BioC 3.5: CHECK report for biomaRt on oaxaca

Package: biomaRt

Version: 2.31.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biomaRt_2.31.4.tar.gz

StartedAt: 2017-03-03 23:42:21 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:44:06 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 104.5 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_2.31.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/biomaRt.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘2.31.4’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
getBM 0.361  0.016  11.195
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/biomaRt.Rcheck/00check.log’
for details.

* 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
* DONE (biomaRt)

name	user	system	elapsed
NP2009code	0.000	0.000	0.001
attributePages	0.000	0.000	0.001
exportFASTA	0.000	0.000	0.001
filterOptions	0	0	0
filterType	0.000	0.000	0.001
getBM	0.361	0.016	11.195
getBMlist	0	0	0
getGene	0.001	0.000	0.002
getLDS	0.001	0.000	0.001
getSequence	0.001	0.000	0.002
getXML	0.000	0.000	0.001
listAttributes	0.001	0.000	0.001
listDatasets	0.000	0.000	0.001
listEnsembl	0	0	0
listFilters	0.001	0.000	0.001
listMarts	0.001	0.000	0.000
select	0.697	0.022	4.183
useDataset	0.000	0.000	0.001
useEnsembl	0.001	0.000	0.001
useMart	0.001	0.001	0.000