[med-svn] [Git][med-team/genometester][master] 7 commits: d/{install, rules}: replace gdistribution by gassembler.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Jan 30 15:57:10 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / genometester
Commits:
7acb37e7 by Étienne Mollier at 2026-01-30T12:12:23+01:00
d/{install,rules}: replace gdistribution by gassembler.
The former binary fails to build from source and is not advertised in
upstream Read Me files, which suggests limited usefulness. On the
other hand gassembler is documented upstream and may be worth
including in the binary package.
- - - - -
ae948d25 by Étienne Mollier at 2026-01-30T12:14:05+01:00
default-wordlength.patch: new: set a sane default.
glistmaker defaults to have a wordlength of 0, out of the acceptable
length of 1 to 32. This patch restores the previous behavior, which
looks to have been to default to a wordlength of 16, given autopkgtest
expectations.
- - - - -
dff38dd4 by Étienne Mollier at 2026-01-30T16:52:36+01:00
gdistribution.patch: new: fix build failure of this binary.
- - - - -
b153ac12 by Étienne Mollier at 2026-01-30T16:53:20+01:00
d/{install,rules}: restore gdistribution now that it's repaired.
- - - - -
4f2bd6aa by Étienne Mollier at 2026-01-30T16:54:05+01:00
buildflags.patch: new: improve hardening by passing CPP and LDFLAGS.
- - - - -
1df39278 by Étienne Mollier at 2026-01-30T16:54:31+01:00
d/patches/*: normalize Last-Update timestamps.
- - - - -
7b84518b by Étienne Mollier at 2026-01-30T16:56:20+01:00
d/changelog: update the changelog.
- - - - -
9 changed files:
- debian/changelog
- debian/install
- debian/patches/add_debug_symbols.patch
- + debian/patches/buildflags.patch
- + debian/patches/default-wordlength.patch
- + debian/patches/gdistribution.patch
- debian/patches/hardening.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,7 @@
genometester (4.0+git20221122.71e6625-1) UNRELEASED; urgency=medium
+ * Team upload.
+
[ Andreas Tille ]
* New upstream version
* d/watch:
@@ -15,7 +17,19 @@ genometester (4.0+git20221122.71e6625-1) UNRELEASED; urgency=medium
* Fix C vs C++ confusion by rather calling CC for C code
Closes: #1107684
- -- Andreas Tille <tille at debian.org> Thu, 11 Dec 2025 14:49:37 +0100
+ [ Étienne Mollier ]
+ * default-wordlength.patch: new: set a sane default.
+ glistmaker defaults to have a wordlength of 0, out of the acceptable
+ length of 1 to 32. This patch restores the previous behavior, which
+ looks to have been to default to a wordlength of 16, given autopkgtest
+ expectations.
+ * gdistribution.patch: new: fix build failure of this binary.
+ * d/{install,rules}: restore gdistribution now that it's repaired.
+ * d/{install,rules}: build gassembler.
+ * buildflags.patch: new: improve hardening by passing CPP and LDFLAGS.
+ * d/patches/*: normalize Last-Update timestamps.
+
+ -- Étienne Mollier <emollier at debian.org> Fri, 30 Jan 2026 16:54:58 +0100
genometester (4.0+git20200511.91cecb5+dfsg-1) unstable; urgency=medium
=====================================
debian/install
=====================================
@@ -1,3 +1,4 @@
+src/gassembler usr/bin
src/gdistribution usr/bin
src/glistcompare usr/bin
src/glistmaker usr/bin
=====================================
debian/patches/add_debug_symbols.patch
=====================================
@@ -1,5 +1,5 @@
Author: Liubov Chuprikova <chuprikovalv at gmail.com>
-Last-Update: Fri, 1 June 2018 01:13:17 +0200
+Last-Update: 2018-06-01
Description: Add debug symbols
--- a/src/Makefile
=====================================
debian/patches/buildflags.patch
=====================================
@@ -0,0 +1,59 @@
+Description: propagate build flags.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2026-01-30
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- genometester.orig/src/Makefile
++++ genometester/src/Makefile
+@@ -201,39 +201,39 @@
+ all: all-before $(BINS) all-after
+
+ glistmaker: $(LISTMAKER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
+- $(CC) $(LISTMAKER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o glistmaker $(LIBS) $(CFLAGS) $(AZ_FLAGS)
++ $(CC) $(CPPFLAGS) $(LISTMAKER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o glistmaker $(LIBS) $(CFLAGS) $(AZ_FLAGS) $(LDFLAGS)
+
+ glistquery: $(LISTQUERY_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
+- $(CC) $(LISTQUERY_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o glistquery $(LIBS) $(CFLAGS) $(AZ_FLAGS)
++ $(CC) $(CPPFLAGS) $(LISTQUERY_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o glistquery $(LIBS) $(CFLAGS) $(AZ_FLAGS) $(LDFLAGS)
+
+ glistcompare: $(LISTCOMPARE_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
+- $(CC) $(LISTCOMPARE_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o glistcompare $(LIBS) $(CFLAGS) $(AZ_FLAGS)
++ $(CC) $(CPPFLAGS) $(LISTCOMPARE_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o glistcompare $(LIBS) $(CFLAGS) $(AZ_FLAGS) $(LDFLAGS)
+
+ gindexer: $(GINDEXER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
+- $(CC) $(GINDEXER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gindexer $(LIBS) $(CFLAGS) $(AZ_FLAGS)
++ $(CC) $(CPPFLAGS) $(GINDEXER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gindexer $(LIBS) $(CFLAGS) $(AZ_FLAGS) $(LDFLAGS)
+
+ gmer_counter: $(GMER_COUNTER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
+- $(CC) $(GMER_COUNTER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gmer_counter $(LIBS) $(CFLAGS) $(AZ_FLAGS)
++ $(CC) $(CPPFLAGS) $(GMER_COUNTER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gmer_counter $(LIBS) $(CFLAGS) $(AZ_FLAGS) $(LDFLAGS)
+
+ gmer_caller: $(GMER_CALLER_SOURCES)
+- $(CC) $(GMER_CALLER_SOURCES) -o gmer_caller $(LIBS) $(CFLAGS) -Wall
++ $(CC) $(CPPFLAGS) $(GMER_CALLER_SOURCES) -o gmer_caller $(LIBS) $(CFLAGS) -Wall $(LDFLAGS)
+
+ gassembler: $(GASSEMBLER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
+- $(CC) $(GASSEMBLER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gassembler $(LIBS) $(CFLAGS) $(AZ_FLAGS)
++ $(CC) $(CPPFLAGS) $(GASSEMBLER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gassembler $(LIBS) $(CFLAGS) $(AZ_FLAGS) $(LDFLAGS)
+
+ gdistribution: $(GDISTRIBUTION_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
+- $(CC) $(GDISTRIBUTION_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gdistribution $(LIBS) $(CFLAGS) $(AZ_FLAGS)
++ $(CC) $(CPPFLAGS) $(GDISTRIBUTION_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gdistribution $(LIBS) $(CFLAGS) $(AZ_FLAGS) $(LDFLAGS)
+
+ aleq: $(ALEQ_SOURCES)
+- $(CC) $(ALEQ_SOURCES) -o aleq $(LIBS) $(CFLAGS) -Wall
++ $(CC) $(CPPFLAGS) $(ALEQ_SOURCES) -o aleq $(LIBS) $(CFLAGS) -Wall $(LDFLAGS)
+
+ kmer_predictor: $(KMER_PREDICTOR_SOURCES)
+- $(CC) $(KMER_PREDICTOR_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o kmer_predictor $(LIBS) $(AZ_FLAGS) $(CFLAGS)
++ $(CC) $(CPPFLAGS) $(KMER_PREDICTOR_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o kmer_predictor $(LIBS) $(AZ_FLAGS) $(CFLAGS) $(LDFLAGS)
+
+ clean: clean-custom
+ rm -f *.o $(BINS)
+
+ depend:
+- $(CC) $(CFLAGS) -M *.c > .depend
++ $(CC) $(CPPFLAGS) $(CFLAGS) -M *.c $(LDFLAGS) > .depend
+
+ include .depend
=====================================
debian/patches/default-wordlength.patch
=====================================
@@ -0,0 +1,25 @@
+Description: provide a sane default wordlength to glistmaker.
+ When forgetting to pass the wordlenght, glistmaker errors out with:
+ .
+ ---glistmaker test---
+ Error: Invalid word-length 0 (must be 1 - 32)!
+ .
+ This change restores the past behavior, which was to pass a wordlength
+ of 16. Note that the autopkgtest is written in such a way that it
+ expects such wordlength.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2026-01-30
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- genometester.orig/src/glistmaker.c
++++ genometester/src/glistmaker.c
+@@ -144,7 +144,7 @@
+ char *end;
+
+ /* default values */
+- unsigned int wordlength = 0;
++ unsigned int wordlength = 16;
+ unsigned int nthreads = DEFAULT_NUM_THREADS;
+ unsigned long long tablesize = DEFAULT_TABLE_SIZE;
+ unsigned int ntables = DEFAULT_NUM_TABLES;
=====================================
debian/patches/gdistribution.patch
=====================================
@@ -0,0 +1,117 @@
+Description: restore buildability of gdistribution.
+ It seems that gdistribution has been left out upstream and is not in a
+ buildable state right now, in such a way that Makefile targets have gone
+ missing. This patch restores build recipes to construction
+ gdistribution and fix several build failures affecting gdistribution.c's
+ source code.
+Author: Étienne Mollier <emollier at debian.org>
+Bug: https://github.com/bioinfo-ut/GenomeTester4/issues/29
+Forwarded: no
+Last-Update: 2026-01-30
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- genometester.orig/src/gdistribution.c
++++ genometester/src/gdistribution.c
+@@ -29,7 +29,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+
+-#include "wordmap.h"
++#include "word-map.h"
+
+ #define ELSIZE (sizeof (unsigned long long) + sizeof (unsigned int))
+ #define MAP_WORD(m,i) *((unsigned long long *) ((m)->wordlist + (i) * ELSIZE))
+@@ -40,7 +40,7 @@
+ unsigned int count;
+ } Freq;
+
+-static void get_distribution (wordmap *maps[2]);
++static void get_distribution (GT4WordMap *maps[2]);
+
+ static void
+ print_usage (FILE *ofs) {
+@@ -51,7 +51,7 @@
+ main (int argc, const char *argv[])
+ {
+ const char *names[2];
+- wordmap *maps[2];
++ GT4WordMap *maps[2];
+ Freq *freqs;
+
+ if (argc < 3) {
+@@ -64,8 +64,8 @@
+
+ if (debug) fprintf (stderr, "%s %s\n", names[0], names[1]);
+
+- maps[0] = wordmap_new (names[0], 1);
+- maps[1] = wordmap_new (names[1], 1);
++ maps[0] = gt4_word_map_new (names[0], 1, 0, 0);
++ maps[1] = gt4_word_map_new (names[1], 1, 0, 0);
+
+ get_distribution (maps);
+
+@@ -79,13 +79,13 @@
+ }
+
+ static void
+-get_distribution (wordmap *maps[2])
++get_distribution (GT4WordMap *maps[2])
+ {
+ unsigned long long size, i0, i1, fidx;
+ unsigned int j, count;
+ float *flist, current;
+
+- size = maps[0]->header->nwords + maps[1]->header->nwords;
++ size = maps[0]->header.n_words + maps[1]->header.n_words;
+ if (debug) fprintf (stderr, "Total size %llu\n", size);
+ flist = (float *) malloc (size * sizeof (float));
+
+@@ -94,7 +94,7 @@
+ fidx = 0;
+
+ if (debug) fprintf (stderr, "Finding intersection\n");
+- while ((i0 < maps[0]->header->nwords) && (i1 < maps[1]->header->nwords)) {
++ while ((i0 < maps[0]->header.n_words) && (i1 < maps[1]->header.n_words)) {
+ if (MAP_WORD(maps[0], i0) == MAP_WORD(maps[1], i1)) {
+ unsigned int c0, c1;
+ float freq;
+--- genometester.orig/src/Makefile
++++ genometester/src/Makefile
+@@ -165,6 +165,27 @@
+ az/serialization.c az/serialization.h \
+ az/types.c az/types.h
+
++GDISTRIBUTION_SOURCES = \
++ bloom.h \
++ sequence.h \
++ utils.h \
++ word-array-sorted.h \
++ word-dict.h \
++ word-list.h \
++ word-list-sorted.h \
++ word-map.h \
++ word-table.h \
++ bloom.c \
++ sequence.c \
++ utils.c \
++ word-array-sorted.c \
++ word-dict.c \
++ word-list.c \
++ word-list-sorted.c \
++ word-map.c \
++ word-table.c \
++ gdistribution.c
++
+ RELEASEFLAGS = -O3 -g
+ DEBUGFLAGS = -O0 -g
+ AZ_FLAGS = -DAZ_NO_PROPERTIES -DAZ_NO_STRING -DAZ_NO_VALUE
+@@ -200,6 +221,9 @@
+ gassembler: $(GASSEMBLER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
+ $(CC) $(GASSEMBLER_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gassembler $(LIBS) $(CFLAGS) $(AZ_FLAGS)
+
++gdistribution: $(GDISTRIBUTION_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES)
++ $(CC) $(GDISTRIBUTION_SOURCES) $(AZ_SOURCES) $(ARIKKEI_SOURCES) -o gdistribution $(LIBS) $(CFLAGS) $(AZ_FLAGS)
++
+ aleq: $(ALEQ_SOURCES)
+ $(CC) $(ALEQ_SOURCES) -o aleq $(LIBS) $(CFLAGS) -Wall
+
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,5 +1,5 @@
Author: Liubov Chuprikova <chuprikovalv at gmail.com>
-Last-Update: Fri, 1 June 2018 01:33:17 +0200
+Last-Update: 2018-06-01
Description: Propagate hardening options
--- a/src/Makefile
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,6 @@
add_debug_symbols.patch
hardening.patch
cross.patch
+default-wordlength.patch
+gdistribution.patch
+buildflags.patch
=====================================
debian/rules
=====================================
@@ -15,6 +15,7 @@ override_dh_auto_build:
dh_auto_build
dh_auto_build -- gmer_counter
dh_auto_build -- gmer_caller
+ dh_auto_build -- gassembler
dh_auto_build -- gdistribution
override_dh_auto_clean:
View it on GitLab: https://salsa.debian.org/med-team/genometester/-/compare/ea15009de4b175e1ae37943a0e82121af390a211...7b84518b3b640ef179668b48016228b9e9578320
--
View it on GitLab: https://salsa.debian.org/med-team/genometester/-/compare/ea15009de4b175e1ae37943a0e82121af390a211...7b84518b3b640ef179668b48016228b9e9578320
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