BioC 3.4: CHECK report for GenomeInfoDb on morelia

Package: GenomeInfoDb

Version: 1.10.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.10.3.tar.gz

StartedAt: 2017-04-15 02:41:12 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 02:43:31 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 139.2 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeInfoDb.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 GenomeInfoDb_1.10.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.10.3’
* package encoding: UTF-8
* 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 ‘GenomeInfoDb’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data  13.6Mb
* 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: ‘utils:::.roman2numeric’
  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 ... NOTE
.lookupSpeciesFromTaxId: no visible binding for global variable
  ‘specData’
Undefined global functions or variables:
  specData
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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
available.species              7.524  0.162   7.691
GenomeDescription-class        6.158  0.181   6.472
fetchExtendedChromInfoFromUCSC 1.028  0.325  17.696
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomeInfoDb’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomeInfoDb)

name	user	system	elapsed
GenomeDescription-class	6.158	0.181	6.472
Seqinfo-class	0.068	0.013	0.083
available.species	7.524	0.162	7.691
fetchExtendedChromInfoFromUCSC	1.028	0.325	17.696
mapGenomeBuilds	0.053	0.003	0.056
rankSeqlevels	0.142	0.009	0.481
seqinfo	2.926	0.096	3.511
seqlevels-wrappers	2.960	0.163	3.414
seqlevelsStyle	0.567	0.025	0.592
speciesMap	4.683	0.144	4.835