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

[Brian Long]

Sorry for the additional email. It turns out there is additional
information in the file
/Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/tests/test-all.Rout.fail
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
​

On Wed, Nov 11, 2015 at 12:29 PM, Brian Long <brian at bioconductor.org> wrote:

> 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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