[med-svn] [Git][med-team/seqtools][master] 9 commits: Partial revert to be in sync with version 4.44.1+dfsg-7.1
Santiago Vila (@sanvila)
gitlab at salsa.debian.org
Wed Nov 26 20:44:03 GMT 2025
Santiago Vila pushed to branch master at Debian Med / seqtools
Commits:
24c3577b by Santiago Vila at 2025-11-25T12:00:00+01:00
Partial revert to be in sync with version 4.44.1+dfsg-7.1
- - - - -
6200b5c2 by Santiago Vila at 2025-11-26T21:33:00+01:00
d/libgbtools-dev.examples: Specify the exact files to be put in examples. Closes: #962589.
- - - - -
3348f5ce by Santiago Vila at 2025-11-26T21:34:00+01:00
d/rules: Do not remove Makefile.in or Makefile.am in the working tree, as it breaks "make distclean". Closes: #1047310.
- - - - -
319451e8 by Santiago Vila at 2025-11-26T21:35:00+01:00
d/control: Drop "Rules-Requires-Root: no" (default).
- - - - -
5726285a by Santiago Vila at 2025-11-26T21:36:00+01:00
d/control: Drop "Priority: optional" (default).
- - - - -
f56bf7b3 by Santiago Vila at 2025-11-26T21:37:00+01:00
d/control: Update standards-version.
- - - - -
b3e7a4c7 by Santiago Vila at 2025-11-26T21:38:00+01:00
d/control: Fix Conflicts line (lintian error).
Instead of updating it at every upload, freeze the version used in
conflicts at the version where the time_t transition happened.
- - - - -
8e686142 by Santiago Vila at 2025-11-26T21:39:00+01:00
d/salsa-ci.yml: Use the simplified version.
- - - - -
5f8487c3 by Santiago Vila at 2025-11-26T21:40:00+01:00
Upload for unstable as 4.44.1+dfsg-8
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/libgbtools-dev.examples
- − debian/patches/no_gtk2+.patch
- debian/patches/series
- debian/rules
- debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,18 @@
-seqtools (4.44.1+dfsg-8) UNRELEASED; urgency=medium
+seqtools (4.44.1+dfsg-8) unstable; urgency=medium
- * Standards-Version: 4.6.2 (routine-update)
- * Add patch removing dependency from libgtk2.0-dev - unfortunately this
- removes all binaries this package is shipping and the patch is
- useless and will not fix #967743.
-
- -- Andreas Tille <tille at debian.org> Sat, 09 Dec 2023 16:53:48 +0100
+ * Team upload.
+ * Acknowledge NMU.
+ * d/libgbtools-dev.examples: Specify here the exact files to be put
+ in examples. Closes: #962589 in a better way.
+ * d/rules: Do not remove Makefile.in or Makefile.am in the working tree,
+ as it breaks "make distclean". Closes: #1047310.
+ * d/control: Drop "Rules-Requires-Root: no" (default).
+ * d/control: Drop "Priority: optional" (default).
+ * d/control: Update standards-version.
+ * d/control: Fix Conflicts line (lintian error).
+ * d/salsa-ci.yml: Use the simplified version.
+
+ -- Santiago Vila <sanvila at debian.org> Wed, 26 Nov 2025 21:40:00 +0100
seqtools (4.44.1+dfsg-7.1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -2,23 +2,21 @@ Source: seqtools
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Section: science
-Priority: optional
Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
- libglib2.0-dev,
+ libgtk2.0-dev,
libsqlite3-dev,
libcurl4-openssl-dev | libcurl4-dev,
libjsoncpp-dev,
d-shlibs (>= 0.106),
-Standards-Version: 4.6.2
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/seqtools
Vcs-Git: https://salsa.debian.org/med-team/seqtools.git
Homepage: https://www.sanger.ac.uk/science/tools/seqtools
-Rules-Requires-Root: no
Package: libgbtools0t64
Provides: ${t64:Provides}
Replaces: libgbtools0
-Conflicts: libgbtools0 (<< ${source:Version})
+Conflicts: libgbtools0 (<< 4.44.1+dfsg-7.1)
Architecture: any
Multi-Arch: same
Section: libs
=====================================
debian/libgbtools-dev.examples
=====================================
@@ -1 +1,9 @@
-examples/*
+examples/DA730641.fasta
+examples/PF02171_seed.stock
+examples/Q9H8G1.fasta
+examples/README
+examples/chr4_dna_align.gff
+examples/chr4_protein_align.gff
+examples/chr4_ref_seq.fasta
+examples/chr4_ref_seq_short.fasta
+examples/chr4_translation_frame1.fasta
=====================================
debian/patches/no_gtk2+.patch deleted
=====================================
@@ -1,185 +0,0 @@
-Description: Attempt to build without libgtk2.0-dev
-FIXME: Unfortunately this removes all binaries - so the
- patches need to be more carefully or the package needs
- to be removed.
-Bug-Debian: https://bugs.debian.org/967743
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 09 Dec 2023 16:53:48 +0100
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -6,15 +6,11 @@ m4_include([./seqtools_version.m4])
- AC_PREREQ([2.50])
- AC_INIT([SeqTools], VERSION_NUMBER, [gb10 at sanger.ac.uk])
- AC_CONFIG_AUX_DIR([config])
--AC_CONFIG_SRCDIR([blixemApp/blxmain.cpp])
- AM_INIT_AUTOMAKE([1.9 foreign])
- AC_CONFIG_HEADERS([config.h])
-
- # Set up calling of Makefiles in toplevel directory and subdirectories
- AC_CONFIG_FILES([Makefile
--blixemApp/Makefile
--dotterApp/Makefile
--belvuApp/Makefile
- seqtoolsUtils/Makefile
- doc/Makefile
- doc/User_doc/Makefile
-@@ -59,7 +55,7 @@ AC_CHECK_PROG(GLIB_GENMARSHAL, glib-genm
- # Checks for libraries.
-
- # Checks for header files.
--AC_CHECK_HEADERS([arpa/inet.h netdb.h netinet/in.h stdlib.h string.h sys/socket.h unistd.h gtk.h sqlite3.h])
-+AC_CHECK_HEADERS([arpa/inet.h netdb.h netinet/in.h stdlib.h string.h sys/socket.h unistd.h sqlite3.h])
-
- # Checks for typedefs, structures, and compiler characteristics.
- AC_TYPE_PID_T
-@@ -70,7 +66,7 @@ AC_FUNC_FORK
- AC_CHECK_FUNCS([dup2 floor gethostbyname memset socket sqrt strcasecmp strchr strcspn strerror strncasecmp strrchr strstr strtol uname])
-
- # Check for dependencies required by all executables
--PKG_CHECK_MODULES([DEPS], [glib-2.0 gtk+-2.0 >= 2.10 jsoncpp])
-+PKG_CHECK_MODULES([DEPS], [glib-2.0 jsoncpp])
-
- # Check for dependencies required by sqlite code
- PKG_CHECK_MODULES([DEPS_SQLITE3], [sqlite3], [HAVE_SQLITE3=1], [HAVE_SQLITE3=0])
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -9,7 +9,7 @@ if USE_GBTOOLS
- SUBDIRS += gbtools
- endif
-
--SUBDIRS += seqtoolsUtils dotterApp blixemApp belvuApp doc test examples
-+SUBDIRS += seqtoolsUtils doc test examples
-
- # these are included in the distribution, but are not installed
- EXTRA_DIST = INSTALL.windows INSTALL.linux INSTALL.mac
---- a/gbtools/configure.ac
-+++ b/gbtools/configure.ac
-@@ -6,7 +6,6 @@ m4_include([./gbtools_version.m4])
- AC_PREREQ([2.50])
- AC_INIT([gbtools], VERSION_NUMBER, [annosoft at sanger.ac.uk])
- AC_CONFIG_AUX_DIR([config])
--AC_CONFIG_SRCDIR([src/gbtoolsGUI/gbtoolsGUI.cpp])
- AM_INIT_AUTOMAKE([1.9 foreign])
- AC_CONFIG_HEADERS([config.h])
-
-@@ -14,8 +13,6 @@ AC_CONFIG_HEADERS([config.h])
- AC_CONFIG_FILES([Makefile
- src/Makefile
- src/include/Makefile
--src/gbtoolsUtils/Makefile
--src/gbtoolsGUI/Makefile
- src/gbtoolsCurl/Makefile
- src/gbtoolsTrackhub/Makefile
- src/gbtoolsPfetch/Makefile
-@@ -66,7 +63,7 @@ AC_FUNC_MALLOC
- AC_CHECK_FUNCS([dup2 floor gethostbyname memset socket sqrt strcasecmp strchr strcspn strerror strncasecmp strrchr strstr strtol uname])
-
- # Check for dependencies required by all executables
--PKG_CHECK_MODULES([DEPS], [glib-2.0 gtk+-2.0 >= 2.10 jsoncpp])
-+PKG_CHECK_MODULES([DEPS], [glib-2.0 jsoncpp])
-
- # Check for optional dependencies
- AX_CHECK_OPENSSL()
---- a/gbtools/Makefile.am
-+++ b/gbtools/Makefile.am
-@@ -8,7 +8,7 @@ lib_LTLIBRARIES = libgbtools.la
-
- libgbtools_la_SOURCES =
-
--libgbtools_la_LIBADD = src/gbtoolsGUI/libgbtoolsGUI.la src/gbtoolsUtils/libgbtoolsUtils.la
-+libgbtools_la_LIBADD =
-
- libgbtools_la_LIBADD += -ljsoncpp
-
---- a/gbtools/src/Makefile.am
-+++ b/gbtools/src/Makefile.am
-@@ -1,5 +1,5 @@
-
--SUBDIRS = include gbtoolsUtils gbtoolsGUI
-+SUBDIRS = include
-
- if USE_LIBCURL
- SUBDIRS += gbtoolsCurl gbtoolsPfetch
---- a/gbtools/src/include/gbtools/gbtoolsUtils.hpp
-+++ b/gbtools/src/include/gbtools/gbtoolsUtils.hpp
-@@ -30,7 +30,7 @@
- #ifndef _gbtoolsUtils_h_included_
- #define _gbtoolsUtils_h_included_
-
--#include <gtk/gtk.h>
-+#include <glib.h>
-
- namespace gbtools
- {
---- a/seqtoolsUtils/utilities.hpp
-+++ b/seqtoolsUtils/utilities.hpp
-@@ -38,7 +38,7 @@
- #ifndef _utilities_h_included_
- #define _utilities_h_included_
-
--#include <gtk/gtk.h>
-+#include <glib.h>
-
- #define UNSET_INT -1 /* this value indicates an unset integer */
- #define DEFAULT_LABEL_X_PAD 0 /* default x padding to use for header labels */
-@@ -678,6 +678,7 @@ char* revCo
- char complementChar(const char inputChar, GError **error);
-
-
-+/*
- void gtk_text_buffer_insert_markup (GtkTextBuffer *buffer,
- GtkTextIter *iter,
- const gchar *markup);
-@@ -693,6 +694,6 @@ void gtk_text_buffer_set_markup_with_
-
- void gtk_text_buffer_set_markup (GtkTextBuffer *buffer,
- const gchar *markup);
--
-+*/
-
- #endif /* _utilities_h_included_ */
---- a/seqtoolsUtils/blxGff3Parser.hpp
-+++ b/seqtoolsUtils/blxGff3Parser.hpp
-@@ -38,7 +38,7 @@
- #ifndef BLX_GFF_P_H
- #define BLX_GFF_P_H
-
--#include <gtk/gtk.h>
-+#include <glib.h>
- #include <seqtoolsUtils/blxmsp.hpp>
-
- /* We follow glib convention in error domain naming:
---- a/seqtoolsUtils/blxmsp.hpp
-+++ b/seqtoolsUtils/blxmsp.hpp
-@@ -45,7 +45,7 @@
-
- #include <seqtoolsUtils/utilities.hpp>
- #include <stdlib.h>
--#include <gtk/gtk.h>
-+#include <glib.h>
-
-
- //extern GArray *fsArr; /* in dotter.c */
---- a/gbtools/src/include/gbtools/gbtoolsGUI.hpp
-+++ b/gbtools/src/include/gbtools/gbtoolsGUI.hpp
-@@ -30,7 +30,7 @@
- #define gbtoolsGUI_h_included
-
- #include <gbtools/gbtoolsUtils.hpp>
--#include <gtk/gtk.h>
-+#include <glib.h>
-
- namespace gbtools
- {
---- a/seqtoolsUtils/Makefile.am
-+++ b/seqtoolsUtils/Makefile.am
-@@ -9,7 +9,7 @@ endif
-
- noinst_LIBRARIES = libSeqtoolsUtils.a
-
--libSeqtoolsUtils_a_SOURCES = iupac.hpp version.hpp utilities.hpp utilities.cpp blxmsp.hpp blxmsp.cpp translate.cpp seqtoolsWebBrowser.cpp blxGff3Parser.hpp blxGff3Parser.cpp blxparser.hpp blxparser.cpp seqtoolsFetch.hpp seqtoolsFetch.cpp
-+libSeqtoolsUtils_a_SOURCES = iupac.hpp version.hpp blxparser.hpp seqtoolsFetch.hpp seqtoolsFetch.cpp
- libSeqtoolsUtils_a_LIBADD =
- libSeqtoolsUtils_a_CFLAGS =
-
=====================================
debian/patches/series
=====================================
@@ -4,4 +4,3 @@ use_debian_packaged_jsoncpp.patch
fix_missing_includes.patch
spelling.patch
ksh2sh.patch
-#no_gtk2+.patch
=====================================
debian/rules
=====================================
@@ -18,4 +18,3 @@ override_dh_install:
--movedev debian/tmp/usr/include/* usr/include \
debian/tmp/usr/lib/*/*.so
find debian -name "*.la" -delete
- rm -f examples/Makefile.in examples/Makefile
=====================================
debian/salsa-ci.yml
=====================================
@@ -1,4 +1,3 @@
---
include:
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
View it on GitLab: https://salsa.debian.org/med-team/seqtools/-/compare/b7f4072a072799fa00915794f2cf1f1f88c86e2f...5f8487c37dbb49a66b69266c4b6e2b6d22b4994a
--
View it on GitLab: https://salsa.debian.org/med-team/seqtools/-/compare/b7f4072a072799fa00915794f2cf1f1f88c86e2f...5f8487c37dbb49a66b69266c4b6e2b6d22b4994a
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