From 34f0f43e33d1ac2b2efbb5548e43d804daa68cbe Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Wed, 3 Aug 2016 18:58:57 -0400 Subject: [PATCH] Refresh patches; drop fix_kfreebsd_ftbs.patch (applied upstream). --- debian/changelog | 7 ++++++ debian/patches/fix_kfreebsd_ftbs.patch | 34 -------------------------- debian/patches/fix_lib_deps | 22 ++++++++--------- debian/patches/no_multiarch_rpath | 4 +-- debian/patches/series | 1 - debian/patches/use_pie_for_apps | 2 +- 6 files changed, 21 insertions(+), 49 deletions(-) delete mode 100644 debian/patches/fix_kfreebsd_ftbs.patch diff --git a/debian/changelog b/debian/changelog index 05d47462..e74d1fdf 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +ncbi-blast+ (2.4.0-1) UNRELEASED; urgency=medium + + * New upstream release. (NOT RELEASED YET.) + * Refresh patches; drop fix_kfreebsd_ftbs.patch (applied upstream). + + -- Aaron M. Ucko Wed, 03 Aug 2016 18:58:57 -0400 + ncbi-blast+ (2.3.0-2) unstable; urgency=medium * Team upload. diff --git a/debian/patches/fix_kfreebsd_ftbs.patch b/debian/patches/fix_kfreebsd_ftbs.patch deleted file mode 100644 index eadc9d23..00000000 --- a/debian/patches/fix_kfreebsd_ftbs.patch +++ /dev/null @@ -1,34 +0,0 @@ -Subject: Fix missing colon -Description: colon missing causing FTBS on some archs -Author: Olivier Sallou -Forwarded: yes -Comment: updated upstream at revision 70194 ---- a/c++/src/corelib/ncbifile.cpp -+++ b/c++/src/corelib/ncbifile.cpp -@@ -4427,7 +4427,7 @@ static const SFileSystem s_FileSystem[] - if (statvfs(path.c_str(), &st) != 0) { \ - NCBI_THROW(CFileErrnoException, eFileSystemInfo, msg); \ - } \ -- info->total_space = (Uint8)st.f_bsize * st.f_blocks \ -+ info->total_space = (Uint8)st.f_bsize * st.f_blocks; \ - if (st.f_frsize) { \ - info->free_space = (Uint8)st.f_frsize * st.f_bavail; \ - info->block_size = (unsigned long)st.f_frsize; \ -@@ -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; \ - } \ -- info->used_space = info->total_space - info->free_space -+ info->used_space = info->total_space - info->free_space; - - - #define GET_STATFS_INFO \ -@@ -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; \ -- info->block_size = (unsigned long)st.f_bsize -+ info->block_size = (unsigned long)st.f_bsize; - - - diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index 7d6ad7c5..3b17332a 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -59,14 +59,14 @@ 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 @@ LIB = blast - CFLAGS = $(FAST_CFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = composition_adjustment xconnect tables +@@ -23,6 +23,7 @@ LDFLAGS = $(FAST_LDFLAGS) WATCHERS = madden camacho fongah2 ++DLL_LIB = composition_adjustment xconnect tables + + USES_LIBRARIES = \ + 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 @@ SRC = sequence_istream_fasta \ @@ -124,10 +124,10 @@ Last-Update: 2014-12-02 seqmasks_io --- a/c++/src/build-system/library_relations.txt +++ b/c++/src/build-system/library_relations.txt -@@ -1268,7 +1268,7 @@ xasmcompare needs $(SEQ_LIBS) - xasmcompare needs pub - xasn needs xhtml - xasn needs3party $(NCBI_C_ncbi) +@@ -1331,7 +1331,7 @@ xbiosample_util needs $(OBJEDIT_LIBS) + xbiosample_util needs $(XFORMAT_LIBS) + xbiosample_util needs xalnmgr + xbiosample_util needs xmlwrapp -xblast includes blast +xblast needs blast xblast needs xalgoblastdbindex @@ -154,7 +154,7 @@ Last-Update: 2014-12-02 + LIBS = $(NETWORK_LIBS) $(ORIG_LIBS) - WATCHERS = lavr + WATCHERS = lavr elisovdn --- a/c++/src/corelib/Makefile.test_boost.lib +++ b/c++/src/corelib/Makefile.test_boost.lib @@ -3,6 +3,8 @@ @@ -576,7 +576,7 @@ Last-Update: 2014-12-02 +DLL_LIB = seq general xser xncbi + - WATCHERS = dicuccio shchekot + WATCHERS = dicuccio shchekot zherikov --- a/c++/src/objects/medline/Makefile.medline.lib diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath index 94c158ef..70543bb9 100644 --- a/debian/patches/no_multiarch_rpath +++ b/debian/patches/no_multiarch_rpath @@ -10,7 +10,7 @@ Author: Aaron M. Ucko Last-Update: 2011-08-28 --- a/c++/src/build-system/configure +++ b/c++/src/build-system/configure -@@ -7758,7 +7758,7 @@ echo "$as_me: WARNING: Unable to find st +@@ -9107,7 +9107,7 @@ echo "$as_me: WARNING: Unable to find st break ;; /* ) @@ -21,7 +21,7 @@ Last-Update: 2011-08-28 esac --- a/c++/src/build-system/configure.ac +++ b/c++/src/build-system/configure.ac -@@ -1951,7 +1951,7 @@ case "$compiler:$compiler_version:$with_ +@@ -1961,7 +1961,7 @@ case "$compiler:$compiler_version:$with_ break ;; /* ) diff --git a/debian/patches/series b/debian/patches/series index 11e1ab38..40551826 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -6,4 +6,3 @@ no_multiarch_rpath use_pie_for_apps skip_services_unit_test fix_configure -fix_kfreebsd_ftbs.patch diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps index 15dc1906..b43c7b4f 100644 --- a/debian/patches/use_pie_for_apps +++ b/debian/patches/use_pie_for_apps @@ -18,7 +18,7 @@ Last-Update: 2012-05-10 SOURCES = @UNIX_SRC@ $(SRC) ### Standard application build rules -@@ -52,7 +52,7 @@ ifneq "" "$(wildcard Makefile.$(TMPL).ap +@@ -53,7 +53,7 @@ ifneq "" "$(wildcard Makefile.$(TMPL).ap endif endif -- 2.30.2