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CHECK report for biomaRt on tokay2

This page was generated on 2018-10-17 08:32:22 -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: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomaRt.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings biomaRt_2.36.1.tar.gz
StartedAt: 2018-10-17 00:45:50 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:49:44 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 233.8 seconds
RetCode: 1
Status:  ERROR  
CheckDir: biomaRt.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomaRt.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings biomaRt_2.36.1.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/biomaRt.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
select 0.29   0.05   46.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
select 0.36      0    48.2
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  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
** running tests for arch 'x64' ...
  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: 2 ERRORs, 1 NOTE
See
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/biomaRt_2.36.1.tar.gz && rm -rf biomaRt.buildbin-libdir && mkdir biomaRt.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biomaRt.buildbin-libdir biomaRt_2.36.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL biomaRt_2.36.1.zip && rm biomaRt_2.36.1.tar.gz biomaRt_2.36.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 38670  100 38670    0     0   487k      0 --:--:-- --:--:-- --:--:--  539k

install for i386

* installing *source* package 'biomaRt' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biomaRt'
    finding HTML links ... done
    Mart-class                              html  
    NP2009code                              html  
    attributePages                          html  
    exportFASTA                             html  
    filterOptions                           html  
    filterType                              html  
    getBM                                   html  
    getBMlist                               html  
    getGene                                 html  
    getLDS                                  html  
    getSequence                             html  
    getXML                                  html  
    listAttributes                          html  
    listDatasets                            html  
    listEnsembl                             html  
    listEnsemblArchives                     html  
    listFilters                             html  
    listMarts                               html  
    select                                  html  
    useDataset                              html  
    useEnsembl                              html  
    useMart                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'biomaRt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biomaRt' as biomaRt_2.36.1.zip
* DONE (biomaRt)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'biomaRt' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

biomaRt.Rcheck/tests_i386/testthat.Rout.fail


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

biomaRt.Rcheck/tests_x64/testthat.Rout.fail


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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/examples_i386/biomaRt-Ex.timings

nameusersystemelapsed
NP2009code000
attributePages000
exportFASTA000
filterOptions000
filterType000
getBM0.260.123.44
getBMlist000
getGene000
getLDS000
getSequence0.010.000.02
getXML000
listAttributes000
listDatasets000
listEnsembl000
listEnsemblArchives0.030.010.69
listFilters000
listMarts000
select 0.29 0.0546.77
useDataset000
useEnsembl000
useMart000

biomaRt.Rcheck/examples_x64/biomaRt-Ex.timings

nameusersystemelapsed
NP2009code0.020.000.02
attributePages000
exportFASTA000
filterOptions0.010.000.01
filterType000
getBM0.290.003.30
getBMlist000
getGene000
getLDS0.010.000.02
getSequence000
getXML000
listAttributes000
listDatasets0.020.000.01
listEnsembl000
listEnsemblArchives0.010.000.32
listFilters000
listMarts000
select 0.36 0.0048.20
useDataset000
useEnsembl000
useMart000