[med-svn] [Git][med-team/libsonlib][master] 15 commits: Fix: error: comparison between pointer and zero character constant "[-Werror=pointer-compare]"
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Oct 21 16:20:14 BST 2026
Andreas Tille pushed to branch master at Debian Med / libsonlib
Commits:
2ef9a2e1 by Andreas Tille at 2020-07-04T07:59:58+02:00
Fix: error: comparison between pointer and zero character constant "[-Werror=pointer-compare]"
- - - - -
572ca14c by Andreas Tille at 2026-10-21T17:16:30+02:00
d/watch: version=5
- - - - -
11649d62 by Andreas Tille at 2026-10-21T17:16:52+02:00
New upstream version
- - - - -
30d08e05 by Andreas Tille at 2026-10-21T17:16:53+02:00
New upstream version 1.1+git20220915.5cbc158+dfsg
- - - - -
1e595edf by Andreas Tille at 2026-10-21T17:16:53+02:00
Update upstream source from tag 'upstream/1.1+git20220915.5cbc158+dfsg'
Update to upstream version '1.1+git20220915.5cbc158+dfsg'
with Debian dir 438538612edaba1a47c00f27374693baaf441794
- - - - -
0d750c04 by Andreas Tille at 2026-10-21T17:16:53+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
14a7ebe7 by Andreas Tille at 2026-10-21T17:17:01+02:00
Changes made by cme
- - - - -
eb9bb490 by Andreas Tille at 2026-10-21T17:17:03+02:00
Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
- - - - -
bf6922f4 by Andreas Tille at 2026-10-21T16:17:04+01:00
Reformat the Last-Update date as ISO YYYY-MM-DD.
Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/use_debian_packaged_quicktree.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/2to3.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/fix_test.patch]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/rpath.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html
- - - - -
7584d8a8 by Andreas Tille at 2026-10-21T16:17:04+01:00
Remove unused dh-exec usage from debian/libsonlib-dev.install.
Changes-By: lintian-brush
Fixes: lintian: source: dh-exec-script-without-dh-exec-features [debian/libsonlib-dev.install]
See-also: https://lintian.debian.org/tags/dh-exec-script-without-dh-exec-features.html
- - - - -
68add605 by Andreas Tille at 2026-10-21T16:17:07+01:00
Set upstream metadata fields: Bug-Database, Repository-Browse.
Changes-By: lintian-brush
- - - - -
7ce75e73 by Andreas Tille at 2026-10-21T17:17:09+02:00
debputy lint --auto-fix (routine-update)
- - - - -
1fdaf4df by Andreas Tille at 2026-10-21T17:18:01+02:00
Remove autopkgtest template
- - - - -
e66ccab0 by Andreas Tille at 2026-10-21T17:18:47+02:00
Cleanup d/changelog
- - - - -
f7c2fde3 by Andreas Tille at 2026-10-21T17:19:42+02:00
Remove README.test
- - - - -
17 changed files:
- C/impl/sonLibList.c
- C/inc/sonLibList.h
- − debian/README.test
- debian/changelog
- debian/control
- debian/libsonlib-dev.install
- debian/patches/2to3.patch
- debian/patches/fix_test.patch
- + debian/patches/fix_warnings.patch
- debian/patches/rpath.patch
- debian/patches/series
- debian/patches/use_debian_packaged_quicktree.patch
- debian/rules
- − debian/tests/control
- − debian/tests/run-unit-test
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
C/impl/sonLibList.c
=====================================
@@ -388,3 +388,7 @@ void stList_mapReplace(stList *l, void *(*mapFn)(void *, void *), void *extraArg
stList_set(l, i, mapFn(stList_get(l, i), extraArg));
}
}
+
+void *stList_getBackingArray(stList *list) {
+ return list->list;
+}
=====================================
C/inc/sonLibList.h
=====================================
@@ -220,6 +220,11 @@ stList *stList_join(stList *listOfLists);
*/
void stList_mapReplace(stList *l, void *(*mapFn)(void *, void *), void *extraArg);
+/*
+ * Returns the underlying array.
+ */
+void *stList_getBackingArray(stList *list);
+
#ifdef __cplusplus
}
#endif
=====================================
debian/README.test deleted
=====================================
@@ -1,8 +0,0 @@
-Notes on how this package can be tested.
-────────────────────────────────────────
-
-This package can be tested by running the provided test:
-
- sh run-unit-test
-
-in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-libsonlib (1.1+git20200429.1040ab0+dfsg-1) UNRELEASED; urgency=medium
+libsonlib (1.1+git20220915.5cbc158+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #963598)
- -- Shayan Doust <hello at shayandoust.me> Wed, 24 Jun 2020 11:06:35 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 21 Oct 2026 17:16:52 +0200
=====================================
debian/control
=====================================
@@ -1,30 +1,31 @@
Source: libsonlib
-Section: science
-Priority: optional
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Shayan Doust <hello at shayandoust.me>
-Build-Depends: debhelper-compat (= 13),
- dh-exec,
- dh-python,
- python3,
- python3-setuptools,
- libquicktree-dev,
- zlib1g-dev,
- libtokyocabinet-dev,
- libbz2-dev
-Standards-Version: 4.5.0
+Uploaders:
+ Andreas Tille <tille at debian.org>,
+Section: science
+Build-Depends:
+ debhelper-compat (= 14),
+ dh-exec,
+ dh-sequence-python3,
+ libbz2-dev,
+ libquicktree-dev,
+ libtokyocabinet-dev,
+ python3,
+ python3-setuptools,
+ zlib1g-dev,
Vcs-Browser: https://salsa.debian.org/med-team/libsonlib
Vcs-Git: https://salsa.debian.org/med-team/libsonlib.git
Homepage: https://github.com/ArtRand/sonLib
Package: libsonlib-dev
-Section: libdevel
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${python3:Depends},
- libquicktree-dev
+Section: libdevel
+Depends:
+ libquicktree-dev,
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends},
Description: compact C/Python library for sequence analysis in bioinformatics
SonLib is a small general purpose library for C and Python for sequence
analysis with focus on bioinformatics.
=====================================
debian/libsonlib-dev.install
=====================================
@@ -1,4 +1,2 @@
-#!/usr/bin/dh-exec
-
#include/*.h usr/include/sonlib
lib/* usr/lib/${DEB_HOST_MULTIARCH}
=====================================
debian/patches/2to3.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 16 Jun 2020 08:23:45 +0200
+Last-Update: 2020-06-16
Description: Port to Python3
--- libsonlib.orig/treeTest.py
=====================================
debian/patches/fix_test.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 16 Jun 2020 08:23:45 +0200
+Last-Update: 2020-06-16
Description: Somehow the test suite was non-functional. Fix some PATHs here
--- libsonlib.orig/C/Makefile
=====================================
debian/patches/fix_warnings.patch
=====================================
@@ -0,0 +1,34 @@
+Author: Andreas Tille <tille at debian.org>
+Description: When compiling with CGL_DEBUG=ultra the build ends in
+ error: comparison between pointer and zero character constant "[-Werror=pointer-compare]"
+ This should be fixed here.
+
+--- a/C/impl/bioioC.c
++++ b/C/impl/bioioC.c
+@@ -265,7 +265,7 @@ int64_t parseInt(char **string, int64_t
+ i = sscanf(*string, INT_STRING, j);
+ if(i == 1) {
+ *string = eatWhiteSpace(*string);
+- while(*string != '\0' && !isspace(**string)) {
++ while(**string != '\0' && !isspace(**string)) {
+ (*string)++;
+ }
+ *string = eatWhiteSpace(*string);
+@@ -286,7 +286,7 @@ int64_t parseFloat(char **string, float
+ i = sscanf(*string, "%f", j);
+ if(i == 1) {
+ *string = eatWhiteSpace(*string);
+- while(*string != '\0' && !isspace(**string)) {
++ while(**string != '\0' && !isspace(**string)) {
+ (*string)++;
+ }
+ *string = eatWhiteSpace(*string);
+@@ -307,7 +307,7 @@ int64_t parseString(char **string, char
+ i = sscanf(*string, "%s", cA);
+ if(i == 1) {
+ *string = eatWhiteSpace(*string);
+- while(*string != '\0' && !isspace(**string)) {
++ while(**string != '\0' && !isspace(**string)) {
+ (*string)++;
+ }
+ *string = eatWhiteSpace(*string);
=====================================
debian/patches/rpath.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 16 Jun 2020 08:23:45 +0200
+Last-Update: 2020-06-16
Description: No rpath
--- libsonlib.orig/include.mk
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ use_debian_packaged_quicktree.patch
2to3.patch
fix_test.patch
rpath.patch
+fix_warnings.patch
=====================================
debian/patches/use_debian_packaged_quicktree.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 16 Jun 2020 08:23:45 +0200
+Last-Update: 2020-06-16
Description: To avoid a code copy of quicktree here inside the quicktree
package a static lib is built and used to link here
=====================================
debian/rules
=====================================
@@ -6,17 +6,17 @@ export LC_ALL=C.UTF-8
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
- dh $@ --with python3
+ dh $@
override_dh_auto_build:
# Somehow Makefile does not deal with this ...
#mkdir -p bin
#cp -a src/sonLib/test/sonLib_daemonize.py .
- dh_auto_build
+ CGL_DEBUG=ultra dh_auto_build
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_test || true
+ CGL_DEBUG=ultra dh_auto_test || true
endif
override_dh_install:
=====================================
debian/tests/control deleted
=====================================
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test deleted
=====================================
@@ -1,19 +0,0 @@
-#!/bin/bash
-set -e
-
-pkg=#PACKAGENAME#
-
-export LC_ALL=C.UTF-8
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
- AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- # Double quote below to expand the temporary directory variable now versus
- # later is on purpose.
- # shellcheck disable=SC2064
- trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-#do_stuff_to_test_package#
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/ArtRand/sonLib/issues
Registry:
- Name: conda:bioconda
Entry: sonlib
+Repository-Browse: https://github.com/ArtRand/sonLib
=====================================
debian/watch
=====================================
@@ -1,6 +1,8 @@
-version=4
+Version: 5
-opts="mode=git,pretty=1.1+git%cd.%h,repacksuffix=+dfsg,dversionmangle=auto" \
- https://github.com/benedictpaten/sonLib.git HEAD
-
-# FIXME: open issue asking for release tags
+Source: https://github.com/benedictpaten/sonLib.git
+Matching-Pattern: HEAD
+Dversion-Mangle: auto
+Mode: git
+Git-Pretty: 1.1+git%cd.%h
+Repack-Suffix: +dfsg
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/compare/ea2f51958597771ff26a105ee539d7f3dab55b6b...f7c2fde3d385dca85e1897bbbaac4c79e93dbef0
--
View it on GitLab: https://salsa.debian.org/med-team/libsonlib/-/compare/ea2f51958597771ff26a105ee539d7f3dab55b6b...f7c2fde3d385dca85e1897bbbaac4c79e93dbef0
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