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CHECK report for GA4GHclient on merida2

This page was generated on 2018-10-17 08:58:00 -0400 (Wed, 17 Oct 2018).

Package 535/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GA4GHclient 1.4.0
Welliton Souza
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GA4GHclient
Branch: RELEASE_3_7
Last Commit: 2abcb37
Last Changed Date: 2018-04-30 10:35:45 -0400 (Mon, 30 Apr 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
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### Running 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
###
##############################################################################
##############################################################################


* 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


Installation output

GA4GHclient.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GA4GHclient
###
##############################################################################
##############################################################################


* 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)

Tests output

GA4GHclient.Rcheck/tests/testthat.Rout


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 

Example timings

GA4GHclient.Rcheck/GA4GHclient-Ex.timings

nameusersystemelapsed
HGVSnames0.0040.0010.005
getBiosample0.0010.0010.002
getCallSet0.0010.0010.002
getDataset0.0010.0000.001
getExpressionLevel0.0020.0000.002
getFeature0.0010.0000.001
getFeatureSet0.0010.0000.001
getIndividual0.0020.0000.002
getReadGroupSet0.0010.0000.002
getReference0.0020.0010.002
getReferenceSet0.0010.0000.001
getRnaQuantification0.0020.0000.002
getRnaQuantificationSet0.0010.0000.002
getVariant0.0020.0000.002
getVariantAnnotationSet0.0020.0000.001
getVariantSet0.0020.0000.002
listReferenceBases0.0010.0000.001
makeVCFFromGA4GHResponse0.0030.0000.002
makeVCFHeaderFromGA4GHResponse0.0020.0000.002
searchBiosamples0.0010.0000.001
searchCallSets0.0010.0000.001
searchDatasets0.0010.0000.001
searchExpressionLevels0.0020.0000.002
searchFeatureSets0.0010.0010.001
searchFeatures0.0020.0000.002
searchIndividuals0.0020.0000.002
searchPhenotypeAssociationSets0.0010.0000.001
searchPhenotypeAssociations0.0010.0000.002
searchReadGroupSets0.0020.0000.001
searchReads0.0010.0000.001
searchReferenceSets0.0020.0010.002
searchReferences0.0010.0000.001
searchRnaQuantificationSets0.0010.0000.002
searchRnaQuantifications0.0020.0000.002
searchVariantAnnotationSets0.0020.0000.002
searchVariantAnnotations0.0020.0000.001
searchVariantSets0.0010.0000.002
searchVariants0.0020.0000.002
searchVariantsByGRanges0.0600.0070.069