[med-svn] r13602 - in trunk/packages/ffindex/tags: . 0.9.9.1-1/debian 0.9.9.1-1/debian/patches
Laszlo Kajan
lkajan at alioth.debian.org
Thu May 16 13:41:55 UTC 2013
Author: lkajan
Date: 2013-05-16 13:41:55 +0000 (Thu, 16 May 2013)
New Revision: 13602
Added:
trunk/packages/ffindex/tags/0.9.9.1-1/
trunk/packages/ffindex/tags/0.9.9.1-1/debian/changelog
trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/Makefile
trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/basename
trunk/packages/ffindex/tags/0.9.9.1-1/debian/rules
Removed:
trunk/packages/ffindex/tags/0.9.9.1-1/debian/changelog
trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/Makefile
trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/basename
trunk/packages/ffindex/tags/0.9.9.1-1/debian/rules
Log:
[svn-buildpackage] Tagging ffindex 0.9.9.1-1
Deleted: trunk/packages/ffindex/tags/0.9.9.1-1/debian/changelog
===================================================================
--- trunk/packages/ffindex/trunk/debian/changelog 2013-05-16 13:12:23 UTC (rev 13599)
+++ trunk/packages/ffindex/tags/0.9.9.1-1/debian/changelog 2013-05-16 13:41:55 UTC (rev 13602)
@@ -1,38 +0,0 @@
-ffindex (0.9.9-2) unstable; urgency=low
-
- * Fixed 'bc' not found issue in d/rules (Closes: #696285).
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 19 Dec 2012 00:39:51 +0100
-
-ffindex (0.9.9-1) unstable; 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.
- * Added symbols control file.
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 27 Jun 2012 15:27:47 +0200
-
-ffindex (0.9.6.1-1) unstable; urgency=low
-
- * New upstream release.
- * Fixed many bugs.
-
- -- Laszlo Kajan <lkajan at rostlab.org> Tue, 26 Jun 2012 11:43:41 +0200
-
-ffindex (0.9.3-2) unstable; urgency=low
-
- * Included full text of CC-BY-SA-3.0 license (Closes: #667698)
-
- -- Laszlo Kajan <lkajan at rostlab.org> Mon, 23 Apr 2012 11:30:03 +0200
-
-ffindex (0.9.3-1) unstable; urgency=low
-
- * Initial release (Closes: #661111)
-
- -- Laszlo Kajan <lkajan at rostlab.org> Fri, 24 Feb 2012 10:38:57 +0100
-
Copied: trunk/packages/ffindex/tags/0.9.9.1-1/debian/changelog (from rev 13600, trunk/packages/ffindex/trunk/debian/changelog)
===================================================================
--- trunk/packages/ffindex/tags/0.9.9.1-1/debian/changelog (rev 0)
+++ trunk/packages/ffindex/tags/0.9.9.1-1/debian/changelog 2013-05-16 13:41:55 UTC (rev 13602)
@@ -0,0 +1,44 @@
+ffindex (0.9.9.1-1) unstable; urgency=low
+
+ * New upstream release. Shared library sources did not change.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 16 May 2013 14:40:05 +0200
+
+ffindex (0.9.9-2) unstable; urgency=low
+
+ * Fixed 'bc' not found issue in d/rules (Closes: #696285).
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 19 Dec 2012 00:39:51 +0100
+
+ffindex (0.9.9-1) unstable; 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.
+ * Added symbols control file.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 27 Jun 2012 15:27:47 +0200
+
+ffindex (0.9.6.1-1) unstable; urgency=low
+
+ * New upstream release.
+ * Fixed many bugs.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 26 Jun 2012 11:43:41 +0200
+
+ffindex (0.9.3-2) unstable; urgency=low
+
+ * Included full text of CC-BY-SA-3.0 license (Closes: #667698)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 23 Apr 2012 11:30:03 +0200
+
+ffindex (0.9.3-1) unstable; urgency=low
+
+ * Initial release (Closes: #661111)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Fri, 24 Feb 2012 10:38:57 +0100
+
Deleted: trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/Makefile
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/Makefile 2013-05-16 13:12:23 UTC (rev 13599)
+++ trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/Makefile 2013-05-16 13:41:55 UTC (rev 13602)
@@ -1,86 +0,0 @@
-From: Laszlo Kajan <lkajan at rostlab.org>
-Subject: Makefile fixes
- * make Makefile DESTDIR-aware
- * other changes to allow help2man to work better.
- * deinstall -> uninstall
- .
- Upstream is aware but not interested in DESTDIR.
-Forwarded: yes
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -1,15 +1,18 @@
--INSTALL_DIR?=..
--libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
-+PREFIX?=/usr
-+INSTALL_DIR=$(DESTDIR)$(PREFIX)
-+libdir=lib
- LANG=C
--CC=gcc -fopenmp
--#CC=icc -openmp
-+CC=gcc
- CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic
--LDFLAGS=-lffindex -L.
-+SOCURRENT=1
-+SOAGE=1
-+SOVERSION=$(SOCURRENT).0.$(SOAGE)
-+SOMAJORV=$(shell echo $$(( $(SOCURRENT)-$(SOAGE) )) )
- ifdef FFINDEX_STATIC
- LDFLAGS+=-static
- FFINDEX_OBJECTS=libffindex.a
- else
-- FFINDEX_OBJECTS=libffindex.so libffindex.so.0.1
-+ FFINDEX_OBJECTS=libffindex.so libffindex.so.$(SOVERSION)
- endif
-
- #-Wl,--version-script=libffindex.map
-@@ -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.$(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.$(SOMAJORV)
-+ ln -sf libffindex.so.$(SOVERSION) libffindex.so
-
- libffindex.a: ffindex.o ffutil.o
- ar rcs libffindex.a ffutil.o ffindex.o
-
--test:
-+check:
- 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 +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.$(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)
-+
-+distclean: clean
-
- install:
- mkdir -p $(INSTALL_DIR)/bin
-@@ -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
-- install libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1
-+ 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.$(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
- ifdef HAVE_MPI
Copied: trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/Makefile (from rev 13601, trunk/packages/ffindex/trunk/debian/patches/Makefile)
===================================================================
--- trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/Makefile (rev 0)
+++ trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/Makefile 2013-05-16 13:41:55 UTC (rev 13602)
@@ -0,0 +1,86 @@
+From: Laszlo Kajan <lkajan at rostlab.org>
+Subject: Makefile fixes
+ * make Makefile DESTDIR-aware
+ * other changes to allow help2man to work better.
+ * deinstall -> uninstall
+ .
+ Upstream is aware but not interested in DESTDIR.
+Forwarded: yes
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,15 +1,18 @@
+-INSTALL_DIR?=..
+-libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
++PREFIX?=/usr
++INSTALL_DIR=$(DESTDIR)$(PREFIX)
++libdir=lib
+ LANG=C
+-CC=gcc -fopenmp
+-#CC=icc -openmp
++CC=gcc
+ CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic
+-LDFLAGS=-lffindex -L.
++SOCURRENT=1
++SOAGE=1
++SOVERSION=$(SOCURRENT).0.$(SOAGE)
++SOMAJORV=$(shell echo $$(( $(SOCURRENT)-$(SOAGE) )) )
+ ifdef FFINDEX_STATIC
+ LDFLAGS+=-static
+ FFINDEX_OBJECTS=libffindex.a
+ else
+- FFINDEX_OBJECTS=libffindex.so libffindex.so.0.1
++ FFINDEX_OBJECTS=libffindex.so libffindex.so.$(SOVERSION)
+ endif
+
+ #-Wl,--version-script=libffindex.map
+@@ -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) $(LDFLAGS) -Wl,-z,defstack -shared -Wl,-soname,libffindex.so.$(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.$(SOVERSION) libffindex.so.$(SOMAJORV)
++ ln -sf libffindex.so.$(SOVERSION) libffindex.so
+
+ libffindex.a: ffindex.o ffutil.o
+ ar rcs libffindex.a ffutil.o ffindex.o
+
+-test:
++check:
+ rm -f /tmp/test.data /tmp/test.ffindex
+ LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
+ LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_get /tmp/test.data /tmp/test.ffindex a b foo | tee /tmp/test.out
+@@ -76,8 +80,11 @@
+ LD_LIBRARY_PATH=".:$(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.$(SOMAJORV)* libffindex.so.$(SOCURRENT)* ffindex_modify ffindex_modify.o \
++ libffindex.a ffindex_from_fasta.o ffindex_from_fasta ffindex_apply_mpi.o ffindex_apply.o \
++ $(OBJECTS) $(OBJECTS:%=%.o)
++
++distclean: clean
+
+ install:
+ mkdir -p $(INSTALL_DIR)/bin
+@@ -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
+- install libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1
++ 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.$(SOMAJORV)
++ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so
+ install ffindex.h $(INSTALL_DIR)/include/ffindex.h
+ install ffutil.h $(INSTALL_DIR)/include/ffutil.h
+ ifdef HAVE_MPI
Deleted: trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/basename
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/basename 2013-05-16 13:12:23 UTC (rev 13599)
+++ trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/basename 2013-05-16 13:41:55 UTC (rev 13602)
@@ -1,150 +0,0 @@
-Author: Laszlo Kajan <lkajan at rostlab.org>
-Author: Elso Andras <elso.andras at gmail.com>
-Subject: 40000000 bug and basename
- [Laszlo Kajan]
- The default value 40000000 for FFINDEX_MAX_INDEX_ENTRIES_DEFAULT is too high for a machine with 2G (or less) RAM.
- Bug fixed by introducing an environment variable FFINDEX_MAX_INDEX_ENTRIES to control the value.
- [Elso Andras]
- using basename for usage print, this helps help2man if a packager is using it
-Forwarded: yes
-
---- a/src/ffindex_apply.c
-+++ b/src/ffindex_apply.c
-@@ -34,8 +34,10 @@
- if(argn < 4)
- {
- fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME PROGRAM [PROGRAM_ARGS]*\n"
-+ "ENVIRONMENT\n"
-+ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
- "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
-- argv[0]);
-+ basename(argv[0]));
- return -1;
- }
- char *data_filename = argv[1];
---- a/src/ffindex_apply_mpi.c
-+++ b/src/ffindex_apply_mpi.c
-@@ -186,7 +186,7 @@
- fprintf(stderr, "Not enough arguments %d.\n", optind - argn);
- fprintf(stderr, "USAGE: %s -d DATA_FILENAME_OUT -i INDEX_FILENAME_OUT DATA_FILENAME INDEX_FILENAME -- PROGRAM [PROGRAM_ARGS]*\n"
- "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
-- argv[0]);
-+ basename(argv[0]));
- return -1;
- }
- read_buffer = malloc(400 * 1024 * 1024);
---- a/src/ffindex_build.c
-+++ b/src/ffindex_build.c
-@@ -40,6 +40,8 @@
- "\t-s\t\tsort index file, so that the index can queried.\n"
- "\t\t\tAnother append operations can be done without sorting.\n"
- "\t-v\t\tprint version and other info then exit\n"
-+ "ENVIRONMENT\n"
-+ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
- "\nEXAMPLES:\n"
- "\tCreate a new ffindex containing all files from the \"bar/\" directory containing\n"
- "\tsay myfile1.txt, myfile2.txt and sort (-s) it so that e.g. ffindex_get can use it.\n"
-@@ -52,7 +54,7 @@
- "\tMaximum key/filename length is %d and maximum entries are by default %d\n"
- "\tThis can be changed in the sources.\n"
- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
-- program_name, MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT);
-+ basename(program_name), MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT);
- }
-
- int main(int argn, char **argv)
---- a/src/ffindex_from_fasta.c
-+++ b/src/ffindex_from_fasta.c
-@@ -33,7 +33,9 @@
- {
- fprintf(stderr, "USAGE: %s -v | [-s] data_filename index_filename fasta_filename\n"
- "\t-s\tsort index file\n"
-- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n", program_name);
-+ "ENVIRONMENT\n"
-+ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
-+ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n", basename(program_name));
- }
-
- int main(int argn, char **argv)
-@@ -127,4 +129,4 @@
- return err;
- }
-
--/* vim: ts=2 sw=2 et: */
-+// vim: ts=2 sw=2 et:
---- a/src/ffindex_get.c
-+++ b/src/ffindex_get.c
-@@ -26,8 +26,10 @@
- {
- fprintf(stderr, "USAGE: %s data_filename index_filename entry name(s)\n"
- "-n\tuse index of entry instead of entry name\n"
-+ "ENVIRONMENT\n"
-+ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
- "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
-- program_name);
-+ basename(program_name));
- }
-
- int main(int argn, char **argv)
---- a/src/ffindex_modify.c
-+++ b/src/ffindex_modify.c
-@@ -37,7 +37,7 @@
- "\t-u\tunlink entry (remove from index only)\n"
- "\t-v\tprint version and other info then exit\n"
- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
-- program_name, MAX_FILENAME_LIST_FILES);
-+ basename(program_name), MAX_FILENAME_LIST_FILES);
- }
-
- int main(int argn, char **argv)
-@@ -124,7 +124,7 @@
- }
- else
- {
-- char** sorted_names_to_unlink = malloc(FFINDEX_MAX_INDEX_ENTRIES_DEFAULT * sizeof(char *));
-+ char** sorted_names_to_unlink = malloc(ffindex_max_index_entries() * sizeof(char *));
- if(sorted_names_to_unlink == NULL)
- fferror_print(__FILE__, __LINE__, __func__, "malloc failed");
- /* For each list_file unlink all entries */
---- a/src/ffindex_unpack.c
-+++ b/src/ffindex_unpack.c
-@@ -35,7 +35,7 @@
- {
- fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME OUT_DIR\n"
- "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
-- argv[0]);
-+ basename(argv[0]));
- return -1;
- }
- char *data_filename = argv[1];
---- a/src/ffindex.c
-+++ b/src/ffindex.c
-@@ -227,7 +227,7 @@
- ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries)
- {
- if(num_max_entries == 0)
-- num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT;
-+ num_max_entries = ffindex_max_index_entries();
- size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries);
- ffindex_index_t *index = (ffindex_index_t *)malloc(nbytes);
- if(index == NULL)
---- a/src/ffindex.h
-+++ b/src/ffindex.h
-@@ -22,6 +22,8 @@
- #include <stdio.h>
-
- #define FFINDEX_VERSION 0.980
-+// lkajan: with ~72 bytes per entry, the below makes a default allocation over 2G. malloc in ffindex.c:225 fails on a machine with 'only' 2G of RAM.
-+// lkajan: let the default remain 40000000, and let the actual value be controlled by the env var FFINDEX_MAX_INDEX_ENTRIES wherever FFINDEX_MAX_INDEX_ENTRIES_DEFAULT is used.
- #define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 40000000
- #define FFINDEX_MAX_ENTRY_NAME_LENTH 32
-
-@@ -45,6 +47,8 @@
- ffindex_entry_t entries[]; /* This array is as big as the excess memory allocated for this struct. */
- } ffindex_index_t;
-
-+inline size_t ffindex_max_index_entries(){ char *FMIE = getenv("FFINDEX_MAX_INDEX_ENTRIES"); if( FMIE ) { return atol( FMIE ); } else { return FFINDEX_MAX_INDEX_ENTRIES_DEFAULT; } }
-+
- int ffindex_insert_memory(FILE *data_file, FILE *index_file, size_t *offset, char *from_start, size_t from_length, char *name);
-
- int ffindex_insert_file(FILE *data_file, FILE *index_file, size_t *offset, const char *path, char *name);
Copied: trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/basename (from rev 13600, trunk/packages/ffindex/trunk/debian/patches/basename)
===================================================================
--- trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/basename (rev 0)
+++ trunk/packages/ffindex/tags/0.9.9.1-1/debian/patches/basename 2013-05-16 13:41:55 UTC (rev 13602)
@@ -0,0 +1,150 @@
+Author: Laszlo Kajan <lkajan at rostlab.org>
+Author: Elso Andras <elso.andras at gmail.com>
+Subject: 40000000 bug and basename
+ [Laszlo Kajan]
+ The default value 40000000 for FFINDEX_MAX_INDEX_ENTRIES_DEFAULT is too high for a machine with 2G (or less) RAM.
+ Bug fixed by introducing an environment variable FFINDEX_MAX_INDEX_ENTRIES to control the value.
+ [Elso Andras]
+ using basename for usage print, this helps help2man if a packager is using it
+Forwarded: yes
+
+--- a/src/ffindex_apply.c
++++ b/src/ffindex_apply.c
+@@ -34,8 +34,10 @@
+ if(argn < 4)
+ {
+ fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME PROGRAM [PROGRAM_ARGS]*\n"
++ "ENVIRONMENT\n"
++ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
+ "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
+- argv[0]);
++ basename(argv[0]));
+ return -1;
+ }
+ char *data_filename = argv[1];
+--- a/src/ffindex_apply_mpi.c
++++ b/src/ffindex_apply_mpi.c
+@@ -195,7 +195,7 @@
+ "\t-m\tDo not merge the FFindex parts generated by the different MPI processes\n"
+ "\t\tThis is useful for large MPI Jobs where merge time might be accounted.\n"
+ "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
+- argv[0]);
++ basename(argv[0]));
+ return -1;
+ }
+ read_buffer = malloc(400 * 1024 * 1024);
+--- a/src/ffindex_build.c
++++ b/src/ffindex_build.c
+@@ -40,6 +40,8 @@
+ "\t-s\t\tsort index file, so that the index can queried.\n"
+ "\t\t\tAnother append operations can be done without sorting.\n"
+ "\t-v\t\tprint version and other info then exit\n"
++ "ENVIRONMENT\n"
++ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
+ "\nEXAMPLES:\n"
+ "\tCreate a new ffindex containing all files from the \"bar/\" directory containing\n"
+ "\tsay myfile1.txt, myfile2.txt and sort (-s) it so that e.g. ffindex_get can use it.\n"
+@@ -52,7 +54,7 @@
+ "\tMaximum key/filename length is %d and maximum entries are by default %d\n"
+ "\tThis can be changed in the sources.\n"
+ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
+- program_name, MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT);
++ basename(program_name), MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT);
+ }
+
+ int main(int argn, char **argv)
+--- a/src/ffindex_from_fasta.c
++++ b/src/ffindex_from_fasta.c
+@@ -33,7 +33,9 @@
+ {
+ fprintf(stderr, "USAGE: %s -v | [-s] data_filename index_filename fasta_filename\n"
+ "\t-s\tsort index file\n"
+- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n", program_name);
++ "ENVIRONMENT\n"
++ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
++ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n", basename(program_name));
+ }
+
+ int main(int argn, char **argv)
+@@ -127,4 +129,4 @@
+ return err;
+ }
+
+-/* vim: ts=2 sw=2 et: */
++// vim: ts=2 sw=2 et:
+--- a/src/ffindex_get.c
++++ b/src/ffindex_get.c
+@@ -26,8 +26,10 @@
+ {
+ fprintf(stderr, "USAGE: %s data_filename index_filename entry name(s)\n"
+ "-n\tuse index of entry instead of entry name\n"
++ "ENVIRONMENT\n"
++ "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
+ "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
+- program_name);
++ basename(program_name));
+ }
+
+ int main(int argn, char **argv)
+--- a/src/ffindex_modify.c
++++ b/src/ffindex_modify.c
+@@ -37,7 +37,7 @@
+ "\t-u\tunlink entry (remove from index only)\n"
+ "\t-v\tprint version and other info then exit\n"
+ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
+- program_name, MAX_FILENAME_LIST_FILES);
++ basename(program_name), MAX_FILENAME_LIST_FILES);
+ }
+
+ int main(int argn, char **argv)
+@@ -124,7 +124,7 @@
+ }
+ else
+ {
+- char** sorted_names_to_unlink = malloc(FFINDEX_MAX_INDEX_ENTRIES_DEFAULT * sizeof(char *));
++ char** sorted_names_to_unlink = malloc(ffindex_max_index_entries() * sizeof(char *));
+ if(sorted_names_to_unlink == NULL)
+ fferror_print(__FILE__, __LINE__, __func__, "malloc failed");
+ /* For each list_file unlink all entries */
+--- a/src/ffindex_unpack.c
++++ b/src/ffindex_unpack.c
+@@ -35,7 +35,7 @@
+ {
+ fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME OUT_DIR\n"
+ "\nDesigned and implemented by Andy Hauser <hauser at genzentrum.lmu.de>.\n",
+- argv[0]);
++ basename(argv[0]));
+ return -1;
+ }
+ char *data_filename = argv[1];
+--- a/src/ffindex.c
++++ b/src/ffindex.c
+@@ -227,7 +227,7 @@
+ ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries)
+ {
+ if(num_max_entries == 0)
+- num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT;
++ num_max_entries = ffindex_max_index_entries();
+ size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries);
+ ffindex_index_t *index = (ffindex_index_t *)malloc(nbytes);
+ if(index == NULL)
+--- a/src/ffindex.h
++++ b/src/ffindex.h
+@@ -22,6 +22,8 @@
+ #include <stdio.h>
+
+ #define FFINDEX_VERSION 0.980
++// lkajan: with ~72 bytes per entry, the below makes a default allocation over 2G. malloc in ffindex.c:225 fails on a machine with 'only' 2G of RAM.
++// lkajan: let the default remain 40000000, and let the actual value be controlled by the env var FFINDEX_MAX_INDEX_ENTRIES wherever FFINDEX_MAX_INDEX_ENTRIES_DEFAULT is used.
+ #define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 40000000
+ #define FFINDEX_MAX_ENTRY_NAME_LENTH 32
+
+@@ -45,6 +47,8 @@
+ ffindex_entry_t entries[]; /* This array is as big as the excess memory allocated for this struct. */
+ } ffindex_index_t;
+
++inline size_t ffindex_max_index_entries(){ char *FMIE = getenv("FFINDEX_MAX_INDEX_ENTRIES"); if( FMIE ) { return atol( FMIE ); } else { return FFINDEX_MAX_INDEX_ENTRIES_DEFAULT; } }
++
+ int ffindex_insert_memory(FILE *data_file, FILE *index_file, size_t *offset, char *from_start, size_t from_length, char *name);
+
+ int ffindex_insert_file(FILE *data_file, FILE *index_file, size_t *offset, const char *path, char *name);
Deleted: trunk/packages/ffindex/tags/0.9.9.1-1/debian/rules
===================================================================
--- trunk/packages/ffindex/trunk/debian/rules 2013-05-16 13:12:23 UTC (rev 13599)
+++ trunk/packages/ffindex/tags/0.9.9.1-1/debian/rules 2013-05-16 13:41:55 UTC (rev 13602)
@@ -1,52 +0,0 @@
-#!/usr/bin/make -f
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
-export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
-export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-
-# lkajan: work in progress, enable this in next upstream release, after speaking to upstream
-#export HAVE_MPI:=1
-
-%:
- dh $@ --parallel
-
-FFMANPAGES = ffindex_apply.1 ffindex_build.1 ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.1 ffindex_unpack.1
-.PHONY: ffmanpages
-ffmanpages: $(FFMANPAGES)
-BINNAMES = \
- ffindex_apply="apply a program to each FFindex entry";\
- ffindex_build="build file index from files in directories";\
- ffindex_from_fasta="populate index from FASTA file";\
- ffindex_get="retrieve entries from file index";\
- ffindex_modify="modify file index entries";\
- ffindex_unpack="unpack file index entries";
-
-.PHONY: override_dh_installman
-override_dh_installman: $(FFMANPAGES)
- dh_installman
-
-$(FFMANPAGES): %.1 : debian/tmp/usr/bin/%
- unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && eval '$(BINNAMES)' && help2man --no-info --no-discard-stderr '--help-option= ' -n "$$$*" --version-option="-v" '$<' -o '$@' --include debian/man_notes.nroff
-
-.PHONY: override_dh_clean
-override_dh_clean:
- rm -f $(FFMANPAGES)
- dh_clean
-
-.PHONY: override_dh_strip
-override_dh_strip:
- dh_strip --dbg-package=ffindex-dbg
-
-# [Laszlo Kajan <lkajan at rostlab.org>]
-# ffindex has an overly large default for FFINDEX_MAX_INDEX_ENTRIES (40000000). In order to require less RAM for testing the package (make check), a more modest value is set below.
-.PHONY: override_dh_auto_test
-override_dh_auto_test:
- dh_auto_test -- FFINDEX_MAX_INDEX_ENTRIES=20000
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
Copied: trunk/packages/ffindex/tags/0.9.9.1-1/debian/rules (from rev 13601, trunk/packages/ffindex/trunk/debian/rules)
===================================================================
--- trunk/packages/ffindex/tags/0.9.9.1-1/debian/rules (rev 0)
+++ trunk/packages/ffindex/tags/0.9.9.1-1/debian/rules 2013-05-16 13:41:55 UTC (rev 13602)
@@ -0,0 +1,52 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
+export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+
+# lkajan: work in progress, enable this in next upstream release, after speaking to upstream
+#export HAVE_MPI:=1
+
+%:
+ dh $@ --parallel
+
+FFMANPAGES = ffindex_apply.1 ffindex_build.1 ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.1 ffindex_unpack.1
+.PHONY: ffmanpages
+ffmanpages: $(FFMANPAGES)
+BINNAMES = \
+ ffindex_apply="apply a program to each FFindex entry";\
+ ffindex_build="build file index from files in directories";\
+ ffindex_from_fasta="populate index from FASTA file";\
+ ffindex_get="retrieve entries from file index";\
+ ffindex_modify="modify file index entries";\
+ ffindex_unpack="unpack file index entries";
+
+.PHONY: override_dh_installman
+override_dh_installman: $(FFMANPAGES)
+ dh_installman
+
+$(FFMANPAGES): %.1 : debian/tmp/usr/bin/%
+ unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && eval '$(BINNAMES)' && help2man --no-info --no-discard-stderr '--help-option= ' -n "$$$*" --version-option="-v" '$<' -o '$@' --include debian/man_notes.nroff
+
+.PHONY: override_dh_clean
+override_dh_clean:
+ rm -f $(FFMANPAGES)
+ dh_clean
+
+.PHONY: override_dh_strip
+override_dh_strip:
+ dh_strip --dbg-package=ffindex-dbg
+
+# [Laszlo Kajan <lkajan at rostlab.org>]
+# ffindex has an overly large default for FFINDEX_MAX_INDEX_ENTRIES (40000000). In order to require less RAM for testing the package (make check), a more modest value is set below.
+.PHONY: override_dh_auto_test
+override_dh_auto_test:
+ dh_auto_test -- FFINDEX_MAX_INDEX_ENTRIES=20000 check
+
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --destdir=../tarballs
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