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BioC 3.5: CHECK report for GenomeInfoDb on veracruz2

This page was generated on 2017-10-18 14:31:45 -0400 (Wed, 18 Oct 2017).

Package 534/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeInfoDb 1.12.3
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/GenomeInfoDb
Branch: RELEASE_3_5
Last Commit: 2deef3f
Last Changed Date: 2017-10-04 10:51:06 -0400 (Wed, 04 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomeInfoDb
Version: 1.12.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.12.3.tar.gz
StartedAt: 2017-10-18 04:04:10 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 04:06:26 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 136.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomeInfoDb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomeInfoDb_1.12.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenomeInfoDb.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 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
seqlevels-wrappers             19.124  0.182  19.879
seqinfo                        17.761  0.320  19.040
available.species               7.981  0.203   8.489
GenomeDescription-class         6.206  0.215   6.635
fetchExtendedChromInfoFromUCSC  2.123  0.204   5.251
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenomeInfoDb.Rcheck/00check.log’
for details.


GenomeInfoDb.Rcheck/00install.out:

* 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)

GenomeInfoDb.Rcheck/GenomeInfoDb-Ex.timings:

nameusersystemelapsed
GenomeDescription-class6.2060.2156.635
Seqinfo-class0.5620.0070.602
available.species7.9810.2038.489
fetchExtendedChromInfoFromUCSC2.1230.2045.251
mapGenomeBuilds0.1380.0200.160
rankSeqlevels0.1220.0160.143
seqinfo17.761 0.32019.040
seqlevels-wrappers19.124 0.18219.879
seqlevelsStyle0.5370.0240.583