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BioC 3.5: CHECK report for biomaRt on tokay2

This page was generated on 2017-08-16 13:18:53 -0400 (Wed, 16 Aug 2017).

Package 126/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomaRt 2.32.1
Steffen Durinck
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/biomaRt
Last Changed Rev: 130159 / Revision: 131943
Last Changed Date: 2017-06-07 12:08:53 -0400 (Wed, 07 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biomaRt
Version: 2.32.1
Command: rm -rf biomaRt.buildbin-libdir biomaRt.Rcheck && mkdir biomaRt.buildbin-libdir biomaRt.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomaRt.buildbin-libdir biomaRt_2.32.1.tar.gz >biomaRt.Rcheck\00install.out 2>&1 && cp biomaRt.Rcheck\00install.out biomaRt-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=biomaRt.buildbin-libdir --install="check:biomaRt-install.out" --force-multiarch --no-vignettes --timings biomaRt_2.32.1.tar.gz
StartedAt: 2017-08-15 22:18:28 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:21:38 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 190.2 seconds
RetCode: 0
Status:  OK  
CheckDir: biomaRt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biomaRt.buildbin-libdir biomaRt.Rcheck && mkdir biomaRt.buildbin-libdir biomaRt.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomaRt.buildbin-libdir biomaRt_2.32.1.tar.gz >biomaRt.Rcheck\00install.out 2>&1 && cp biomaRt.Rcheck\00install.out biomaRt-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=biomaRt.buildbin-libdir --install="check:biomaRt-install.out" --force-multiarch --no-vignettes --timings biomaRt_2.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/biomaRt.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.32.1'
* 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 installed files from 'inst/doc' ... 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 0.83   0.02   16.70
getBM  0.74   0.06   13.46
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
select 0.89   0.02   12.36
getBM  0.70   0.13   13.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/biomaRt.Rcheck/00check.log'
for details.


biomaRt.Rcheck/00install.out:


install for i386

* installing *source* package 'biomaRt' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'biomaRt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biomaRt' as biomaRt_2.32.1.zip
* DONE (biomaRt)

biomaRt.Rcheck/examples_i386/biomaRt-Ex.timings:

nameusersystemelapsed
NP2009code000
attributePages000
exportFASTA0.010.000.01
filterOptions000
filterType000
getBM 0.74 0.0613.46
getBMlist0.010.000.01
getGene000
getLDS000
getSequence000
getXML000
listAttributes000
listDatasets000
listEnsembl000
listFilters000
listMarts000
select 0.83 0.0216.70
useDataset000
useEnsembl000
useMart000

biomaRt.Rcheck/examples_x64/biomaRt-Ex.timings:

nameusersystemelapsed
NP2009code000
attributePages000
exportFASTA000
filterOptions000
filterType000
getBM 0.70 0.1313.03
getBMlist000
getGene000
getLDS000
getSequence000
getXML000
listAttributes000
listDatasets0.010.000.02
listEnsembl000
listFilters000
listMarts000
select 0.89 0.0212.36
useDataset000
useEnsembl000
useMart000