[med-svn] [ncbi-blast+] 02/08: Refresh patches; drop fix_kfreebsd_ftbs.patch (applied upstream).
Aaron M. Ucko
ucko at moszumanska.debian.org
Thu Aug 4 02:29:36 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 34f0f43e33d1ac2b2efbb5548e43d804daa68cbe
Author: Aaron M. Ucko <ucko at debian.org>
Date: Wed Aug 3 18:58:57 2016 -0400
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(-)
diff --git a/debian/changelog b/debian/changelog
index 05d4746..e74d1fd 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 <ucko at debian.org> 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 eadc9d2..0000000
--- 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 <olivier.sallou at irisa.fr>
-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 7d6ad7c..3b17332 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) $(ORIG_LIBS)
- WATCHERS = lavr
+ WATCHERS = lavr elisovdn
--- a/c++/src/corelib/Makefile.test_boost.lib
+++ b/c++/src/corelib/Makefile.test_boost.lib
@@ -3,6 +3,8 @@
@@ -576,7 +576,7 @@ Last-Update: 2014-12-02
+DLL_LIB = seq general xser xncbi
+
- WATCHERS = dicuccio shchekot
+ WATCHERS = dicuccio shchekot zherikov
--- a/c++/src/objects/medline/Makefile.medline.lib
diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 94c158e..70543bb 100644
--- a/debian/patches/no_multiarch_rpath
+++ b/debian/patches/no_multiarch_rpath
@@ -10,7 +10,7 @@ Author: Aaron M. Ucko <ucko at debian.org>
Last-Update: 2011-08-28
--- a/c++/src/build-system/configure
+++ b/c++/src/build-system/configure
-@@ -7758,7 +7758,7 @@ echo "$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 11e1ab3..4055182 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 15dc190..b43c7b4 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
--
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