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

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### Running command:
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###   /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.

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### Running command:
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###   /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)

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

name	user	system	elapsed
NP2009code	0.002	0.000	0.001
attributePages	0.002	0.001	0.002
exportFASTA	0.001	0.000	0.002
filterOptions	0.002	0.000	0.001
filterType	0.002	0.000	0.002
getBM	0.305	0.043	6.651
getBMlist	0.002	0.000	0.002
getGene	0.003	0.000	0.004
getLDS	0.002	0.000	0.002
getSequence	0.003	0.000	0.002
getXML	0.002	0.001	0.002
listAttributes	0.002	0.000	0.001
listDatasets	0.002	0.000	0.001
listEnsembl	0.001	0.000	0.001
listEnsemblArchives	0.026	0.002	0.269
listFilters	0.002	0.000	0.002
listMarts	0.002	0.000	0.002
select	0.282	0.033	57.382
useDataset	0.002	0.000	0.002
useEnsembl	0.002	0.000	0.002
useMart	0.002	0.001	0.002