[med-svn] r23000 - in trunk/packages/R/r-bioc-metagenomeseq/trunk/debian: . tests
Andreas Tille
tille at moszumanska.debian.org
Fri Nov 4 14:14:54 UTC 2016
Author: tille
Date: 2016-11-04 14:14:53 +0000 (Fri, 04 Nov 2016)
New Revision: 23000
Modified:
trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/README.test
trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/changelog
trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/control
trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/copyright
trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/docs
trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/rules
trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/tests/run-unit-test
Log:
* New upstream version
* Convert to dh-r
* Generic BioConductor homepage
* Use testthat for autopkgtest since other unittest is empty
Modified: trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/README.test 2016-11-04 13:48:08 UTC (rev 22999)
+++ trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/README.test 2016-11-04 14:14:53 UTC (rev 23000)
@@ -1,10 +1,8 @@
Notes on how this package can be tested.
────────────────────────────────────────
-You can run the test suite by doing
+This package can be tested by running the provided test:
-R --no-save <<EOT
-BiocGenerics:::testPackage("metagenomeSeq")
-EOT
+ sh ./run-unit-test
- -- Andreas Tille <tille at debian.org> Mon, 16 Jun 2014 16:28:55 +0200
+in order to confirm its integrity.
Modified: trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/changelog 2016-11-04 13:48:08 UTC (rev 22999)
+++ trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/changelog 2016-11-04 14:14:53 UTC (rev 23000)
@@ -1,3 +1,12 @@
+r-bioc-metagenomeseq (1.16.0-1) unstable; urgency=medium
+
+ * New upstream version
+ * Convert to dh-r
+ * Generic BioConductor homepage
+ * Use testthat for autopkgtest since other unittest is empty
+
+ -- Andreas Tille <tille at debian.org> Fri, 04 Nov 2016 14:55:51 +0100
+
r-bioc-metagenomeseq (1.14.2-1) unstable; urgency=low
* Initial release (closes: #835135)
Modified: trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/control 2016-11-04 13:48:08 UTC (rev 22999)
+++ trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/control 2016-11-04 14:14:53 UTC (rev 23000)
@@ -4,7 +4,7 @@
Section: gnu-r
Priority: optional
Build-Depends: debhelper (>= 9),
- cdbs,
+ dh-r,
r-base-dev,
r-bioc-biobase,
r-bioc-limma,
@@ -17,20 +17,14 @@
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-metagenomeseq/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-metagenomeseq/trunk/
-Homepage: http://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html
+Homepage: https://bioconductor.org/packages/metagenomeSeq/
Package: r-bioc-metagenomeseq
Architecture: all
Depends: ${R:Depends},
- ${misc:Depends},
- r-bioc-biobase,
- r-bioc-limma,
- r-cran-glmnet,
- r-cran-rcolorbrewer,
- r-cran-matrixstats,
- r-cran-foreach,
- r-cran-matrix,
- r-cran-gplots
+ ${misc:Depends}
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
Description: GNU R statistical analysis for sparse high-throughput sequencing
MetagenomeSeq is designed to determine features (be it Operational
Taxanomic Unit (OTU), species, etc.) that are differentially abundant
Modified: trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/copyright 2016-11-04 13:48:08 UTC (rev 22999)
+++ trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/copyright 2016-11-04 14:14:53 UTC (rev 23000)
@@ -1,7 +1,7 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: metagenomeSeq
Upstream-Contact: Joseph N. Paulson <jpaulson at jimmy.harvard.edu>
-Source: http://www.bioconductor.org/packages/release/bioc/html/metagenomeSeq.html
+Source: https://bioconductor.org/packages/metagenomeSeq/
Files: *
Copyright: © 2010-2016 Joseph N. Paulson <jpaulson at jimmy.harvard.edu>
Modified: trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/docs 2016-11-04 13:48:08 UTC (rev 22999)
+++ trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/docs 2016-11-04 14:14:53 UTC (rev 23000)
@@ -1 +1,3 @@
+tests
debian/README.test
+debian/tests/run-unit-test
Modified: trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/rules 2016-11-04 13:48:08 UTC (rev 22999)
+++ trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/rules 2016-11-04 14:14:53 UTC (rev 23000)
@@ -1,4 +1,4 @@
#!/usr/bin/make -f
-debRreposname=bioc
-include /usr/share/R/debian/r-cran.mk
+%:
+ dh $@ --buildsystem R
Modified: trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/tests/run-unit-test 2016-11-04 13:48:08 UTC (rev 22999)
+++ trunk/packages/R/r-bioc-metagenomeseq/trunk/debian/tests/run-unit-test 2016-11-04 14:14:53 UTC (rev 23000)
@@ -1,5 +1,13 @@
#!/bin/sh -e
-LC_ALL=C R --no-save <<EOT
-BiocGenerics:::testPackage("metagenomeSeq")
-EOT
+oname=metagenomeSeq
+pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'`
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+find . -name "*.gz" -exec gunzip \{\} \;
+LC_ALL=C R --no-save < testthat.R
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