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 <[email protected]> Wed, 19 Dec 2012 00:39:51 +0100 - -ffindex (0.9.9-1) unstable; urgency=low - - * New upstream release - - -- Laszlo Kajan <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 23 Apr 2012 11:30:03 +0200 - -ffindex (0.9.3-1) unstable; urgency=low - - * Initial release (Closes: #661111) - - -- Laszlo Kajan <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 19 Dec 2012 00:39:51 +0100 + +ffindex (0.9.9-1) unstable; urgency=low + + * New upstream release + + -- Laszlo Kajan <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 23 Apr 2012 11:30:03 +0200 + +ffindex (0.9.3-1) unstable; urgency=low + + * Initial release (Closes: #661111) + + -- Laszlo Kajan <[email protected]> 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 <[email protected]> -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 <[email protected]> +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 <[email protected]> -Author: Elso Andras <[email protected]> -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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\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 <[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)); - } - - 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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]> +Author: Elso Andras <[email protected]> +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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\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 <[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)); + } + + 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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>.\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 <[email protected]>] -# 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 <[email protected]>] +# 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
