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 :
* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck’ * using R Under development (unstable) (2015-11-08 r69614) * using platform: x86_64-apple-darwin13.4.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SWATH2stats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SWATH2stats’ version ‘1.1.2’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘imsbInfer’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SWATH2stats’ can be installed ... [2s/2s] OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [14s/16s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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 NOTEHope 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