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[Bioc-devel] Access check.log file after error

2 messages · Blattmann Peter, James W. MacDonald

Original
Blattmann Peter
# 
Dear all,

I am maintaining the R package SWATH2stats and I received an error after having added a new test and committed it to the devel branch. As I cannot reproduce the error on my own computer I wanted to have a look at the error log that exists from the CHECK report on the Bioconductor devel branch.

So my question is how do I access the error log file? I don't mean the html website that is produced but it says at the end that there is further details in: '/Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/00check.log' and I don't know where to find this "00check.log" file?

Thanks for the help.

Peter

__________________________________________

ETH Zurich
Dr. Peter Blattmann
Institute of Molecular Systems Biology
Aebersold group
HPT E58
Auguste-Piccard-Hof 1
8093 Zurich
Switzerland

phone: +41 44 633 0473
cellphone: +41 79 745 8061
fax: +41 44 633 1532
e-mail: blattmann at imsb.biol.ethz.ch<mailto:blattmann at imsb.biol.ethz.ch>
James W. MacDonald
# 
As I already told you on the support site, everything you need to know is
in the Command output (the 00check.log is the same output) found by
clicking on the Error for each build machine. For Moscato, you have:

Warning: replacing previous import by 'data.table::melt' when loading
'MSstats'
Error in library.dynam(lib, package, package.lib) :
  DLL 'mzR' not found: maybe not installed for this architecture?

Error: processing vignette 'SWATH2stats_vignette.Rnw' failed with
diagnostics:
 chunk 33
Error : package or namespace load failed for 'MSstats'

That seems pretty clear to me - MStats appears not to be installed, maybe
because mzR isn't installed either? Anyway, neither one is really your
problem.

For Zin2 (linux) the Command output says

  Running ?test-all.R? [6s/6s]
 ERROR
Running the tests in ?tests/test-all.R? failed.
Last 13 lines of output:
  7: with_sink(temp, withCallingHandlers(withVisible(code), warning =
wHandler, message = mHandler))
  8: withCallingHandlers(withVisible(code), warning = wHandler, message =
mHandler)
  9: withVisible(code)
  10: disaggregate(data.max.test2)
  11: stop(paste("The number of transitions annotated and measured do not
match in the following transitions:\n",
         paste(unlist(n.transitions[n.transitions2 != n.transitions4]),
collapse = ", ")))

  testthat results
================================================================
  OK: 46 SKIPPED: 0 FAILED: 1
  1. Error: data conversion

Which says to me 'I tried to run all 46 of your unit tests, and bombed out
on the first one'.



On Wed, Nov 11, 2015 at 10:38 AM, Blattmann Peter <
blattmann at imsb.biol.ethz.ch> wrote: