[med-svn] [Git][med-team/genometools][master] 9 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Sun Oct 28 14:11:10 GMT 2018
Andreas Tille pushed to branch master at Debian Med / genometools
Commits:
b56add75 by Andreas Tille at 2018-10-28T11:40:18Z
debhelper 11
- - - - -
f094d915 by Andreas Tille at 2018-10-28T11:43:23Z
Point Vcs fields to salsa.debian.org
- - - - -
0acb5529 by Andreas Tille at 2018-10-28T11:43:23Z
Standards-Version: 4.2.1
- - - - -
1753c83a by Andreas Tille at 2018-10-28T11:43:24Z
Secure URI in copyright format
- - - - -
1f66df0b by Andreas Tille at 2018-10-28T12:05:01Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
3cbf05e7 by Andreas Tille at 2018-10-28T12:06:59Z
Do not parse d/changelog
- - - - -
ec5a4b8a by Andreas Tille at 2018-10-28T13:42:34Z
Fix docbase location
- - - - -
ee895fe6 by Andreas Tille at 2018-10-28T13:54:13Z
Remove unused patches
- - - - -
9ea70945 by Andreas Tille at 2018-10-28T14:10:08Z
Upload to unstable
- - - - -
18 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/genometools-doc.doc-base
- − debian/patches/add-libtre
- − debian/patches/arm64-no-m64
- − debian/patches/fix-unsigned-char
- − debian/patches/fix_caption.patch
- − debian/patches/manual_fixed_dates.patch
- − debian/patches/mips-64
- − debian/patches/sort-inputs
- − debian/patches/spelling
- − debian/patches/spelling.patch
- − debian/patches/strip-nonpublic
- − debian/patches/typecheck-fixes
- − debian/patches/use-pkgconfig
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+genometools (1.5.10+ds-3) unstable; urgency=medium
+
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.2.1
+ * Secure URI in copyright format
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Do not parse d/changelog
+ * Remove unused patches
+
+ -- Andreas Tille <tille at debian.org> Sun, 28 Oct 2018 14:54:51 +0100
+
genometools (1.5.10+ds-2) unstable; urgency=medium
* Ensure that src/external is not repopulated by patches.
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Sascha Steinbiss <satta at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
dh-python,
liblua5.1-0-dev,
lua-md5-dev,
@@ -32,9 +32,9 @@ Build-Depends: debhelper (>= 9),
docbook-xml,
faketime,
imagemagick
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/genometools.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/genometools.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/genometools
+Vcs-Git: https://salsa.debian.org/med-team/genometools.git
Homepage: http://genometools.org
Package: genometools
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: genometools
Source: http://genometools.org
Files-Excluded: src/external
=====================================
debian/genometools-doc.doc-base
=====================================
@@ -11,4 +11,4 @@ Abstract: User manuals for GenomeTools
Section: Science/Biology
Format: PDF
-Files: /usr/share/doc/genometools-doc/*.pdf.gz
+Files: /usr/share/doc/genometools/*.pdf.gz
=====================================
debian/patches/add-libtre deleted
=====================================
@@ -1,16 +0,0 @@
-Description: add soname to linker call in Makefile
- Upstream Makefile does not build a shared object with soname or version
- number. This patch adds support for sonames, as well a symlink from
- the .so to the .so.X file.
-Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
---- a/Makefile
-+++ b/Makefile
-@@ -191,7 +191,7 @@
- # add necessary shared lib dependencies then not building them ourselves
- ifeq ($(useshared),yes)
- DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
-- -llua5.1-filesystem -llua5.1-des56 -lbam
-+ -llua5.1-filesystem -llua5.1-des56 -lbam -ltre
- else
- DEPLIBS:=
- endif
=====================================
debian/patches/arm64-no-m64 deleted
=====================================
@@ -1,13 +0,0 @@
-Description: Do not use -m64 in arm64.
-Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
---- a/Makefile
-+++ b/Makefile
-@@ -308,7 +308,7 @@
- endif
-
- ifeq ($(m64),yes)
-- ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el))
-+ ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el aarch64))
- GT_CFLAGS += -m64
- GT_LDFLAGS += -m64
- SQLITE_CFLAGS += -m64
=====================================
debian/patches/fix-unsigned-char deleted
=====================================
@@ -1,117 +0,0 @@
-Description: Adapt code to work with char being unsigned by default.
-Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
---- a/src/core/safearith.c
-+++ b/src/core/safearith.c
-@@ -182,8 +182,10 @@
- gt_error_check(err);
-
- {
-+ /* This is not always true, e.g. on PPC and ARM!
-+ cf. http://www.network-theory.co.uk/docs/gccintro/gccintro_71.html
- gt_ensure(__MIN(char) == -128);
-- gt_ensure(__MAX(char) == 127);
-+ gt_ensure(__MAX(char) == 127); */
- gt_ensure(__MIN(unsigned char) == 0);
- gt_ensure(__MAX(unsigned char) == 255);
-
---- a/src/core/tokenizer.c
-+++ b/src/core/tokenizer.c
-@@ -45,7 +45,9 @@
-
- GtStr* gt_tokenizer_get_token(GtTokenizer *t)
- {
-- char c = EOF;
-+ char c;
-+ bool has_eof = true;
-+ int rval = 0;
- gt_assert(t);
-
- /* if we have no current token, get it if possible */
-@@ -53,32 +55,44 @@
- if (t->skip_comment_lines && gt_io_line_start(t->io)) {
- for (;;) {
- gt_assert(gt_io_line_start(t->io));
-- if ((gt_io_get_char(t->io, &c) != -1)) {
-- if (c == '#') {
-+ if ((gt_io_get_char(t->io, (char*) &c) != -1)) {
-+ if ((char) c == '#') {
- /* skip line */
- while ((gt_io_get_char(t->io, &c) != -1) && c != '\n');
-- c = EOF;
-+ has_eof = true;
- }
- else {
- gt_io_unget_char(t->io, c);
-+ has_eof = false;
- break;
- }
- }
-- else
-+ else {
-+ c = EOF;
- break;
-+ }
- }
-- }
-- while ((gt_io_get_char(t->io, &c) != -1) && c == ' '); /* skip blanks */
-+ } /* skip blanks */
-+ while (((rval = gt_io_get_char(t->io, &c)) != -1) && c == ' ');
-+ if (rval == -1)
-+ has_eof = true;
-+ else
-+ has_eof = false;
- do {
-- if (c != EOF) {
-+ if (!has_eof) {
- if (!t->token)
- t->token = gt_str_new();
- if (c == '\n')
- break;
- gt_str_append_char(t->token, c);
- }
-- } while ((gt_io_get_char(t->io, &c) != -1) && c != ' ' && c != '\n');
-- if (c == '\n' && c != EOF) {
-+ } while (((rval = gt_io_get_char(t->io, &c)) != -1)
-+ && c != ' ' && c != '\n');
-+ if (rval == -1)
-+ has_eof = true;
-+ else
-+ has_eof = false;
-+ if (c == '\n' && !has_eof) {
- gt_assert(t->token);
- gt_str_append_char(t->token, c);
- }
---- a/src/core/tokenizer.h
-+++ b/src/core/tokenizer.h
-@@ -33,7 +33,7 @@
- bool gt_tokenizer_has_token(GtTokenizer*);
- bool gt_tokenizer_line_start(const GtTokenizer*);
- void gt_tokenizer_next_token(GtTokenizer*); /* go to the next token */
--GtUword gt_tokenizer_get_line_number(const GtTokenizer*);
-+GtUword gt_tokenizer_get_line_number(const GtTokenizer*);
- const char* gt_tokenizer_get_filename(const GtTokenizer*);
- int gt_tokenizer_unit_test(GtError*);
- void gt_tokenizer_delete(GtTokenizer*);
---- a/src/core/trans_table.c
-+++ b/src/core/trans_table.c
-@@ -21,7 +21,7 @@
- #include "core/ma.h"
- #include "core/trans_table.h"
-
--#define GT_AMINOACIDFAIL -1
-+#define GT_AMINOACIDFAIL ((char) 0)
-
- /* The integer which a T is encoded to. */
- #define GT_T_CODE 0
---- a/src/extended/gff3_escaping.c
-+++ b/src/extended/gff3_escaping.c
-@@ -64,7 +64,8 @@
- unsigned char d;
- gt_assert(str && out);
- if (!(GtIsHexChar[(int) *(str+1)] & 2)
-- || !(GtIsHexChar[(int) *(str+2)] & 1)) {
-+ || !(GtIsHexChar[(int) *(str+2)] & 1)
-+ || !strncmp(str, "%7F", 3 * (sizeof (char)))) {
- return -1;
- }
- d = (GtHexToDec[(int) *(str+1)] << 4) | (GtHexToDec[(int) *(str+2)]);
=====================================
debian/patches/fix_caption.patch deleted
=====================================
@@ -1,13 +0,0 @@
-Description: change test caption to be less problematic
-Author: Sascha Steinbiss <satta at debian.org>
-Origin: https://github.com/genometools/genometools/commit/d86b83dda1eb43a5adf27f831b103f817e1dc48f#commitcomment-20423074
---- a/testdata/gt_sketch_textwidth.gff3
-+++ b/testdata/gt_sketch_textwidth.gff3
-@@ -1,6 +1,6 @@
- ##gff-version 3
- ##sequence-region ctg123 1 1497228
- ctg123 . gene 1000 2000 . + 0 ID=g00001;Name=thisisalongname123
--ctg123 . gene 2001 3000 . + 0 ID=g00002;Name=anotherlongname123
-+ctg123 . gene 2001 3000 . + 0 ID=g00002;Name=anotherlongname
- ctg123 . gene 3001 4000 . + 0 ID=g00003;Name=stillanotherlonglonglonglonglonglonglongname
- ctg123 . gene 4001 5000 . + 0 ID=g00004;Name=shortname
=====================================
debian/patches/manual_fixed_dates.patch deleted
=====================================
@@ -1,170 +0,0 @@
-From 3bf0e31b3a020c415d99d8661c5aca32647c7a6f Mon Sep 17 00:00:00 2001
-From: Sascha Steinbiss <ss34 at sanger.ac.uk>
-Date: Thu, 7 Apr 2016 10:25:25 +0100
-Subject: [PATCH] introduce dates for manuals
-
-IMHO manuals should have a specific date, and the build date should not be
-relevant here. This commit initialises the date fields in the manuals by
-setting the date to the last modification date of the file in git, as
-given by:
-
-for f in doc/manuals/*.tex; do
- export OUT=`TZ=UTC LC_ALL=C date -d "$(git log -1 --format='%aD' -- $f )" +'%d\/%m\/%Y'`;
- sed -ri "s/.begin.document./\\\date{$OUT}\n\\\begin{document}/g" $f;
- unset OUT;
-done
----
- doc/manuals/annotationsketch.tex | 1 +
- doc/manuals/genomediff.tex | 1 +
- doc/manuals/hop.tex | 1 +
- doc/manuals/ltrdigest.tex | 1 +
- doc/manuals/ltrharvest.tex | 1 +
- doc/manuals/mgth.tex | 1 +
- doc/manuals/packedindex.tex | 1 +
- doc/manuals/readjoiner.tex | 1 +
- doc/manuals/repfind.tex | 1 +
- doc/manuals/tagerator.tex | 1 +
- doc/manuals/tallymer.tex | 1 +
- doc/manuals/uniquesub.tex | 1 +
- 12 files changed, 12 insertions(+)
-
---- a/doc/manuals/annotationsketch.tex
-+++ b/doc/manuals/annotationsketch.tex
-@@ -50,6 +50,7 @@
- \subject{Supplementary Information}
- \author{Sascha Steinbiss, Gordon Gremme, Christin Sch\"arfer, Malte Mader\\ and Stefan Kurtz}
-
-+\date{11/07/2012}
- \begin{document}
-
- \maketitle
---- a/doc/manuals/genomediff.tex
-+++ b/doc/manuals/genomediff.tex
-@@ -59,6 +59,7 @@
- \url{willrodt at zbh.uni-hamburg.de}\\
- \end{tabular}}
-
-+\date{02/10/2012}
- \begin{document}
- %\tsuhhfamily
- \maketitle
---- a/doc/manuals/hop.tex
-+++ b/doc/manuals/hop.tex
-@@ -32,6 +32,7 @@
- \url{kurtz at zbh.uni-hamburg.de}\\[1cm]
- \end{tabular}}
-
-+\date{15/05/2014}
- \begin{document}
- \maketitle
-
---- a/doc/manuals/ltrdigest.tex
-+++ b/doc/manuals/ltrdigest.tex
-@@ -41,6 +41,7 @@
- \end{tabular}
- \end{tabular}}
-
-+\date{26/08/2013}
- \begin{document}
- \maketitle
-
---- a/doc/manuals/ltrharvest.tex
-+++ b/doc/manuals/ltrharvest.tex
-@@ -41,6 +41,7 @@
- \url{http://www.biomedcentral.com/1471-2105/9/18}
- \end{tabular}
- \end{tabular}}
-+\date{26/08/2013}
- \begin{document}
- \maketitle
-
---- a/doc/manuals/mgth.tex
-+++ b/doc/manuals/mgth.tex
-@@ -37,6 +37,7 @@
- 20146 Hamburg\\
- Germany\\[1cm]
- \end{tabular}}
-+\date{26/08/2013}
- \begin{document}
- \maketitle
-
---- a/doc/manuals/packedindex.tex
-+++ b/doc/manuals/packedindex.tex
-@@ -38,6 +38,7 @@
- % BMC Bioinformatics 2008, 9:18
- \end{tabular}
- \end{tabular}}
-+\date{26/08/2013}
- \begin{document}
- \maketitle
-
---- a/doc/manuals/readjoiner.tex
-+++ b/doc/manuals/readjoiner.tex
-@@ -45,6 +45,7 @@
- \url{kurtz at zbh.uni-hamburg.de}\\[1cm]
- \end{tabular}}
-
-+\date{18/02/2014}
- \begin{document}
- \maketitle
-
---- a/doc/manuals/repfind.tex
-+++ b/doc/manuals/repfind.tex
-@@ -28,6 +28,7 @@
- University of Hamburg
- \end{tabular}}
-
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- This manual describes the options of the program \Repfind. It also gives
---- a/doc/manuals/tagerator.tex
-+++ b/doc/manuals/tagerator.tex
-@@ -22,6 +22,7 @@
- University of Hamburg
- \end{tabular}}
-
-+\date{26/08/2013}
- \begin{document}
- \maketitle
-
---- a/doc/manuals/tallymer.tex
-+++ b/doc/manuals/tallymer.tex
-@@ -95,6 +95,7 @@
- University of Hamburg
- \end{tabular}}
-
-+\date{26/08/2013}
- \begin{document}
- \maketitle
- This manual describes the \textit{Tallymer}-software, a collection of programs
---- a/doc/manuals/uniquesub.tex
-+++ b/doc/manuals/uniquesub.tex
-@@ -24,6 +24,7 @@
- University of Hamburg
- \end{tabular}}
-
-+\date{26/08/2013}
- \begin{document}
- \maketitle
-
---- a/doc/devguide/devguide.tex
-+++ b/doc/devguide/devguide.tex
-@@ -36,6 +36,7 @@
- \author{Sascha Steinbiss, Gordon Gremme and Stefan
- Kurtz\thanks{please send comments to:
- \texttt{steinbiss at zbh.uni-hamburg.de}}}
-+\date{18/02/2016}
-
-
- \begin{document}
---- a/doc/manuals/matstat.tex
-+++ b/doc/manuals/matstat.tex
-@@ -23,6 +23,7 @@
- Center for Bioinformatics,\\
- University of Hamburg
- \end{tabular}}
-+\date{26/01/2008}
-
- \begin{document}
- \maketitle
=====================================
debian/patches/mips-64 deleted
=====================================
@@ -1,21 +0,0 @@
-Description: Fix compilation on mips64.
-Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
---- a/Makefile
-+++ b/Makefile
-@@ -308,12 +308,10 @@
- endif
-
- ifeq ($(m64),yes)
-- ifneq ($(MACHINE),ia64)
-- ifneq ($(MACHINE),alpha)
-- GT_CFLAGS += -m64
-- GT_LDFLAGS += -m64
-- SQLITE_CFLAGS += -m64
-- endif
-+ ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el))
-+ GT_CFLAGS += -m64
-+ GT_LDFLAGS += -m64
-+ SQLITE_CFLAGS += -m64
- endif
- endif
-
=====================================
debian/patches/sort-inputs deleted
=====================================
@@ -1,78 +0,0 @@
-Description: Sort inputs
---- a/Makefile
-+++ b/Makefile
-@@ -115,7 +115,7 @@
- EXAMPLES_SRC:=src/example.c
- EXAMPLES_DEP:=$(EXAMPLES_SRC:%.c=obj/%.d)
-
--TOOLS_SRC:=$(wildcard src/tools/*.c)
-+TOOLS_SRC:=$(sort $(wildcard src/tools/*.c))
- TOOLS_OBJ:=$(TOOLS_SRC:%.c=obj/%.o)
- TOOLS_DEP:=$(TOOLS_SRC:%.c=obj/%.d)
-
-@@ -449,7 +449,7 @@
- endif
-
- # the GenomeTools library
--LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard $(DIR)/*.c))
-+LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard $(DIR)/*.c)))
- # remove AnnotationSketch-only bindings
- LIBGENOMETOOLS_PRESRC:=$(filter-out $(CAIRO_FILTER_OUT),\
- $(LIBGENOMETOOLS_PRESRC))
-@@ -664,7 +664,7 @@
- @test -d $(@D) || mkdir -p $(@D)
- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $^ -lm $(LUA_LDLIB) -o $@
-
--API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard $(DIR)/*_api.h))
-+API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard $(DIR)/*_api.h)))
-
- obj/public_symbols.lst: $(API_HEADERS) $(LIBGENOMETOOLS_SRC)
- @echo '[gathering public API symbols to $@]'
-@@ -999,8 +999,8 @@
- ABTOOLS=${shell grep -l Blaufelder src/tools/*.c}
-
- ALLSPLINT=${addprefix obj/,${notdir ${subst .c,.splint,\
-- ${filter-out ${EISFILES},${wildcard ${CURDIR}/src/match/*.c}}\
-- ${wildcard ${CURDIR}/src/ltr/*.c}\
-+ ${filter-out ${EISFILES},${sort ${wildcard ${CURDIR}/src/match/*.c}}}\
-+ ${sort ${wildcard ${CURDIR}/src/ltr/*.c}}\
- ${SKTOOLS} ${SKCORE} ${SKEXT} \
- ${DWTOOLS} ${DWCORE} ${DWEXT} \
- ${GGTOOLS} ${GGCORE} ${GGEXT} \
---- a/gtscripts/gtdoc.lua
-+++ b/gtscripts/gtdoc.lua
-@@ -104,6 +104,25 @@
- end
- end
-
-+local function iter (a, i) -- taken from PiL, page 59
-+ i = i + 1
-+ local v = a[i]
-+ if v then
-+ return i, v
-+ end
-+end
-+
-+function sorted_dir(dir)
-+ local entries = {}
-+ local i = 0
-+ for name in lfs.dir(dir) do
-+ i = i + 1
-+ entries[i] = name
-+ end
-+ table.sort(entries)
-+ return iter, entries, 0
-+end
-+
- local export = nil
- local is_lua = nil
-
-@@ -127,7 +146,7 @@
- for _, v in ipairs(export) do
- local filename = gt_home .. "/" .. v
- if is_dir(filename) then
-- for f in lfs.dir(filename) do
-+ for _, f in sorted_dir(filename) do
- local filename = filename .. "/" .. f
- process_file(filename, be_verbose, is_lua)
- end
=====================================
debian/patches/spelling deleted
=====================================
@@ -1,5 +0,0 @@
-Description: fix spelling issues
-Author: Sascha Steinbiss <satta at debian.org>
-Forwarded: https://github.com/genometools/genometools/pull/727, https://github.com/genometools/genometools/pull/762, https://github.com/genometools/genometools/pull/767
-Applied-Upstream: 1.5.9, commit:f47cc4a6e13d037d6342b0213a5739031ada59c1
-Last-Update: 2016-03-15
=====================================
debian/patches/spelling.patch deleted
=====================================
@@ -1,117 +0,0 @@
-Description: fix minor spelling issues
-Author: Sascha Steinbiss <satta at debian.org>
---- a/src/extended/condenseq_creator.c
-+++ b/src/extended/condenseq_creator.c
-@@ -1723,7 +1723,7 @@
- if (!had_err) {
- if (gt_showtime_enabled())
- gt_timer_show_progress(timer, "write data, alphabet", stderr);
-- gt_log_log(GT_WU " kmer positons in final kmer_db",
-+ gt_log_log(GT_WU " kmer positions in final kmer_db",
- gt_kmer_database_get_kmer_count(condenseq_creator->kmer_db));
- gt_log_log(GT_WU " xdrop calls.", ces_c_xdrops);
- gt_log_log(GT_WU " uniques", condenseq_creator->ces->udb_nelems);
---- a/src/extended/intset.h
-+++ b/src/extended/intset.h
-@@ -74,7 +74,7 @@
- size_t gt_intset_best_memory_size(GtUword maxelement, GtUword num_of_elems);
-
- /* Write <intset> to file <fp>. Fails with exit on IO-error. Returns NULL if
-- data error occures and writes it to <err>, <intset> will be deleted at that
-+ data error occurs and writes it to <err>, <intset> will be deleted at that
- point. */
- GtIntset* gt_intset_write(GtIntset *intset, FILE *fp, GtError *err);
-
---- a/src/extended/wtree_encseq.c
-+++ b/src/extended/wtree_encseq.c
-@@ -84,7 +84,7 @@
-
- if (bit == 0) {
- pos = gt_compressed_bitsequence_rank_0(we->c_bits, node_start + pos) -
-- zero_rank_prefix - 1; /*convert count (rank) to positon */
-+ zero_rank_prefix - 1; /*convert count (rank) to position */
- alpha_end = middle;
- node_start += we->parent_instance.members->length;
- node_size = left_child_size;
-@@ -96,7 +96,7 @@
- one_rank_prefix =
- gt_compressed_bitsequence_rank_1(we->c_bits, node_start - 1);
- pos = gt_compressed_bitsequence_rank_1(we->c_bits, node_start + pos) -
-- one_rank_prefix - 1; /*convert count (rank) to positon */
-+ one_rank_prefix - 1; /*convert count (rank) to position */
- alpha_start = middle + 1;
- node_size =
- gt_compressed_bitsequence_rank_1(we->c_bits,
---- a/src/match/seqabstract.h
-+++ b/src/match/seqabstract.h
-@@ -71,7 +71,7 @@
- /* return the length of <sa> */
- GtUword gt_seqabstract_length(const GtSeqabstract *sa);
-
--/* return character at positon <idx> (relative to <startpos>) of <sa> */
-+/* return character at position <idx> (relative to <startpos>) of <sa> */
- GtUchar gt_seqabstract_encoded_char(const GtSeqabstract *sa,
- GtUword idx);
-
---- a/src/match/sfx-diffcov.c
-+++ b/src/match/sfx-diffcov.c
-@@ -491,7 +491,7 @@
- return countderived;
- }
-
--static int dc_compareCodeatpositon(const void *vala,const void *valb)
-+static int dc_compareCodeatposition(const void *vala,const void *valb)
- {
- const Codeatposition *a = (const Codeatposition *) vala;
- const Codeatposition *b = (const Codeatposition *) valb;
-@@ -516,7 +516,7 @@
- return 0;
- }
-
--static void dc_validate_samplepositons(const GtDifferencecover *dcov)
-+static void dc_validate_samplepositions(const GtDifferencecover *dcov)
- {
- GtUword pos;
- unsigned int modvalue;
-@@ -1268,7 +1268,7 @@
- gt_assert(codelist.spaceCodeatposition != NULL);
- qsort(codelist.spaceCodeatposition,
- (size_t) codelist.nextfreeCodeatposition,
-- sizeof (*codelist.spaceCodeatposition),dc_compareCodeatpositon);
-+ sizeof (*codelist.spaceCodeatposition),dc_compareCodeatposition);
- }
- if (dcov->effectivesamplesize > 0)
- {
-@@ -1690,7 +1690,7 @@
- printf("v=%u (size=%u)\n",dcov->vparam,dcov->size);
- if (withcheck)
- {
-- dc_validate_samplepositons(dcov);
-+ dc_validate_samplepositions(dcov);
- }
- dc_differencecover_sortsample(dcov,NULL,NULL,NULL,withcheck);
- gt_differencecover_delete(dcov);
---- a/src/tools/gt_kmer_database.c
-+++ b/src/tools/gt_kmer_database.c
-@@ -126,8 +126,8 @@
- gt_option_exclude(option_mean_cutoff, option);
-
- /* -disable_prune */
-- option = gt_option_new_bool("disable_prune", "disables the removel of kmers, "
-- "which occure more often than the cutoff.",
-+ option = gt_option_new_bool("disable_prune", "disables the removal of kmers "
-+ "which occur more often than the cutoff.",
- &arguments->prune, false);
- gt_option_parser_add_option(op, option);
- gt_option_imply(option, option_use_cutoff);
---- a/src/tools/gt_show_seedext.c
-+++ b/src/tools/gt_show_seedext.c
-@@ -119,7 +119,7 @@
-
- /* -sort */
- op_sortmatches = gt_option_new_bool("sort","sort matches in ascending order "
-- "of their end positon on the "
-+ "of their end position on the "
- "query",
- &arguments->sortmatches,false);
- gt_option_parser_add_option(op, op_sortmatches);
=====================================
debian/patches/strip-nonpublic deleted
=====================================
@@ -1,17 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -894,8 +894,13 @@
- $(RANLIB) $(prefix)/lib/libgenometools.a
- endif
- ifneq ($(sharedlib),no)
-- cp lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) $(prefix)/lib
-+ find src -name '*_api.h' | xargs egrep -ho '(gt_[0-9a-zA-Z_]+)(\[|\()' \
-+ | sort | uniq | sed s'/.$$//' > apisyms
-+ objcopy --strip-all --keep-symbols apisyms \
-+ lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) \
-+ $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION)
- ln -fs $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)
-+ rm apisyms
- endif
- @echo '[build config script $(@F)]'
- sed -e 's!@CC@!$(CC)!' -e 's!@CFLAGS@!$(EXP_CFLAGS)!' \
=====================================
debian/patches/typecheck-fixes deleted
=====================================
@@ -1,224 +0,0 @@
-Description: Type conversion problem fixes.
-Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
---- a/src/gtlua/encseq_lua.c
-+++ b/src/gtlua/encseq_lua.c
-@@ -80,8 +80,10 @@
- GtReadmode readmode;
- reader = check_encseq_reader(L, 1);
- encseq = check_encseq(L, 2);
-- readmode = luaL_checknumber(L, 3);
-- startpos = luaL_checknumber(L, 4);
-+ readmode = luaL_checklong(L, 3);
-+ startpos = luaL_checklong(L, 4);
-+ luaL_argcheck(L, readmode <= 3, 3,
-+ "invalid readmode value, must be <= 3");
- luaL_argcheck(L, startpos < gt_encseq_total_length(*encseq), 4,
- "cannot exceed total length of encoded sequence");
- gt_encseq_reader_reinit_with_readmode(*reader, *encseq, readmode, startpos);
-@@ -113,10 +115,12 @@
- int readmode;
- unsigned char cc;
- encseq = check_encseq(L, 1);
-- pos = luaL_checknumber(L, 2);
-- readmode = luaL_checknumber(L, 3);
-+ pos = luaL_checklong(L, 2);
-+ readmode = luaL_checklong(L, 3);
- luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
- "cannot exceed total length of encoded sequence");
-+ luaL_argcheck(L, readmode <= 3, 3,
-+ "invalid readmode value, must be <= 3");
- cc = gt_encseq_get_encoded_char(*encseq, pos, readmode);
- lua_pushnumber(L, cc);
- return 1;
-@@ -129,10 +133,12 @@
- int readmode;
- char cc;
- encseq = check_encseq(L, 1);
-- pos = luaL_checknumber(L, 2);
-- readmode = luaL_checknumber(L, 3);
-+ pos = luaL_checklong(L, 2);
-+ readmode = luaL_checklong(L, 3);
- luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
- "cannot exceed total length of encoded sequence");
-+ luaL_argcheck(L, readmode <= 3, 3,
-+ "invalid readmode value, must be <= 3");
- cc = gt_encseq_get_decoded_char(*encseq, pos, readmode);
- lua_pushlstring(L, &cc, sizeof (char));
- return 1;
-@@ -192,8 +198,8 @@
- GtUword from, to;
- unsigned char *string;
- encseq = check_encseq(L, 1);
-- from = luaL_checknumber(L, 2);
-- to = luaL_checknumber(L, 3);
-+ from = luaL_checklong(L, 2);
-+ to = luaL_checklong(L, 3);
- luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
- luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
- "cannot exceed total length of encoded sequence");
-@@ -209,8 +215,8 @@
- GtUword from, to;
- char *string;
- encseq = check_encseq(L, 1);
-- from = luaL_checknumber(L, 2);
-- to = luaL_checknumber(L, 3);
-+ from = luaL_checklong(L, 2);
-+ to = luaL_checklong(L, 3);
- luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
- luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
- "cannot exceed total length of encoded sequence");
-@@ -226,7 +232,7 @@
- GtEncseq **encseq;
- GtUword pos;
- encseq = check_encseq(L, 1);
-- pos = luaL_checknumber(L, 2);
-+ pos = luaL_checklong(L, 2);
- luaL_argcheck(L, pos < gt_encseq_num_of_sequences(*encseq), 2,
- "cannot exceed number of sequences");
- lua_pushnumber(L, gt_encseq_seqlength(*encseq, pos));
-@@ -238,7 +244,7 @@
- GtEncseq **encseq;
- GtUword pos;
- encseq = check_encseq(L, 1);
-- pos = luaL_checknumber(L, 2);
-+ pos = luaL_checklong(L, 2);
- luaL_argcheck(L, pos < gt_encseq_num_of_sequences(*encseq), 2,
- "cannot exceed number of sequences");
- lua_pushnumber(L, gt_encseq_seqstartpos(*encseq, pos));
-@@ -250,7 +256,7 @@
- GtEncseq **encseq;
- GtUword pos;
- encseq = check_encseq(L, 1);
-- pos = luaL_checknumber(L, 2);
-+ pos = luaL_checklong(L, 2);
- luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
- "cannot exceed total length of encoded sequence");
- lua_pushnumber(L, gt_encseq_seqnum(*encseq, pos));
-@@ -279,7 +285,7 @@
- GtUword seqno, desclen;
- const char *string;
- encseq = check_encseq(L, 1);
-- seqno = luaL_checknumber(L, 2);
-+ seqno = luaL_checklong(L, 2);
- luaL_argcheck(L, seqno < gt_encseq_num_of_sequences(*encseq), 2,
- "cannot exceed number of sequences");
- string = gt_encseq_description(*encseq, &desclen, seqno);
-@@ -300,7 +306,7 @@
- GtEncseq **encseq;
- GtUword fileno;
- encseq = check_encseq(L, 1);
-- fileno = luaL_checknumber(L, 2);
-+ fileno = luaL_checklong(L, 2);
- luaL_argcheck(L, fileno < gt_encseq_num_of_files(*encseq), 2,
- "cannot exceed number of files");
- lua_pushnumber(L, gt_encseq_effective_filelength(*encseq, fileno));
-@@ -312,7 +318,7 @@
- GtEncseq **encseq;
- GtUword fileno;
- encseq = check_encseq(L, 1);
-- fileno = luaL_checknumber(L, 2);
-+ fileno = luaL_checklong(L, 2);
- luaL_argcheck(L, fileno < gt_encseq_num_of_files(*encseq), 2,
- "cannot exceed number of files");
- lua_pushnumber(L, gt_encseq_filestartpos(*encseq, fileno));
-@@ -324,7 +330,7 @@
- GtEncseq **encseq;
- GtUword pos;
- encseq = check_encseq(L, 1);
-- pos = luaL_checknumber(L, 2);
-+ pos = luaL_checklong(L, 2);
- luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
- "cannot exceed total length of encoded sequence");
- lua_pushnumber(L, gt_encseq_filenum(*encseq, pos));
-@@ -397,8 +403,10 @@
- GtUword startpos;
- GtReadmode readmode;
- encseq = check_encseq(L, 1);
-- readmode = luaL_checknumber(L, 2);
-- startpos = luaL_checknumber(L, 3);
-+ readmode = luaL_checklong(L, 2);
-+ startpos = luaL_checklong(L, 3);
-+ luaL_argcheck(L, readmode <= 3, 2,
-+ "invalid readmode value, must be <= 3");
- luaL_argcheck(L, startpos < gt_encseq_total_length(*encseq), 3,
- "cannot exceed total length of encoded sequence");
- reader = gt_encseq_create_reader_with_readmode(*encseq, readmode, startpos);
---- a/src/gtlua/mathsupport_lua.c
-+++ b/src/gtlua/mathsupport_lua.c
-@@ -21,7 +21,7 @@
-
- static int gt_lua_mathsupport_rand_max(lua_State *L)
- {
-- GtUword max = luaL_checknumber(L, 1);
-+ GtUword max = luaL_checklong(L, 1);
-
- lua_pushnumber(L, gt_rand_max(max));
- return 1;
---- a/src/match/eis-bwtseq.c
-+++ b/src/match/eis-bwtseq.c
-@@ -473,7 +473,7 @@
- CONTEXT_INTERVAL = 128,
- };
-
--int
-+enum verifyBWTSeqErrCode
- gt_BWTSeqVerifyIntegrity(BWTSeq *bwtSeq, const char *projectName,
- int checkFlags,
- GtUword tickPrint, FILE *fp,
---- a/src/tools/gt_tir.c
-+++ b/src/tools/gt_tir.c
-@@ -394,9 +394,9 @@
- GtNodeVisitor *pdom_v;
- ms = gt_pdom_model_set_new(arguments->hmm_files, err);
- if (ms != NULL) {
-- pdom_v = gt_ltrdigest_pdom_visitor_new(ms, arguments->cutoff,
-+ pdom_v = gt_ltrdigest_pdom_visitor_new(ms, arguments->evalue_cutoff,
- arguments->chain_max_gap_length,
-- arguments->evalue_cutoff, rmap,
-+ arguments->cutoff, rmap,
- err);
- if (pdom_v == NULL)
- had_err = -1;
---- a/testdata/gtscripts/encseq.lua
-+++ b/testdata/gtscripts/encseq.lua
-@@ -60,6 +60,9 @@
- rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 100, 0)
- assert(not rval)
- assert(string.find(err, "cannot exceed"))
-+ rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 10, 6)
-+ assert(not rval)
-+ assert(string.find(err, "invalid readmode"))
- end
-
- function run_test_seq_startpos(es)
-@@ -99,6 +102,9 @@
- rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
- assert(not rval)
- assert(string.find(err, "cannot exceed"))
-+ rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 10, 6)
-+ assert(not rval)
-+ assert(string.find(err, "invalid readmode"))
- end
-
- function run_test_file_length_protein(es)
-@@ -128,7 +134,7 @@
- rval, err = pcall(GenomeTools_encseq.extract_encoded, es, 300, 500)
- assert(not rval)
- assert(string.find(err, "cannot exceed"))
--
-+
- end
-
- function run_test_seq_substr_decoded(es, seq1, seq2)
-@@ -168,7 +174,10 @@
- rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 0, 300)
- assert(not rval)
- assert(string.find(err, "cannot exceed"))
--end
-+ rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 7, 3)
-+ assert(not rval)
-+ assert(string.find(err, "invalid readmode"))
-+end
-
- ee = gt.encseq_encoder_new()
- ee:encode({dnaseqfile}, "dnaseqfile")
=====================================
debian/patches/use-pkgconfig deleted
=====================================
@@ -1,53 +0,0 @@
-From afaed82084071e9d11663b7ce593fa83e6eabbe5 Mon Sep 17 00:00:00 2001
-From: Justus Winter <justus at gnupg.org>
-Date: Fri, 19 Feb 2016 14:06:41 +0100
-Subject: [PATCH 1/6] Makefile: Drop spurious '$(3)'
-
-* Makefile: Drop spurious '$(3)', likely a left-over from copying
-'COMPILE_template'.
----
- Makefile | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
---- /dev/null
-+++ b/src/external/lpeg-0.10.2/lua-lpeg.h
-@@ -0,0 +1,39 @@
-+/*
-+** $Id: lpeg.h,v 1.1 2009/12/23 16:15:36 roberto Exp $
-+** LPeg - PEG pattern matching for Lua
-+** Copyright 2009, Lua.org & PUC-Rio (see 'lpeg.html' for license)
-+** written by Roberto Ierusalimschy
-+*/
-+
-+#ifndef lpeg_h
-+#define lpeg_h
-+
-+#include "lua.h"
-+
-+int luaopen_lpeg (lua_State *L);
-+
-+#define KEYNEWPATT "lpeg.newpf"
-+
-+
-+/*
-+** type of extension functions that define new "patterns" for LPEG
-+** It should return the new current position or NULL if match fails
-+*/
-+typedef const char *(*PattFunc) (const char *s, /* current position */
-+ const char *e, /* string end */
-+ const char *o, /* string start */
-+ const void *ud); /* user data */
-+
-+/*
-+** function to create new patterns based on 'PattFunc' functions.
-+** This function is available at *registry[KEYNEWPATT]. (Notice
-+** the extra indirection; the userdata at the registry points to
-+** a variable that points to the function. In ANSI C a void* cannot
-+** point to a function.)
-+*/
-+typedef void (*Newpf) (lua_State *L,
-+ PattFunc f, /* pattern */
-+ const void *ud, /* (user) data to be passed to 'f' */
-+ size_t l); /* size of data to be passed to 'f' */
-+
-+#endif
=====================================
debian/rules
=====================================
@@ -5,13 +5,14 @@
export DESTDIR=$(CURDIR)/debian/tmp
export DH_ALWAYS_EXCLUDE=.gitignore
export PATH := $(CURDIR)/debian/strip-nondeterminism:$(PATH)
-export SOURCE_DATE_EPOCH = $(shell date -d "$$(dpkg-parsechangelog -SDate)" +%s)
+
+include /usr/share/dpkg/default.mk
+
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
DARCH:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH= | cut -f 2 -d'=')
BITS:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH_BITS= | cut -f 2 -d'=')
-
ifeq ($(DARCH),x32)
X32:=yes
else
@@ -57,8 +58,10 @@ override_dh_auto_build:
$(FAKETIME) dh_auto_build -- verbose=yes useshared=yes x32=$(X32) 64bit=$(64BIT) errorcheck=no all docs manuals
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
bin/gt -test
cd testsuite; ./testsuite.rb -keywords 'gt_sketch and not gt_python and not gt_ruby'
+endif
override_dh_auto_install:
dh_auto_install -- installmanpages useshared=yes \
View it on GitLab: https://salsa.debian.org/med-team/genometools/compare/a9a0de07038801f3bd495523818651d776f08dce...9ea7094540eef6c6e78cd20dbf19d01404813e19
--
View it on GitLab: https://salsa.debian.org/med-team/genometools/compare/a9a0de07038801f3bd495523818651d776f08dce...9ea7094540eef6c6e78cd20dbf19d01404813e19
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