Author: tille Date: 2016-05-07 22:53:31 +0000 (Sat, 07 May 2016) New Revision: 21858
Modified: trunk/packages/ffindex/trunk/debian/changelog trunk/packages/ffindex/trunk/debian/control trunk/packages/ffindex/trunk/debian/patches/Makefile.patch trunk/packages/ffindex/trunk/debian/patches/basename.patch trunk/packages/ffindex/trunk/debian/rules Log: * New upstream version * cme fix dpkg-control * enable mpi Modified: trunk/packages/ffindex/trunk/debian/changelog =================================================================== --- trunk/packages/ffindex/trunk/debian/changelog 2016-05-05 05:48:58 UTC (rev 21857) +++ trunk/packages/ffindex/trunk/debian/changelog 2016-05-07 22:53:31 UTC (rev 21858) @@ -1,3 +1,11 @@ +ffindex (0.9.9.7-1) unstable; urgency=medium + + * New upstream version + * cme fix dpkg-control + * enable mpi + + -- Andreas Tille <[email protected]> Sun, 08 May 2016 00:43:21 +0200 + ffindex (0.9.9.6-2) unstable; urgency=medium * Install ffindex_posix_search.h (see #802076) Modified: trunk/packages/ffindex/trunk/debian/control =================================================================== --- trunk/packages/ffindex/trunk/debian/control 2016-05-05 05:48:58 UTC (rev 21857) +++ trunk/packages/ffindex/trunk/debian/control 2016-05-07 22:53:31 UTC (rev 21858) @@ -6,10 +6,10 @@ Priority: optional Build-Depends: debhelper (>= 9), help2man, -# libopenmpi-dev, -# openmpi-bin ... needs another Build-Depends to create the manpage - but which one? -Standards-Version: 3.9.6 -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ffindex/trunk/ + libopenmpi-dev, + openmpi-bin +Standards-Version: 3.9.8 +Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/ffindex/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ffindex/trunk/ Homepage: http://www.splashground.de/~andy/programs/FFindex/ Modified: trunk/packages/ffindex/trunk/debian/patches/Makefile.patch =================================================================== --- trunk/packages/ffindex/trunk/debian/patches/Makefile.patch 2016-05-05 05:48:58 UTC (rev 21857) +++ trunk/packages/ffindex/trunk/debian/patches/Makefile.patch 2016-05-07 22:53:31 UTC (rev 21858) @@ -18,7 +18,7 @@ LANG=C #CC=musl-gcc #OMPI_CC=musl-gcc -@@ -7,7 +8,11 @@ CC=gcc +@@ -7,11 +8,15 @@ LANG=C #CC=icc #CC=clang CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. @@ -31,41 +31,30 @@ OS:= $(shell uname) -@@ -15,7 +20,7 @@ ifdef FFINDEX_STATIC - LDFLAGS+=-static - FFINDEX_OBJECTS=libffindex.a - else -- FFINDEX_OBJECTS=libffindex.so libffindex.so.0.1 -+ FFINDEX_OBJECTS=libffindex.so libffindex.so.$(SOVERSION) - endif +-FFINDEX_LIBS=libffindex.so libffindex.so.0.1 libffindex.a ++FFINDEX_LIBS=libffindex.so libffindex.so.$(SOVERSION) libffindex.a - OBJECTS=ffindex_apply ffindex_from_fasta ffindex_get ffindex_build ffindex_modify libffindex.a libffindex.so ffindex_unpack ffindex_from_tsv -@@ -35,10 +40,10 @@ ffindex_apply.o: ffindex_apply_mpi.c ffi - $(CC) $(CFLAGS) -c ffindex_apply_mpi.c -o $@ + FFINDEX_HEADERS=ffindex.h ffindex_posix_search.h ffutil.h + FFINDEX_OBJECTS=$(FFINDEX_HEADERS:.h=.o) +@@ -34,30 +39,30 @@ libffindex.a: $(FFINDEX_OBJECTS) + ar rcs libffindex.a $^ - ffindex_apply: $(FFINDEX_OBJECTS) ffindex_apply.o ffindex.h -- $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS) -+ $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS) -L. -lffindex - - ffindex_apply_mpi: $(FFINDEX_OBJECTS) ffindex_apply_mpi.o ffindex.h -- mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS) -+ mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex - - ffindex_apply_mpi.o: ffindex_apply_mpi.c ffindex.h - mpicc $(CFLAGS) -DHAVE_MPI -c ffindex_apply_mpi.c -o $@ -@@ -68,20 +73,20 @@ ffindex_unpack: $(FFINDEX_OBJECTS) ffind - $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) -L. -lffindex - ifeq ($(OS), Darwin) --libffindex.so.0.1: ffindex.o ffutil.o ffindex_posix_search.o ext/fmemopen.o +-libffindex.so.0.1: $(FFINDEX_OBJECTS) ext/fmemopen.o - $(CC) -shared -o libffindex.so.0.1 $^ -+libffindex.so.$(SOVERSION): ffindex.o ffutil.o ffindex_posix_search.o ext/fmemopen.o ++libffindex.so.$(SOVERSION): $(FFINDEX_OBJECTS) ext/fmemopen.o + $(CC) -shared -o libffindex.so.$(SOVERSION) $^ else --libffindex.so.0.1: ffindex.o ffutil.o ffindex_posix_search.o + + ifdef FFINDEX_STATIC + STATIC=-static + endif + +-libffindex.so.0.1: $(FFINDEX_OBJECTS) - $(CC) -Wl,-z,defs -Wl,-soname,libffindex.so.0.1 -shared -o libffindex.so.0.1 $^ -+libffindex.so.$(SOVERSION): ffindex.o ffutil.o ffindex_posix_search.o -+ $(CC) $(LDFLAGS) -Wl,-z,defstack -Wl,-soname,libffindex.so.$(SOVERSION) -shared -o libffindex.so.$(SOVERSION) $^ ++libffindex.so.$(SOVERSION): $(FFINDEX_OBJECTS) ++ $(CC) -Wl,-z,defs -Wl,-soname,libffindex.so.$(SOVERSION) -shared -o libffindex.so.$(SOVERSION) $^ + endif -libffindex.so: libffindex.so.0.1 @@ -73,30 +62,66 @@ +libffindex.so: libffindex.so.$(SOVERSION) + ln -sf libffindex.so.$(SOVERSION) libffindex.so - libffindex.a: ffindex.o ffutil.o ffindex_posix_search.o - ar rcs libffindex.a $^ + ffindex_apply.o: ffindex_apply_mpi.c $(FFINDEX_LIBS) + $(CC) $(CFLAGS) -c ffindex_apply_mpi.c -o $@ + ffindex_apply: ffindex_apply.o $(FFINDEX_LIBS) +- $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS) $(STATIC) ++ $(CC) $(CFLAGS) -o $@ ffindex_apply.o $(LDFLAGS) -L. -lffindex + + ffindex_apply_mpi: ffindex_apply_mpi.o $(FFINDEX_LIBS) +- mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS) ++ mpicc $(CFLAGS) -DHAVE_MPI -o $@ ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex + + ffindex_apply_mpi.o: ffindex_apply_mpi.c $(FFINDEX_HEADERS) + mpicc $(CFLAGS) -DHAVE_MPI -c ffindex_apply_mpi.c -o $@ +@@ -69,24 +74,24 @@ ffindex_apply_mpi_spawn.o: ffindex_apply + mpicc $(CFLAGS) -c ffindex_apply_mpi_spawn.c -o $@ + + ffindex_from_fasta: ffindex_from_fasta.o $(FFINDEX_LIBS) +- $(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) $(STATIC) ++ $(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) -L. -lffindex + + ffindex_from_tsv: ffindex_from_tsv.o $(FFINDEX_LIBS) +- $(CC) -o $@ ffindex_from_tsv.o $(LDFLAGS) $(STATIC) ++ $(CC) -o $@ ffindex_from_tsv.o $(LDFLAGS) -L. -lffindex + + ffindex_get: ffindex_get.o $(FFINDEX_LIBS) +- $(CC) -o $@ ffindex_get.o $(LDFLAGS) $(STATIC) ++ $(CC) -o $@ ffindex_get.o $(LDFLAGS) -L. -lffindex + + ffindex_build: ffindex_build.o $(FFINDEX_LIBS) +- $(CC) -o $@ ffindex_build.o $(LDFLAGS) $(STATIC) ++ $(CC) -o $@ ffindex_build.o $(LDFLAGS) -L. -lffindex + + ffindex_modify: ffindex_modify.o $(FFINDEX_LIBS) +- $(CC) -o $@ ffindex_modify.o $(LDFLAGS) $(STATIC) ++ $(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex + + ffindex_unpack: ffindex_unpack.o $(FFINDEX_LIBS) +- $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC) ++ $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) -L. -lffindex + -test: +check: rm -f /tmp/test.data /tmp/test.ffindex LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2 LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_get /tmp/test.data /tmp/test.ffindex a b foo | tee /tmp/test.out -@@ -101,10 +106,11 @@ time: - LD_LIBRARY_PATH=".:$(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" +@@ -107,9 +112,10 @@ time: clean: -- rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.0.1 \ -+ rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.$(SOVERSION) \ - ffindex_modify ffindex_modify.o libffindex.a ffindex_from_fasta.o ffindex_from_fasta ffindex_apply_mpi.o \ - ffindex_apply.o ffindex_apply ffindex_from_tsv ffindex_khget ffindex_unpack ffindex_from_tsv.o ffindex_unpack.o \ -- ffindex_posix_search.o -+ ffindex_posix_search.o \ + rm -f $(FFINDEX_PROGRAMS) $(FFINDEX_OBJECTS) $(FFINDEX_LIBS) \ +- libffindex.so libffindex.so.0.1 libffindex.a \ ++ libffindex.so libffindex.so.$(SOVERSION) libffindex.a \ + ffindex_build.o ffindex_get.o ffindex_modify.o ffindex_from_fasta.o ffindex_apply_mpi.o \ +- ffindex_apply.o ffindex_from_tsv.o ffindex_unpack.o ffindex_posix_search.o ffindex_apply_mpi_spawn.o ++ ffindex_apply.o ffindex_from_tsv.o ffindex_unpack.o ffindex_posix_search.o ffindex_apply_mpi_spawn.o \ + $(OBJECTS) $(OBJECTS:%=%.o) install: mkdir -p $(INSTALL_DIR)/bin -@@ -116,9 +122,10 @@ install: - install ffindex_from_fasta $(INSTALL_DIR)/bin/ffindex_from_fasta +@@ -122,9 +128,10 @@ install: + install ffindex_from_tsv $(INSTALL_DIR)/bin/ffindex_from_tsv 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 @@ -107,13 +132,13 @@ + 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 -@@ -127,7 +134,7 @@ endif + install ffindex_posix_search.h $(INSTALL_DIR)/include/ffindex_posix_search.h +@@ -134,7 +141,7 @@ endif 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.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.a \ $(INSTALL_DIR)/$(libdir)/libffindex.so $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h\ - $(INSTALL_DIR)/bin/ffindex_from_fasta + $(INSTALL_DIR)/include/ffindex_posix_search.h $(INSTALL_DIR)/bin/ffindex_from_fasta $(INSTALL_DIR)/bin/ffindex_from_tsv rmdir $(INSTALL_DIR)/bin || true Modified: trunk/packages/ffindex/trunk/debian/patches/basename.patch =================================================================== --- trunk/packages/ffindex/trunk/debian/patches/basename.patch 2016-05-05 05:48:58 UTC (rev 21857) +++ trunk/packages/ffindex/trunk/debian/patches/basename.patch 2016-05-07 22:53:31 UTC (rev 21858) @@ -10,17 +10,17 @@ --- a/src/ffindex_build.c +++ b/src/ffindex_build.c -@@ -40,6 +40,8 @@ void usage(char *program_name) - "\t-s\t\tsort index file, so that the index can queried.\n" +@@ -41,6 +41,8 @@ void usage(char *program_name) "\t\t\tAnother append operations can be done without sorting.\n" "\t-v\t\tprint version and other info then exit\n" + "\t-h\t\tdisplay this help message\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 @@ void usage(char *program_name) - "\tMaximum key/filename length is %d and maximum entries are by default %d\n" +@@ -54,7 +56,7 @@ void usage(char *program_name) + "\tdefault maximum entries %d.\n" "\tThis can be changed in the sources.\n" FFINDEX_COPYRIGHT, - program_name, MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT); @@ -59,21 +59,10 @@ return -1; } char *data_filename = argv[1]; ---- a/src/ffindex.c -+++ b/src/ffindex.c -@@ -307,7 +307,7 @@ ffindex_entry_t* ffindex_bsearch_get_ent - 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 @@ -24,6 +24,8 @@ - #define FFINDEX_VERSION 0.996 + #define FFINDEX_VERSION 0.997 #define FFINDEX_COPYRIGHT "\nDesigned and implemented by Andreas Hauser <[email protected]>.\n" +// lkajan: the below makes a default allocation over 2G. malloc in ffindex.c:225 fails on a machine with 'only' 2G of RAM. @@ -81,7 +70,7 @@ #define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 80000000 #define FFINDEX_MAX_ENTRY_NAME_LENTH 63 -@@ -71,6 +73,8 @@ ffindex_db_t * ffindex_index_db_open(ffi +@@ -76,6 +78,8 @@ int ffindex_index_close(ffindex_index_t* /* return *out_data_file, *out_index_file, out_offset. */ int ffindex_index_open(char *data_filename, char *index_filename, char* mode, FILE **out_data_file, FILE **out_index_file, size_t *out_offset); @@ -105,9 +94,9 @@ } --- a/src/ffindex_get.c +++ b/src/ffindex_get.c -@@ -27,8 +27,10 @@ void usage(char* program_name) - fprintf(stderr, "USAGE: %s data_filename index_filename entry name(s)\n" +@@ -28,8 +28,10 @@ void usage(char* program_name) "\t-f FILE\t\tfile containing a list of file names, one per line\n" + "\t-h\t\tdisplay this help message\n" "\t-n\t\tuse index of entry instead of entry name\n" + "ENVIRONMENT\n" + "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n" @@ -128,3 +117,14 @@ } int main(int argn, char **argv) +--- a/src/ffindex.c ++++ b/src/ffindex.c +@@ -373,7 +373,7 @@ ffindex_entry_t* ffindex_bsearch_get_ent + 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 *)mmap(0, nbytes, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0); Modified: trunk/packages/ffindex/trunk/debian/rules =================================================================== --- trunk/packages/ffindex/trunk/debian/rules 2016-05-05 05:48:58 UTC (rev 21857) +++ trunk/packages/ffindex/trunk/debian/rules 2016-05-07 22:53:31 UTC (rev 21858) @@ -6,8 +6,10 @@ # lkajan: work in progress, enable this in next upstream release, after speaking to upstream # [email protected]: If enabled only ffindex_apply_mpi and for creating the manpage another (not yet # known) Build-Depends is needed. -# export HAVE_MPI:=1 +export HAVE_MPI:=1 +export DEB_BUILD_MAINT_OPTIONS = hardening=+all + %: dh $@ --parallel _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
