[med-svn] r15280 - in trunk/packages/ffindex/trunk/debian: . patches
Laszlo Kajan
lkajan at moszumanska.debian.org
Wed Nov 27 07:00:15 UTC 2013
Author: lkajan
Date: 2013-11-27 07:00:15 +0000 (Wed, 27 Nov 2013)
New Revision: 15280
Modified:
trunk/packages/ffindex/trunk/debian/README.source
trunk/packages/ffindex/trunk/debian/changelog
trunk/packages/ffindex/trunk/debian/control
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
trunk/packages/ffindex/trunk/debian/watch
Log:
new upstream release - commit before upload (lkajan will upload)
Modified: trunk/packages/ffindex/trunk/debian/README.source
===================================================================
--- trunk/packages/ffindex/trunk/debian/README.source 2013-11-26 19:24:16 UTC (rev 15279)
+++ trunk/packages/ffindex/trunk/debian/README.source 2013-11-27 07:00:15 UTC (rev 15280)
@@ -1,5 +1,5 @@
ffindex for Debian
-------------------
+==================
O: libffindex0: shlib-with-executable-stack usr/lib/libffindex.so.0.1.0
.......................................................................
@@ -9,4 +9,8 @@
.......
Patches are documented in their headers.
+src/ffindex_optimize.c in version 0.9.9.3
+-----------------------------------------
+This source probably should not have made it into the upstream release. It does not build, and it is not built from the upstream src/Makefile.
+
# vim:et:ts=2:
Modified: trunk/packages/ffindex/trunk/debian/changelog
===================================================================
--- trunk/packages/ffindex/trunk/debian/changelog 2013-11-26 19:24:16 UTC (rev 15279)
+++ trunk/packages/ffindex/trunk/debian/changelog 2013-11-27 07:00:15 UTC (rev 15280)
@@ -1,8 +1,10 @@
-ffindex (0.9.9.1-2) UNRELEASED; urgency=low
+ffindex (0.9.9.3-1) unstable; urgency=low
- * NOT RELEASED YET
+ * New upstream release.
+ * Up-to-date standards-version.
+ * Vcs fields updated.
- -- Laszlo Kajan <lkajan at rostlab.org> Thu, 16 May 2013 15:41:56 +0200
+ -- Laszlo Kajan <lkajan at debian.org> Mon, 25 Nov 2013 20:01:02 +0100
ffindex (0.9.9.1-1) unstable; urgency=low
Modified: trunk/packages/ffindex/trunk/debian/control
===================================================================
--- trunk/packages/ffindex/trunk/debian/control 2013-11-26 19:24:16 UTC (rev 15279)
+++ trunk/packages/ffindex/trunk/debian/control 2013-11-27 07:00:15 UTC (rev 15280)
@@ -2,13 +2,12 @@
Section: science
Priority: extra
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+Uploaders: Laszlo Kajan <lkajan at debian.org>
Build-Depends: debhelper (>= 8.0.0), help2man
-Standards-Version: 3.9.3
-Homepage: http://pubshare.genzentrum.lmu.de/scientific_computing/software/ffindex/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ffindex/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ffindex/trunk/
-DM-Upload-Allowed: yes
+Standards-Version: 3.9.4
+Homepage: http://www.splashground.de/~andy/programs/FFindex/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ffindex/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ffindex/trunk/
Package: ffindex
Architecture: any
Modified: trunk/packages/ffindex/trunk/debian/libffindex0.lintian-overrides
===================================================================
--- trunk/packages/ffindex/trunk/debian/libffindex0.lintian-overrides 2013-11-26 19:24:16 UTC (rev 15279)
+++ trunk/packages/ffindex/trunk/debian/libffindex0.lintian-overrides 2013-11-27 07:00:15 UTC (rev 15280)
@@ -1 +1 @@
-libffindex0: shlib-with-executable-stack usr/lib/libffindex.so.1.0.1
+libffindex0: shlib-with-executable-stack usr/lib/libffindex.so.2.0.2
Modified: trunk/packages/ffindex/trunk/debian/libffindex0.symbols
===================================================================
--- trunk/packages/ffindex/trunk/debian/libffindex0.symbols 2013-11-26 19:24:16 UTC (rev 15279)
+++ trunk/packages/ffindex/trunk/debian/libffindex0.symbols 2013-11-27 07:00:15 UTC (rev 15280)
@@ -12,8 +12,10 @@
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_open at Base 0.9.9.3
ffindex_index_parse at Base 0.9.8
ffindex_insert_dir at Base 0.9.8
+ ffindex_insert_ffindex at Base 0.9.9.3
ffindex_insert_file at Base 0.9.8
ffindex_insert_filestream at Base 0.9.8
ffindex_insert_list_file at Base 0.9.8
Modified: trunk/packages/ffindex/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/Makefile 2013-11-26 19:24:16 UTC (rev 15279)
+++ trunk/packages/ffindex/trunk/debian/patches/Makefile 2013-11-27 07:00:15 UTC (rev 15280)
@@ -9,7 +9,7 @@
--- a/src/Makefile
+++ b/src/Makefile
-@@ -1,15 +1,18 @@
+@@ -1,15 +1,19 @@
-INSTALL_DIR?=..
-libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
+PREFIX?=/usr
@@ -19,11 +19,12 @@
-CC=gcc -fopenmp
-#CC=icc -openmp
+CC=gcc
- CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic
+ CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1
-LDFLAGS=-lffindex -L.
-+SOCURRENT=1
-+SOAGE=1
-+SOVERSION=$(SOCURRENT).0.$(SOAGE)
++SOCURRENT=2
++SOREVISION=0
++SOAGE=2
++SOVERSION=$(SOCURRENT).$(SOREVISION).$(SOAGE)
+SOMAJORV=$(shell echo $$(( $(SOCURRENT)-$(SOAGE) )) )
ifdef FFINDEX_STATIC
LDFLAGS+=-static
@@ -34,7 +35,7 @@
endif
#-Wl,--version-script=libffindex.map
-@@ -47,16 +50,17 @@
+@@ -47,16 +51,17 @@
ffindex_unpack: $(FFINDEX_OBJECTS) ffindex_unpack.o ffindex.h
$(CC) -o $@ ffindex_unpack.o $(LDFLAGS) -L. -lffindex
@@ -57,7 +58,7 @@
rm -f /tmp/test.data /tmp/test.ffindex
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_get /tmp/test.data /tmp/test.ffindex a b foo | tee /tmp/test.out
-@@ -76,8 +80,11 @@
+@@ -76,8 +81,11 @@
LD_LIBRARY_PATH=".:$(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:
@@ -71,7 +72,7 @@
install:
mkdir -p $(INSTALL_DIR)/bin
-@@ -89,9 +96,10 @@
+@@ -89,9 +97,10 @@
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
Modified: trunk/packages/ffindex/trunk/debian/patches/basename
===================================================================
--- trunk/packages/ffindex/trunk/debian/patches/basename 2013-11-26 19:24:16 UTC (rev 15279)
+++ trunk/packages/ffindex/trunk/debian/patches/basename 2013-11-27 07:00:15 UTC (rev 15280)
@@ -16,7 +16,7 @@
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",
+ FFINDEX_COPYRIGHT,
- argv[0]);
+ basename(argv[0]));
return -1;
@@ -24,15 +24,15 @@
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",
+@@ -207,7 +207,7 @@
+ "\t-d\tFFDATA output file, stdout of program will be captured\n"
+ "\t-i\tFFINDEX output file, entries get the same name as input entry\n"
+ FFINDEX_COPYRIGHT,
- argv[0]);
+ basename(argv[0]));
- return -1;
+ errno = EINVAL;
+ goto EXCEPTION;
}
- read_buffer = malloc(400 * 1024 * 1024);
--- a/src/ffindex_build.c
+++ b/src/ffindex_build.c
@@ -40,6 +40,8 @@
@@ -47,7 +47,7 @@
@@ -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",
+ FFINDEX_COPYRIGHT,
- 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);
}
@@ -55,18 +55,19 @@
int main(int argn, char **argv)
--- a/src/ffindex_from_fasta.c
+++ b/src/ffindex_from_fasta.c
-@@ -33,7 +33,9 @@
+@@ -33,8 +33,10 @@
{
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));
+ FFINDEX_COPYRIGHT,
+- program_name);
++ basename(program_name));
}
int main(int argn, char **argv)
-@@ -127,4 +129,4 @@
+@@ -123,4 +125,4 @@
return err;
}
@@ -80,7 +81,7 @@
"-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",
+ FFINDEX_COPYRIGHT,
- program_name);
+ basename(program_name));
}
@@ -88,18 +89,18 @@
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);
+@@ -41,7 +41,7 @@
+ "\tTo clean up the data file after unlinking insert it to an new one:\n"
+ "\tffindex_build -as cleaned.ffdata cleaned.ffindex -d foo.ffdata -i foo.ffindex\n"
+ FFINDEX_COPYRIGHT,
+- program_name, MAX_FILENAME_LIST_FILES, program_name);
++ basename(program_name), MAX_FILENAME_LIST_FILES, program_name);
}
int main(int argn, char **argv)
-@@ -124,7 +124,7 @@
+@@ -128,7 +128,7 @@
}
- else
+ else // unused
{
- 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 *));
@@ -111,7 +112,7 @@
@@ -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",
+ FFINDEX_COPYRIGHT,
- argv[0]);
+ basename(argv[0]));
return -1;
@@ -119,7 +120,7 @@
char *data_filename = argv[1];
--- a/src/ffindex.c
+++ b/src/ffindex.c
-@@ -227,7 +227,7 @@
+@@ -284,7 +284,7 @@
ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries)
{
if(num_max_entries == 0)
@@ -130,19 +131,19 @@
if(index == NULL)
--- a/src/ffindex.h
+++ b/src/ffindex.h
-@@ -22,6 +22,8 @@
- #include <stdio.h>
+@@ -24,6 +24,8 @@
+ #define FFINDEX_VERSION 0.993
+ #define FFINDEX_COPYRIGHT "\nDesigned and implemented by Andreas Hauser <andy at splashground.de>.\n"
- #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
++// lkajan: 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 80000000, 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 80000000
+ #define FFINDEX_MAX_ENTRY_NAME_LENTH 63
-@@ -45,6 +47,8 @@
- ffindex_entry_t entries[]; /* This array is as big as the excess memory allocated for this struct. */
- } ffindex_index_t;
+@@ -51,6 +53,8 @@
+ int ffindex_index_open(char *data_filename, char *index_filename, char* mode, FILE **out_data_file, FILE **out_index_file, size_t *out_offset);
+
+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);
Modified: trunk/packages/ffindex/trunk/debian/watch
===================================================================
--- trunk/packages/ffindex/trunk/debian/watch 2013-11-26 19:24:16 UTC (rev 15279)
+++ trunk/packages/ffindex/trunk/debian/watch 2013-11-27 07:00:15 UTC (rev 15280)
@@ -1,5 +1,5 @@
version=3
# Homepage Pattern [Version [Action]]
-http://pubshare.genzentrum.lmu.de/scientific_computing/software/ffindex/ \
- ffindex-([0-9][0-9.]*)\.tar\.[gzbl2]{2,3}
+http://www.splashground.de/~andy/programs/FFindex/ \
+ ffindex-([0-9][0-9.]*)\.tar\.[gzbl2]{2,3}
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