[Bioc-devel] Obtain unitTest reports from build machines ?

Dan Tenenbaum dtenenba at fhcrc.org
Mon Jan 30 19:04:59 CET 2012

Hi Steggen,

On Mon, Jan 30, 2012 at 12:22 AM, Steffen Neumann <sneumann at ipb-halle.de> wrote:
> Hi,
> a while ago one of the packages I am involved in (xcms)
> turned "red" for the check on windows builds. As there was no
> commit from our side at or before the failure, it must be
> some other interaction or side-effect.
> Getting the output of the actual RUnit test failure
> would be an enormous help, and has the top rank
> on my wishlist for the build machines.

What you see in the build report is the full output of
R CMD check
as well as the contents of the file 00install.out.

I ran the check for xcms manually and I see that R crashes with the
following output:

Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  Loading required package: caTools
  Loading required package: bitops
  3: >C:\Users\BIOCBU~1\AppData\Local\Temp\5\RtmpsnCFwB/ko15.mzData
  tracemem[0x0000000008140960 -> 0x0000000008140960]: data.frame eval
evalq rcpp_doTryCatc
h rcpp_tryCatch .External <Anonymous> .local header header mzRRawData
xcmsRaw func system.
time doTryCatch tryCatchOne tryCatchList tryCatch try .executeTestCase
.sourceTestFile run
  Timing stopped at: 12.75 0.22 12.97
  Error in structure(list(message = as.character(message), call = call),  :
    value of 'SET_ATTRIB' must be a pairlist or NULL, not a 'character'
  In addition: There were 50 or more warnings (use warnings() to see
the first 50)
   done successfully.

  Executing test function test.rawMat  ...

I'll look into this further, but there isn't much of a way for us to
capture the output when R crashes unexpectedly.


> Yours,
> Steffen
> --
> IPB Halle                    AG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann          http://www.IPB-Halle.DE
> Weinberg 3                   http://msbi.bic-gh.de
> 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
>                                  +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> _______________________________________________
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