BioC 3.5: CHECK report for GA4GHclient on malbec2

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

##############################################################################
##############################################################################
###
### 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

* 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)

name	user	system	elapsed
HGVSnames	0.000	0.000	0.001
getBiosample	0	0	0
getCallSet	0.000	0.000	0.001
getDataset	0.000	0.004	0.000
getExpressionLevel	0	0	0
getFeature	0	0	0
getFeatureSet	0.000	0.000	0.001
getIndividual	0.000	0.000	0.001
getReadGroupSet	0	0	0
getReference	0	0	0
getReferenceSet	0	0	0
getRnaQuantification	0.000	0.000	0.001
getRnaQuantificationSet	0.000	0.000	0.001
getVariant	0.004	0.000	0.000
getVariantAnnotationSet	0	0	0
getVariantSet	0.000	0.000	0.001
listReferenceBases	0.004	0.000	0.001
makeVCFFromGA4GHResponse	0	0	0
makeVCFHeaderFromGA4GHResponse	0	0	0
searchBiosamples	0.000	0.000	0.001
searchCallSets	0.000	0.000	0.001
searchDatasets	0	0	0
searchExpressionLevels	0	0	0
searchFeatureSets	0.000	0.000	0.001
searchFeatures	0.000	0.000	0.001
searchIndividuals	0	0	0
searchPhenotypeAssociationSets	0.004	0.000	0.000
searchPhenotypeAssociations	0.000	0.000	0.001
searchReadGroupSets	0	0	0
searchReads	0	0	0
searchReferenceSets	0.000	0.000	0.001
searchReferences	0	0	0
searchRnaQuantificationSets	0	0	0
searchRnaQuantifications	0.000	0.000	0.001
searchVariantAnnotationSets	0.000	0.000	0.001
searchVariantAnnotations	0	0	0
searchVariantSets	0	0	0
searchVariants	0	0	0
searchVariantsByGRanges	0.06	0.00	0.06