BioC 3.3: CHECK report for BgeeDB on oaxaca

Package: BgeeDB

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BgeeDB_1.0.3.tar.gz

StartedAt: 2016-10-12 23:32:24 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:39:35 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 431.1 seconds

RetCode: 0

Status:  OK

CheckDir: BgeeDB.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 BgeeDB_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/BgeeDB.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeDB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeDB’ version ‘1.0.3’
* 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 ‘BgeeDB’ 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: ‘topGO:::mapGenes2GOgraph’
  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 ... 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
Bgee-class      62.867  4.098 103.753
loadTopAnatData  5.615  0.323  33.477
listBgeeSpecies  0.025  0.004   6.452
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘biomaRt’
* 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/BgeeDB.Rcheck/00check.log’
for details.

* installing *source* package ‘BgeeDB’ ...
** R
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (BgeeDB)

name	user	system	elapsed
Bgee-class	62.867	4.098	103.753
listBgeeSpecies	0.025	0.004	6.452
loadTopAnatData	5.615	0.323	33.477
makeTable	3.843	0.073	3.921
topAnat	3.354	0.059	3.420