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CHECK report for biomaRt on merida2

This page was generated on 2018-10-17 08:46:31 -0400 (Wed, 17 Oct 2018).

Package 140/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomaRt 2.36.1
Mike Smith
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/biomaRt
Branch: RELEASE_3_7
Last Commit: 5634e57
Last Changed Date: 2018-05-23 11:57:32 -0400 (Wed, 23 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: biomaRt
Version: 2.36.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biomaRt_2.36.1.tar.gz
StartedAt: 2018-10-16 20:07:38 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:10:24 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 166.1 seconds
RetCode: 1
Status:  ERROR 
CheckDir: biomaRt.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biomaRt_2.36.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/biomaRt.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.36.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘biomaRt’ can be installed ... 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::smartKeys’
  See the note in ?`:::` about the use of this operator.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
getBM  0.305  0.043   6.651
select 0.282  0.033  57.382
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: getBM(filter = "ensembl_gene_id", values = "ENSMUSG00000000103", attributes = attributes, 
         mart = mart) at testthat/test_colnames.R:37
  2: read.table(con, sep = "\t", header = callHeader, quote = quote, comment.char = "", 
         check.names = FALSE, stringsAsFactors = FALSE)
  3: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, 
         skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, 
         blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, 
         allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: Renaming columns - real data (@test_colnames.R#37) 
  
  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-3.7-bioc/meat/biomaRt.Rcheck/00check.log’
for details.


Installation output

biomaRt.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL biomaRt
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘biomaRt’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomaRt)

Tests output

biomaRt.Rcheck/tests/testthat.Rout.fail


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
> library(biomaRt)
> 
> test_check("biomaRt", encoding = "UTF-8")
── 1. Error: Renaming columns - real data (@test_colnames.R#37)  ───────────────
line 1 did not have 3 elements
1: getBM(filter = "ensembl_gene_id", values = "ENSMUSG00000000103", attributes = attributes, 
       mart = mart) at testthat/test_colnames.R:37
2: read.table(con, sep = "\t", header = callHeader, quote = quote, comment.char = "", 
       check.names = FALSE, stringsAsFactors = FALSE)
3: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, 
       skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, 
       blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, 
       allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul)

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 9 SKIPPED: 0 FAILED: 1
1. Error: Renaming columns - real data (@test_colnames.R#37) 

Error: testthat unit tests failed
Execution halted

Example timings

biomaRt.Rcheck/biomaRt-Ex.timings

nameusersystemelapsed
NP2009code0.0020.0000.001
attributePages0.0020.0010.002
exportFASTA0.0010.0000.002
filterOptions0.0020.0000.001
filterType0.0020.0000.002
getBM0.3050.0436.651
getBMlist0.0020.0000.002
getGene0.0030.0000.004
getLDS0.0020.0000.002
getSequence0.0030.0000.002
getXML0.0020.0010.002
listAttributes0.0020.0000.001
listDatasets0.0020.0000.001
listEnsembl0.0010.0000.001
listEnsemblArchives0.0260.0020.269
listFilters0.0020.0000.002
listMarts0.0020.0000.002
select 0.282 0.03357.382
useDataset0.0020.0000.002
useEnsembl0.0020.0000.002
useMart0.0020.0010.002