BioC 3.1: CHECK report for biomaRt on morelia

Package: biomaRt

Version: 2.24.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biomaRt_2.24.1.tar.gz

StartedAt: 2015-10-08 23:36:03 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:37:29 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 86.4 seconds

RetCode: 0

Status:  OK

CheckDir: biomaRt.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biomaRt_2.24.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/biomaRt.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biomaRt’ can be installed ... [8s/8s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/biomaRt.Rcheck/00check.log’
for details.

* 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’
* DONE (biomaRt)

name	user	system	elapsed
NP2009code	0	0	0
attributePages	0.001	0.000	0.000
exportFASTA	0.001	0.001	0.001
filterOptions	0	0	0
filterType	0.001	0.000	0.000
getBM	0.001	0.000	0.001
getBMlist	0	0	0
getGene	0.001	0.000	0.001
getLDS	0.000	0.001	0.001
getSequence	0.001	0.000	0.001
getXML	0	0	0
listAttributes	0	0	0
listDatasets	0.001	0.000	0.001
listEnsembl	0.000	0.001	0.001
listFilters	0.001	0.000	0.001
listMarts	0	0	0
select	0.209	0.021	2.515
useDataset	0.000	0.000	0.001
useEnsembl	0.001	0.000	0.001
useMart	0	0	0