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 Bioconductor devel branch. Can anyone tell me how I access the error log file on the subversion respository or similar?
If someone has an idea on how to troubleshoot such a problem most efficiently this is of course also highly appreciated.
Thank you very much.
Peter
part of the BioC 3.3: CHECK report for SWATH2stats:
Running ‘test-all.R’ [7s/7s]
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
Error: testthat unit tests failed Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/00check.log’ for details.
Hi Peter, Jim is right, the content of /Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/00check.log is nearly identical to what you see on the web. The only difference, is that the copy on web is a day older (since the build report for today hasn't been generated yet). Here's content of /Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/00check.log from the morelia build server :
Hope this helps,
Brian
Presumably, you both saw my email on the mailing list, but if you didn't (or if you prefer HTML formatted messages), here's what I said :
It turns out there is additional information in the file <pre>/Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/tests/test-all.Rout.fail</pre> on morelia (and similar on zin2). Below are the contents of each.
From morelia
From zin2
Hope this helps,
Brian