[med-svn] [Git][med-team/seqtools][master] 3 commits: routine-update: Packaging update
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Dec 9 17:37:52 GMT 2023
Andreas Tille pushed to branch master at Debian Med / seqtools
Commits:
aaee9708 by Andreas Tille at 2023-12-09T16:53:49+01:00
routine-update: Packaging update
- - - - -
d028d9f1 by Andreas Tille at 2023-12-09T16:53:49+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
8d541e32 by Andreas Tille at 2023-12-09T18:37:29+01:00
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.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/no_gtk2+.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+seqtools (4.44.1+dfsg-8) UNRELEASED; 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
+
seqtools (4.44.1+dfsg-7) unstable; urgency=medium
* Versioned Build-Depends: d-shlibs (>= 0.80)
=====================================
debian/control
=====================================
@@ -4,12 +4,12 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- libgtk2.0-dev,
+ libglib2.0-dev,
libsqlite3-dev,
libcurl4-openssl-dev | libcurl4-dev,
libjsoncpp-dev,
d-shlibs
-Standards-Version: 4.6.0
+Standards-Version: 4.6.2
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
=====================================
debian/patches/no_gtk2+.patch
=====================================
@@ -0,0 +1,185 @@
+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
=====================================
@@ -4,3 +4,4 @@ use_debian_packaged_jsoncpp.patch
fix_missing_includes.patch
spelling.patch
ksh2sh.patch
+#no_gtk2+.patch
View it on GitLab: https://salsa.debian.org/med-team/seqtools/-/compare/77de348af00fa29340f8db6ff52a8941c4f8a83f...8d541e326c0a451856e089f38a5b19d0bec7512d
--
View it on GitLab: https://salsa.debian.org/med-team/seqtools/-/compare/77de348af00fa29340f8db6ff52a8941c4f8a83f...8d541e326c0a451856e089f38a5b19d0bec7512d
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20231209/a75cd822/attachment-0001.htm>
More information about the debian-med-commit
mailing list