[med-svn] r15194 - in trunk/packages/readseq/trunk/debian: . patches tests
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 21:54:06 UTC 2013
Author: tille
Date: 2013-11-20 21:54:06 +0000 (Wed, 20 Nov 2013)
New Revision: 15194
Added:
trunk/packages/readseq/trunk/debian/README.test
trunk/packages/readseq/trunk/debian/patches/enable_tests.patch
trunk/packages/readseq/trunk/debian/patches/hardening.patch
trunk/packages/readseq/trunk/debian/tests/
trunk/packages/readseq/trunk/debian/tests/Makefile
Removed:
trunk/packages/readseq/trunk/debian/README.source
Modified:
trunk/packages/readseq/trunk/debian/changelog
trunk/packages/readseq/trunk/debian/compat
trunk/packages/readseq/trunk/debian/control
trunk/packages/readseq/trunk/debian/copyright
trunk/packages/readseq/trunk/debian/docs
trunk/packages/readseq/trunk/debian/install
trunk/packages/readseq/trunk/debian/patches/gcc-4.6_format-security.patch
trunk/packages/readseq/trunk/debian/patches/series
trunk/packages/readseq/trunk/debian/rules
Log:
Mass changes for 1-10
Deleted: trunk/packages/readseq/trunk/debian/README.source
===================================================================
--- trunk/packages/readseq/trunk/debian/README.source 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/README.source 2013-11-20 21:54:06 UTC (rev 15194)
@@ -1,4 +0,0 @@
-This packages uses the quilt patch system. Please read
-/usr/share/doc/quilt/README.source for more information.
-
- -- Andreas Tille <tille at debian.org> Mon, 31 Aug 2009 14:50:19 +0200
Added: trunk/packages/readseq/trunk/debian/README.test
===================================================================
--- trunk/packages/readseq/trunk/debian/README.test (rev 0)
+++ trunk/packages/readseq/trunk/debian/README.test 2013-11-20 21:54:06 UTC (rev 15194)
@@ -0,0 +1,10 @@
+You can test this package by
+
+ cd `mktemp -d`
+ cp -a /usr/share/doc/readseq/tests/* .
+ make test
+
+Note: It is known that not all tests are passing but it is
+ not known whether the tests itself are correctly implemented
+ Feel free to use `reportbug readseq` if you have some idea
+ how to fix the tests.
Modified: trunk/packages/readseq/trunk/debian/changelog
===================================================================
--- trunk/packages/readseq/trunk/debian/changelog 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/changelog 2013-11-20 21:54:06 UTC (rev 15194)
@@ -1,8 +1,17 @@
-readseq (1-10) UNRELEASED; urgency=low
+readseq (1-10) unstable; urgency=low
* debian/upstream: citation information
+ * debian/control:
+ - cme fix dpkg-control
+ - debhelper 9
+ - canonical Vcs URLs
+ * debian/README.source: removed because redundant
+ * debian/patches/enable_tests.patch: Fix test target
+ * debian/patches/hardening.patch: Propagate hardening options
+ * debian/copyright: DEP5
+ * provide test after installing the package
- -- Andreas Tille <tille at debian.org> Tue, 08 May 2012 09:19:59 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 18 Nov 2013 14:22:50 +0100
readseq (1-9) unstable; urgency=low
Modified: trunk/packages/readseq/trunk/debian/compat
===================================================================
--- trunk/packages/readseq/trunk/debian/compat 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/compat 2013-11-20 21:54:06 UTC (rev 15194)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/readseq/trunk/debian/control
===================================================================
--- trunk/packages/readseq/trunk/debian/control 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/control 2013-11-20 21:54:06 UTC (rev 15194)
@@ -1,18 +1,19 @@
Source: readseq
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), quilt, ncbi-tools-dev
-Standards-Version: 3.9.2
+Build-Depends: debhelper (>= 9),
+ ncbi-tools-dev
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/readseq/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/readseq/trunk/
Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/readseq/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/readseq/trunk/
Package: readseq
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
Description: Conversion between sequence formats
Reads and writes nucleic/protein sequences in various
formats. Data files may have multiple sequences.
Modified: trunk/packages/readseq/trunk/debian/copyright
===================================================================
--- trunk/packages/readseq/trunk/debian/copyright 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/copyright 2013-11-20 21:54:06 UTC (rev 15194)
@@ -1,38 +1,31 @@
-This package was debianized by Andreas Tille tille at debian.org on
-Thu, 25 Oct 2001 09:42:26 +0200.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Readseq
+Source: http://iubio.bio.indiana.edu/soft/molbio/readseq/version1/src/
-It was downloaded from
- http://iubio.bio.indiana.edu/soft/molbio/readseq/version1/src/
-
-Upstream Author: D. Gilbert <gilbertd at bio.indiana.edu>
-
-Copyright: 1990-1993 D. Gilbert
-
-(From the Readme:)
-
- * Copyright 1990 by d.g.gilbert
- * biology dept., indiana university, bloomington, in 47405
- * e-mail: gilbertd at bio.indiana.edu
- *
+Files: *
+Copyright: 1990-1993 D. Gilbert <gilbertd at bio.indiana.edu>
+ biology dept., indiana university
+License: PD
* This program may be freely copied and used by anyone.
* Developers are encourged to incorporate parts in their
* programs, rather than devise their own private sequence
* format.
+ .
+ From gilbertd at bio.indiana.edu Tue Oct 30 08:18:23 2001
+ Date: Mon, 29 Oct 2001 13:07:26 -0500 (EST)
+ From: Don Gilbert <gilbertd at bio.indiana.edu>
+ Subject: Re: [ITA] Intent To Adopt Readseq
+ .
+ Andreas,
+ .
+ Please feel free to use readseq code as you like; I've placed
+ it in the public domain.
+ .
+ - Don
+Files: debian/*
+Copyright: © 2001-2013 Andreas Tille <tille at debian.org>
+License: GPLv2+
+ The Debian packaging is licensed under the GPL which is available at
+ `/usr/share/common-licenses/GPL'.
-From gilbertd at bio.indiana.edu Tue Oct 30 08:18:23 2001
-Date: Mon, 29 Oct 2001 13:07:26 -0500 (EST)
-From: Don Gilbert <gilbertd at bio.indiana.edu>
-To: TilleA at rki.de
-Subject: Re: [ITA] Intent To Adopt Readseq
-
-Andreas,
-
-Please feel free to use readseq code as you like; I've placed
-it in the public domain.
-
-- Don
-
-The Debian packaging is © 2001-2009 Andreas Tille <tille at debian.org>
-and is licensed under the GPL which is available at
-`/usr/share/common-licenses/GPL'.
Modified: trunk/packages/readseq/trunk/debian/docs
===================================================================
--- trunk/packages/readseq/trunk/debian/docs 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/docs 2013-11-20 21:54:06 UTC (rev 15194)
@@ -2,3 +2,4 @@
Readme
Stdfiles
Readseq.help
+debian/README.test
Modified: trunk/packages/readseq/trunk/debian/install
===================================================================
--- trunk/packages/readseq/trunk/debian/install 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/install 2013-11-20 21:54:06 UTC (rev 15194)
@@ -1,3 +1,3 @@
readseq usr/bin
-Makefile usr/share/doc/readseq/tests
+debian/tests/Makefile usr/share/doc/readseq/tests
*.std usr/share/doc/readseq/tests
Added: trunk/packages/readseq/trunk/debian/patches/enable_tests.patch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/enable_tests.patch (rev 0)
+++ trunk/packages/readseq/trunk/debian/patches/enable_tests.patch 2013-11-20 21:54:06 UTC (rev 15194)
@@ -0,0 +1,70 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Mon, 18 Nov 2013 14:22:50 +0100
+Description: Make sure the just builded readseq will be used for testing
+
+--- a/Makefile
++++ b/Makefile
+@@ -53,41 +53,41 @@ build: $(SOURCES)
+ test:
+ @echo ""
+ @echo "Test for general read/write of all chars:"
+- readseq -p alphabet.std -otest.alpha
++ ./readseq -p alphabet.std -otest.alpha
+ -diff test.alpha alphabet.std
+
+ @echo ""
+ @echo "Test for valid format conversions:"
+- readseq -v -p -f=ig nucleic.std -otest.ig
+- readseq -v -p -f=gb test.ig -otest.gb
+- readseq -v -p -f=nbrf test.gb -otest.nbrf
+- readseq -v -p -f=embl test.nbrf -otest.embl
+- readseq -v -p -f=gcg test.embl -otest.gcg
+- readseq -v -p -f=strider test.gcg -otest.strider
+- readseq -v -p -f=fitch test.strider -otest.fitch
+- readseq -v -p -f=fasta test.fitch -otest.fasta
+- readseq -v -p -f=pir test.fasta -otest.pir
+- readseq -v -p -f=ig test.pir -otest.ig-b
++ ./readseq -v -p -f=ig nucleic.std -otest.ig
++ ./readseq -v -p -f=gb test.ig -otest.gb
++ ./readseq -v -p -f=nbrf test.gb -otest.nbrf
++ ./readseq -v -p -f=embl test.nbrf -otest.embl
++ ./readseq -v -p -f=gcg test.embl -otest.gcg
++ ./readseq -v -p -f=strider test.gcg -otest.strider
++ ./readseq -v -p -f=fitch test.strider -otest.fitch
++ ./readseq -v -p -f=fasta test.fitch -otest.fasta
++ ./readseq -v -p -f=pir test.fasta -otest.pir
++ ./readseq -v -p -f=ig test.pir -otest.ig-b
+ -diff test.ig test.ig-b
+
+ @echo ""
+ @echo "Test for multiple-sequence format conversions:"
+- readseq -p -f=ig multi.std -otest.m-ig
+- readseq -p -f=gb test.m-ig -otest.m-gb
+- readseq -p -f=nbrf test.m-gb -otest.m-nbrf
+- readseq -p -f=embl test.m-nbrf -otest.m-embl
+- readseq -p -f=fasta test.m-embl -otest.m-fasta
+- readseq -p -f=pir test.m-fasta -otest.m-pir
+- readseq -p -f=msf test.m-pir -otest.m-msf
+- readseq -p -f=paup test.m-msf -otest.m-paup
+- readseq -p -f=ig test.m-paup -otest.m-ig-b
++ ./readseq -p -f=ig multi.std -otest.m-ig
++ ./readseq -p -f=gb test.m-ig -otest.m-gb
++ ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
++ ./readseq -p -f=embl test.m-nbrf -otest.m-embl
++ ./readseq -p -f=fasta test.m-embl -otest.m-fasta
++ ./readseq -p -f=pir test.m-fasta -otest.m-pir
++ ./readseq -p -f=msf test.m-pir -otest.m-msf
++ ./readseq -p -f=paup test.m-msf -otest.m-paup
++ ./readseq -p -f=ig test.m-paup -otest.m-ig-b
+ -diff test.m-ig test.m-ig-b
+ #
+ # if using NCBI, uncomment these lines
+ @echo ""
+ @echo "Test of NCBI ASN.1 conversions:"
+- readseq -p -f=asn test.m-ig -otest.m-asn
+- readseq -p -f=ig test.m-asn -otest.m-ig-c
++ ./readseq -p -f=asn test.m-ig -otest.m-asn
++ ./readseq -p -f=ig test.m-asn -otest.m-ig-c
+ -diff test.m-ig test.m-ig-c
+ #
+ @echo ""
Modified: trunk/packages/readseq/trunk/debian/patches/gcc-4.6_format-security.patch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/gcc-4.6_format-security.patch 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/patches/gcc-4.6_format-security.patch 2013-11-20 21:54:06 UTC (rev 15194)
@@ -5,9 +5,9 @@
calls are throwing erros. This patch replates [f]printf by [f]puts to
fix the problem
---- readseq-1.orig/readseq.c
-+++ readseq-1/readseq.c
-@@ -335,7 +335,7 @@
+--- a/readseq.c
++++ b/readseq.c
+@@ -335,7 +335,7 @@ void usage()
{
short i, midi;
@@ -16,7 +16,7 @@
fprintf(stderr,
"usage: readseq [-options] in.seq > out.seq\n");
fprintf(stderr," options\n");
-@@ -988,7 +988,7 @@
+@@ -988,7 +988,7 @@ char** argv;
if (seqout == 0) fprintf( foo,"\\\\\\\n");
break;
case kASN1:
Added: trunk/packages/readseq/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/hardening.patch (rev 0)
+++ trunk/packages/readseq/trunk/debian/patches/hardening.patch 2013-11-20 21:54:06 UTC (rev 15194)
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Mon, 18 Nov 2013 14:22:50 +0100
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -10,7 +10,7 @@ CC=gcc # Gnu C Compiler
+ #CC=cc # SGI Irix
+ #CC=vcc # some DEC Ultrix
+
+-CFLAGS= -g -O2
++CFLAGS+= -g -O2
+ #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
+ # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+
+@@ -48,7 +48,7 @@ all: build
+ # if using NCBI, uncomment these lines in place of build: above
+ build: $(SOURCES)
+ @echo "Compiling readseq with NCBI toolkit support and ARB patches";
+- $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS)
++ $(CC) -o readseq $(NLDFLAGS) $(NCFLAGS) $(ARBFLAGS) readseq.c ureadseq.c ureadasn.c $(NLIBS) $(LDFLAGS)
+
+ test:
+ @echo ""
Modified: trunk/packages/readseq/trunk/debian/patches/series
===================================================================
--- trunk/packages/readseq/trunk/debian/patches/series 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/patches/series 2013-11-20 21:54:06 UTC (rev 15194)
@@ -3,3 +3,5 @@
30-arb-code-patches.patch
552830.patch
gcc-4.6_format-security.patch
+enable_tests.patch
+hardening.patch
Modified: trunk/packages/readseq/trunk/debian/rules
===================================================================
--- trunk/packages/readseq/trunk/debian/rules 2013-11-20 21:53:31 UTC (rev 15193)
+++ trunk/packages/readseq/trunk/debian/rules 2013-11-20 21:54:06 UTC (rev 15194)
@@ -9,9 +9,5 @@
dh_clean
rm -f readseq
-override_dh_auto_test:
- # Sorry, I'm too lazy for now to fix this test
- # Any help is welcome!!!
-
get-orig-source:
. debian/get-orig-source
Added: trunk/packages/readseq/trunk/debian/tests/Makefile
===================================================================
--- trunk/packages/readseq/trunk/debian/tests/Makefile (rev 0)
+++ trunk/packages/readseq/trunk/debian/tests/Makefile 2013-11-20 21:54:06 UTC (rev 15194)
@@ -0,0 +1,59 @@
+#
+# Makefile for testing readseq
+# to use, command me:
+# % make test
+#
+
+test:
+ @echo ""
+ @echo "Test for general read/write of all chars:"
+ /usr/bin/readseq -p alphabet.std -otest.alpha
+ -diff test.alpha alphabet.std
+
+ @echo ""
+ @echo "Test for valid format conversions:"
+ /usr/bin/readseq -v -p -f=ig nucleic.std -otest.ig
+ /usr/bin/readseq -v -p -f=gb test.ig -otest.gb
+ /usr/bin/readseq -v -p -f=nbrf test.gb -otest.nbrf
+ /usr/bin/readseq -v -p -f=embl test.nbrf -otest.embl
+ /usr/bin/readseq -v -p -f=gcg test.embl -otest.gcg
+ /usr/bin/readseq -v -p -f=strider test.gcg -otest.strider
+ /usr/bin/readseq -v -p -f=fitch test.strider -otest.fitch
+ /usr/bin/readseq -v -p -f=fasta test.fitch -otest.fasta
+ /usr/bin/readseq -v -p -f=pir test.fasta -otest.pir
+ /usr/bin/readseq -v -p -f=ig test.pir -otest.ig-b
+ -diff test.ig test.ig-b
+
+ @echo ""
+ @echo "Test for multiple-sequence format conversions:"
+ /usr/bin/readseq -p -f=ig multi.std -otest.m-ig
+ /usr/bin/readseq -p -f=gb test.m-ig -otest.m-gb
+ /usr/bin/readseq -p -f=nbrf test.m-gb -otest.m-nbrf
+ /usr/bin/readseq -p -f=embl test.m-nbrf -otest.m-embl
+ /usr/bin/readseq -p -f=fasta test.m-embl -otest.m-fasta
+ /usr/bin/readseq -p -f=pir test.m-fasta -otest.m-pir
+ /usr/bin/readseq -p -f=msf test.m-pir -otest.m-msf
+ /usr/bin/readseq -p -f=paup test.m-msf -otest.m-paup
+ /usr/bin/readseq -p -f=ig test.m-paup -otest.m-ig-b
+ -diff test.m-ig test.m-ig-b
+#
+# if using NCBI, uncomment these lines
+ @echo ""
+ @echo "Test of NCBI ASN.1 conversions:"
+ /usr/bin/readseq -p -f=asn test.m-ig -otest.m-asn
+ /usr/bin/readseq -p -f=ig test.m-asn -otest.m-ig-c
+ -diff test.m-ig test.m-ig-c
+#
+ @echo ""
+ @echo "Expect differences in the header lines due to"
+ @echo "different format headers. If any sequence lines"
+ @echo "differ, or if the checksums differ, there is a problem."
+ @echo "----------------------"
+ @echo ""
+ @echo "To clean up test files, command me:"
+ @echo " make clean"
+
+clean:
+ rm -f test.*
+
+
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