Author: tille Date: 2014-08-08 13:01:07 +0000 (Fri, 08 Aug 2014) New Revision: 17649
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/tests/ trunk/packages/R/r-bioc-gviz/trunk/debian/tests/control_unused trunk/packages/R/r-bioc-gviz/trunk/debian/tests/run-unit-test Modified: trunk/packages/R/r-bioc-gviz/trunk/debian/README.test trunk/packages/R/r-bioc-gviz/trunk/debian/changelog Log: New upstream source and add better / more precise advise how the package can be tested. No autopkgtest since it requires 800MB data package Modified: trunk/packages/R/r-bioc-gviz/trunk/debian/README.test =================================================================== --- trunk/packages/R/r-bioc-gviz/trunk/debian/README.test 2014-08-08 12:55:25 UTC (rev 17648) +++ trunk/packages/R/r-bioc-gviz/trunk/debian/README.test 2014-08-08 13:01:07 UTC (rev 17649) @@ -1,5 +1,24 @@ Notes on how this package can be tested. ──────────────────────────────────────── -This package can be tested by loading it into R with the command -‘library(Gviz)’ in order to confirm its integrity. +This package can be tested be rerunning the vignettes. However +you need to install the following stuff from BioConductto first: + + http://bioconductor.org/packages/release/bioc/html/BiocStyle.html + http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html + +To simplify the installation of the large data package you can use the Debian +packaging which is prepared at + + svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-bsgenome.hsapiens.ucsc.hg19/trunk/ + +and create a Debian packagage. Currently there is no preparation done +for a r-bioc-biocstyle package - may be this can be changed at request. +Once you installed this data you can run script which is provided in +the package source as + + debian/tests/run-unit-test + +to confirm the integrity of the package. + + -- Andreas Tille <[email protected]> Fri, 08 Aug 2014 13:37:40 +0200 Modified: trunk/packages/R/r-bioc-gviz/trunk/debian/changelog =================================================================== --- trunk/packages/R/r-bioc-gviz/trunk/debian/changelog 2014-08-08 12:55:25 UTC (rev 17648) +++ trunk/packages/R/r-bioc-gviz/trunk/debian/changelog 2014-08-08 13:01:07 UTC (rev 17649) @@ -1,3 +1,10 @@ +r-bioc-gviz (1.8.4-1) unstable; urgency=medium + + * New upstream version + * Add better advise how the package can be tested + + -- Andreas Tille <[email protected]> Fri, 08 Aug 2014 14:18:07 +0200 + r-bioc-gviz (1.8.3-1) unstable; urgency=medium * New upstream version Added: trunk/packages/R/r-bioc-gviz/trunk/debian/tests/control_unused =================================================================== --- trunk/packages/R/r-bioc-gviz/trunk/debian/tests/control_unused (rev 0) +++ trunk/packages/R/r-bioc-gviz/trunk/debian/tests/control_unused 2014-08-08 13:01:07 UTC (rev 17649) @@ -0,0 +1,4 @@ +Tests: run-unit-test +# The following dependencies are not available so this autopkgtest is disabled +Depends: @, r-bioc-biocstyle, r-bioc-bsgenome.hsapiens.ucsc.hg19 +Restrictions: allow-stderr Added: trunk/packages/R/r-bioc-gviz/trunk/debian/tests/run-unit-test =================================================================== --- trunk/packages/R/r-bioc-gviz/trunk/debian/tests/run-unit-test (rev 0) +++ trunk/packages/R/r-bioc-gviz/trunk/debian/tests/run-unit-test 2014-08-08 13:01:07 UTC (rev 17649) @@ -0,0 +1,18 @@ +#!/bin/sh -e +oname=Gviz +pkg=r-bioc-`echo $oname | tr [A-Z] [a-z]` + +if [ "$ADTTMP" = "" ] ; then + ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi +cd $ADTTMP +cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP +gunzip *.gz +for rnw in `ls *.[rR]nw` ; do +rfile=`echo $rnw | sed 's/\.[rR]nw/.R/'` +R --no-save <<EOT + Stangle("$rnw") + source("$rfile", echo=TRUE) +EOT +done +# rm -rf * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
