Commit 0f57a25bfc78e9395cf4d1450faf455d70573f76 - genometools

+2

-0

debian/changelog less more

1	1
2	2	* Remove hardcoded number of threads from testsuite call.
3	3	Closes: #836283
	4	* Make build reproducible.
	5	- Remove absolute include path to make __FILE__ use relative paths.
4	6
5	7	-- Sascha Steinbiss <satta@debian.org> Thu, 01 Sep 2016 17:16:40 +0000
6	8

+3

-3

debian/patches/adding_soname less more

4	4	Author: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
5	5	--- a/Makefile
6	6	+++ b/Makefile
7		@@ -137,6 +137,7 @@
	7	@@ -138,6 +138,7 @@
8	8	SHARED_OBJ_NAME_EXT:=.so
9	9	SHARED:=-shared
10	10	endif

12	12
13	13	# compiled executables
14	14	GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c
15		@@ -621,8 +622,9 @@
	15	@@ -622,8 +623,9 @@
16	16	$(V_ECHO) "[link $(@F)]"
17	17	$(V_DO)test -d $(@D) \|\| mkdir -p $(@D)
18	18	$(V_DO)$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \

24	24
25	25	define PROGRAM_template
26	26	$(1): $(2)
27		@@ -989,7 +991,8 @@
	27	@@ -990,7 +992,8 @@
28	28	$(RANLIB) $(prefix)/lib/libgenometools.a
29	29	endif
30	30	ifneq ($(sharedlib),no)

+1

-1

debian/patches/ignore-m32-m64.patch less more

1	1	Author: Sascha Steinbiss <satta@debian.org>
2	2	--- a/Makefile
3	3	+++ b/Makefile
4		@@ -354,22 +354,6 @@
	4	@@ -355,22 +355,6 @@
5	5	endif
6	6	endif
7	7

+3

-3

debian/patches/libbam-fix less more

4	4
5	5	--- a/Makefile
6	6	+++ b/Makefile
7		@@ -600,6 +600,10 @@
	7	@@ -601,6 +601,10 @@
8	8	$(V_DO)$(RANLIB) $@
9	9	endif
10	10

15	15	lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ)
16	16	$(V_ECHO) "[link $(@F)]"
17	17	$(V_DO)test -d $(@D) \|\| mkdir -p $(@D)
18		@@ -618,13 +622,14 @@
	18	@@ -619,13 +623,14 @@
19	19	$(LIBGENOMETOOLS_OBJ) \
20	20	$(ADDITIONAL_SO_DEPS) \
21	21	$(ADDITIONAL_ZLIBS) \

31	31
32	32	define PROGRAM_template
33	33	$(1): $(2)
34		@@ -637,46 +642,55 @@
	34	@@ -638,46 +643,55 @@
35	35
36	36	$(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \
37	37	lib/libgenometools.a \

+0

-61

~~debian/patches/remove_png_timestamps~~ less more

0		Description: Remove_png_timestamps
1		--- a/Makefile
2		+++ b/Makefile
3		@@ -910,6 +910,10 @@
4		bin/examples/sketch_constructed gtdata/sketch/default.style \
5		www/genometools.org/htdocs/images/constructed.png
6		endif
7		+ mogrify -format jpg +set date:create +set date:modify \
8		+ -define png:exclude-chunk=time \
9		+ www/genometools.org/htdocs/images/*.png && \
10		+ rm -rf www/genometools.org/htdocs/images/*.png
11		sed -nf scripts/incl.sed \
12		www/genometools.org/htdocs/examples_tmpl.html \| \
13		sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \
14		--- a/doc/manuals/annotationsketch.tex
15		+++ b/doc/manuals/annotationsketch.tex
16		@@ -241,7 +241,7 @@
17		We will call the second part (after the ``\texttt{\|}'') of these track titles \emph{track identifier strings} in the rest of this document.
18
19		\begin{figure}[ht]
20		-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect.png}}
21		+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect}}
22		\caption{Default AnnotationSketch output for a simple GFF3 file with simple \emph{exon}$\to$\emph{mRNA} collapsing.}
23		\label{tsexample1}
24		\end{figure}
25		@@ -271,7 +271,7 @@
26		Using this track selector function would produce the desired result of separate tracks for the \emph{mRNA} features for each strand (see Fig. \ref{tsexample2}).
27
28		\begin{figure}[ht]
29		-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect.png}}
30		+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect}}
31		\caption{AnnotationSketch output with \texttt{strand\_track\_se\-lector()} track selector function. This image now shows separate tracks for plus and minus strand features.}
32		\label{tsexample2}
33		\end{figure}
34		@@ -313,7 +313,7 @@
35		This code results in the image shown in Fig.~\ref{tsexample3} :
36
37		\begin{figure}[ht]
38		-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect.png}}
39		+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect}}
40		\caption{\AnnotationSketch output with \texttt{filter\_track\_selector()} track selector function. This image now shows a separate track for features with a specific caption.}
41		\label{tsexample3}
42		\end{figure}
43		@@ -322,7 +322,7 @@
44		There are kinds of data which may be interesting to see together with annotation renderings, but that can not be expressed -- or only in a complicated way -- in GFF3 format. It may even be too difficult or counterintuitive to properly represent this data as typical \AnnotationSketch box graphics. For example, this may be sequence data, numerical sequence analysis results, or other kinds of data which does not fit into the simple ‘genomic feature’ scheme. For an example, see Fig. \ref{ctexample1}.
45
46		\begin{figure}[ht]
47		-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct.png}}
48		+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct}}
49		\caption{Example \AnnotationSketch output with a custom track at the bottom, displaying the GC content over a window size of 200 bp.}
50		\label{ctexample1}
51		\end{figure}
52		@@ -415,7 +415,7 @@
53		Running layout and drawing functions on this diagram then produces the desired image (see Fig.~\ref{ctexample2}
54
55		\begin{figure}[ht]
56		-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2.png}}
57		+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2}}
58		\caption{The example insertion site custom track (at the bottom), displaying three sample data points.}
59		\label{ctexample2}
60		\end{figure}

+70

-0

debian/patches/reproducible less more

	0	Description: Make build reproducible
	1	Author: Sascha Steinbiss <satta@debian.org>
	2	--- a/Makefile
	3	+++ b/Makefile
	4	@@ -16,6 +16,7 @@
	5	# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
	6	#
	7
	8	+CURDIR=.
	9	INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/obj
	10
	11	ifeq ($(shell pkg-config --version > /dev/null 2> /dev/null; echo $$?),0)
	12	@@ -910,6 +911,10 @@
	13	bin/examples/sketch_constructed gtdata/sketch/default.style \
	14	www/genometools.org/htdocs/images/constructed.png
	15	endif
	16	+ mogrify -format jpg +set date:create +set date:modify \
	17	+ -define png:exclude-chunk=time \
	18	+ www/genometools.org/htdocs/images/*.png && \
	19	+ rm -rf www/genometools.org/htdocs/images/*.png
	20	sed -nf scripts/incl.sed \
	21	www/genometools.org/htdocs/examples_tmpl.html \| \
	22	sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \
	23	--- a/doc/manuals/annotationsketch.tex
	24	+++ b/doc/manuals/annotationsketch.tex
	25	@@ -241,7 +241,7 @@
	26	We will call the second part (after the ``\texttt{\|}'') of these track titles \emph{track identifier strings} in the rest of this document.
	27
	28	\begin{figure}[ht]
	29	-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect.png}}
	30	+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect}}
	31	\caption{Default AnnotationSketch output for a simple GFF3 file with simple \emph{exon}$\to$\emph{mRNA} collapsing.}
	32	\label{tsexample1}
	33	\end{figure}
	34	@@ -271,7 +271,7 @@
	35	Using this track selector function would produce the desired result of separate tracks for the \emph{mRNA} features for each strand (see Fig. \ref{tsexample2}).
	36
	37	\begin{figure}[ht]
	38	-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect.png}}
	39	+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect}}
	40	\caption{AnnotationSketch output with \texttt{strand\_track\_se\-lector()} track selector function. This image now shows separate tracks for plus and minus strand features.}
	41	\label{tsexample2}
	42	\end{figure}
	43	@@ -313,7 +313,7 @@
	44	This code results in the image shown in Fig.~\ref{tsexample3} :
	45
	46	\begin{figure}[ht]
	47	-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect.png}}
	48	+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect}}
	49	\caption{\AnnotationSketch output with \texttt{filter\_track\_selector()} track selector function. This image now shows a separate track for features with a specific caption.}
	50	\label{tsexample3}
	51	\end{figure}
	52	@@ -322,7 +322,7 @@
	53	There are kinds of data which may be interesting to see together with annotation renderings, but that can not be expressed -- or only in a complicated way -- in GFF3 format. It may even be too difficult or counterintuitive to properly represent this data as typical \AnnotationSketch box graphics. For example, this may be sequence data, numerical sequence analysis results, or other kinds of data which does not fit into the simple ‘genomic feature’ scheme. For an example, see Fig. \ref{ctexample1}.
	54
	55	\begin{figure}[ht]
	56	-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct.png}}
	57	+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct}}
	58	\caption{Example \AnnotationSketch output with a custom track at the bottom, displaying the GC content over a window size of 200 bp.}
	59	\label{ctexample1}
	60	\end{figure}
	61	@@ -415,7 +415,7 @@
	62	Running layout and drawing functions on this diagram then produces the desired image (see Fig.~\ref{ctexample2}
	63
	64	\begin{figure}[ht]
	65	-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2.png}}
	66	+\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2}}
	67	\caption{The example insertion site custom track (at the bottom), displaying three sample data points.}
	68	\label{ctexample2}
	69	\end{figure}

+1

-1

debian/patches/series less more

0		remove_png_timestamps
	0	reproducible
1	1	use-pkgconfig
2	2	adding_soname
3	3	libbam-fix

+1

-1

debian/patches/use-mx32 less more

0	0	Description: Use mx32
1	1	--- a/Makefile
2	2	+++ b/Makefile
3		@@ -354,17 +354,19 @@
	3	@@ -355,17 +355,19 @@
4	4	endif
5	5	endif
6	6