Question: How to access error log from build report
0
gravatar for blattmann
4.0 years ago by
blattmann0
Switzerland/Zurich/ETH Zurich
blattmann0 wrote:

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.
cmd check testthat build • 829 views
ADD COMMENTlink modified 4.0 years ago by James W. MacDonald51k • written 4.0 years ago by blattmann0
Answer: How to access error log from build report
1
gravatar for James W. MacDonald
4.0 years ago by
United States
James W. MacDonald51k wrote:

This sort of question should be directed towards the devel list (bioc-devel@r-project.org).

That said, the entire log can be accessed by clicking on the error messages here. There are two problems. One for windows and one for linux. The former is sort of boring - there appears to be a missing package dependency on the windows build machine. The linux (and by linux I mean both linux and MacOS) you are failing in one of your unit tests.

ADD COMMENTlink written 4.0 years ago by James W. MacDonald51k

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 NOTE

Hope this helps,

Brian

ADD REPLYlink written 4.0 years ago by brian.long10

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

R Under development (unstable) (2015-11-08 r69614) -- "Unsuffered Consequences"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("SWATH2stats")
Loading required package: SWATH2stats
1. Error: data conversion ------------------------------------------------------
The number of transitions annotated and measured do not match in the following transitions:
 1069078_FIIDPAAVITGR_2, 1069082_FIIDPAAVITGR_2, 1069080_FIIDPAAVITGR_2, 1069071_FIIDPAAVITGR_2, 1069078_FIIDPAAVITGR_2, 1069082_FIIDPAAVITGR_2, 1069080_FIIDPAAVITGR_2, 1069071_FIIDPAAVITGR_2, 1069084_FIIDPAAVITGR_2, 1069076_FIIDPAAVITGR_2
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_that(disaggregate(data.max.test2), shows_message("The library contains between 4 and 6 transitions per precursor.", 
       fixed = TRUE)) at test_convert.R:50
5: condition(object)
6: evaluate_promise(expr)
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

From zin2

R Under development (unstable) (2015-11-08 r69614) -- "Unsuffered Consequences"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("SWATH2stats")
Loading required package: SWATH2stats
1. Error: data conversion ------------------------------------------------------
The number of transitions annotated and measured do not match in the following transitions:
 1069078_FIIDPAAVITGR_2, 1069082_FIIDPAAVITGR_2, 1069080_FIIDPAAVITGR_2, 1069071_FIIDPAAVITGR_2, 1069078_FIIDPAAVITGR_2, 1069082_FIIDPAAVITGR_2, 1069080_FIIDPAAVITGR_2, 1069071_FIIDPAAVITGR_2, 1069084_FIIDPAAVITGR_2, 1069076_FIIDPAAVITGR_2
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_that(disaggregate(data.max.test2), shows_message("The library contains between 4 and 6 transitions per precursor.", 
       fixed = TRUE)) at test_convert.R:50
5: condition(object)
6: evaluate_promise(expr)
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

Hope this helps,
Brian

ADD REPLYlink written 4.0 years ago by brian.long10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 201 users visited in the last hour