[Debian-med-packaging] Bug#727693: autopkgtest fails: there is no package called ‘statmod’

[Martin Pitt]

Package: r-bioc-limma 
Version: 3.16.7~dfsg-1

The latest version of this package grew an XS-Testsuite header which
made it get picked up by our automatic Jenkins runners. However, it
seems that they fail without giving any useful output [1]:

| adt-run: & dsc0t-upstream: [----------------------------------------
| adt-run1: teeing to stdout: /tmp/adt-run.KRNBNH/dsc0t-upstream-testtmp/test_stdout, stderr: /tmp/adt-run.KRNBNH/dsc0t-upstream-testtmp/test_stderr
| adt-run1: testbed executing test finished with exit status 1
| adt-run: & dsc0t-upstream: ----------------------------------------]
| adt-run: & dsc0t-upstream:  - - - - - - - - - - results - - - - - - - - - -
| dsc0t-upstream       FAIL non-zero exit status 1

I installed r-bioc-limma into a clean VM and ran the test manually with sh -x:

| ~/r-bioc-limma-3.16.7~dfsg⟫ sh -ex debian/tests/upstream                                     
| + mktemp -d
| + TEMPORARY_DIR=/tmp/tmp.ngEhS1PLVf
| + cd /tmp/tmp.ngEhS1PLVf
| + cp /usr/share/doc/r-bioc-limma/tests/limma-Tests.R.gz /usr/share/doc/r-bioc-limma/tests/limma-Tests.Rout.save.gz .
| + basename limma-Tests.R.gz .gz
| + zcat limma-Tests.R.gz
| + basename limma-Tests.R.gz .gz
| + R CMD BATCH limma-Tests.R

Then I cd'ed into the temporary directory and tried with --verbose:

/tmp/tmp.AHzbzjmcPP⟫ R --verbose CMD BATCH limma-Tests.R
/tmp/tmp.AHzbzjmcPP⟫

I finally found limma-Tests.Rout which seems to have some detail at
last. At the end it says:

| > cor.out <- duplicateCorrelation(M)
| Loading required package: statmod
| Error: could not find function "mixedModel2Fit"
| In addition: Warning message:
| In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
|   there is no package called ‘statmod’
| Execution halted

apt-cache search statmod does not give anything. Is that a missing
dependency or some missing configuration? Also, could the autopkgtest
perhaps do something like "R [...] || { cat <logfile>; exit 1 }" to
make the test fail usefully?

Thank you!

Martin

P.S. r-bioc-edger fails in a similar way, bug coming.

[1] https://jenkins.qa.ubuntu.com/job/trusty-adt-r-bioc-limma/1/ARCH=amd64,label=adt/
-- 
Martin Pitt                        | http://www.piware.de
Ubuntu Developer (www.ubuntu.com)  | Debian Developer  (www.debian.org)