Author: sascha-guest Date: 2016-01-09 12:30:24 +0000 (Sat, 09 Jan 2016) New Revision: 21050
Added: trunk/packages/aegean/trunk/debian/patches/spelling Modified: trunk/packages/aegean/trunk/debian/aegean.docs trunk/packages/aegean/trunk/debian/changelog trunk/packages/aegean/trunk/debian/patches/add_hardening trunk/packages/aegean/trunk/debian/patches/add_version trunk/packages/aegean/trunk/debian/patches/adjust_datapath trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs trunk/packages/aegean/trunk/debian/patches/follow_links trunk/packages/aegean/trunk/debian/patches/includepaths trunk/packages/aegean/trunk/debian/patches/remove_license trunk/packages/aegean/trunk/debian/patches/series Log: new upstream release Modified: trunk/packages/aegean/trunk/debian/aegean.docs =================================================================== --- trunk/packages/aegean/trunk/debian/aegean.docs 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/aegean.docs 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,3 +1 @@ README.md -VERSION -CHANGELOG.md Modified: trunk/packages/aegean/trunk/debian/changelog =================================================================== --- trunk/packages/aegean/trunk/debian/changelog 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/changelog 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,3 +1,9 @@ +aegean (0.15.1+dfsg-1) UNRELEASED; urgency=medium + + * New upstream release. + + -- Sascha Steinbiss <[email protected]> Sat, 09 Jan 2016 11:36:04 +0000 + aegean (0.14.1+dfsg2-2) unstable; urgency=low * d/rules: build w/o parallelism, set LC_ALL Modified: trunk/packages/aegean/trunk/debian/patches/add_hardening =================================================================== --- trunk/packages/aegean/trunk/debian/patches/add_hardening 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/patches/add_hardening 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,12 +1,70 @@ -Description: Add_hardening +Description: Add hardening +Author: Sascha Steinbiss <[email protected]> --- a/Makefile +++ b/Makefile -@@ -48,7 +48,7 @@ +@@ -49,7 +49,7 @@ ifneq ($(debug),no) CFLAGS += -g endif --LDFLAGS=-lgenometools -lm \ -+LDFLAGS+=-lgenometools -lm \ +-LDFLAGS=-lgenometools -lm -ldl \ ++LDFLAGS+=-lgenometools -lm -ldl \ -L$(prefix)/lib \ -L/usr/local/lib ifdef lib +@@ -99,47 +99,47 @@ + $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h + @- mkdir -p obj + @ echo "[compile $*]" +- @ $(CC) $(CFLAGS) $(INCS) -c -o $@ $< ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $< + + $(PE_EXE): src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c src/ParsEval/pe_options.h src/ParsEval/pe_utils.h $(AGN_OBJS) + @ mkdir -p bin + @ echo "[compile ParsEval]" +- @ $(CC) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS) ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS) + + $(CN_EXE): src/canon-gff3.c $(AGN_OBJS) + @ mkdir -p bin + @ echo "[compile CanonGFF3]" +- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS) ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS) + + $(LP_EXE): src/locuspocus.c $(AGN_OBJS) + @ mkdir -p bin + @ echo "[compile LocusPocus]" +- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS) ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS) + + $(GV_EXE): src/gaeval.c $(AGN_OBJS) + @ mkdir -p bin + @ echo "[compile GAEVAL]" +- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS) ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS) + + $(XT_EXE): src/xtractore.c $(AGN_OBJS) + @ mkdir -p bin + @ echo "[compile Xtractore]" +- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS) ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS) + + $(RP_EXE): src/pmrna.c $(AGN_OBJS) + @ mkdir -p bin + @ echo "[compile $@]" +- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS) ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS) + + $(TD_EXE): src/tidygff3.c $(AGN_OBJS) + @ mkdir -p bin + @ echo "[compile $@]" +- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS) ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS) + + $(UT_EXE): test/unittests.c $(AGN_OBJS) + @ mkdir -p bin + @ echo "[compile unit tests]" +- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS) ++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS) + + libaegean.a: $(AGN_OBJS) + @ echo "[create libaegean]" Modified: trunk/packages/aegean/trunk/debian/patches/add_version =================================================================== --- trunk/packages/aegean/trunk/debian/patches/add_version 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/patches/add_version 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,7 +1,7 @@ Description: Add_version --- a/Makefile +++ b/Makefile -@@ -95,47 +95,47 @@ +@@ -99,47 +99,47 @@ $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h @- mkdir -p obj @ echo "[compile $*]" Modified: trunk/packages/aegean/trunk/debian/patches/adjust_datapath =================================================================== --- trunk/packages/aegean/trunk/debian/patches/adjust_datapath 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/patches/adjust_datapath 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,32 +1,18 @@ -Description: Adjust_datapath +Description: Adjust datapath + Debian uses /usr/share. +Author: Sascha Steinbiss <[email protected]> --- a/Makefile +++ b/Makefile -@@ -27,7 +27,7 @@ +@@ -29,7 +29,7 @@ # Compilation settings CC=gcc --CFLAGS += -Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result -+CFLAGS += -Wall -DAGN_DATA_PATH='"/usr/share/aegean"' -Wno-unused-result +-CFLAGS=-Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result ++CFLAGS+=-Wall -DAGN_DATA_PATH='"/usr/share/aegean"' -Wno-unused-result GTFLAGS=prefix=$(prefix) SYSTEM:=$(shell uname -s) MACHINE:=$(shell uname -m) -@@ -87,13 +87,13 @@ - @ mkdir -p $(prefix)/bin/ - cp data/scripts/*.p? $(prefix)/bin/. - --uninstall: -+uninstall: - for exe in $(INSTALL_BINS); do rm -r $(prefix)/$$exe; done - rm -r $(prefix)/include/aegean/ - rm -r $(prefix)/share/aegean/ - rm $(prefix)/lib/libaegean.a - --clean: -+clean: - rm -rf README $(BINS) libaegean.a $(AGN_OBJS) inc/core/AgnVersion.h bin/*.dSYM - - $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h -@@ -145,12 +145,12 @@ +@@ -149,12 +149,12 @@ @ echo "[create libaegean]" @ ar ru libaegean.a $(AGN_OBJS) Modified: trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs =================================================================== --- trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,16 +1,17 @@ -Description: Fix_m64_on_some_archs +Description: Fix -m64 on some archs +Author: Sascha Steinbiss <[email protected]> --- a/Makefile +++ b/Makefile -@@ -29,6 +29,8 @@ +@@ -31,6 +31,8 @@ CC=gcc - CFLAGS += -Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result + CFLAGS=-Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result GTFLAGS=prefix=$(prefix) +SYSTEM:=$(shell uname -s) +MACHINE:=$(shell uname -m) ifeq ($(cairo),no) CFLAGS += -DWITHOUT_CAIRO GTFLAGS += cairo=no -@@ -40,8 +42,10 @@ +@@ -43,8 +45,10 @@ CFLAGS += -O3 endif ifneq ($(64bit),no) @@ -23,7 +24,7 @@ endif ifneq ($(debug),no) CFLAGS += -g -@@ -66,7 +70,7 @@ +@@ -70,7 +74,7 @@ # Targets all: $(BINS) libaegean.a @@ -32,7 +33,7 @@ install: all @ mkdir -p $(prefix)/bin/ -@@ -142,7 +146,7 @@ +@@ -146,7 +150,7 @@ @ ar ru libaegean.a $(AGN_OBJS) inc/core/AgnVersion.h: Modified: trunk/packages/aegean/trunk/debian/patches/follow_links =================================================================== --- trunk/packages/aegean/trunk/debian/patches/follow_links 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/patches/follow_links 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,7 +1,9 @@ -Description: Follow_links +Description: Follow links + Honor symlinks when copying files. +Author: Sascha Steinbiss <[email protected]> --- a/src/ParsEval/pe_options.c +++ b/src/ParsEval/pe_options.c -@@ -265,7 +265,7 @@ +@@ -262,7 +262,7 @@ } char copy_cmd[1024]; Modified: trunk/packages/aegean/trunk/debian/patches/includepaths =================================================================== --- trunk/packages/aegean/trunk/debian/patches/includepaths 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/patches/includepaths 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,25 +1,9 @@ -Description: Includepaths +Description: Adjust include paths + Debian uses /usr/include. +Author: Sascha Steinbiss <[email protected]> --- a/Makefile +++ b/Makefile -@@ -1,8 +1,6 @@ - #---Begin configuration---# - #---Begin configuration---# - --prefix=/usr/local -- - #----End configuration----# - #----End configuration----# - -@@ -29,7 +27,7 @@ - - # Compilation settings - CC=gcc --CFLAGS=-Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result -+CFLAGS += -Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result - GTFLAGS=prefix=$(prefix) - ifeq ($(cairo),no) - CFLAGS += -DWITHOUT_CAIRO -@@ -57,6 +55,7 @@ +@@ -62,6 +62,7 @@ INCS=$(shell pkg-config --silence-errors --cflags-only-I cairo) \ -I inc/core \ -I /usr/local/include/genometools \ @@ -27,12 +11,3 @@ -I $(prefix)/include/genometools ifeq ($(memcheck),yes) MEMCHECK=valgrind --leak-check=full --show-reachable=yes --error-exitcode=1 \ -@@ -91,7 +90,7 @@ - rm $(prefix)/lib/libaegean.a - - clean: -- rm -rf $(BINS) libaegean.a $(AGN_OBJS) inc/core/AgnVersion.h bin/*.dSYM -+ rm -rf README $(BINS) libaegean.a $(AGN_OBJS) inc/core/AgnVersion.h bin/*.dSYM - - $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h - @- mkdir -p obj Modified: trunk/packages/aegean/trunk/debian/patches/remove_license =================================================================== --- trunk/packages/aegean/trunk/debian/patches/remove_license 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/patches/remove_license 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,4 +1,5 @@ -Description: Remove_license +Description: Remove license file not to be installed in wrong location +Author: Sascha Steinbiss <[email protected]> --- a/data/share/LICENSE +++ /dev/null @@ -1,13 +0,0 @@ @@ -15,3 +16,19 @@ -WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN -ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF -OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. +--- a/data/misc/amel-ogs-vs-ncbi-parseval-html/LICENSE ++++ /dev/null +@@ -1,13 +0,0 @@ +-Copyright (c) 2010-2014, Daniel S. Standage and CONTRIBUTORS +- +-Permission to use, copy, modify, and/or distribute this software for any +-purpose with or without fee is hereby granted, provided that the above +-copyright notice and this permission notice appear in all copies. +- +-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES +-WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF +-MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR +-ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES +-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN +-ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF +-OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. Modified: trunk/packages/aegean/trunk/debian/patches/series =================================================================== --- trunk/packages/aegean/trunk/debian/patches/series 2016-01-09 07:21:28 UTC (rev 21049) +++ trunk/packages/aegean/trunk/debian/patches/series 2016-01-09 12:30:24 UTC (rev 21050) @@ -1,8 +1,7 @@ add_hardening -remove_license -includepaths -add_version fix_m64_on_some_archs +remove_license adjust_datapath follow_links -sort_source_files +includepaths +spelling Added: trunk/packages/aegean/trunk/debian/patches/spelling =================================================================== --- trunk/packages/aegean/trunk/debian/patches/spelling (rev 0) +++ trunk/packages/aegean/trunk/debian/patches/spelling 2016-01-09 12:30:24 UTC (rev 21050) @@ -0,0 +1,14 @@ +Description: Fix spelling unknow->unknown +Author: Sascha Steinbiss <[email protected]> +Forwarded: https://github.com/standage/AEGeAn/pull/161 +--- a/src/core/AgnLocus.c ++++ b/src/core/AgnLocus.c +@@ -344,7 +344,7 @@ + break; + default: + desc = NULL; +- fprintf(stderr, "error: unknow comp classification %d\n", c); ++ fprintf(stderr, "error: unknown comp classification %d\n", c); + break; + } + desc->comparison_count++; _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
