BioC 3.2: CHECK report for GenomeInfoDb on perceval

Package: GenomeInfoDb

Version: 1.5.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.5.13.tar.gz

StartedAt: 2015-08-24 01:02:41 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:05:30 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 168.2 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_1.5.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.5.13’
* 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 ... [7s/7s] OK
* checking installed package size ... NOTE
  installed size is 20.7Mb
  sub-directories of 1Mb or more:
    data  20.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘S4Vectors’
A package should be listed in only one of these fields.
* 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’
* 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 ... [46s/48s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
availableSpecies        17.431  0.509  18.033
speciesMap               8.651  0.408   9.084
GenomeDescription-class  7.080  0.257   7.429
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/10s]
 [11s/11s] 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	7.080	0.257	7.429
Seqinfo-class	0.092	0.013	0.107
availableSpecies	17.431	0.509	18.033
fetchExtendedChromInfoFromUCSC	1.251	0.160	2.161
rankSeqlevels	0.357	0.013	0.435
seqinfo	3.867	0.252	4.189
seqlevels-wrappers	1.860	0.200	2.183
seqlevelsStyle	0.308	0.025	0.333
speciesMap	8.651	0.408	9.084