[med-svn] r4073 - trunk/packages/infernal/trunk/debian

Tue Sep 29 15:17:04 UTC 2009

Author: tille
Date: 2009-09-29 15:17:04 +0000 (Tue, 29 Sep 2009)
New Revision: 4073

Modified:
   trunk/packages/infernal/trunk/debian/changelog
   trunk/packages/infernal/trunk/debian/control
   trunk/packages/infernal/trunk/debian/copyright
   trunk/packages/infernal/trunk/debian/infernal-doc.doc-base
   trunk/packages/infernal/trunk/debian/infernal.install
   trunk/packages/infernal/trunk/debian/rules
Log:
Several changes towards a lintian clean package


Modified: trunk/packages/infernal/trunk/debian/changelog
===================================================================

--- trunk/packages/infernal/trunk/debian/changelog	2009-09-29 15:13:30 UTC (rev 4072)
+++ trunk/packages/infernal/trunk/debian/changelog	2009-09-29 15:17:04 UTC (rev 4073)
@@ -22,6 +22,10 @@
   * debian/infernal.install: install src/{trcyk,truncyk_check} to
     /usr/bin
 
+  * TODO: Convince upstream to release libeazel which is also used in
+    hmmer as a separate library instead of copying the code into
+    different projects
+
  -- Andreas Tille <tille at debian.org>  Fri, 25 Sep 2009 15:17:22 +0200
 
 infernal (0.81-1) experimental; urgency=low

Modified: trunk/packages/infernal/trunk/debian/control
===================================================================
--- trunk/packages/infernal/trunk/debian/control	2009-09-29 15:13:30 UTC (rev 4072)
+++ trunk/packages/infernal/trunk/debian/control	2009-09-29 15:17:04 UTC (rev 4073)
@@ -33,6 +33,7 @@
 
 Package: infernal-doc
 Architecture: all
+Section: doc
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: inference of RNA secondary structural alignments
  Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
@@ -44,7 +45,5 @@
  identifying RNA homologs that conserve their secondary structure more
  than their primary sequence.
  .
- The tool is an integral component of the Rfam database.
- .
  This package provides the documentation which is shipped with the
  code of infernal.

Modified: trunk/packages/infernal/trunk/debian/copyright
===================================================================
--- trunk/packages/infernal/trunk/debian/copyright	2009-09-29 15:13:30 UTC (rev 4072)
+++ trunk/packages/infernal/trunk/debian/copyright	2009-09-29 15:17:04 UTC (rev 4073)
@@ -47,14 +47,60 @@
  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
  IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
+Files: easel/{esl_sse.c,esl_vmx.c}
+Copyright: © 2007 Julien Pommier
+           © 1992 Stephen Moshier
+License: BSD
 
-Files: easel/documentation/figures/evd*.pdf, easel/documentation/figures/gev*.pdf
-X-Comment: Those files are figures with only a few words of text, that probably
- have been generated in a command line session. Most of these will not be possible
- to recreate without the raw data at hand. As an interim solution, the folder
- easel/documentation was removed from the source.
+Files: easel/easel.c::esl_tmpfile()
+Copyright: © 1999-2001 David A. Wheeler
+License: MIT
 
+Files: easel/esl_regexp.c
+Copyright: © 1986, 1993, 1995 by University of Toronto
+License: BSD
 
+Files: easel/*
+Copyright: © 2004-2008 Sean R. Eddy
+           © 2006-2008 Howard Hughes Medical Institute
+License: Easel - a library of C functions for biological sequence analysis
+ @EASEL_COPYRIGHT@
+ .
+ The Easel library is freely modifiable and redistributable under the
+ Janelia Farm Software License, a BSD license:
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+ .
+ 3. Neither the name of the Howard Hughes Medical Institute nor the
+    names of its contributors may be used to endorse or promote
+    products derived from this software without specific prior written
+    permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,
+ NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+ TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+ DAMAGE.
+
+
 Files: Userguide.pdf
 X-Comment: The PDFs that are coming with the sources from which the userguide is
  built are indeed upstream's original sources. They are edited with a PDF

Modified: trunk/packages/infernal/trunk/debian/infernal-doc.doc-base
===================================================================
--- trunk/packages/infernal/trunk/debian/infernal-doc.doc-base	2009-09-29 15:13:30 UTC (rev 4072)
+++ trunk/packages/infernal/trunk/debian/infernal-doc.doc-base	2009-09-29 15:17:04 UTC (rev 4073)
@@ -13,4 +13,4 @@
 Section: Science/Biology
 
 Format: pdf
-Index: /usr/share/doc/infernal/Userguide.pdf
+Files: /usr/share/doc/infernal/Userguide.pdf

Modified: trunk/packages/infernal/trunk/debian/infernal.install
===================================================================
--- trunk/packages/infernal/trunk/debian/infernal.install	2009-09-29 15:13:30 UTC (rev 4072)
+++ trunk/packages/infernal/trunk/debian/infernal.install	2009-09-29 15:17:04 UTC (rev 4073)
@@ -1,3 +1,9 @@
+src/cmalign       usr/bin
+src/cmbuild       usr/bin
+src/cmcalibrate   usr/bin
+src/cmemit        usr/bin
+src/cmscore       usr/bin
+src/cmsearch      usr/bin
+src/cmstat        usr/bin
 src/trcyk         usr/bin
 src/truncyk_check usr/bin
-

Modified: trunk/packages/infernal/trunk/debian/rules
===================================================================
--- trunk/packages/infernal/trunk/debian/rules	2009-09-29 15:13:30 UTC (rev 4072)
+++ trunk/packages/infernal/trunk/debian/rules	2009-09-29 15:17:04 UTC (rev 4073)
@@ -4,8 +4,13 @@
 %:
 	dh $@
 
+override_dh_compress:
+	dh_compress --exclude=.pdf
+
 override_dh_auto_clean:
 	if [ -r Makefile ]; then $(MAKE) distclean; fi
+	cd documentation/userguide; make distclean
+	cd easel/documentation; make distclean
 	dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1
 
 override_dh_auto_install:


