[med-svn] [Git][med-team/genometools][debian/buster-backports] 4 commits: use static images for AnnotationSketch manual
Sascha Steinbiss
gitlab at salsa.debian.org
Wed Jul 29 12:14:43 BST 2020
Sascha Steinbiss pushed to branch debian/buster-backports at Debian Med / genometools
Commits:
b55f9502 by Sascha Steinbiss at 2020-02-09T09:53:54+01:00
use static images for AnnotationSketch manual
- - - - -
bb3bf8ab by Sascha Steinbiss at 2020-07-22T13:33:29+02:00
add patch to fix build on GCC10
- - - - -
b5308391 by Sascha Steinbiss at 2020-07-29T13:01:41+02:00
Merge branch 'master' into debian/buster-backports
- - - - -
cf1c416f by Sascha Steinbiss at 2020-07-29T13:13:47+02:00
rebuild for buster-backports
- - - - -
11 changed files:
- debian/changelog
- + debian/doc-imgs/callbacks.png
- + debian/doc-imgs/constructed.png
- + debian/doc-imgs/parsed.png
- debian/patches/adding_soname
- + debian/patches/gcc10.patch
- debian/patches/reproducible
- debian/patches/series
- debian/rules
- + debian/source/include-binaries
- − www/genometools.org/htdocs/libgenometools.html
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,24 @@
+genometools (1.6.1+ds-3~bpo10+1) buster-backports; urgency=medium
+
+ * Rebuild for buster-backports.
+
+ -- Sascha Steinbiss <satta at debian.org> Wed, 29 Jul 2020 13:01:49 +0200
+
+genometools (1.6.1+ds-3) unstable; urgency=medium
+
+ * Add patch to fix build on GCC 10.
+ Closes: #957268
+
+ -- Sascha Steinbiss <satta at debian.org> Wed, 22 Jul 2020 13:00:06 +0200
+
+genometools (1.6.1+ds-2) unstable; urgency=medium
+
+ * Use static images for AnnotationSketch documentation.
+ This improves reproducibility in cases where (on some platforms)
+ different runs would create different images.
+
+ -- Sascha Steinbiss <satta at debian.org> Sun, 09 Feb 2020 09:33:24 +0100
+
genometools (1.6.1+ds-1~bpo10+1) buster-backports; urgency=medium
* Rebuild for buster-backports.
=====================================
debian/doc-imgs/callbacks.png
=====================================
Binary files /dev/null and b/debian/doc-imgs/callbacks.png differ
=====================================
debian/doc-imgs/constructed.png
=====================================
Binary files /dev/null and b/debian/doc-imgs/constructed.png differ
=====================================
debian/doc-imgs/parsed.png
=====================================
Binary files /dev/null and b/debian/doc-imgs/parsed.png differ
=====================================
debian/patches/adding_soname
=====================================
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
define PROGRAM_template
$(1): $(2)
-@@ -1003,7 +1005,8 @@
+@@ -999,7 +1001,8 @@
$(RANLIB) $(prefix)/lib/libgenometools.a
endif
ifneq ($(sharedlib),no)
=====================================
debian/patches/gcc10.patch
=====================================
@@ -0,0 +1,88 @@
+From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001
+From: Sascha Steinbiss <satta at debian.org>
+Date: Wed, 22 Apr 2020 21:59:57 +0200
+Subject: [PATCH 1/2] make sure to not ignore snprintf output
+
+GCC 10 will warn about the (here intended) silent string truncation
+done by snprintf() unless the return value is handled.
+Obviously this will break the build as we use -Werror. We
+circumvent the problem by checking the output value and printing a
+warning if we notice a truncation.
+---
+ src/ltr/ltrdigest_file_out_stream.c | 17 ++++++++++++-----
+ 1 file changed, 12 insertions(+), 5 deletions(-)
+
+diff --git a/src/ltr/ltrdigest_file_out_stream.c b/src/ltr/ltrdigest_file_out_stream.c
+index 723b8cf9a..61325b693 100644
+--- a/src/ltr/ltrdigest_file_out_stream.c
++++ b/src/ltr/ltrdigest_file_out_stream.c
+@@ -1,5 +1,5 @@
+ /*
+- Copyright (c) 2008-2015 Sascha Steinbiss <sascha at steinbiss.name>
++ Copyright (c) 2008-2020 Sascha Steinbiss <sascha at steinbiss.name>
+ Copyright (c) 2008-2013 Center for Bioinformatics, University of Hamburg
+
+ Permission to use, copy, modify, and distribute this software for any
+@@ -33,6 +33,7 @@
+ #include "core/symbol.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
++#include "core/warning_api.h"
+ #include "extended/extract_feature_sequence.h"
+ #include "extended/feature_node.h"
+ #include "extended/feature_node_iterator_api.h"
+@@ -416,6 +417,8 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
+
+ if (!had_err) {
+ GtRange rng;
++ int ret = 0;
++
+ ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char));
+ (void) snprintf(ls->element.seqid,
+ GT_MIN((size_t) gt_str_length(sdesc),
+@@ -425,12 +428,16 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
+ if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen)
+ ls->element.seqid[ls->seqnamelen] = '\0';
+
+- (void) gt_ltrelement_format_description(&ls->element,
+- ls->seqnamelen,
+- desc,
+- (size_t) (GT_MAXFASTAHEADER-1));
++ ret = gt_ltrelement_format_description(&ls->element,
++ ls->seqnamelen,
++ desc,
++ (size_t) (GT_MAXFASTAHEADER-1));
++ if (ret < 0) {
++ gt_warning("FASTA header truncated: %s", desc);
++ }
+ gt_str_delete(sdesc);
+
++
+ /* output basic retrotransposon data */
+ lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR);
+ rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR);
+
+From 30ae36037228dc4ed174e8462f3489638e6f5e76 Mon Sep 17 00:00:00 2001
+From: Sascha Steinbiss <satta at debian.org>
+Date: Wed, 22 Apr 2020 22:01:00 +0200
+Subject: [PATCH 2/2] declare hashmap type as extern
+
+This fixes a build issue with GCC 10.
+Closes #941.
+---
+ src/mgth/metagenomethreader.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/mgth/metagenomethreader.h b/src/mgth/metagenomethreader.h
+index 92f16d498..7f76fffb9 100644
+--- a/src/mgth/metagenomethreader.h
++++ b/src/mgth/metagenomethreader.h
+@@ -221,7 +221,7 @@ typedef struct
+ } ParseStruct;
+
+ /* specific access mode of queryhash */
+-DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp,,)
++DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp, extern,)
+ DECLARE_SAFE_DEREF(GtUword *, ulp)
+
+ /* Funktion, mit der der Metagenomethreader gestartet wird
=====================================
debian/patches/reproducible
=====================================
@@ -19,17 +19,15 @@ Author: Sascha Steinbiss <satta at debian.org>
echo '$(EXP_CPPFLAGS) $(GT_CPPFLAGS)' | \
sed -e 's/\([^\]\)"/\1\\"/g' -e 's/^"/\\"/g' -e 's/$$/"/' \
-e 's/^/#define GT_CPPFLAGS "/'; \
-@@ -922,6 +923,10 @@
- bin/examples/sketch_constructed gtdata/sketch/default.style \
- www/genometools.org/htdocs/images/constructed.png
- endif
-+ mogrify -format jpg +set date:create +set date:modify \
-+ -define png:exclude-chunk=time \
-+ www/genometools.org/htdocs/images/*.png && \
-+ rm -rf www/genometools.org/htdocs/images/*.png
- sed -nf scripts/incl.sed \
- www/genometools.org/htdocs/examples_tmpl.html | \
- sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \
+@@ -911,7 +912,7 @@
+ > www/genometools.org/htdocs/libgenometools.html
+ bin/gt gtscripts/gtdoc.lua -lua -html $(CURDIR) \
+ > www/genometools.org/htdocs/docs.html
+-ifdef SKETCH_EXTRA_BINARIES
++ifdef ___SKETCH_EXTRA_BINARIES
+ bin/examples/sketch_parsed gtdata/sketch/default.style \
+ www/genometools.org/htdocs/images/parsed.png \
+ testdata/eden.gff3
--- a/doc/manuals/annotationsketch.tex
+++ b/doc/manuals/annotationsketch.tex
@@ -51,6 +51,7 @@
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ split-manuals
use-mx32
gtdoc-traverse-sorted
ignore-m32-m64.patch
+gcc10.patch
=====================================
debian/rules
=====================================
@@ -55,6 +55,7 @@ override_dh_auto_clean:
rm -rf obj
override_dh_auto_build:
+ cp debian/doc-imgs/*png www/genometools.org/htdocs/images
$(FAKETIME) dh_auto_build -- verbose=yes useshared=yes x32=$(X32) 64bit=$(64BIT) errorcheck=no all docs manuals
override_dh_auto_test:
=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1,3 @@
+debian/doc-imgs/constructed.png
+debian/doc-imgs/parsed.png
+debian/doc-imgs/callbacks.png
=====================================
www/genometools.org/htdocs/libgenometools.html deleted
=====================================
The diff for this file was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/genometools/-/compare/025c54c8736493aceb6cf2f726d75c09845c8241...cf1c416f6df665f670eaca5c6279a5c0c2a4f7b0
--
View it on GitLab: https://salsa.debian.org/med-team/genometools/-/compare/025c54c8736493aceb6cf2f726d75c09845c8241...cf1c416f6df665f670eaca5c6279a5c0c2a4f7b0
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200729/c5e4a19b/attachment-0001.html>
More information about the debian-med-commit
mailing list