[med-svn] r21050 - in trunk/packages/aegean/trunk/debian: . patches
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sat Jan 9 12:30:25 UTC 2016
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 <sascha at steinbiss.name> 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 <sascha at steinbiss.name>
--- 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 $*]"
Modified: trunk/packages/aegean/trunk/debian/patches/adjust_datapath
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/adjust_datapath 2016-01-09 07:21:28 UTC (rev 21049)
+++ trunk/packages/aegean/trunk/debian/patches/adjust_datapath 2016-01-09 12:30:24 UTC (rev 21050)
@@ -1,32 +1,18 @@
-Description: Adjust_datapath
+Description: Adjust datapath
+ Debian uses /usr/share.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/Makefile
+++ b/Makefile
-@@ -27,7 +27,7 @@
+@@ -29,7 +29,7 @@
# Compilation settings
CC=gcc
--CFLAGS += -Wall -DAGN_DATA_PATH='"$(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 $(AGN_OBJS)
Modified: trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs 2016-01-09 07:21:28 UTC (rev 21049)
+++ trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs 2016-01-09 12:30:24 UTC (rev 21050)
@@ -1,16 +1,17 @@
-Description: Fix_m64_on_some_archs
+Description: Fix -m64 on some archs
+Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/Makefile
+++ b/Makefile
-@@ -29,6 +29,8 @@
+@@ -31,6 +31,8 @@
CC=gcc
- CFLAGS += -Wall -DAGN_DATA_PATH='"$(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 $(AGN_OBJS)
inc/core/AgnVersion.h:
Modified: trunk/packages/aegean/trunk/debian/patches/follow_links
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/follow_links 2016-01-09 07:21:28 UTC (rev 21049)
+++ trunk/packages/aegean/trunk/debian/patches/follow_links 2016-01-09 12:30:24 UTC (rev 21050)
@@ -1,7 +1,9 @@
-Description: Follow_links
+Description: Follow links
+ Honor symlinks when copying files.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/src/ParsEval/pe_options.c
+++ b/src/ParsEval/pe_options.c
-@@ -265,7 +265,7 @@
+@@ -262,7 +262,7 @@
}
char copy_cmd[1024];
Modified: trunk/packages/aegean/trunk/debian/patches/includepaths
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/includepaths 2016-01-09 07:21:28 UTC (rev 21049)
+++ trunk/packages/aegean/trunk/debian/patches/includepaths 2016-01-09 12:30:24 UTC (rev 21050)
@@ -1,25 +1,9 @@
-Description: Includepaths
+Description: Adjust include paths
+ Debian uses /usr/include.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/Makefile
+++ b/Makefile
-@@ -1,8 +1,6 @@
- #---Begin configuration---#
- #---Begin configuration---#
-
--prefix=/usr/local
--
- #----End configuration----#
- #----End configuration----#
-
-@@ -29,7 +27,7 @@
-
- # Compilation settings
- CC=gcc
--CFLAGS=-Wall -DAGN_DATA_PATH='"$(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 <sascha at steinbiss.name>
--- 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 <sascha at steinbiss.name>
+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++;
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