This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-ebseq.
commit ae20873097056b874ce9490494e53a0598f5dc23 Author: Andreas Tille <[email protected]> Date: Sun Nov 8 21:26:54 2015 +0100 Add autopkgtest --- debian/README.test | 8 ++++++++ debian/control | 7 +++++-- debian/docs | 2 ++ debian/examples | 1 + debian/tests/control | 5 +++++ debian/tests/run-unit-test | 19 +++++++++++++++++++ 6 files changed, 40 insertions(+), 2 deletions(-) diff --git a/debian/README.test b/debian/README.test new file mode 100644 index 0000000..55a9142 --- /dev/null +++ b/debian/README.test @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +To run the unit tests provided by the package you can do + + sh run-unit-test + +in this directory. diff --git a/debian/control b/debian/control index d87c723..b6e1a4a 100644 --- a/debian/control +++ b/debian/control @@ -7,7 +7,8 @@ Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-cran-gplots, - r-cran-blockmodeling + r-cran-blockmodeling, + r-cran-testthat Standards-Version: 3.9.6 Homepage: https://www.biostat.wisc.edu/~kendzior/EBSEQ/ @@ -15,7 +16,9 @@ Package: r-bioc-ebseq Architecture: all Depends: ${R:Depends}, ${misc:Depends}, - r-cran-gplots + r-cran-gplots, + r-cran-blockmodeling, + r-cran-testthat Description: R package for RNA-Seq Differential Expression Analysis r-bioc-ebseq is an R package for identifying genes and isoforms differentially expressed (DE) across two or more biological conditions in an RNA-seq diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..9a4f4f8 --- /dev/null +++ b/debian/docs @@ -0,0 +1,2 @@ +debian/README.test +debian/tests/run-unit-test diff --git a/debian/examples b/debian/examples new file mode 100644 index 0000000..18244c8 --- /dev/null +++ b/debian/examples @@ -0,0 +1 @@ +vignettes diff --git a/debian/tests/control b/debian/tests/control new file mode 100644 index 0000000..3edd424 --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,5 @@ +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 diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test new file mode 100644 index 0000000..d134fec --- /dev/null +++ b/debian/tests/run-unit-test @@ -0,0 +1,19 @@ +#!/bin/sh -e +oname=ebseq +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 +find . -name "*.gz" -exec gunzip \{\} \; +export LC_ALL=C +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 * -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-ebseq.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
