Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:17 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GA4GHclient on nebbiolo1


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? 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 712/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GA4GHclient 1.20.0  (landing page)
Welliton Souza
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/GA4GHclient
git_branch: RELEASE_3_15
git_last_commit: 22ed961
git_last_commit_date: 2022-04-26 11:39:48 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GA4GHclient
Version: 1.20.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GA4GHclient.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GA4GHclient_1.20.0.tar.gz
StartedAt: 2022-10-18 19:48:31 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:52:56 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 265.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GA4GHclient.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GA4GHclient.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GA4GHclient_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GA4GHclient.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.20.0’
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GA4GHclient
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

Attaching package: 'BiocGenerics'

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")
[ FAIL 0 | WARN 0 | SKIP 84 | PASS 10 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (84)

[ FAIL 0 | WARN 0 | SKIP 84 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
 13.081   0.750  13.818 

Example timings

GA4GHclient.Rcheck/GA4GHclient-Ex.timings

nameusersystemelapsed
HGVSnames0.0010.0000.001
getBiosample000
getCallSet0.0010.0000.000
getDataset0.0000.0010.000
getExpressionLevel0.0000.0010.000
getFeature000
getFeatureSet0.0000.0000.001
getIndividual000
getReadGroupSet0.0000.0010.000
getReference000
getReferenceSet0.0000.0000.001
getRnaQuantification000
getRnaQuantificationSet000
getVariant0.0000.0010.000
getVariantAnnotationSet000
getVariantSet0.0000.0000.001
listReferenceBases000
makeVCFFromGA4GHResponse000
makeVCFHeaderFromGA4GHResponse0.0000.0010.000
searchBiosamples000
searchCallSets0.0000.0000.001
searchDatasets000
searchExpressionLevels0.0000.0010.000
searchFeatureSets000
searchFeatures0.0000.0000.001
searchIndividuals000
searchPhenotypeAssociationSets0.0010.0000.000
searchPhenotypeAssociations000
searchReadGroupSets0.0000.0000.001
searchReads000
searchReferenceSets0.0010.0000.000
searchReferences000
searchRnaQuantificationSets000
searchRnaQuantifications0.0000.0000.001
searchVariantAnnotationSets000
searchVariantAnnotations000
searchVariantSets0.0000.0010.000
searchVariants000
searchVariantsByGRanges0.0560.0000.057