BioC 3.5: CHECK report for GenomeInfoDb on malbec2

Package: GenomeInfoDb

Version: 1.12.3

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.12.3.tar.gz

StartedAt: 2017-10-17 23:29:02 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:31:01 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 119.1 seconds

RetCode: 0

Status:  OK

CheckDir: GenomeInfoDb.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.12.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.12.3’
* 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 ... 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: ‘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
.getTaxonomyId: no visible binding for global variable ‘speciesMap’
.lookupSpeciesFromTaxId: no visible binding for global variable
  ‘specData’
available.species: no visible binding for global variable ‘speciesMap’
Undefined global functions or variables:
  specData speciesMap
* 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
seqinfo                        16.092  0.060  16.616
seqlevels-wrappers             15.396  0.008  15.437
available.species               7.232  0.220   7.467
GenomeDescription-class         5.508  0.120   6.287
fetchExtendedChromInfoFromUCSC  2.300  0.116   5.186
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomeInfoDb’ ...
** R
** 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	5.508	0.120	6.287
Seqinfo-class	0.548	0.000	0.549
available.species	7.232	0.220	7.467
fetchExtendedChromInfoFromUCSC	2.300	0.116	5.186
mapGenomeBuilds	0.140	0.016	0.158
rankSeqlevels	0.128	0.008	0.229
seqinfo	16.092	0.060	16.616
seqlevels-wrappers	15.396	0.008	15.437
seqlevelsStyle	0.384	0.004	0.393