Adapt patches to new upstream version (please verify!)

diff --git a/debian/patches/allow_gcc5 b/debian/patches/allow_gcc5
deleted file mode 100644 (file)
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@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 75434fb848fb3254792d43073e0e329704bf720c..e57f4923d84615bc4a4da09863733d6c75248fbb 100644 (file)
--- 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 (file)
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@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 8a82e614e65eb6a4806ab70a4ad4b84bfccf70a7..eadc9d23c4ec00cc1940d677834e4b76d5320db9 100644 (file)
--- 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 086900a80e01e0a9c1104ea6890104ca10f765e6..7d6ad7c54a81271fce2356357ec217637eaf4d60 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -15,7 +15,7 @@ Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2014-12-02\r
 --- 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 f40204b183e760b48aa5c4d84c6d11d7219efaaf..5b23961373e047c6742e846a5962371c9aeafb57 100644 (file)
--- 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 169cc2fe85174e4d8adac4d32037b165a14a6fe8..94c158ef786a88e1f6d5d1bf56b139a27d103276 100644 (file)
--- a/debian/patches/no_multiarch_rpath
+++ b/debian/patches/no_multiarch_rpath
@@ -10,7 +10,7 @@ Author: Aaron M. Ucko <ucko@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 f60154b67cb24d89a9c18fb33b6d961c6e821554..11e1ab388f6a2efa436f997b77e505b302f8579b 100644 (file)
--- 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 d23a16438b540c5728e13252e74c384e53407799..a4d03234077f36464f532361c86c42041238a337 100644 (file)
--- 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 1900f33539e41afd658182d9088a11761dcca238..15dc1906edcb4eadb5f7485f239374a41d2f9241 100644 (file)
--- a/debian/patches/use_pie_for_apps
+++ b/debian/patches/use_pie_for_apps
@@ -7,7 +7,7 @@ Author: Aaron M. Ucko <ucko@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)