[med-svn] [Git][med-team/staden][master] 11 commits: d/patches/use_mkstemp_instead_of_tmpnam.patch: add missing stdlib include. Closes: #1066508
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Mar 13 14:46:22 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / staden
Commits:
999a11ca by Michael R. Crusoe at 2024-03-13T15:24:06+01:00
d/patches/use_mkstemp_instead_of_tmpnam.patch: add missing stdlib include. Closes: #1066508
- - - - -
bc351ce7 by Michael R. Crusoe at 2024-03-13T15:24:07+01:00
d/control: libncurses-dev replaced libncurses5-dev.
- - - - -
ae8f0499 by Michael R. Crusoe at 2024-03-13T15:31:47+01:00
fix my email address
- - - - -
51815ed0 by Michael R. Crusoe at 2024-03-13T15:31:56+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
61a9dfa5 by Michael R. Crusoe at 2024-03-13T15:31:57+01:00
routine-update: debhelper-compat 13
- - - - -
aaa13535 by Michael R. Crusoe at 2024-03-13T15:32:01+01:00
routine-update: Rules-Requires-Root: no
- - - - -
71f3fde5 by Michael R. Crusoe at 2024-03-13T15:32:01+01:00
routine-update: No tab in license text
- - - - -
88dc98f4 by Michael R. Crusoe at 2024-03-13T15:32:04+01:00
Update lintian override info format in d/staden-common.lintian-overrides on line 2.
Changes-By: lintian-brush
Fixes: lintian: mismatched-override
See-also: https://lintian.debian.org/tags/mismatched-override.html
- - - - -
08e20aa3 by Michael R. Crusoe at 2024-03-13T15:32:30+01:00
routine-update: watch file standard 4
- - - - -
bad60dd7 by Michael R. Crusoe at 2024-03-13T15:40:49+01:00
d/upstream/metadata: add links to Sourceforge issue tracker, VCS
- - - - -
f54da3b0 by Michael R. Crusoe at 2024-03-13T15:40:50+01:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/patches/use_mkstemp_instead_of_tmpnam.patch
- debian/staden-common.lintian-overrides
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,22 @@
-staden (2.0.0+b11-5) UNRELEASED; urgency=medium
+staden (2.0.0+b11-5) unstable; urgency=medium
* Team upload.
* Mark staden-commen as Multi-Arch: foreign
* Standards-Version: 4.5.0
* Correctly detect 64bit host architectures
-
- -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 19 Feb 2020 16:32:52 +0100
+ * d/patches/use_mkstemp_instead_of_tmpnam.patch: add missing stdlib
+ include. Closes: #1066508
+ * d/control: libncurses-dev replaced libncurses5-dev.
+ * Standards-Version: 4.6.2 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * No tab in license text (routine-update)
+ * Update lintian override info format in d/staden-common.lintian-overrides on
+ line 2.
+ * watch file standard 4 (routine-update)
+ * d/upstream/metadata: add links to Sourceforge issue tracker, VCS
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 13 Mar 2024 15:32:32 +0100
staden (2.0.0+b11-4) unstable; urgency=medium
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -4,8 +4,8 @@ Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~),
- libstaden-read-dev (>= 1.14.6),
+Build-Depends: debhelper-compat (= 13),
+ libstaden-read-dev,
itcl3-dev,
itk3-dev,
zlib1g-dev,
@@ -15,13 +15,14 @@ Build-Depends: debhelper (>= 12~),
tk-dev,
tklib,
libpng-dev,
- libncurses5-dev,
+ libncurses-dev,
iwidgets4,
libcurl4-gnutls-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/staden
Vcs-Git: https://salsa.debian.org/med-team/staden.git
Homepage: https://sourceforge.net/projects/staden/
+Rules-Requires-Root: no
Package: staden
Architecture: any
@@ -30,7 +31,7 @@ Depends: ${misc:Depends},
staden-common (= ${source:Version}),
staden-io-lib-utils,
tklib
-Recommends: med-config (>= 2.1)
+Recommends: med-config
Description: DNA sequence assembly (Gap4/Gap5), editing and analysis tools
Staden is a fully developed set of DNA sequence assembly (Gap4 and
Gap5), editing and analysis tools (Spin).
=====================================
debian/copyright
=====================================
@@ -9,7 +9,7 @@ Files: *
Copyright: 1995-2001 Medical Research Council, Laboratory of Molecular Biology
2005-2013, James Bonfield
2005-2013, Andrew Whitwham
- Rodger Staden
+ Rodger Staden
Kathryn Beal
Mark Jordan
Yaping Cheng
=====================================
debian/patches/use_mkstemp_instead_of_tmpnam.patch
=====================================
@@ -3,26 +3,43 @@ Bug-Debian: https://bugs.debian.org/825461
Author: Andreas Tille <tille at debian.org>
Last-Update: Fri, 27 May 2016 08:58:49 +0200
---- a/tk_utils/capture.c
-+++ b/tk_utils/capture.c
-@@ -17,7 +17,7 @@ int tcl_capture(ClientData clientData, T
+--- staden.orig/tk_utils/capture.c
++++ staden/tk_utils/capture.c
+@@ -5,6 +5,7 @@
+ #include <sys/types.h>
+ #include <sys/stat.h>
+ #include <unistd.h>
++#include <stdlib.h>
+
+ #include "os.h"
+ #include "capture.h"
+@@ -17,7 +18,7 @@
static int fd = 0;
char *buf;
struct stat statbuf;
- char *tmpfile;
-+ /* char *tmpfile; */
++ char template[] = "/tmp/tcl_capture.XXXXXX";
int result;
if (argc != 2 && argc != 3) {
-@@ -28,8 +28,9 @@ int tcl_capture(ClientData clientData, T
+@@ -28,8 +29,7 @@
/* File descriptor mangling */
if (!fd) {
- tmpfile = tmpnam(NULL);
- fd = open(tmpfile, O_RDWR|O_CREAT|O_TRUNC, 0666);
-+ /* tmpfile = tmpnam(NULL);
-+ fd = open(tmpfile, O_RDWR|O_CREAT|O_TRUNC, 0666); */
-+ fd = mkostemp(NULL, 0666);
++ fd = mkostemp(template, 0666);
} else {
lseek(fd, 0, SEEK_SET);
}
+--- staden.orig/tk_utils/Makefile
++++ staden/tk_utils/Makefile
+@@ -13,7 +13,7 @@
+ INCLUDES_E += $(MISC_INC) $(TKUTILS_INC) $(IOLIB_INC) $(TK_INC) \
+ $(SEQUTILS_INC) $(BIOLIMS_INC) $(PNG_INC)
+
+-CFLAGS += $(SHLIB_CFLAGS) $(TK_UTILS_DLL)
++CFLAGS += $(SHLIB_CFLAGS) $(TK_UTILS_DLL) -D_GNU_SOURCE
+
+ #DEFINES += -DCHECK_LICENCE -DTCL_LOCAL_APPINIT=Stash_AppInit
+ #DEFINES += -DTCL_LOCAL_APPINIT=Stash_AppInit
=====================================
debian/staden-common.lintian-overrides
=====================================
@@ -1,3 +1,3 @@
# This is actually no license file but a script showing the license text
-staden-common: extra-license-file usr/share/staden/tcl/tk_utils/licence.tcl
+staden-common: extra-license-file [usr/share/staden/tcl/tk_utils/licence.tcl]
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,7 @@
+Bugs-Database: https://sourceforge.net/p/staden/bugs/
+Bugs-Sumbit: https://sourceforge.net/p/staden/bugs/new/
+Repository-Browse: https://sourceforge.net/p/staden/code/HEAD/tree/staden/
+Repository: https://svn.code.sf.net/p/staden/code/
Reference:
- Author: James K. Bonfield and Andrew Whitwham
Title: Gap5--editing the billion fragment sequence assembly
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
-version=3
+version=4
opts=dversionmangle=s/[+~]b/b/ \
http://sf.net/staden/staden-(\d[\dab.]*)-[-\dsrc]*\.tar\.(?:bz2|gz)
View it on GitLab: https://salsa.debian.org/med-team/staden/-/compare/667e20a99269381700d65ba7325c9753e99c9d54...f54da3b054940d0c3ee214f76f36526b23133b92
--
View it on GitLab: https://salsa.debian.org/med-team/staden/-/compare/667e20a99269381700d65ba7325c9753e99c9d54...f54da3b054940d0c3ee214f76f36526b23133b92
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