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 <[email protected]> Thu, 16 May 2013 15:41:56 +0200 + -- Laszlo Kajan <[email protected]> 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 <[email protected]> -Uploaders: Laszlo Kajan <[email protected]> +Uploaders: Laszlo Kajan <[email protected]> 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@Base 0.9.8 ffindex_get_entry_by_name@Base 0.9.9 ffindex_index_as_tree@Base 0.9.8 + ffindex_index_open@Base 0.9.9.3 ffindex_index_parse@Base 0.9.8 ffindex_insert_dir@Base 0.9.8 + ffindex_insert_ffindex@Base 0.9.9.3 ffindex_insert_file@Base 0.9.8 ffindex_insert_filestream@Base 0.9.8 ffindex_insert_list_file@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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\n", program_name); + "ENVIRONMENT\n" + "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n" -+ "\nDesigned and implemented by Andreas W. Hauser <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\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} _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
