BioC 3.6: CHECK report for biomaRt on tokay1

Package: biomaRt

Version: 2.33.4

Command: rm -rf biomaRt.buildbin-libdir biomaRt.Rcheck && mkdir biomaRt.buildbin-libdir biomaRt.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomaRt.buildbin-libdir biomaRt_2.33.4.tar.gz >biomaRt.Rcheck\00install.out 2>&1 && cp biomaRt.Rcheck\00install.out biomaRt-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biomaRt.buildbin-libdir --install="check:biomaRt-install.out" --force-multiarch --no-vignettes --timings biomaRt_2.33.4.tar.gz

StartedAt: 2017-08-15 22:00:52 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:03:51 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 179.1 seconds

RetCode: 0

Status:  OK

CheckDir: biomaRt.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf biomaRt.buildbin-libdir biomaRt.Rcheck && mkdir biomaRt.buildbin-libdir biomaRt.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomaRt.buildbin-libdir biomaRt_2.33.4.tar.gz >biomaRt.Rcheck\00install.out 2>&1 && cp biomaRt.Rcheck\00install.out biomaRt-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biomaRt.buildbin-libdir --install="check:biomaRt-install.out" --force-multiarch --no-vignettes --timings biomaRt_2.33.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-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 '2.33.4'
* 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 ... NOTE
prepare_Rd: listEnsemblArchives.Rd:10: Dropping empty section \arguments
* 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 0.45   0.02   15.19
getBM  0.38   0.08   17.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
select 0.54   0.02   14.16
getBM  0.42   0.03   11.78
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/biomaRt.Rcheck/00check.log'
for details.

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_2.33.4.zip
* DONE (biomaRt)

name	user	system	elapsed
NP2009code	0	0	0
attributePages	0	0	0
exportFASTA	0	0	0
filterOptions	0	0	0
filterType	0	0	0
getBM	0.38	0.08	17.28
getBMlist	0	0	0
getGene	0	0	0
getLDS	0	0	0
getSequence	0	0	0
getXML	0.01	0.00	0.02
listAttributes	0	0	0
listDatasets	0	0	0
listEnsembl	0	0	0
listEnsemblArchives	0.00	0.00	0.42
listFilters	0	0	0
listMarts	0	0	0
select	0.45	0.02	15.19
useDataset	0	0	0
useEnsembl	0	0	0
useMart	0	0	0

name	user	system	elapsed
NP2009code	0	0	0
attributePages	0	0	0
exportFASTA	0	0	0
filterOptions	0	0	0
filterType	0.02	0.00	0.01
getBM	0.42	0.03	11.78
getBMlist	0	0	0
getGene	0	0	0
getLDS	0.02	0.00	0.02
getSequence	0	0	0
getXML	0	0	0
listAttributes	0	0	0
listDatasets	0	0	0
listEnsembl	0	0	0
listEnsemblArchives	0.00	0.00	0.39
listFilters	0	0	0
listMarts	0	0	0
select	0.54	0.02	14.16
useDataset	0	0	0
useEnsembl	0	0	0
useMart	0	0	0