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This page was generated on 2021-09-13 15:06:57 -0400 (Mon, 13 Sep 2021).

CHECK results for GA4GHclient on machv2

To the developers/maintainers of the GA4GHclient package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GA4GHclient.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 682/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GA4GHclient 1.16.0  (landing page)
Welliton Souza
Snapshot Date: 2021-09-12 04:50:10 -0400 (Sun, 12 Sep 2021)
git_url: https://git.bioconductor.org/packages/GA4GHclient
git_branch: RELEASE_3_13
git_last_commit: d3644e7
git_last_commit_date: 2021-05-19 12:26:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GA4GHclient
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2021-09-12 19:08:13 -0400 (Sun, 12 Sep 2021)
EndedAt: 2021-09-12 19:13:39 -0400 (Sun, 12 Sep 2021)
EllapsedTime: 325.8 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GA4GHclient.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/GA4GHclient.Rcheck/00check.log’
for details.



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/4.1/Resources/library’
* installing *source* package ‘GA4GHclient’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘BiocGenerics’ for request: ‘lengths’ when loading ‘GA4GHclient’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘BiocGenerics’ for request: ‘lengths’ when loading ‘GA4GHclient’
** testing if installed package can be loaded from final location
No methods found in package ‘BiocGenerics’ for request: ‘lengths’ when loading ‘GA4GHclient’
** testing if installed package keeps a record of temporary installation path
* DONE (GA4GHclient)

Tests output

GA4GHclient.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient'
> 
> test_check("GA4GHclient")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (84)

[ FAIL 0 | WARN 0 | SKIP 84 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
 17.138   0.741  17.869 

Example timings

GA4GHclient.Rcheck/GA4GHclient-Ex.timings

nameusersystemelapsed
HGVSnames0.0010.0010.002
getBiosample0.0000.0010.001
getCallSet000
getDataset000
getExpressionLevel0.0010.0000.001
getFeature000
getFeatureSet0.0000.0010.001
getIndividual0.0000.0010.001
getReadGroupSet0.0000.0000.001
getReference0.0000.0000.001
getReferenceSet000
getRnaQuantification000
getRnaQuantificationSet0.0000.0000.001
getVariant000
getVariantAnnotationSet0.0000.0000.001
getVariantSet000
listReferenceBases0.0000.0000.001
makeVCFFromGA4GHResponse0.0000.0000.001
makeVCFHeaderFromGA4GHResponse0.0010.0000.000
searchBiosamples000
searchCallSets0.0000.0010.001
searchDatasets000
searchExpressionLevels0.0000.0000.001
searchFeatureSets0.0000.0010.000
searchFeatures0.0000.0000.001
searchIndividuals000
searchPhenotypeAssociationSets000
searchPhenotypeAssociations0.0000.0010.001
searchReadGroupSets0.0000.0000.001
searchReads000
searchReferenceSets000
searchReferences000
searchRnaQuantificationSets0.0000.0000.001
searchRnaQuantifications0.0000.0000.001
searchVariantAnnotationSets000
searchVariantAnnotations000
searchVariantSets000
searchVariants0.0000.0010.001
searchVariantsByGRanges0.0690.0040.073