[med-svn] r1977 - in trunk/packages/ncbi-epcr/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Fri Jun 6 00:07:02 UTC 2008
Author: plessy
Date: 2008-06-06 00:07:02 +0000 (Fri, 06 Jun 2008)
New Revision: 1977
Removed:
trunk/packages/ncbi-epcr/trunk/debian/patches/10_assert.patch
trunk/packages/ncbi-epcr/trunk/debian/patches/10_gcc4.3.patch
trunk/packages/ncbi-epcr/trunk/debian/patches/series
Modified:
trunk/packages/ncbi-epcr/trunk/debian/changelog
trunk/packages/ncbi-epcr/trunk/debian/control
trunk/packages/ncbi-epcr/trunk/debian/copyright
trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs
trunk/packages/ncbi-epcr/trunk/debian/rules
Log:
New upstream release in which the patches made by Andreas have been accepted. Converted copyright to machine-readable format. Package does not build, I have to figure out why.
Modified: trunk/packages/ncbi-epcr/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/changelog 2008-06-05 21:30:18 UTC (rev 1976)
+++ trunk/packages/ncbi-epcr/trunk/debian/changelog 2008-06-06 00:07:02 UTC (rev 1977)
@@ -1,11 +1,22 @@
-epcr (2.3.9-2) UNRELEASED; urgency=low
+epcr (2.3.10-1) UNRELEASED; urgency=low
- * Raised from priority extra to optional according to policy
- * Added description to tags according to suggested format
- http://lists.debian.org/debian-med/2008/05/msg00053.html
+ FIXME: Does not build, not time to investigate.
- -- Andreas Tille <tille at debian.org> Wed, 16 Apr 2008 19:45:31 +0200
+ [ Charles Plessy ]
+ * New upstream release applying Andreases patches introduced
+ in the previous Debian package.
+ * debian/patches: removed 10_assert.patch and 10_gcc4.3.patch
+ (Removed debian/patches/series as well.)
+ * debian/copyright converted to machine-readable format.
+ * debian/control: downgraded recommendation on bioperl to `Suggests:'
+ because BioPerl provides a parser for e-PCR results, but e-PCR
+ does not need BioPerl for running.
+ [ Andreas Tille ]
+ * Raised from priority extra to optional according to policy.
+
+ -- Charles Plessy <plessy at debian.org> Fri, 06 Jun 2008 09:01:17 +0900
+
epcr (2.3.9-1) unstable; urgency=low
* New upstream version
Modified: trunk/packages/ncbi-epcr/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/control 2008-06-05 21:30:18 UTC (rev 1976)
+++ trunk/packages/ncbi-epcr/trunk/debian/control 2008-06-06 00:07:02 UTC (rev 1977)
@@ -14,7 +14,7 @@
Package: ncbi-epcr
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: bioperl
+Suggests: bioperl
Description: Tool to test a DNA sequence for the presence of sequence tagged sites
Electronic PCR (e-PCR) is computational procedure that is used to identify
sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential
Modified: trunk/packages/ncbi-epcr/trunk/debian/copyright
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/copyright 2008-06-05 21:30:18 UTC (rev 1976)
+++ trunk/packages/ncbi-epcr/trunk/debian/copyright 2008-06-06 00:07:02 UTC (rev 1977)
@@ -1,32 +1,85 @@
-This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
-Thu, 20 Nov 2003 12:50:19 +0100.
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129
+Upstream-Author: Gregory D. Schuler <schuler at ncbi.nlm.nih.gov>
+Packaged-By: Steffen Moeller <moeller at debian.org>
+Packaged-Date: Thu, 20 Nov 2003 12:50:19 +0100
+Original-Source-Location: ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-2.3.10-src.tar.gz
-It was downloaded from ftp://ftp.ncbi.nih.gov/pub/schuler
+Files: *
+Authors: Greg Schuler, NCBI
+ Kirill Rotmistrovsky, NCBI
+Licence: PD
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+ .
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the author's official duties as a United States Government employee and
+ thus cannot be copyrighted. This software/database is freely available
+ to the public for use. The National Library of Medicine and the U.S.
+ Government have not placed any restriction on its use or reproduction.
+ .
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+ .
+ Please cite the author in any work or product based on this material.
-Upstream Authors: Gregory D. Schuler <schuler at ncbi.nlm.nih.gov>
+Files: debian/*
+Copyright: © 2003-2004 Steffen Moeller <moeller at debian.org>
+ © 2008 Andreas Tille <tille at debian.org>
+License: unknown
+ There was not statement of copyright for the whole package when I
+ reformatted debian/copyright -- Charles Plessy
-Copyright:
+Files: debian/*.1
+Copyright: © 2003-2004 Steffen Moeller <moeller at debian.org>
+ © 2008 Andreas Tille <tille at debian.org>
+License: GPL-2+
+ debian/*.1: manual pages for e-PCR.
+ Copyright © 2008 Steffen Moeller <moeller at debian.org> and
+ Andreas Tille <tille at debian.org>
+ .
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-Public domain. No particular license. To quote an email the upstream author sent:
+Files: debian/rules
+Copyright: © 2008 Andreas Tille <tille at debian.org>
+License: GPL-1+
+ debian/rules: file to build the ncbi-epcr Debian package
+ Copyright © 2008 Andreas Tille <tille at debian.org>
+ .
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+X-Comment: On Debian systems, you can find the full text of the latest
+ GNU General Public License in the file `/usr/share/common-licenses/GPL'
-"
-Steffen,
-
-I don't know what Debian is, but the e-PCR code is
-in the public domain, so anyone can do anything
-with it.
-
-Cheers,
--greg
-"
-
-As this license apparently passes the
-
- Island test
-
- Dissident test
-
- and the "tentacles of evil" test
-
-(http://people.debian.org/~bap/dfsg-faq.html) this program is considered
-to be DFSGL conform.
+Files: debian/copyright
+Copyright: © 2008 Charles Plessy <plessy at debian.org>
+License: PD
+ Please treat my contributions as if they were in the public domain.
Modified: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs 2008-06-05 21:30:18 UTC (rev 1976)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs 2008-06-06 00:07:02 UTC (rev 1977)
@@ -1,3 +1,2 @@
README.txt
README.html
-
Deleted: trunk/packages/ncbi-epcr/trunk/debian/patches/10_assert.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/10_assert.patch 2008-06-05 21:30:18 UTC (rev 1976)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/10_assert.patch 2008-06-06 00:07:02 UTC (rev 1977)
@@ -1,16 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Forwarded: "Upstream author Gregory D. Schuler" <schuler at ncbi.nlm.nih.gov>
-Date: Mon, 21 Apr 2008 13:21:39 +0200 (CEST)
-Description: Missing header file assert.h
-License: Same as epcr itself.
-
---- e-PCR-2.3.9.orig/e-PCR_main.cpp
-+++ e-PCR-2.3.9/e-PCR_main.cpp
-@@ -32,6 +32,7 @@
-
- #include <epcr/stsmatch.hpp>
-
-+#include <assert.h>
- #include <errno.h>
- #include <time.h>
-
Deleted: trunk/packages/ncbi-epcr/trunk/debian/patches/10_gcc4.3.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/10_gcc4.3.patch 2008-06-05 21:30:18 UTC (rev 1976)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/10_gcc4.3.patch 2008-06-06 00:07:02 UTC (rev 1977)
@@ -1,81 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Forwarded: "Upstream author Gregory D. Schuler" <schuler at ncbi.nlm.nih.gov>
-Date: Mon, 21 Apr 2008 13:21:39 +0200 (CEST)
-Description: Missing header files to compile successfully with gcc4.3
-License: Same as epcr itself.
-
---- e-PCR-2.3.9.orig/re-PCR_main.cpp
-+++ e-PCR-2.3.9/re-PCR_main.cpp
-@@ -37,6 +37,8 @@
- #include <errno.h>
-
- #include <stdexcept>
-+#include <cstring>
-+#include <memory>
-
- USING_NCBI_SCOPE;
- USING_SCOPE(EPCR_SCOPE);
---- e-PCR-2.3.9.orig/strref.hpp
-+++ e-PCR-2.3.9/strref.hpp
-@@ -32,6 +32,7 @@
-
- #include <epcr/build_cfg.h>
- #include <string>
-+#include <cstring>
-
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(EPCR_SCOPE)
---- e-PCR-2.3.9.orig/fahash_main.cpp
-+++ e-PCR-2.3.9/fahash_main.cpp
-@@ -37,6 +37,8 @@
- #include <math.h>
- #include <time.h>
-
-+#include <memory>
-+
- USING_NCBI_SCOPE;
- USING_SCOPE(EPCR_SCOPE);
-
---- e-PCR-2.3.9.orig/bin-io.hpp
-+++ e-PCR-2.3.9/bin-io.hpp
-@@ -35,6 +35,7 @@
- #include <stdio.h>
- #include <errno.h>
-
-+#include <cstring>
- #include <string>
- #include <vector>
- #include <stdexcept>
---- e-PCR-2.3.9.orig/e-PCR_main.cpp
-+++ e-PCR-2.3.9/e-PCR_main.cpp
-@@ -36,6 +36,8 @@
- #include <errno.h>
- #include <time.h>
-
-+#include <memory>
-+
- #ifndef STANDALONE
- #include <objtools/readers/seqdb/seqdb.hpp>
- #endif
---- e-PCR-2.3.9.orig/famap_main.cpp
-+++ e-PCR-2.3.9/famap_main.cpp
-@@ -32,6 +32,8 @@
- #include <string.h>
- #include <errno.h>
-
-+#include <cstdlib>
-+
- USING_NCBI_SCOPE;
- USING_SCOPE(EPCR_SCOPE);
-
---- e-PCR-2.3.9.orig/fahash_create2.cpp
-+++ e-PCR-2.3.9/fahash_create2.cpp
-@@ -38,6 +38,8 @@
- #include <errno.h>
- #include <assert.h>
-
-+#include <memory>
-+
- USING_NCBI_SCOPE;
- USING_SCOPE(EPCR_SCOPE);
-
Deleted: trunk/packages/ncbi-epcr/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/series 2008-06-05 21:30:18 UTC (rev 1976)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/series 2008-06-06 00:07:02 UTC (rev 1977)
@@ -1,2 +0,0 @@
-10_assert.patch
-10_gcc4.3.patch
Modified: trunk/packages/ncbi-epcr/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/rules 2008-06-05 21:30:18 UTC (rev 1976)
+++ trunk/packages/ncbi-epcr/trunk/debian/rules 2008-06-06 00:07:02 UTC (rev 1977)
@@ -12,6 +12,6 @@
rm -f libepcr.a
rm -f e-PCR famap fahash re-PCR
-DEB_OPT_FLAG += -I. -g2 -DDEALLOCATE=0 `getconf LFS_CFLAGS` -DVERSION=\\\"2.3.9\\\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=9 -DSTANDALONE=1
+DEB_OPT_FLAG += -I. -g2 -DDEALLOCATE=0 `getconf LFS_CFLAGS` -DVERSION=\\\"2.3.10\\\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=10 -DSTANDALONE=1
LDFLAGS += `getconf LFS_LDFLAGS` `getconf LFS_LIBS` -L.
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