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 M�ller 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 <[email protected]> +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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 16 Mar 2005 23:21:37 +0100 + -- Steffen Moeller <[email protected]> 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 <[email protected]> -Build-Depends: debhelper (>= 4.0.0) -Standards-Version: 3.6.1 +Maintainer: Steffen Moeller <[email protected]> +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 <[email protected]> on -Wed Mar 16 23:57:06 CET 2005. +This package was first debianized by Steffen Moeller <[email protected]> +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 + <[email protected]> Upstream Author: Rob Russel <[email protected]> @@ -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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