BioC 3.1: CHECK report for biomaRt on moscato2

Package: biomaRt

Version: 2.24.1

Command: rm -rf biomaRt.buildbin-libdir biomaRt.Rcheck && mkdir biomaRt.buildbin-libdir biomaRt.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomaRt.buildbin-libdir biomaRt_2.24.1.tar.gz >biomaRt.Rcheck\00install.out 2>&1 && cp biomaRt.Rcheck\00install.out biomaRt-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=biomaRt.buildbin-libdir --install="check:biomaRt-install.out" --force-multiarch --no-vignettes --timings biomaRt_2.24.1.tar.gz

StartedAt: 2015-10-08 23:44:03 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:46:13 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 130.0 seconds

RetCode: 0

Status:  OK

CheckDir: biomaRt.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biomaRt.buildbin-libdir biomaRt.Rcheck && mkdir biomaRt.buildbin-libdir biomaRt.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomaRt.buildbin-libdir biomaRt_2.24.1.tar.gz >biomaRt.Rcheck\00install.out 2>&1 && cp biomaRt.Rcheck\00install.out biomaRt-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=biomaRt.buildbin-libdir --install="check:biomaRt-install.out" --force-multiarch --no-vignettes --timings biomaRt_2.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/biomaRt.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '2.24.1'
* 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.
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' ... [7s] OK
** running examples for arch 'x64' ... [7s] 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-3.1-bioc/meat/biomaRt.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'biomaRt' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'biomaRt' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'biomaRt' as biomaRt_2.24.1.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	0	0
getBMlist	0	0	0
getGene	0	0	0
getLDS	0	0	0
getSequence	0.01	0.00	0.01
getXML	0	0	0
listAttributes	0	0	0
listDatasets	0	0	0
listEnsembl	0	0	0
listFilters	0	0	0
listMarts	0	0	0
select	0.77	0.00	3.18
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	0	0
getBM	0	0	0
getBMlist	0	0	0
getGene	0	0	0
getLDS	0	0	0
getSequence	0	0	0
getXML	0	0	0
listAttributes	0	0	0
listDatasets	0	0	0
listEnsembl	0	0	0
listFilters	0	0	0
listMarts	0	0	0
select	0.53	0.06	2.80
useDataset	0	0	0
useEnsembl	0	0	0
useMart	0	0	0