast/Makefile.blast_macros.mk
++++ b/c++/src/algo/blast/Makefile.blast_macros.mk
+@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \
+ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
+
+ # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
+-BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
++BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment blast \
+ xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \
+ xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables
+ # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ncbi-blast+.git
More information about the debian-med-commit
mailing list