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BioC 3.3: CHECK report for biomaRt on moscato2

This page was generated on 2016-10-13 12:47:31 -0700 (Thu, 13 Oct 2016).

Package 110/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomaRt 2.28.0
Steffen Durinck
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/biomaRt
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biomaRt
Version: 2.28.0
Command: rm -rf biomaRt.buildbin-libdir biomaRt.Rcheck && mkdir biomaRt.buildbin-libdir biomaRt.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomaRt.buildbin-libdir biomaRt_2.28.0.tar.gz >biomaRt.Rcheck\00install.out 2>&1 && cp biomaRt.Rcheck\00install.out biomaRt-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=biomaRt.buildbin-libdir --install="check:biomaRt-install.out" --force-multiarch --no-vignettes --timings biomaRt_2.28.0.tar.gz
StartedAt: 2016-10-13 01:27:28 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:30:16 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 168.6 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomaRt.buildbin-libdir biomaRt_2.28.0.tar.gz >biomaRt.Rcheck\00install.out 2>&1 && cp biomaRt.Rcheck\00install.out biomaRt-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=biomaRt.buildbin-libdir --install="check:biomaRt-install.out" --force-multiarch --no-vignettes --timings biomaRt_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/biomaRt.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.28.0'
* 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.keys'
* 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 0.39   0.01   19.18
** running examples for arch 'x64' ... 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
  'E:/biocbld/bbs-3.3-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_2.28.0.zip
* DONE (biomaRt)

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

nameusersystemelapsed
NP2009code000
attributePages000
exportFASTA000
filterOptions000
filterType000
getBM0.020.000.01
getBMlist000
getGene000
getLDS000
getSequence000
getXML000
listAttributes000
listDatasets000
listEnsembl000
listFilters000
listMarts000
select 0.39 0.0119.18
useDataset000
useEnsembl000
useMart000

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

nameusersystemelapsed
NP2009code0.020.000.01
attributePages000
exportFASTA000
filterOptions000
filterType000
getBM000
getBMlist000
getGene000
getLDS000
getSequence000
getXML000
listAttributes000
listDatasets000
listEnsembl000
listFilters000
listMarts000
select0.390.064.23
useDataset000
useEnsembl000
useMart000