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

[Brian Long]

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
<http://bioconductor.org/checkResults/devel/bioc-LATEST/SWATH2stats/morelia-checksrc.html>.
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 NOTE

Hope this helps,
Brian
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