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BioC 3.5: CHECK report for GA4GHclient on malbec2

This page was generated on 2017-08-16 13:18:18 -0400 (Wed, 16 Aug 2017).

Package 486/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GA4GHclient 1.0.0
Welliton Souza
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/GA4GHclient
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GA4GHclient
Version: 1.0.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GA4GHclient_1.0.0.tar.gz
StartedAt: 2017-08-15 23:08:45 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:12:10 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 205.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GA4GHclient.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings GA4GHclient_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/GA4GHclient.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GA4GHclient/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GA4GHclient’ version ‘1.0.0’
* 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 ‘GA4GHclient’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK

GA4GHclient.Rcheck/00install.out:

* installing *source* package ‘GA4GHclient’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GA4GHclient)

GA4GHclient.Rcheck/GA4GHclient-Ex.timings:

nameusersystemelapsed
HGVSnames0.0000.0000.001
getBiosample000
getCallSet0.0000.0000.001
getDataset0.0000.0040.000
getExpressionLevel000
getFeature000
getFeatureSet0.0000.0000.001
getIndividual0.0000.0000.001
getReadGroupSet000
getReference000
getReferenceSet000
getRnaQuantification0.0000.0000.001
getRnaQuantificationSet0.0000.0000.001
getVariant0.0040.0000.000
getVariantAnnotationSet000
getVariantSet0.0000.0000.001
listReferenceBases0.0040.0000.001
makeVCFFromGA4GHResponse000
makeVCFHeaderFromGA4GHResponse000
searchBiosamples0.0000.0000.001
searchCallSets0.0000.0000.001
searchDatasets000
searchExpressionLevels000
searchFeatureSets0.0000.0000.001
searchFeatures0.0000.0000.001
searchIndividuals000
searchPhenotypeAssociationSets0.0040.0000.000
searchPhenotypeAssociations0.0000.0000.001
searchReadGroupSets000
searchReads000
searchReferenceSets0.0000.0000.001
searchReferences000
searchRnaQuantificationSets000
searchRnaQuantifications0.0000.0000.001
searchVariantAnnotationSets0.0000.0000.001
searchVariantAnnotations000
searchVariantSets000
searchVariants000
searchVariantsByGRanges0.060.000.06