[med-svn] [ncbi-blast+] 04/04: Adapt patches to new upstream version (please verify!)
Andreas Tille
tille at debian.org
Tue Apr 12 14:08:42 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ncbi-blast+.
commit f9839bafc6f0966d5d66b96023a944d00a2aed89
Author: Andreas Tille <tille at debian.org>
Date: Tue Apr 12 15:37:25 2016 +0200
Adapt patches to new upstream version (please verify!)
---
debian/patches/allow_gcc5 | 47 ----
debian/patches/enable_clean_after_failed_compile | 2 +-
debian/patches/fix_compilation | 32 ---
debian/patches/fix_kfreebsd_ftbs.patch | 6 +-
debian/patches/fix_lib_deps | 273 ++++++++++-------------
debian/patches/legacy_rename_rpsblast | 2 +-
debian/patches/no_multiarch_rpath | 4 +-
debian/patches/series | 2 -
debian/patches/skip_services_unit_test | 2 +-
debian/patches/use_pie_for_apps | 20 +-
10 files changed, 133 insertions(+), 257 deletions(-)
diff --git a/debian/patches/allow_gcc5 b/debian/patches/allow_gcc5
deleted file mode 100644
index 3814965..0000000
--- a/debian/patches/allow_gcc5
+++ /dev/null
@@ -1,47 +0,0 @@
-Subject: allow compilation with GCC 5
-Description: Formally allow compilation with GCC 5, otherwise okay
-Author: Aaron M. Ucko <ucko at debian.org>
-Forwarded: yes
-Last-Updated: 2015-02-16
---- a/c++/src/build-system/configure
-+++ b/c++/src/build-system/configure
-@@ -5819,14 +5819,10 @@
-
- if test "$GCC" = "yes" ; then
- compiler_ver="`$real_CXX -dumpversion 2>&1`"
-- case "$compiler_ver" in
-- 2.95* | 2.96* | 3.* | 4.* )
-- compiler="GCC"
-- ncbi_compiler="GCC"
-- ncbi_compiler_ver="$compiler_ver"
-- WithFeatures="$WithFeatures${WithFeaturesSep}GCC"; WithFeaturesSep=" "
-- ;;
-- esac
-+ compiler="GCC"
-+ ncbi_compiler="GCC"
-+ ncbi_compiler_ver="$compiler_ver"
-+ WithFeatures="$WithFeatures${WithFeaturesSep}GCC"; WithFeaturesSep=" "
- elif test "$KCC" = "yes" ; then
- compiler_ver="$kcc_ver"
- compiler="KCC"
---- a/c++/src/build-system/configure.ac
-+++ b/c++/src/build-system/configure.ac
-@@ -800,14 +800,10 @@
-
- if test "$GCC" = "yes" ; then
- compiler_ver="`$real_CXX -dumpversion 2>&1`"
-- case "$compiler_ver" in
-- 2.95* | 2.96* | 3.* | 4.* )
-- compiler="GCC"
-- ncbi_compiler="GCC"
-- ncbi_compiler_ver="$compiler_ver"
-- NCBI_FEATURE(GCC)
-- ;;
-- esac
-+ compiler="GCC"
-+ ncbi_compiler="GCC"
-+ ncbi_compiler_ver="$compiler_ver"
-+ NCBI_FEATURE(GCC)
- elif test "$KCC" = "yes" ; then
- compiler_ver="$kcc_ver"
- compiler="KCC"
diff --git a/debian/patches/enable_clean_after_failed_compile b/debian/patches/enable_clean_after_failed_compile
index 75434fb..e57f492 100644
--- a/debian/patches/enable_clean_after_failed_compile
+++ b/debian/patches/enable_clean_after_failed_compile
@@ -5,7 +5,7 @@ Last-Updated: 2013-06-01
Forwarded: no
--- a/c++/src/build-system/new_module.sh.in
+++ b/c++/src/build-system/new_module.sh.in
-@@ -180,7 +180,7 @@
+@@ -180,7 +180,7 @@ if test -z "$datatool"; then # keep look
if test -x "$bindir/datatool"; then
datatool=$bindir/datatool
COMMON_AddRunpath "$libdir"
diff --git a/debian/patches/fix_compilation b/debian/patches/fix_compilation
deleted file mode 100644
index f5a8940..0000000
--- a/debian/patches/fix_compilation
+++ /dev/null
@@ -1,32 +0,0 @@
-Subject: Fix compilation error
-Description: error in compilation, bug sent by mail to upstream
-Forwarded: yes
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2014-12-14
---- a/c++/src/util/regexp/pcretest.c
-+++ b/c++/src/util/regexp/pcretest.c
-@@ -250,7 +250,7 @@ for (;;)
- /* Read the next line by normal means, prompting if the file is stdin. */
-
- {
-- if (f == stdin) printf(prompt);
-+ if (f == stdin) printf("%s",prompt);
- if (fgets((char *)here, rlen, f) == NULL)
- return (here == start)? NULL : start;
- }
---- a/c++/include/util/bitset/bmconst.h
-+++ b/c++/include/util/bitset/bmconst.h
-@@ -147,11 +147,11 @@ const unsigned DeBruijn_bit_position<T>:
- */
- template<bool T> struct first_bit_table
- {
-- static const char _idx[256];
-+ static const signed char _idx[256];
- };
-
- template<bool T>
--const char first_bit_table<T>::_idx[256] = {
-+const signed char first_bit_table<T>::_idx[256] = {
- -1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
- 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
- 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
diff --git a/debian/patches/fix_kfreebsd_ftbs.patch b/debian/patches/fix_kfreebsd_ftbs.patch
index 8a82e61..eadc9d2 100644
--- a/debian/patches/fix_kfreebsd_ftbs.patch
+++ b/debian/patches/fix_kfreebsd_ftbs.patch
@@ -5,7 +5,7 @@ Forwarded: yes
Comment: updated upstream at revision 70194
--- a/c++/src/corelib/ncbifile.cpp
+++ b/c++/src/corelib/ncbifile.cpp
-@@ -4423,7 +4423,7 @@
+@@ -4427,7 +4427,7 @@ static const SFileSystem s_FileSystem[]
if (statvfs(path.c_str(), &st) != 0) { \
NCBI_THROW(CFileErrnoException, eFileSystemInfo, msg); \
} \
@@ -14,7 +14,7 @@ Comment: updated upstream at revision 70194
if (st.f_frsize) { \
info->free_space = (Uint8)st.f_frsize * st.f_bavail; \
info->block_size = (unsigned long)st.f_frsize; \
-@@ -4431,7 +4431,7 @@
+@@ -4435,7 +4435,7 @@ static const SFileSystem s_FileSystem[]
info->free_space = (Uint8)st.f_bsize * st.f_bavail; \
info->block_size = (unsigned long)st.f_bsize; \
} \
@@ -23,7 +23,7 @@ Comment: updated upstream at revision 70194
#define GET_STATFS_INFO \
-@@ -4443,7 +4443,7 @@
+@@ -4447,7 +4447,7 @@ static const SFileSystem s_FileSystem[]
info->total_space = (Uint8)st.f_bsize * st.f_blocks; \
info->free_space = (Uint8)st.f_bsize * st.f_bavail; \
info->used_space = info->total_space - info->free_space; \
diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 086900a..7d6ad7c 100644
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -15,7 +15,7 @@ Author: Aaron M. Ucko <ucko at debian.org>
Last-Update: 2014-12-02
--- a/c++/src/algo/blast/Makefile.blast_macros.mk
+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -18,7 +18,7 @@
+@@ -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
@@ -26,7 +26,7 @@ Last-Update: 2014-12-02
# BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
--- a/c++/src/algo/blast/api/Makefile.xblast.lib
+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,14 +74,15 @@
+@@ -74,14 +74,15 @@ cdd_pssm_input \
deltablast_options \
deltablast
@@ -46,7 +46,7 @@ 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
-@@ -24,7 +24,9 @@
+@@ -24,7 +24,9 @@ SRC = $(SRC_CXX)
LIB = blastinput
@@ -59,7 +59,7 @@ 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
-@@ -21,6 +21,7 @@
+@@ -21,6 +21,7 @@ LIB = blast
CFLAGS = $(FAST_CFLAGS)
LDFLAGS = $(FAST_LDFLAGS)
@@ -69,7 +69,7 @@ Last-Update: 2014-12-02
--- 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)
@@ -80,7 +80,7 @@ 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 \
@@ -89,21 +89,9 @@ Last-Update: 2014-12-02
LIB = $(LIB_:%=%$(STATIC))
CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -7,7 +7,8 @@
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
--DLL_LIB = align_format blastxml blastxml2 xhtml xcgi
-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
-+ seq general xser tables xncbi blastxml2
-
- WATCHERS = jianye zaretska madden camacho fongah2
-
--- 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
@@ -114,7 +102,7 @@ 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
@@ -125,7 +113,7 @@ 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)
@@ -136,7 +124,7 @@ Last-Update: 2014-12-02
seqmasks_io
--- a/c++/src/build-system/library_relations.txt
+++ b/c++/src/build-system/library_relations.txt
-@@ -1163,7 +1163,7 @@
+@@ -1268,7 +1268,7 @@ xasmcompare needs $(SEQ_LIBS)
xasmcompare needs pub
xasn needs xhtml
xasn needs3party $(NCBI_C_ncbi)
@@ -147,7 +135,7 @@ 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
@@ -158,7 +146,7 @@ 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
@@ -191,7 +179,7 @@ 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
@@ -200,42 +188,21 @@ Last-Update: 2014-12-02
WATCHERS = ivanov
---- a/c++/src/objects/biblio/Makefile.biblio.lib
-+++ b/c++/src/objects/biblio/Makefile.biblio.lib
-@@ -1,6 +1,8 @@
- LIB = biblio
- SRC = biblio__ biblio___ citation_base
-
-+DLL_LIB = general xser xncbi
-+
-
- USES_LIBRARIES = \
- general
--- a/c++/src/objects/blast/Makefile.blast.lib
+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -1,6 +1,8 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
+@@ -3,6 +3,8 @@ SRC = blast__ blast___ names
+
+ DLL_LIB = seqset scoremat
+DLL_LIB = scoremat seqset seq xser xncbi
+
WATCHERS = camacho
---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -3,6 +3,7 @@
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-
-+DLL_LIB = xnetblast xser xconnect xutil xncbi
-
- USES_LIBRARIES = \
- xconnect xnetblast
--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
@@ -1,5 +1,7 @@
- # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $
+ # $Id: Makefile.blastdb.lib 468761 2015-05-27 20:14:39Z ucko $
+
+DLL_LIB = seq xser xncbi
@@ -253,33 +220,11 @@ Last-Update: 2014-12-02
USES_LIBRARIES = \
xser
---- a/c++/src/objects/general/Makefile.general.lib
-+++ b/c++/src/objects/general/Makefile.general.lib
-@@ -1,6 +1,8 @@
- LIB = general
- SRC = general__ general___ uoconv
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-@@ -3,6 +3,8 @@
- LIB = genome_collection
- SRC = genome_collection__ genome_collection___
-
-+DLL_LIB = seq general xser xncbi
-+
- WATCHERS = dicuccio
-
-
--- a/c++/src/objects/id1/Makefile.id1.lib
+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -3,6 +3,8 @@
- LIB = id1
- SRC = id1__ id1___
+@@ -5,6 +5,8 @@ SRC = id1__ id1___
+
+ DLL_LIB = seqset
+DLL_LIB = seqset seq xser xncbi
+
@@ -297,44 +242,11 @@ Last-Update: 2014-12-02
WATCHERS = vasilche
---- a/c++/src/objects/medline/Makefile.medline.lib
-+++ b/c++/src/objects/medline/Makefile.medline.lib
-@@ -1,6 +1,8 @@
- LIB = medline
- SRC = medline__ medline___
-
-+DLL_LIB = biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- biblio
---- a/c++/src/objects/pub/Makefile.pub.lib
-+++ b/c++/src/objects/pub/Makefile.pub.lib
-@@ -1,6 +1,8 @@
- LIB = pub
- SRC = pub__ pub___
-
-+DLL_LIB = medline biblio xser xncbi
-+
-
- USES_LIBRARIES = \
- medline
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
-@@ -1,6 +1,8 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-
-+DLL_LIB = seqset seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
--- a/c++/src/objects/seq/Makefile.seq.lib
+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,6 +12,8 @@
- seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
- seq_loc_from_string seq_loc_reverse_complementer
+@@ -14,6 +14,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport
+
+ DLL_LIB = seqcode pub general xser sequtil
+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
+
@@ -398,7 +310,7 @@ 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)
@@ -409,9 +321,9 @@ Last-Update: 2014-12-02
--- a/c++/src/objmgr/util/Makefile.util.lib
+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -8,6 +8,8 @@
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
- LIB = xobjutil
+@@ -11,6 +11,8 @@ LIB = xobjutil
+
+ DLL_LIB = $(SOBJMGR_LIBS)
+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
+
@@ -420,7 +332,7 @@ 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)
@@ -433,7 +345,7 @@ Last-Update: 2014-12-02
# CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -12,7 +12,7 @@
+@@ -14,7 +14,7 @@ DLL_LIB = tables
WATCHERS = todorov dicuccio grichenk
@@ -444,7 +356,7 @@ 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)
@@ -454,9 +366,9 @@ 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
-@@ -24,6 +24,8 @@
-
+@@ -25,6 +25,8 @@ seqdbobj
LIB = seqdb
+ DLL_LIB = blastdb $(SOBJMGR_LIBS)
+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
+
@@ -465,7 +377,7 @@ 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
@@ -477,9 +389,9 @@ 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
-@@ -8,6 +8,8 @@
+@@ -10,6 +10,8 @@ LIB = blast_services
- LIB = blast_services
+ DLL_LIB = xnetblastcli xnetblast
+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
+
@@ -488,7 +400,7 @@ Last-Update: 2014-12-02
CXXFLAGS = $(FAST_CXXFLAGS)
--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -7,6 +7,8 @@
+@@ -9,6 +9,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_
ASN_DEP = blastdb seqset
@@ -499,7 +411,7 @@ 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
-@@ -5,6 +5,8 @@
+@@ -7,6 +7,8 @@ DLL_LIB = blast_services
CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
@@ -510,7 +422,7 @@ Last-Update: 2014-12-02
WATCHERS = camacho
--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,9 @@
+@@ -12,6 +12,9 @@ LIB_OR_DLL = both
# Dependencies for shared library
DLL_LIB = ncbi_xreader$(DLL)
@@ -522,9 +434,9 @@ 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
-@@ -15,6 +15,9 @@
- DLL_LIB =
- DLL_DLIB = $(GENBANK_READER_LDEP)
+@@ -14,6 +14,9 @@ LIB_OR_DLL = both
+ # Dependencies for shared library
+ DLL_LIB = $(GENBANK_READER_LDEP)
+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
+ xser xconnect xcompress xutil xncbi
@@ -534,7 +446,7 @@ Last-Update: 2014-12-02
--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-@@ -12,6 +12,8 @@
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
# Dependencies for shared library
DLL_LIB = ncbi_xreader$(DLL)
@@ -545,7 +457,7 @@ 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)
@@ -556,7 +468,7 @@ 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)
@@ -568,20 +480,9 @@ Last-Update: 2014-12-02
WATCHERS = vasilche
---- a/c++/src/objtools/readers/Makefile.xobjread.lib
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -21,7 +21,7 @@
- message_listener line_error
-
-
--DLL_LIB = creaders
-+DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi
-
-
-
--- 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
@@ -592,7 +493,7 @@ 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
@@ -603,9 +504,9 @@ Last-Update: 2014-12-02
--- a/c++/src/serial/Makefile.serial.lib
+++ b/c++/src/serial/Makefile.serial.lib
-@@ -18,6 +18,8 @@
+@@ -20,6 +20,8 @@ LIB = xser
- LIB = xser
+ DLL_LIB = xutil
+DLL_LIB = xutil xncbi
+
@@ -614,7 +515,7 @@ 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
@@ -624,7 +525,7 @@ Last-Update: 2014-12-02
WATCHERS = vakatov kornbluh
--- 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)
@@ -633,6 +534,29 @@ Last-Update: 2014-12-02
LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)
WATCHERS = ivanov
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib
++++ b/c++/src/util/xregexp/Makefile.xregexp.lib
+@@ -5,7 +5,7 @@ LIB = xregexp
+
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
+
+-DLL_LIB = $(PCRE_LIB)
++DLL_LIB = $(PCRE_LIB) xncbi
+ LIBS = $(PCRE_LIBS)
+
+ USES_LIBRARIES = \
+--- a/c++/src/objtools/readers/Makefile.xobjread.lib
++++ b/c++/src/objtools/readers/Makefile.xobjread.lib
+@@ -20,8 +20,7 @@ SRC = read_util format_guess_ex \
+ ucscregion_reader \
+ message_listener line_error
+
+-
+-DLL_LIB = submit seqset $(SEQ_LIBS) general creaders xutil
++DLL_LIB = submit seqset $(SEQ_LIBS) general creaders xutil pub xser xncbi
+
+
+
--- a/c++/src/util/sequtil/Makefile.sequtil.lib
+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
@@ -3,6 +3,8 @@
@@ -641,17 +565,50 @@ Last-Update: 2014-12-02
+DLL_LIB = xncbi
+
- WATCHERS = shomrat
+ WATCHERS = grichenk ucko
---- a/c++/src/util/xregexp/Makefile.xregexp.lib
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -6,7 +6,7 @@
+--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
++++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+@@ -3,6 +3,8 @@
+ LIB = genome_collection
+ SRC = genome_collection__ genome_collection___
- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
++DLL_LIB = seq general xser xncbi
++
+ WATCHERS = dicuccio shchekot
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
- LIBS = $(PCRE_LIBS)
- WATCHERS = ivanov
+--- a/c++/src/objects/medline/Makefile.medline.lib
++++ b/c++/src/objects/medline/Makefile.medline.lib
+@@ -1,7 +1,7 @@
+ LIB = medline
+ SRC = medline__ medline___
+
+-DLL_LIB = biblio general
++DLL_LIB = biblio general xser xncbi
+
+ USES_LIBRARIES = \
+ biblio
+--- a/c++/src/objects/scoremat/Makefile.scoremat.lib
++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
+@@ -1,7 +1,7 @@
+ LIB = scoremat
+ SRC = scoremat__ scoremat___
+
+-DLL_LIB = seqset
++DLL_LIB = seqset seq general xser xncbi
+
+ USES_LIBRARIES = \
+ seqset
+--- a/c++/src/objects/pub/Makefile.pub.lib
++++ b/c++/src/objects/pub/Makefile.pub.lib
+@@ -1,7 +1,7 @@
+ LIB = pub
+ SRC = pub__ pub___
+
+-DLL_LIB = medline biblio
++DLL_LIB = medline biblio xser xncbi
+
+ USES_LIBRARIES = \
+ medline
diff --git a/debian/patches/legacy_rename_rpsblast b/debian/patches/legacy_rename_rpsblast
index f40204b..5b23961 100644
--- a/debian/patches/legacy_rename_rpsblast
+++ b/debian/patches/legacy_rename_rpsblast
@@ -3,7 +3,7 @@ Description: rename binary as blast+ for package coherency.
Last-Updated: 2011-10-03
--- a/c++/src/app/blast/legacy_blast.pl
+++ b/c++/src/app/blast/legacy_blast.pl
-@@ -1064,7 +1064,7 @@
+@@ -1064,7 +1064,7 @@ sub handle_rpsblast
if (defined $opt_p and $opt_p =~ /f/i) {
$retval .= "/rpstblastn";
} else {
diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 169cc2f..94c158e 100644
--- a/debian/patches/no_multiarch_rpath
+++ b/debian/patches/no_multiarch_rpath
@@ -10,7 +10,7 @@ Author: Aaron M. Ucko <ucko at debian.org>
Last-Update: 2011-08-28
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -7480,7 +7480,7 @@
+@@ -7758,7 +7758,7 @@ echo "$as_me: WARNING: Unable to find st
break
;;
/* )
@@ -21,7 +21,7 @@ Last-Update: 2011-08-28
esac
--- a/c++/src/build-system/configure.ac
+++ b/c++/src/build-system/configure.ac
-@@ -1837,7 +1837,7 @@
+@@ -1951,7 +1951,7 @@ case "$compiler:$compiler_version:$with_
break
;;
/* )
diff --git a/debian/patches/series b/debian/patches/series
index f60154b..11e1ab3 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,6 +6,4 @@ no_multiarch_rpath
use_pie_for_apps
skip_services_unit_test
fix_configure
-fix_compilation
-allow_gcc5
fix_kfreebsd_ftbs.patch
diff --git a/debian/patches/skip_services_unit_test b/debian/patches/skip_services_unit_test
index d23a164..a4d0323 100644
--- a/debian/patches/skip_services_unit_test
+++ b/debian/patches/skip_services_unit_test
@@ -5,7 +5,7 @@ Description: test require internet connection
Last-Updated: 2013-06-01
--- a/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
+++ b/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
-@@ -11,6 +11,7 @@
+@@ -11,6 +11,7 @@ LIB = test_boost blast_services xnetblas
LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS)
diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps
index 1900f33..15dc190 100644
--- a/debian/patches/use_pie_for_apps
+++ b/debian/patches/use_pie_for_apps
@@ -7,7 +7,7 @@ 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 @@
+@@ -24,8 +24,8 @@ default_rule: all
### C/C++ source file compilation setup
@@ -18,12 +18,12 @@ Last-Update: 2012-05-10
SOURCES = @UNIX_SRC@ $(SRC)
### Standard application build rules
-@@ -133,7 +133,7 @@
- else
- $(XAPP): $(XOBJ) $(XOBJ2) $(XLIBDEP)
- @-$(RM) .$(XAPP).stamp
-- $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
-+ $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
- $(STRIP) $(XAPP)
- $(POST_LINK) $(XAPP)
- ifneq "$(BINCOPY)" "@:"
+@@ -52,7 +52,7 @@ ifneq "" "$(wildcard Makefile.$(TMPL).ap
+ endif
+ endif
+
+-CMD_BASE = $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS)
++CMD_BASE = $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS)
+ CMD_TAIL = @f_outexe@$(XAPP) $(LINK_FILTER)
+ CMD = $(CMD_BASE) $(XLIB) $(XAPP_LIBS) $(CMD_TAIL)
+ CMD2 = $(CMD_BASE) $(XLIB2) $(XAPP_LIBS2) $(CMD_TAIL)
--
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