Author: lkajan-guest Date: 2012-06-26 12:57:56 +0000 (Tue, 26 Jun 2012) New Revision: 11478
Added: trunk/packages/ffindex/trunk/debian/man_notes.nroff Modified: trunk/packages/ffindex/trunk/debian/changelog trunk/packages/ffindex/trunk/debian/ffindex.manpages trunk/packages/ffindex/trunk/debian/patches/Makefile trunk/packages/ffindex/trunk/debian/rules Log: New upstream release. Modified: trunk/packages/ffindex/trunk/debian/changelog =================================================================== --- trunk/packages/ffindex/trunk/debian/changelog 2012-06-26 09:39:18 UTC (rev 11477) +++ trunk/packages/ffindex/trunk/debian/changelog 2012-06-26 12:57:56 UTC (rev 11478) @@ -1,3 +1,9 @@ +ffindex (0.9.6.1-1) unstable; urgency=low + + * New upstream release. + + -- 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) Modified: trunk/packages/ffindex/trunk/debian/ffindex.manpages =================================================================== --- trunk/packages/ffindex/trunk/debian/ffindex.manpages 2012-06-26 09:39:18 UTC (rev 11477) +++ trunk/packages/ffindex/trunk/debian/ffindex.manpages 2012-06-26 12:57:56 UTC (rev 11478) @@ -1,3 +1,5 @@ +ffindex_apply.1 ffindex_build.1 +ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.1 Added: trunk/packages/ffindex/trunk/debian/man_notes.nroff =================================================================== --- trunk/packages/ffindex/trunk/debian/man_notes.nroff (rev 0) +++ trunk/packages/ffindex/trunk/debian/man_notes.nroff 2012-06-26 12:57:56 UTC (rev 11478) @@ -0,0 +1,4 @@ +[BUGS] +User feedback is welcome, especially bugs, performance issues and last but not least convenience of the programs and \s-1API\s0. +.PP +Email Andreas Hauser [email protected]. Modified: trunk/packages/ffindex/trunk/debian/patches/Makefile =================================================================== --- trunk/packages/ffindex/trunk/debian/patches/Makefile 2012-06-26 09:39:18 UTC (rev 11477) +++ trunk/packages/ffindex/trunk/debian/patches/Makefile 2012-06-26 12:57:56 UTC (rev 11478) @@ -1,10 +1,8 @@ * make Makefile DESTDIR-aware * deinstall -> uninstall * fix issues where the path in help pages is taken from the build-time location of the executables -Index: ffindex-0.9.3/Makefile -=================================================================== ---- ffindex-0.9.3.orig/Makefile 2012-02-24 11:51:44.275044508 +0100 -+++ ffindex-0.9.3/Makefile 2012-02-24 11:57:11.291044574 +0100 +--- a/Makefile ++++ b/Makefile @@ -6,15 +6,8 @@ MFILE=Makefile endif @@ -24,17 +22,23 @@ - $(MAKE) -C src clean +%: + $(MAKE) -C src -f $(MFILE) $@ -Index: ffindex-0.9.3/src/Makefile -=================================================================== ---- ffindex-0.9.3.orig/src/Makefile 2012-02-24 11:51:44.303044506 +0100 -+++ ffindex-0.9.3/src/Makefile 2012-02-24 14:29:50.919044571 +0100 -@@ -1,12 +1,14 @@ +--- a/src/Makefile ++++ b/src/Makefile +@@ -1,15 +1,19 @@ -INSTALL_DIR?=.. -libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib` +PREFIX?=/usr ++INSTALL_DIR=$(DESTDIR)$(PREFIX) +libdir=lib LANG=C - CFLAGS+=-std=c99 -openmp -g -fPIC -Wall +-CC=gcc -fopenmp +-#CC=icc -openmp ++CC=gcc + CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic +-LDFLAGS=-lffindex -L. ++CFLAGS+=-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security ++CPPFLAGS+=-D_FORTIFY_SOURCE=2 ++LDFLAGS+=-Wl,-z,relro +SOCURRENT=0 +SOVERSION=$(SOCURRENT).1.0 ifdef FFINDEX_STATIC @@ -46,14 +50,36 @@ endif #-Wl,--version-script=libffindex.map -@@ -24,16 +26,17 @@ +@@ -25,33 +29,34 @@ + ffindex_apply: $(FFINDEX_OBJECTS) ffindex_apply.o ffindex.h + + ffindex_apply_mpi: $(FFINDEX_OBJECTS) ffindex_apply_mpi.o ffindex.h +- mpicc $(CFLAGS) -I $(MPI_INCLUDE) -o $@ ffindex_apply_mpi.o $(LDFLAGS) ++ mpicc $(CFLAGS) -I $(MPI_INCLUDE) -o $@ ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex + + ffindex_apply_mpi.o: ffindex_apply_mpi.c ffindex.h + mpicc $(CFLAGS) -I $(MPI_INCLUDE) -c ffindex_apply_mpi.c -o $@ + + ffindex_from_fasta: $(FFINDEX_OBJECTS) ffindex_from_fasta.o ffindex.h +- $(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) -L. -lffindex ++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ ffindex_from_fasta.o $(LDFLAGS) -L. -lffindex + + ffindex_get: $(FFINDEX_OBJECTS) ffindex_get.o ffindex.h +- $(CC) -o $@ ffindex_get.o $(LDFLAGS) -L. -lffindex ++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ ffindex_get.o $(LDFLAGS) -L. -lffindex + + ffindex_build: $(FFINDEX_OBJECTS) ffindex_build.o ffindex.h +- $(CC) -o $@ ffindex_build.o $(LDFLAGS) -L. -lffindex ++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ ffindex_build.o $(LDFLAGS) -L. -lffindex + ffindex_modify: $(FFINDEX_OBJECTS) ffindex_modify.o ffindex.h - $(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex +- $(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex ++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ ffindex_modify.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 -+ $(CC) -Wl,-z,defstack -shared -Wl,-soname,libffindex.so.$(SOCURRENT) -o libffindex.so.$(SOVERSION) ffindex.o ffutil.o -lc ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -Wl,-z,defstack -shared -Wl,-soname,libffindex.so.$(SOCURRENT) -o libffindex.so.$(SOVERSION) ffindex.o ffutil.o -lc -libffindex.so: libffindex.so.0.1 - ln -sf libffindex.so.0.1 libffindex.so @@ -69,59 +95,34 @@ rm -f /tmp/test.data /tmp/test.ffindex LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2 LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_get /tmp/test.data /tmp/test.ffindex a b foo | tee /tmp/test.out -@@ -53,25 +56,28 @@ +@@ -71,9 +76,11 @@ LD_LIBRARY_PATH=".:$(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 -+ 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 libffindex.a +- 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 \ ++ 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 \ + libffindex.a ffindex_from_fasta.o ffindex_from_fasta ffindex_apply_mpi.o ffindex_apply.o + ++distclean: clean + -+distclean: clean - install: -- mkdir -p $(INSTALL_DIR)/bin -- mkdir -p $(INSTALL_DIR)/$(libdir) -- mkdir -p $(INSTALL_DIR)/include -- install ffindex_get $(INSTALL_DIR)/bin/ffindex_get -- install ffindex_build $(INSTALL_DIR)/bin/ffindex_build -- install ffindex_modify $(INSTALL_DIR)/bin/ffindex_modify + mkdir -p $(INSTALL_DIR)/bin + mkdir -p $(INSTALL_DIR)/$(libdir) +@@ -83,9 +90,10 @@ + install ffindex_modify $(INSTALL_DIR)/bin/ffindex_modify + install ffindex_from_fasta $(INSTALL_DIR)/bin/ffindex_from_fasta + install ffindex_apply $(INSTALL_DIR)/bin/ffindex_apply - install libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1 -- install libffindex.a $(INSTALL_DIR)/$(libdir)/libffindex.a ++ 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 -- install ffindex.h $(INSTALL_DIR)/include/ffindex.h -- install ffutil.h $(INSTALL_DIR)/include/ffutil.h -- --deinstall: -- rm -f $(INSTALL_DIR)/bin/ffindex_get $(INSTALL_DIR)/bin/ffindex_build $(INSTALL_DIR)/bin/ffindex_modify \ -- $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.a \ -- $(INSTALL_DIR)/$(libdir)/libffindex.so $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h -- rmdir $(INSTALL_DIR)/bin || true -- rmdir $(INSTALL_DIR)/$(libdir) || true -- rmdir $(INSTALL_DIR)/include || true -+ mkdir -p $(DESTDIR)$(PREFIX)/bin -+ mkdir -p $(DESTDIR)$(PREFIX)/$(libdir) -+ mkdir -p $(DESTDIR)$(PREFIX)/include -+ install ffindex_get $(DESTDIR)$(PREFIX)/bin/ffindex_get -+ install ffindex_build $(DESTDIR)$(PREFIX)/bin/ffindex_build -+ install ffindex_modify $(DESTDIR)$(PREFIX)/bin/ffindex_modify -+ install libffindex.so.$(SOVERSION) $(DESTDIR)$(PREFIX)/$(libdir)/libffindex.so.$(SOVERSION) -+ install libffindex.a $(DESTDIR)$(PREFIX)/$(libdir)/libffindex.a -+ ln -sf libffindex.so.$(SOVERSION) $(DESTDIR)$(PREFIX)/$(libdir)/libffindex.so.$(SOCURRENT) -+ ln -sf libffindex.so.$(SOVERSION) $(DESTDIR)$(PREFIX)/$(libdir)/libffindex.so -+ install ffindex.h $(DESTDIR)$(PREFIX)/include/ffindex.h -+ install ffutil.h $(DESTDIR)$(PREFIX)/include/ffutil.h -+ -+uninstall: -+ rm -f $(PREFIX)/bin/ffindex_get $(PREFIX)/bin/ffindex_build $(PREFIX)/bin/ffindex_modify \ -+ $(PREFIX)/$(libdir)/libffindex.so.$(SOVERSION) $(PREFIX)/$(libdir)/libffindex.a \ -+ $(PREFIX)/$(libdir)/libffindex.so.$(SOCURRENT) $(PREFIX)/$(libdir)/libffindex.so $(PREFIX)/include/ffindex.h $(PREFIX)/include/ffutil.h -+ rmdir $(PREFIX)/bin || true -+ rmdir $(PREFIX)/$(libdir) || true -+ rmdir $(PREFIX)/include || true -Index: ffindex-0.9.3/src/ffindex_build.c -=================================================================== ---- ffindex-0.9.3.orig/src/ffindex_build.c 2012-02-24 11:49:40.279044528 +0100 -+++ ffindex-0.9.3/src/ffindex_build.c 2012-02-24 11:51:49.663044720 +0100 ++ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOCURRENT) ++ ln -sf libffindex.so.$(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 +--- a/src/ffindex_build.c ++++ b/src/ffindex_build.c @@ -31,7 +31,7 @@ void usage(char *program_name) @@ -140,26 +141,8 @@ } int main(int argn, char **argv) -Index: ffindex-0.9.3/src/ffindex_get.c -=================================================================== ---- ffindex-0.9.3.orig/src/ffindex_get.c 2012-02-24 11:49:40.299044548 +0100 -+++ ffindex-0.9.3/src/ffindex_get.c 2012-02-24 11:51:49.671044437 +0100 -@@ -26,9 +26,8 @@ - { - if(argn < 3) - { -- fprintf(stderr, "USAGE: %s data_filename index_filename filename(s)\n" -- "\nDesigned and implemented by Andreas W. Hauser <[email protected]>.\n", -- argv[0]); -+ fprintf(stderr, "USAGE: ffindex_get data_filename index_filename filename(s)\n" -+ "\nDesigned and implemented by Andreas W. Hauser <[email protected]>.\n"); - return -1; - } - char *data_filename = argv[1]; -Index: ffindex-0.9.3/src/ffindex_modify.c -=================================================================== ---- ffindex-0.9.3.orig/src/ffindex_modify.c 2012-02-24 11:49:40.331044474 +0100 -+++ ffindex-0.9.3/src/ffindex_modify.c 2012-02-24 12:53:15.362982150 +0100 +--- a/src/ffindex_modify.c ++++ b/src/ffindex_modify.c @@ -30,7 +30,7 @@ void usage(char *program_name) @@ -194,3 +177,48 @@ } } +--- a/src/ffindex_get.c ++++ b/src/ffindex_get.c +@@ -26,9 +26,8 @@ + { + if(argn < 3) + { +- fprintf(stderr, "USAGE: %s data_filename index_filename filename(s)\n" +- "\nDesigned and implemented by Andy Hauser <[email protected]>.\n", +- argv[0]); ++ fprintf(stderr, "USAGE: ffindex_get data_filename index_filename filename(s)\n" ++ "\nDesigned and implemented by Andreas W. Hauser <[email protected]>.\n"); + return -1; + } + char *data_filename = argv[1]; +--- a/src/ffindex.h ++++ b/src/ffindex.h +@@ -18,7 +18,8 @@ + #include <stdio.h> + + #define FFINDEX_VERSION 0.961 +-#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 40000000 ++// lkajan: with 72 bytes per entry, the below makes a default allocation over 2G. malloc in ffindex.c:225 fails with hardening flags. Let's give a value for approx. 256MB. ++#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 3728270 + #define FFINDEX_MAX_ENTRY_NAME_LENTH 56 + + enum ffindex_type { PLAIN_FILE, SORTED_FILE, SORTED_ARRAY, TREE }; +--- a/src/ffindex.c ++++ b/src/ffindex.c +@@ -223,13 +223,14 @@ + num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT; + size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries); + ffindex_index_t *index = (ffindex_index_t *)malloc(nbytes); +- index->num_max_entries = num_max_entries; + if(index == NULL) + { +- fferror_print(__FILE__, __LINE__, __func__, "malloc failed"); ++ char buf[2048]; snprintf( buf, 2048, "malloc failed to allocate %ld bytes: %s", nbytes, strerror(errno) ); ++ fferror_print(__FILE__, __LINE__, __func__, buf ); + return NULL; + } + ++ index->num_max_entries = num_max_entries; + index->file = index_file; + index->index_data = ffindex_mmap_data(index_file, &(index->index_data_size)); + if(index->index_data_size == 0) Modified: trunk/packages/ffindex/trunk/debian/rules =================================================================== --- trunk/packages/ffindex/trunk/debian/rules 2012-06-26 09:39:18 UTC (rev 11477) +++ trunk/packages/ffindex/trunk/debian/rules 2012-06-26 12:57:56 UTC (rev 11478) @@ -6,8 +6,13 @@ %: dh $@ --parallel -FFMANPAGES = ffindex_build.1 ffindex_get.1 ffindex_modify.1 -BINNAMES = ffindex_build="build file index from files in directories";\ +FFMANPAGES = ffindex_apply.1 ffindex_build.1 ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.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";\ @@ -16,7 +21,7 @@ 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 "$$$*" --version-option="-v" '$<' -o '$@' + unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && eval '$(BINNAMES)' && help2man --no-info --no-discard-stderr '--help-option= ' -n "$$$*" --version-option="-v" '$<' -o '$@' --include debian/man_notes.nroff .PHONY: override_dh_clean override_dh_clean: _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
