BioC 3.2: CHECK report for GenomeInfoDb on zin1

Package: GenomeInfoDb

Version: 1.6.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.6.3.tar.gz

StartedAt: 2016-04-23 01:01:57 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:03:33 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 95.9 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeInfoDb.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.6.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.6.3’
* 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 ‘GenomeInfoDb’ can be installed ... [5s/5s] 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 ... [24s/26s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
availableSpecies 8.834  0.071    8.91
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/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: 4 NOTEs
See
  ‘/home/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	4.011	0.132	4.142
Seqinfo-class	0.047	0.004	0.052
availableSpecies	8.834	0.071	8.910
fetchExtendedChromInfoFromUCSC	0.700	0.056	2.451
rankSeqlevels	0.130	0.000	0.169
seqinfo	2.151	0.052	2.201
seqlevels-wrappers	1.021	0.020	1.040
seqlevelsStyle	0.377	0.013	0.389
speciesMap	4.329	0.043	4.375