This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r-bioc-limma.
commit a52062c4ad5529f0ff9fcddf6753efb159de022b Author: Andreas Tille <[email protected]> Date: Fri Jun 27 21:19:24 2014 +0200 Drop code from unit test that is using locfit since it is not packaged for Debian (and probably can not become part of Debian) --- debian/patches/do_not_attempt_locfit_test.patch | 66 +++++++++++++++++++++++++ debian/patches/series | 1 + debian/tests/control | 4 +- debian/tests/{upstream => run-unit-test} | 15 +++--- 4 files changed, 77 insertions(+), 9 deletions(-) diff --git a/debian/patches/do_not_attempt_locfit_test.patch b/debian/patches/do_not_attempt_locfit_test.patch new file mode 100644 index 0000000..498fe39 --- /dev/null +++ b/debian/patches/do_not_attempt_locfit_test.patch @@ -0,0 +1,66 @@ +Author: Andreas Tille <[email protected]> +Date: Fri, 27 Jun 2014 19:02:17 +0200 +Description: r-cran-locfit has a non-free license and thus can not be packaged + for Debian. So we have to skip this test. Feel free to pick up the + packaging from + svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-locfit/trunk/ + to create a local package and remove this patch from series. + + +--- r-bioc-limma.orig/tests/limma-Tests.R ++++ r-bioc-limma/tests/limma-Tests.R +@@ -48,19 +48,6 @@ + out <- loessFit(y,x,weights=w,method="weightedLowess") + f2 <- quantile(out$fitted) + r2 <- quantile(out$residual) +-out <- loessFit(y,x,weights=w,method="locfit") +-f3 <- quantile(out$fitted) +-r3 <- quantile(out$residual) +-out <- loessFit(y,x,weights=w,method="loess") +-f4 <- quantile(out$fitted) +-r4 <- quantile(out$residual) +-w <- rep(1,100) +-w[2*(1:50)] <- 0 +-out <- loessFit(y,x,weights=w,method="weightedLowess") +-f5 <- quantile(out$fitted) +-r5 <- quantile(out$residual) +-data.frame(f1,f2,f3,f4,f5) +-data.frame(r1,r2,r3,r4,r5) + + ### normalizeWithinArrays + +--- r-bioc-limma.orig/tests/limma-Tests.Rout.save ++++ r-bioc-limma/tests/limma-Tests.Rout.save +@@ -594,32 +594,6 @@ + > out <- loessFit(y,x,weights=w,method="weightedLowess") + > f2 <- quantile(out$fitted) + > r2 <- quantile(out$residual) +-> out <- loessFit(y,x,weights=w,method="locfit") +-> f3 <- quantile(out$fitted) +-> r3 <- quantile(out$residual) +-> out <- loessFit(y,x,weights=w,method="loess") +-> f4 <- quantile(out$fitted) +-> r4 <- quantile(out$residual) +-> w <- rep(1,100) +-> w[2*(1:50)] <- 0 +-> out <- loessFit(y,x,weights=w,method="weightedLowess") +-> f5 <- quantile(out$fitted) +-> r5 <- quantile(out$residual) +-> data.frame(f1,f2,f3,f4,f5) +- f1 f2 f3 f4 f5 +-0% -0.78835384 -0.687432210 -0.78957137 -0.76756060 -0.63778292 +-25% -0.18340154 -0.179683572 -0.18979269 -0.16773223 -0.38064318 +-50% -0.11492924 -0.114796040 -0.12087983 -0.07185314 -0.15971879 +-75% 0.01507921 -0.008145125 -0.01857508 0.04030634 0.07839396 +-100% 0.21653837 0.145106033 0.19214597 0.21417361 0.51836274 +-> data.frame(r1,r2,r3,r4,r5) +- r1 r2 r3 r4 r5 +-0% -2.04434053 -2.05132680 -2.02404318 -2.101242874 -2.22280633 +-25% -0.59321065 -0.57200209 -0.58975649 -0.577887481 -0.71037756 +-50% 0.05874864 0.04514326 0.08335198 -0.001769806 0.06785517 +-75% 0.56010750 0.55124530 0.57618740 0.561454370 0.65383830 +-100% 2.57936026 2.64549799 2.57549257 2.402324533 2.28648835 +-> + > ### normalizeWithinArrays + > + > RG <- new("RGList",list()) diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..d4944cc --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +do_not_attempt_locfit_test.patch diff --git a/debian/tests/control b/debian/tests/control index f08221c..d2aa55a 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -1 +1,3 @@ -Tests: upstream +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr diff --git a/debian/tests/upstream b/debian/tests/run-unit-test old mode 100755 new mode 100644 similarity index 58% rename from debian/tests/upstream rename to debian/tests/run-unit-test index d11cae7..2aeec4a --- a/debian/tests/upstream +++ b/debian/tests/run-unit-test @@ -1,10 +1,11 @@ #!/bin/sh -e -TEMPORARY_DIR=$(mktemp -d) - -cd $TEMPORARY_DIR - -cp /usr/share/doc/r-bioc-limma/tests/* . +pkg=r-bioc-limma +if [ "$ADTTMP" = "" ] ; then + ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +fi +cd $ADTTMP +cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP for test in *R.gz do zcat ${test} > `basename ${test} .gz` @@ -12,7 +13,5 @@ do R CMD Rdiff `basename ${test} .gz`out.save* `basename ${test} .gz`out rm `basename ${test} .gz`out .RData done +rm -f $ADTTMP/* -cd - - -rm -rf $TEMPORARY_DIR -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
