Package: GA4GHclient

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GA4GHclient.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GA4GHclient_1.4.0.tar.gz

StartedAt: 2018-10-16 21:28:13 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:32:18 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 244.1 seconds

RetCode: 0

Status:  OK

CheckDir: GA4GHclient.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GA4GHclient.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GA4GHclient_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GA4GHclient.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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 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 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GA4GHclient
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GA4GHclient’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GA4GHclient)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GA4GHclient)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

> 
> test_check("GA4GHclient")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 10 SKIPPED: 84 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.432   0.607  13.066 

name	user	system	elapsed
HGVSnames	0.004	0.001	0.005
getBiosample	0.001	0.001	0.002
getCallSet	0.001	0.001	0.002
getDataset	0.001	0.000	0.001
getExpressionLevel	0.002	0.000	0.002
getFeature	0.001	0.000	0.001
getFeatureSet	0.001	0.000	0.001
getIndividual	0.002	0.000	0.002
getReadGroupSet	0.001	0.000	0.002
getReference	0.002	0.001	0.002
getReferenceSet	0.001	0.000	0.001
getRnaQuantification	0.002	0.000	0.002
getRnaQuantificationSet	0.001	0.000	0.002
getVariant	0.002	0.000	0.002
getVariantAnnotationSet	0.002	0.000	0.001
getVariantSet	0.002	0.000	0.002
listReferenceBases	0.001	0.000	0.001
makeVCFFromGA4GHResponse	0.003	0.000	0.002
makeVCFHeaderFromGA4GHResponse	0.002	0.000	0.002
searchBiosamples	0.001	0.000	0.001
searchCallSets	0.001	0.000	0.001
searchDatasets	0.001	0.000	0.001
searchExpressionLevels	0.002	0.000	0.002
searchFeatureSets	0.001	0.001	0.001
searchFeatures	0.002	0.000	0.002
searchIndividuals	0.002	0.000	0.002
searchPhenotypeAssociationSets	0.001	0.000	0.001
searchPhenotypeAssociations	0.001	0.000	0.002
searchReadGroupSets	0.002	0.000	0.001
searchReads	0.001	0.000	0.001
searchReferenceSets	0.002	0.001	0.002
searchReferences	0.001	0.000	0.001
searchRnaQuantificationSets	0.001	0.000	0.002
searchRnaQuantifications	0.002	0.000	0.002
searchVariantAnnotationSets	0.002	0.000	0.002
searchVariantAnnotations	0.002	0.000	0.001
searchVariantSets	0.001	0.000	0.002
searchVariants	0.002	0.000	0.002
searchVariantsByGRanges	0.060	0.007	0.069