diff -Nru genometools-1.5.10+ds/debian/changelog genometools-1.5.10+ds/debian/changelog --- genometools-1.5.10+ds/debian/changelog 2017-12-08 11:58:57.000000000 +0000 +++ genometools-1.5.10+ds/debian/changelog 2018-10-28 13:54:51.000000000 +0000 @@ -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 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. diff -Nru genometools-1.5.10+ds/debian/compat genometools-1.5.10+ds/debian/compat --- genometools-1.5.10+ds/debian/compat 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/compat 2018-10-28 13:54:51.000000000 +0000 @@ -1 +1 @@ -9 +11 diff -Nru genometools-1.5.10+ds/debian/control genometools-1.5.10+ds/debian/control --- genometools-1.5.10+ds/debian/control 2017-12-08 11:58:57.000000000 +0000 +++ genometools-1.5.10+ds/debian/control 2018-10-28 13:54:51.000000000 +0000 @@ -4,7 +4,7 @@ Andreas Tille 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 @@ 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 diff -Nru genometools-1.5.10+ds/debian/copyright genometools-1.5.10+ds/debian/copyright --- genometools-1.5.10+ds/debian/copyright 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/copyright 2018-10-28 13:54:51.000000000 +0000 @@ -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 diff -Nru genometools-1.5.10+ds/debian/genometools-doc.doc-base genometools-1.5.10+ds/debian/genometools-doc.doc-base --- genometools-1.5.10+ds/debian/genometools-doc.doc-base 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/genometools-doc.doc-base 2018-10-28 13:54:51.000000000 +0000 @@ -11,4 +11,4 @@ Section: Science/Biology Format: PDF -Files: /usr/share/doc/genometools-doc/*.pdf.gz +Files: /usr/share/doc/genometools/*.pdf.gz diff -Nru genometools-1.5.10+ds/debian/patches/add-libtre genometools-1.5.10+ds/debian/patches/add-libtre --- genometools-1.5.10+ds/debian/patches/add-libtre 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/add-libtre 1970-01-01 00:00:00.000000000 +0000 @@ -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 ---- a/Makefile -+++ b/Makefile -@@ -191,7 +191,7 @@ - # add necessary shared lib dependencies then not building them ourselves - ifeq ($(useshared),yes) - DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ -- -llua5.1-filesystem -llua5.1-des56 -lbam -+ -llua5.1-filesystem -llua5.1-des56 -lbam -ltre - else - DEPLIBS:= - endif diff -Nru genometools-1.5.10+ds/debian/patches/arm64-no-m64 genometools-1.5.10+ds/debian/patches/arm64-no-m64 --- genometools-1.5.10+ds/debian/patches/arm64-no-m64 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/arm64-no-m64 1970-01-01 00:00:00.000000000 +0000 @@ -1,13 +0,0 @@ -Description: Do not use -m64 in arm64. -Author: Sascha Steinbiss ---- a/Makefile -+++ b/Makefile -@@ -308,7 +308,7 @@ - endif - - ifeq ($(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 diff -Nru genometools-1.5.10+ds/debian/patches/fix_caption.patch genometools-1.5.10+ds/debian/patches/fix_caption.patch --- genometools-1.5.10+ds/debian/patches/fix_caption.patch 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/fix_caption.patch 1970-01-01 00:00:00.000000000 +0000 @@ -1,13 +0,0 @@ -Description: change test caption to be less problematic -Author: Sascha Steinbiss -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 diff -Nru genometools-1.5.10+ds/debian/patches/fix-unsigned-char genometools-1.5.10+ds/debian/patches/fix-unsigned-char --- genometools-1.5.10+ds/debian/patches/fix-unsigned-char 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/fix-unsigned-char 1970-01-01 00:00:00.000000000 +0000 @@ -1,117 +0,0 @@ -Description: Adapt code to work with char being unsigned by default. -Author: Sascha Steinbiss ---- 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)]); diff -Nru genometools-1.5.10+ds/debian/patches/manual_fixed_dates.patch genometools-1.5.10+ds/debian/patches/manual_fixed_dates.patch --- genometools-1.5.10+ds/debian/patches/manual_fixed_dates.patch 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/manual_fixed_dates.patch 1970-01-01 00:00:00.000000000 +0000 @@ -1,170 +0,0 @@ -From 3bf0e31b3a020c415d99d8661c5aca32647c7a6f Mon Sep 17 00:00:00 2001 -From: Sascha Steinbiss -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@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@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@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@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 diff -Nru genometools-1.5.10+ds/debian/patches/mips-64 genometools-1.5.10+ds/debian/patches/mips-64 --- genometools-1.5.10+ds/debian/patches/mips-64 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/mips-64 1970-01-01 00:00:00.000000000 +0000 @@ -1,21 +0,0 @@ -Description: Fix compilation on mips64. -Author: Sascha Steinbiss ---- 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 $(MACHINE),ia64 alpha mips64 mips64el)) -+ GT_CFLAGS += -m64 -+ GT_LDFLAGS += -m64 -+ SQLITE_CFLAGS += -m64 - endif - endif - diff -Nru genometools-1.5.10+ds/debian/patches/sort-inputs genometools-1.5.10+ds/debian/patches/sort-inputs --- genometools-1.5.10+ds/debian/patches/sort-inputs 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/sort-inputs 1970-01-01 00:00:00.000000000 +0000 @@ -1,78 +0,0 @@ -Description: Sort inputs ---- a/Makefile -+++ b/Makefile -@@ -115,7 +115,7 @@ - EXAMPLES_SRC:=src/example.c - EXAMPLES_DEP:=$(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 diff -Nru genometools-1.5.10+ds/debian/patches/spelling genometools-1.5.10+ds/debian/patches/spelling --- genometools-1.5.10+ds/debian/patches/spelling 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/spelling 1970-01-01 00:00:00.000000000 +0000 @@ -1,5 +0,0 @@ -Description: fix spelling issues -Author: Sascha Steinbiss -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 diff -Nru genometools-1.5.10+ds/debian/patches/spelling.patch genometools-1.5.10+ds/debian/patches/spelling.patch --- genometools-1.5.10+ds/debian/patches/spelling.patch 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/spelling.patch 1970-01-01 00:00:00.000000000 +0000 @@ -1,117 +0,0 @@ -Description: fix minor spelling issues -Author: Sascha Steinbiss ---- 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 to file . Fails with exit on IO-error. Returns NULL if -- data error occures and writes it to , will be deleted at that -+ data error occurs and writes it to , 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 */ - GtUword gt_seqabstract_length(const GtSeqabstract *sa); - --/* return character at positon (relative to ) of */ -+/* return character at position (relative to ) of */ - 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); diff -Nru genometools-1.5.10+ds/debian/patches/strip-nonpublic genometools-1.5.10+ds/debian/patches/strip-nonpublic --- genometools-1.5.10+ds/debian/patches/strip-nonpublic 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/strip-nonpublic 1970-01-01 00:00:00.000000000 +0000 @@ -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)!' \ diff -Nru genometools-1.5.10+ds/debian/patches/typecheck-fixes genometools-1.5.10+ds/debian/patches/typecheck-fixes --- genometools-1.5.10+ds/debian/patches/typecheck-fixes 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/typecheck-fixes 1970-01-01 00:00:00.000000000 +0000 @@ -1,224 +0,0 @@ -Description: Type conversion problem fixes. -Author: Sascha Steinbiss ---- 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") diff -Nru genometools-1.5.10+ds/debian/patches/use-pkgconfig genometools-1.5.10+ds/debian/patches/use-pkgconfig --- genometools-1.5.10+ds/debian/patches/use-pkgconfig 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/patches/use-pkgconfig 1970-01-01 00:00:00.000000000 +0000 @@ -1,53 +0,0 @@ -From afaed82084071e9d11663b7ce593fa83e6eabbe5 Mon Sep 17 00:00:00 2001 -From: Justus Winter -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 diff -Nru genometools-1.5.10+ds/debian/rules genometools-1.5.10+ds/debian/rules --- genometools-1.5.10+ds/debian/rules 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/rules 2018-10-28 13:54:51.000000000 +0000 @@ -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 @@ $(FAKETIME) dh_auto_build -- verbose=yes useshared=yes x32=$(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 \ diff -Nru genometools-1.5.10+ds/debian/upstream/metadata genometools-1.5.10+ds/debian/upstream/metadata --- genometools-1.5.10+ds/debian/upstream/metadata 2017-12-08 11:58:53.000000000 +0000 +++ genometools-1.5.10+ds/debian/upstream/metadata 2018-10-28 13:54:51.000000000 +0000 @@ -2,17 +2,25 @@ Bug-Database: https://github.com/genometools/genometools/issues Bug-Submit: https://github.com/genometools/genometools/issues/new Contact: Sascha Steinbiss -Homepage: http://genometools.org Reference: - Author: Gremme, Gordon and Steinbiss, Sascha and Kurtz, Stefan - Title: > - GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. - Journal: IEEE/ACM Transactions on Computational Biology and Bioinformatics - Year: 2013 - Volume: 10 - Number: 3 - Pages: 645-656 - DOI: 10.1109/TCBB.2013.68 - PMID: 24091398 - URL: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.68 + Author: Gremme, Gordon and Steinbiss, Sascha and Kurtz, Stefan + Title: > + GenomeTools: a comprehensive software library for efficient + processing of structured genome annotations. + Journal: > + IEEE/ACM Transactions on Computational Biology and Bioinformatics + Year: 2013 + Volume: 10 + Number: 3 + Pages: 645-656 + DOI: 10.1109/TCBB.2013.68 + PMID: 24091398 + URL: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.68 Repository: https://github.com/genometools/genometools.git +Registry: + - Name: OMICtools + Entry: OMICS_16119 + - Name: SciCrunch + Entry: NA + - Name: bio.tools + Entry: genometools