[med-svn] r12632 - in trunk/packages/ffindex/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Sun Dec 16 15:01:25 UTC 2012
Author: lkajan-guest
Date: 2012-12-16 15:01:25 +0000 (Sun, 16 Dec 2012)
New Revision: 12632
Modified:
trunk/packages/ffindex/trunk/debian/changelog
trunk/packages/ffindex/trunk/debian/libffindex0.lintian-overrides
trunk/packages/ffindex/trunk/debian/libffindex0.symbols
trunk/packages/ffindex/trunk/debian/patches/Makefile
trunk/packages/ffindex/trunk/debian/patches/basename
Log:
New upstream release: 0.9.9
Modified: trunk/packages/ffindex/trunk/debian/changelog
===================================================================
--- trunk/packages/ffindex/trunk/debian/changelog 2012-12-15 22:05:46 UTC (rev 12631)
+++ trunk/packages/ffindex/trunk/debian/changelog 2012-12-16 15:01:25 UTC (rev 12632)
@@ -1,3 +1,9 @@
+ffindex (0.9.9-1) UNRELEASED; urgency=low
+
+ * New upstream release
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sun, 16 Dec 2012 14:47:49 +0100
+
ffindex (0.9.8-1) unstable; urgency=low
* New upstream release.
Modified: trunk/packages/ffindex/trunk/debian/libffindex0.lintian-overrides
===================================================================
--- trunk/packages/ffindex/trunk/debian/libffindex0.lintian-overrides 2012-12-15 22:05:46 UTC (rev 12631)
+++ trunk/packages/ffindex/trunk/debian/libffindex0.lintian-overrides 2012-12-16 15:01:25 UTC (rev 12632)
@@ -1 +1 @@
-libffindex0: shlib-with-executable-stack usr/lib/libffindex.so.0.1.0
+libffindex0: shlib-with-executable-stack usr/lib/libffindex.so.1.0.1
Modified: trunk/packages/ffindex/trunk/debian/libffindex0.symbols
===================================================================
--- trunk/packages/ffindex/trunk/debian/libffindex0.symbols 2012-12-15 22:05:46 UTC (rev 12631)
+++ trunk/packages/ffindex/trunk/debian/libffindex0.symbols 2012-12-16 15:01:25 UTC (rev 12632)
@@ -10,6 +10,7 @@
ffindex_get_data_by_name at Base 0.9.8
ffindex_get_data_by_offset at Base 0.9.8
ffindex_get_entry_by_index at Base 0.9.8
+ ffindex_get_entry_by_name at Base 0.9.9
ffindex_index_as_tree at Base 0.9.8
ffindex_index_parse at Base 0.9.8
ffindex_insert_dir at Base 0.9.8
Modified: trunk/packages/ffindex/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/Makefile 2012-12-15 22:05:46 UTC (rev 12631)
+++ trunk/packages/ffindex/trunk/debian/patches/Makefile 2012-12-16 15:01:25 UTC (rev 12632)
@@ -9,7 +9,7 @@
--- a/src/Makefile
+++ b/src/Makefile
-@@ -1,15 +1,16 @@
+@@ -1,15 +1,18 @@
-INSTALL_DIR?=..
-libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
+PREFIX?=/usr
@@ -21,8 +21,10 @@
+CC=gcc
CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic
-LDFLAGS=-lffindex -L.
-+SOCURRENT=0
-+SOVERSION=$(SOCURRENT).1.0
++SOCURRENT=1
++SOAGE=1
++SOVERSION=$(SOCURRENT).0.$(SOAGE)
++SOMAJORV=$(shell echo $(SOCURRENT)-$(SOAGE) | bc)
ifdef FFINDEX_STATIC
LDFLAGS+=-static
FFINDEX_OBJECTS=libffindex.a
@@ -32,19 +34,19 @@
endif
#-Wl,--version-script=libffindex.map
-@@ -47,16 +48,17 @@
+@@ -47,16 +50,17 @@
ffindex_unpack: $(FFINDEX_OBJECTS) ffindex_unpack.o ffindex.h
$(CC) -o $@ ffindex_unpack.o $(LDFLAGS) -L. -lffindex
-libffindex.so.0.1: ffindex.o ffutil.o
- $(CC) -Wl,-z,defs -shared -Wl,-soname,libffindex.so.0.1 -o libffindex.so.0.1 ffindex.o ffutil.o -lc
+libffindex.so.$(SOVERSION): ffindex.o ffutil.o
-+ $(CC) $(LDFLAGS) -Wl,-z,defstack -shared -Wl,-soname,libffindex.so.$(SOCURRENT) -o libffindex.so.$(SOVERSION) ffindex.o ffutil.o -lc
++ $(CC) $(LDFLAGS) -Wl,-z,defstack -shared -Wl,-soname,libffindex.so.$(SOMAJORV) -o libffindex.so.$(SOVERSION) ffindex.o ffutil.o -lc
-libffindex.so: libffindex.so.0.1
- ln -sf libffindex.so.0.1 libffindex.so
+libffindex.so: libffindex.so.$(SOVERSION)
-+ ln -sf libffindex.so.$(SOVERSION) libffindex.so.$(SOCURRENT)
++ ln -sf libffindex.so.$(SOVERSION) libffindex.so.$(SOMAJORV)
+ ln -sf libffindex.so.$(SOVERSION) libffindex.so
libffindex.a: ffindex.o ffutil.o
@@ -55,13 +57,13 @@
rm -f /tmp/test.data /tmp/test.ffindex
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_get /tmp/test.data /tmp/test.ffindex a b foo | tee /tmp/test.out
-@@ -76,8 +78,11 @@
+@@ -76,8 +80,11 @@
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" zsh -c "time ./ffindex_get ../test_big/nr20_11Jan10_a3m_db ../test_big/nr20_11Jan10_a3m_db.ffindex BABBAMIBA.a3m KARDUZEBA.a3m HARPAQIBA.a3m WOQQATEBA.a3m BEBRAQIBA.a3m GIRSAKEBA.a3m NAQTIFIBA.a3m BIWCIQABA.a3m > /dev/null"
clean:
- rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.0.1 ffindex_modify ffindex_modify.o \
- libffindex.a ffindex_from_fasta.o ffindex_from_fasta ffindex_apply_mpi.o ffindex_apply.o
-+ rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.$(SOCURRENT) libffindex.so.$(SOVERSION) ffindex_modify ffindex_modify.o \
++ rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.$(SOMAJORV) libffindex.so.$(SOVERSION) ffindex_modify ffindex_modify.o \
+ libffindex.a ffindex_from_fasta.o ffindex_from_fasta ffindex_apply_mpi.o ffindex_apply.o \
+ $(OBJECTS) $(OBJECTS:%=%.o)
+
@@ -69,7 +71,7 @@
install:
mkdir -p $(INSTALL_DIR)/bin
-@@ -89,9 +94,10 @@
+@@ -89,9 +96,10 @@
install ffindex_from_fasta $(INSTALL_DIR)/bin/ffindex_from_fasta
install ffindex_apply $(INSTALL_DIR)/bin/ffindex_apply
install ffindex_unpack $(INSTALL_DIR)/bin/ffindex_unpack
@@ -77,7 +79,7 @@
+ install libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION)
install libffindex.a $(INSTALL_DIR)/$(libdir)/libffindex.a
- ln -sf libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so
-+ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOCURRENT)
++ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOMAJORV)
+ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so
install ffindex.h $(INSTALL_DIR)/include/ffindex.h
install ffutil.h $(INSTALL_DIR)/include/ffutil.h
Modified: trunk/packages/ffindex/trunk/debian/patches/basename
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/basename 2012-12-15 22:05:46 UTC (rev 12631)
+++ trunk/packages/ffindex/trunk/debian/patches/basename 2012-12-16 15:01:25 UTC (rev 12632)
@@ -119,7 +119,7 @@
char *data_filename = argv[1];
--- a/src/ffindex.c
+++ b/src/ffindex.c
-@@ -223,7 +223,7 @@
+@@ -227,7 +227,7 @@
ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries)
{
if(num_max_entries == 0)
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