[Debian-med-packaging] Bug#727695: autopkgtest fails: copy&paste error, and there is no package called ‘MASS’

[Martin Pitt]

Package: r-bioc-edger
Version: 3.2.4~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-edger into a clean VM and ran the test manually with sh -x:

| r-bioc-edger-3.2.4~dfsg⟫ sh -ex debian/tests/upstream 
| + mktemp -d
| + TEMPORARY_DIR=/tmp/tmp.j2crsonUAL
| + cd /tmp/tmp.j2crsonUAL
| + 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

Please note that this copied the *limma* tests, presumably this is a copy&paste
error from r-bioc-limma?

When I replace that with "edger", I get:

| r-bioc-edger-3.2.4~dfsg⟫ sh -ex debian/tests/upstream 
| + mktemp -d
| + TEMPORARY_DIR=/tmp/tmp.s6FvBqjRVy
| + cd /tmp/tmp.s6FvBqjRVy
| + cp /usr/share/doc/r-bioc-edger/tests/edgeR-Tests.R.gz /usr/share/doc/r-bioc-edger/tests/edgeR-Tests.Rout.save.gz .
| + basename edgeR-Tests.R.gz .gz
| + zcat edgeR-Tests.R.gz
| + basename edgeR-Tests.R.gz .gz
| + R CMD BATCH edgeR-Tests.R

And the log file says

| ~/r-bioc-edger-3.2.4~dfsg⟫ tail -n 20 /tmp/tmp.s6FvBqjRVy/edgeR-Tests.Rout
| Gene61   2.855317 10.27136 10.738307 1.049403e-03 5.247014e-01
| Gene62  -2.123902 10.53174  8.818704 2.981584e-03 8.334758e-01
| Gene134 -1.949073 10.53355  8.125889 4.363759e-03 8.334758e-01
| Gene740 -1.610046 10.94907  8.013408 4.643227e-03 8.334758e-01
| Gene354  2.022698 10.45066  7.826308 5.149116e-03 8.334758e-01
| Gene5    1.856816 10.45249  7.214238 7.232750e-03 8.334758e-01
| Gene746 -1.798331 10.53094  6.846262 8.882690e-03 8.334758e-01
| Gene110  1.623148 10.68607  6.737984 9.438120e-03 8.334758e-01
| Gene383  1.637140 10.75412  6.687530 9.708962e-03 8.334758e-01
| > d <- estimateGLMCommonDisp(d, design, verbose=TRUE)
| Disp = 0.10253 , BCV = 0.3202 
| > glmFit(d,design,dispersion=dispersion.true,method="simple", prior.count=0.5/3)
| Loading required package: MASS
| Error in mglmSimple(y, design = design, dispersion = dispersion, offset = offset,  : 
|   could not find function "negative.binomial"
| Calls: glmFit ... glmFit.DGEList -> glmFit -> glmFit.default -> mglmSimple
| In addition: Warning message:
| In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
|   there is no package called ‘MASS’
| Execution halted

So just like with limma this might be a missing dependency or
mis-configuration?

Thank you!

Martin

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