[med-svn] r4885 - in trunk/packages/coils/trunk: . debian debian/patches debian/source
Steffen Möller
moeller at alioth.debian.org
Sat Jun 12 16:54:34 UTC 2010
Author: moeller
Date: 2010-06-12 16:54:33 +0000 (Sat, 12 Jun 2010)
New Revision: 4885
Added:
trunk/packages/coils/trunk/debian/README.source
trunk/packages/coils/trunk/debian/patches/series
trunk/packages/coils/trunk/debian/patches/strcpy.patch
trunk/packages/coils/trunk/debian/source/
trunk/packages/coils/trunk/debian/source/format
Removed:
trunk/packages/coils/trunk/README
Modified:
trunk/packages/coils/trunk/debian/
trunk/packages/coils/trunk/debian/README.Debian
trunk/packages/coils/trunk/debian/changelog
trunk/packages/coils/trunk/debian/compat
trunk/packages/coils/trunk/debian/control
trunk/packages/coils/trunk/debian/copyright
trunk/packages/coils/trunk/debian/ncoils.1
trunk/packages/coils/trunk/debian/rules
Log:
Uploading coils to the archive (5 year's after initial packaging).
This shall also prepare for GENtle to share this binary, well,
I presume we need to craft a coils library for that, eventually.
Many thanks go to Andreas for having saved my previous work
in the Debian Med archive. So, let's celebrate.
Steffen
Deleted: trunk/packages/coils/trunk/README
===================================================================
--- trunk/packages/coils/trunk/README 2010-06-12 13:32:07 UTC (rev 4884)
+++ trunk/packages/coils/trunk/README 2010-06-12 16:54:33 UTC (rev 4885)
@@ -1,3 +0,0 @@
-Work on this project was started by Steffen Möller but has stalled.
-Feel free to take it over.
-
Property changes on: trunk/packages/coils/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Modified: trunk/packages/coils/trunk/debian/README.Debian
===================================================================
--- trunk/packages/coils/trunk/debian/README.Debian 2010-06-12 13:32:07 UTC (rev 4884)
+++ trunk/packages/coils/trunk/debian/README.Debian 2010-06-12 16:54:33 UTC (rev 4885)
@@ -1,20 +1,27 @@
coils for Debian
----------------
-The software has no version specified. It is said
-to be the same algorithm as published in
+The software has no version specified. It is said to be the same algorithm
+as published in
Lupas, van Dyke & Stock
Predicting coiled coils from protein sequences Science
252:1162-1164(1991)
-The web server is not prepared in this Debian package. A
-separate package will be prepared upon respective requests
-for the CGI. The perl scripts are distributed in
-/usr/share/doc/coils.
+The web server is not prepared in this Debian package. A separate package
+will be prepared upon respective requests for the CGI. The perl scripts
+are distributed in /usr/share/doc/coils.
The source was last modified in 2002, hence the version, as no other
version information was found.
- -- Steffen Moeller <moeller at pzr.uni-rostock.de>
+Interest in this package raised again with the advent of the cloning
+tool GENtle in Debian, which (improvably) ships sources of ncoils with
+it. We will see how we can bring the two packages together.
+The files new.mat and old.mat are installed to /usr/share/ncoils, the
+ncoils binary should be informed explicitly via the environment variable
+COILSDIR of that location. Contact me if this shall be omittable.
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 12 Jun 2010 15:59:57 +0200
+
Added: trunk/packages/coils/trunk/debian/README.source
===================================================================
--- trunk/packages/coils/trunk/debian/README.source (rev 0)
+++ trunk/packages/coils/trunk/debian/README.source 2010-06-12 16:54:33 UTC (rev 4885)
@@ -0,0 +1,10 @@
+coils for Debian
+================
+
+The source is left untouched, except for
+ * the removal of the ncoils-linux binary.
+ * some compiler warnings
+ * some security fixes
+
+--
+ Steffen Moeller <moeller at debian.org> Sat, 12 Jun 2010 16:12:33 +0200
Modified: trunk/packages/coils/trunk/debian/changelog
===================================================================
--- trunk/packages/coils/trunk/debian/changelog 2010-06-12 13:32:07 UTC (rev 4884)
+++ trunk/packages/coils/trunk/debian/changelog 2010-06-12 16:54:33 UTC (rev 4885)
@@ -1,6 +1,11 @@
-coils (2002-0.1) unstable; urgency=low
+coils (2002-1) unstable; urgency=low
- * Initial Release.
+ * Initial Release (Closes: #299856).
+ updated package from 2005
+ * lintian-clean
+ * strcpy -> strncpy fixes
+ * eliminated some compiler warnings
+ * added rudimentary man page
- -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 16 Mar 2005 23:21:37 +0100
+ -- Steffen Moeller <moeller at debian.org> Sat, 12 Jun 2010 16:03:22 +0200
Modified: trunk/packages/coils/trunk/debian/compat
===================================================================
--- trunk/packages/coils/trunk/debian/compat 2010-06-12 13:32:07 UTC (rev 4884)
+++ trunk/packages/coils/trunk/debian/compat 2010-06-12 16:54:33 UTC (rev 4885)
@@ -1 +1 @@
-4
+7
Modified: trunk/packages/coils/trunk/debian/control
===================================================================
--- trunk/packages/coils/trunk/debian/control 2010-06-12 13:32:07 UTC (rev 4884)
+++ trunk/packages/coils/trunk/debian/control 2010-06-12 16:54:33 UTC (rev 4885)
@@ -1,9 +1,12 @@
Source: coils
Section: science
Priority: optional
-Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
-Build-Depends: debhelper (>= 4.0.0)
-Standards-Version: 3.6.1
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7)
+Standards-Version: 3.8.4
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bcoils/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/coils/trunk/
+Homepage: http://www.russell.embl.de/cgi-bin/coils-svr.pl
Package: ncoils
Architecture: any
@@ -14,5 +17,3 @@
from protein sequences. The algorithm was published in
Lupas, van Dyke & Stock, Predicting coiled coils from
protein sequences Science, 252, 1162-1164, 1991.
- .
- Homepage: http://www.russell.embl.de/cgi-bin/coils-svr.pl
Modified: trunk/packages/coils/trunk/debian/copyright
===================================================================
--- trunk/packages/coils/trunk/debian/copyright 2010-06-12 13:32:07 UTC (rev 4884)
+++ trunk/packages/coils/trunk/debian/copyright 2010-06-12 16:54:33 UTC (rev 4885)
@@ -1,9 +1,13 @@
-This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
-Wed Mar 16 23:57:06 CET 2005.
+This package was first debianized by Steffen Moeller <moeller at debian.org>
+on Wed Mar 16 23:57:06 CET 2005, saved by Andreas Tille and is now
+being completed again by Steffen.
It was downloaded from <http://www.russell.embl-heidelberg.de/coils/coils.tar.gz>
-Copyright:
+Copyright: (C) 2002 Robert B. Russel and its employing institute, the
+ EMBL - European Molecular Biology Lab
+ Meyerhofstrasse 1, 69917 Heidelberg, Germany
+ <russell at embl.de>
Upstream Author: Rob Russel <russell at embl.de>
@@ -19,10 +23,8 @@
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
- 02111-1307, USA.
+ along with this program. If not, see <http://www.gnu.org/licenses/>
On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
+Public License can be found in `/usr/share/common-licenses/GPL-2'.
Modified: trunk/packages/coils/trunk/debian/ncoils.1
===================================================================
--- trunk/packages/coils/trunk/debian/ncoils.1 2010-06-12 13:32:07 UTC (rev 4884)
+++ trunk/packages/coils/trunk/debian/ncoils.1 2010-06-12 16:54:33 UTC (rev 4885)
@@ -17,6 +17,8 @@
.SH SYNOPSIS
.B ncoils
-f < sequence.fasta
+.SH ENVIRONMENT
+COILSDIR - specifies the directory containing the file new.mat, for Debian this should be /usr/share/ncoils
.SH SEE ALSO
.BR /usr/share/doc/coils/README
.br
Added: trunk/packages/coils/trunk/debian/patches/series
===================================================================
--- trunk/packages/coils/trunk/debian/patches/series (rev 0)
+++ trunk/packages/coils/trunk/debian/patches/series 2010-06-12 16:54:33 UTC (rev 4885)
@@ -0,0 +1 @@
+strcpy.patch
Added: trunk/packages/coils/trunk/debian/patches/strcpy.patch
===================================================================
--- trunk/packages/coils/trunk/debian/patches/strcpy.patch (rev 0)
+++ trunk/packages/coils/trunk/debian/patches/strcpy.patch 2010-06-12 16:54:33 UTC (rev 4885)
@@ -0,0 +1,60 @@
+Index: coils-2002/ncoils.c
+===================================================================
+--- coils-2002.orig/ncoils.c 2010-06-12 17:29:29.000000000 +0200
++++ coils-2002/ncoils.c 2010-06-12 17:41:00.000000000 +0200
+@@ -35,7 +35,8 @@
+ int mode;
+ int min_seg;
+
+- char heptfile[1000];
++#define HEPTFILELENGTH 1000
++ char heptfile[HEPTFILELENGTH];
+ char *buff;
+ static char *env;
+ char *seq,*title,*ident;
+@@ -56,10 +57,12 @@
+
+ if((env=getenv("COILSDIR"))==NULL) {
+ fprintf(stderr,"error: environment variable COILSDIR must be set\n");
++ fprintf(stderr," Assuming /usr/share/ncoils\n");
++ env=strdup("/usr/share/ncoils"); // a little leak, tolerated as singleton
+ exit(-1);
+ }
+
+- strcpy(&heptfile[0],env);
++ strncpy(&heptfile[0],env,HEPTFILELENGTH-1-8); // -1 for terminal 0, 8 for "/new.mat"
+ strcpy(&heptfile[strlen(heptfile)],"/new.mat");
+
+
+@@ -67,7 +70,7 @@
+ if(argv[i][0]!='-') exit_error();
+ if(strcmp(&argv[i][1],"m")==0) {
+ if((i+1)>=argc) exit_error();
+- strcpy(&heptfile[0],argv[i+1]);
++ strncpy(&heptfile[0],argv[i+1],HEPTFILELENGTH-1);
+ i++;
+ } else if(strcmp(&argv[i][1],"win")==0) {
+ if((i+1)>=argc) exit_error();
+@@ -159,6 +162,10 @@
+ } else {
+ /* printf("Adding |%s| to |%s| = \n",buff,seq); */
+ seq=(char*)realloc(seq,(seqlen+strlen(buff)+1)*sizeof(char));
++ if (NULL == seq) {
++ fprintf(stderr,"Could not allocate memory.\n");
++ exit(-1);
++ }
+ strcpy(&seq[seqlen],buff);
+ seqlen=strlen(seq);
+ /* printf(" |%s|\n",seq); */
+Index: coils-2002/ncoils.h
+===================================================================
+--- coils-2002.orig/ncoils.h 2010-06-12 17:40:01.000000000 +0200
++++ coils-2002/ncoils.h 2010-06-12 17:40:09.000000000 +0200
+@@ -1,6 +1,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <math.h>
++#include <string.h>
+
+ #define AAs "A_CDEFGHI_KLMN_PQRST_VW_Y_"
+ #define PI 3.1415
Modified: trunk/packages/coils/trunk/debian/rules
===================================================================
--- trunk/packages/coils/trunk/debian/rules 2010-06-12 13:32:07 UTC (rev 4884)
+++ trunk/packages/coils/trunk/debian/rules 2010-06-12 16:54:33 UTC (rev 4885)
@@ -41,7 +41,7 @@
install: build
dh_testdir
dh_testroot
- dh_clean -k
+ dh_clean
dh_installdirs
# Add here commands to install the package into debian/ncoils.
@@ -69,5 +69,15 @@
dh_md5sums
dh_builddeb
+version=2002
+d="../coils.upstream.tar.gz"
+
+get-orig-source:
+ echo "Downloading to $(d)." ; \
+ wget -O "$(d)" http://www.russell.embl-heidelberg.de/coils/coils.tar.gz ; \
+ cd `dirname $(d)` ; tar --exclude ncoils-linux -xzf `basename $(d)`
+ cd `dirname $(d)` ; mv coils coils-$(version)
+ cd `dirname $(d)` ; tar --exclude ncoils-linux -czvf coils_$(version).orig.tar.gz coils-$(version)
+
binary: binary-indep binary-arch
.PHONY: build clean binary-indep binary-arch binary install configure
Added: trunk/packages/coils/trunk/debian/source/format
===================================================================
--- trunk/packages/coils/trunk/debian/source/format (rev 0)
+++ trunk/packages/coils/trunk/debian/source/format 2010-06-12 16:54:33 UTC (rev 4885)
@@ -0,0 +1 @@
+3.0 (quilt)
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