[med-svn] r19692 - in trunk/packages/R/r-bioc-qvalue/trunk/debian: . tests
Andreas Tille
tille at moszumanska.debian.org
Fri Jul 24 11:45:18 UTC 2015
Author: tille
Date: 2015-07-24 11:45:17 +0000 (Fri, 24 Jul 2015)
New Revision: 19692
Removed:
trunk/packages/R/r-bioc-qvalue/trunk/debian/vignettes/
Modified:
trunk/packages/R/r-bioc-qvalue/trunk/debian/changelog
trunk/packages/R/r-bioc-qvalue/trunk/debian/control
trunk/packages/R/r-bioc-qvalue/trunk/debian/copyright
trunk/packages/R/r-bioc-qvalue/trunk/debian/docs
trunk/packages/R/r-bioc-qvalue/trunk/debian/examples
trunk/packages/R/r-bioc-qvalue/trunk/debian/rules
trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/run-unit-test
trunk/packages/R/r-bioc-qvalue/trunk/debian/watch
Log:
New upstream version with several adaptions
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/changelog 2015-07-23 08:07:08 UTC (rev 19691)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/changelog 2015-07-24 11:45:17 UTC (rev 19692)
@@ -1,3 +1,12 @@
+r-bioc-qvalue (2.0.0-1) unstable; urgency=medium
+
+ * New upstream version
+ * Add new (Build-)Dependencies: r-cran-ggplot2, r-cran-reshape2
+ * drop debian/vignettes
+ * Adapt autopkgtest
+
+ -- Andreas Tille <tille at debian.org> Fri, 24 Jul 2015 13:31:18 +0200
+
r-bioc-qvalue (1.40.0-1) unstable; urgency=medium
* New upstream version
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/control 2015-07-23 08:07:08 UTC (rev 19691)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/control 2015-07-24 11:45:17 UTC (rev 19692)
@@ -6,7 +6,9 @@
Priority: optional
Build-Depends: debhelper (>= 9),
cdbs,
- r-base-dev (>= 3.0)
+ r-base-dev (>= 3.0),
+ r-cran-ggplot2,
+ r-cran-reshape2
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-qvalue/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-qvalue/trunk/
@@ -15,7 +17,9 @@
Package: r-bioc-qvalue
Architecture: all
Depends: ${R:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ r-cran-ggplot2,
+ r-cran-reshape2
Conflicts: r-cran-qvalue
Provides: r-cran-qvalue
Replaces: r-cran-qvalue
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/copyright 2015-07-23 08:07:08 UTC (rev 19691)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/copyright 2015-07-24 11:45:17 UTC (rev 19692)
@@ -1,16 +1,16 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: qvalue
-Upstream-Contact: John D. Storey <jstorey at u.washington.edu>
+Upstream-Contact: John D. Storey <jstorey at princeton.edu>
Source: http://www.bioconductor.org/packages/release/bioc/html/qvalue.html
Files: *
-Copyright: © 2006-2014 Alan Dabney and John D. Storey
+Copyright: © 2006-2015 Alan Dabney and John D. Storey
License: LGPL
Files: debian/*
Copyright: 2008-2009 Steffen Moeller <moeller at debian.org>
2009-2011 Charles Plessy <plessy at debian.org>
- 2010-2014 Andreas Tille <tille at debian.org>
+ 2010-2015 Andreas Tille <tille at debian.org>
License: LGPL
License: LGPL
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/docs 2015-07-23 08:07:08 UTC (rev 19691)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/docs 2015-07-24 11:45:17 UTC (rev 19692)
@@ -1,3 +1,3 @@
debian/README.test
debian/tests/run-unit-test
-vignettes/manual.pdf
+inst/doc/qvalue.pdf
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/examples
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/examples 2015-07-23 08:07:08 UTC (rev 19691)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/examples 2015-07-24 11:45:17 UTC (rev 19692)
@@ -1,2 +1 @@
vignettes
-debian/vignettes
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/rules 2015-07-23 08:07:08 UTC (rev 19691)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/rules 2015-07-24 11:45:17 UTC (rev 19692)
@@ -7,7 +7,8 @@
chmod 644 debian/$(package)/usr/lib/R/site-library/$(cranName)/doc/*
# does not work but I have given up to understand cdbs - feel free to fix
-binary/$(package)::
+# binary/$(package)::
+post-install/$(package)::
chmod 644 debian/$(package)/usr/share/doc/$(package)/examples/vignettes/*
clean::
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/run-unit-test 2015-07-23 08:07:08 UTC (rev 19691)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/tests/run-unit-test 2015-07-24 11:45:17 UTC (rev 19692)
@@ -8,11 +8,17 @@
cd $ADTTMP
cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
find . -name "*.gz" -exec gunzip \{\} \;
+export LC_ALL=C
for rnw in `ls *.[rRS]nw` ; do
rfile=`echo $rnw | sed 's/\.[rRS]nw/.R/'`
+# Somehow Stangle ends up in error but an R file is created anyway so we ignore this for the moment
+echo "Stangle(\"$rnw\")" > tmp.R
+R --no-save < tmp.R || true
+# help requires user input
+sed -i 's/^help/#&/' $rfile
R --no-save <<EOT
- Stangle("$rnw")
+# Stangle("$rnw")
source("$rfile", echo=TRUE)
EOT
done
-# rm -rf *
+rm -rf *
Modified: trunk/packages/R/r-bioc-qvalue/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-qvalue/trunk/debian/watch 2015-07-23 08:07:08 UTC (rev 19691)
+++ trunk/packages/R/r-bioc-qvalue/trunk/debian/watch 2015-07-24 11:45:17 UTC (rev 19692)
@@ -1,4 +1,4 @@
version=3
-opts=downloadurlmangle=s/\.\./packages\/release\/bioc/,uversionmangle=s/$/+dfsg/ \
+opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
http://www.bioconductor.org/packages/release/bioc/html/qvalue.html \
.*/qvalue_([\d\.]+)\.tar\.gz
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