Your message dated Wed, 08 Jan 2014 09:19:22 +0000
with message-id <[email protected]>
and subject line Bug#727695: fixed in r-bioc-edger 3.4.2+dfsg-2
has caused the Debian Bug report #727695,
regarding autopkgtest fails: copy&paste error, and there is no package called
‘MASS’
to be marked as done.
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727695: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=727695
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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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--- End Message ---
--- Begin Message ---
Source: r-bioc-edger
Source-Version: 3.4.2+dfsg-2
We believe that the bug you reported is fixed in the latest version of
r-bioc-edger, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated r-bioc-edger package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Wed, 08 Jan 2014 10:01:36 +0100
Source: r-bioc-edger
Binary: r-bioc-edger
Architecture: source amd64
Version: 3.4.2+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
r-bioc-edger - Empirical analysis of digital gene expression data in R
Closes: 727695
Changes:
r-bioc-edger (3.4.2+dfsg-2) unstable; urgency=medium
.
[ Martin Pitt ]
* debian/tests/control: Re-add @ test dependency which got dropped in the
previous upload.
* debian/tests/upstream: Run edger tests, not limma (copy&paste error).
(Closes: #727695)
.
[ Andreas Tille ]
* Standards-Version: 3.9.5
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