Author: tille Date: 2015-05-09 21:17:21 +0000 (Sat, 09 May 2015) New Revision: 19186
Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog trunk/packages/R/r-bioc-snpstats/trunk/debian/control trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test trunk/packages/R/r-bioc-snpstats/trunk/debian/watch Log: Exclude tests needing not packaged CRAN packages Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog =================================================================== --- trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog 2015-05-09 21:09:19 UTC (rev 19185) +++ trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog 2015-05-09 21:17:21 UTC (rev 19186) @@ -1,7 +1,8 @@ r-bioc-snpstats (1.18.0+dfsg-1) unstable; urgency=medium * New upstream version - TODO: Testsuite uses http://cran.r-project.org/web/packages/hexbin/ + * Exclude tests needing not packaged CRAN packages + * d/watch: proper versionmangling -- Andreas Tille <[email protected]> Sat, 09 May 2015 08:31:15 +0200 Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/control =================================================================== --- trunk/packages/R/r-bioc-snpstats/trunk/debian/control 2015-05-09 21:09:19 UTC (rev 19185) +++ trunk/packages/R/r-bioc-snpstats/trunk/debian/control 2015-05-09 21:17:21 UTC (rev 19186) @@ -24,6 +24,7 @@ r-cran-survival, r-cran-matrix, r-bioc-biocgenerics (>= 0.12.0) +Suggests: r-cran-hexbin Description: BioConductor SnpMatrix and XSnpMatrix classes and methods This BioConductor package provides R functions to work with SnpMatrix and XSnpMatrix classes and methods. Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test =================================================================== --- trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test 2015-05-09 21:09:19 UTC (rev 19185) +++ trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test 2015-05-09 21:17:21 UTC (rev 19186) @@ -8,12 +8,22 @@ fi cd $ADTTMP cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP -gunzip *.gz +find . -name "*.gz" -exec gunzip \{\} \; +export LC_ALL=C for rnw in *.Rnw ; do -rfile=`basename $rnw nw` -R --no-save <<EOT - Stangle("$rnw") - source("$rfile", echo=TRUE) + echo "====================== $rnw ============================" + rfile=`basename $rnw nw` + if [ "$rnw" = "imputation-vignette.Rnw" ] ; then # -o "$rnw" = "ld-vignette.Rnw" ] + echo "Test "$rnw" needs r-cran-hexbin which is not yet packaged." + else + if [ "$rnw" = "snpStats-vignette.Rnw" ] ; then + echo "Test $rnw needs allest[""rs10882596""] but it is not clear where to get this." + else + R --no-save <<EOT + Stangle("$rnw") + source("$rfile", echo=TRUE) EOT + fi + fi done Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/watch =================================================================== --- trunk/packages/R/r-bioc-snpstats/trunk/debian/watch 2015-05-09 21:09:19 UTC (rev 19185) +++ trunk/packages/R/r-bioc-snpstats/trunk/debian/watch 2015-05-09 21:17:21 UTC (rev 19186) @@ -1,3 +1,3 @@ version=3 -opts=uversionmangle=s/$/+dfsg/,downloadurlmangle=s/\.\./packages\/release\/bioc/ \ +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,downloadurlmangle=s/\.\./packages\/release\/bioc/" \ http://www.bioconductor.org/packages/release/bioc/html/snpStats.html .*/snpStats_([\d\.]+)\.tar\.gz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
