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This page was generated on 2024-02-29 11:37:46 -0500 (Thu, 29 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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

Package 759/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GA4GHclient 1.26.0  (landing page)
Welliton Souza
Snapshot Date: 2024-02-28 14:05:05 -0500 (Wed, 28 Feb 2024)
git_url: https://git.bioconductor.org/packages/GA4GHclient
git_branch: RELEASE_3_18
git_last_commit: 6356ce0
git_last_commit_date: 2023-10-24 10:56:18 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for GA4GHclient on lconway


To the developers/maintainers of the GA4GHclient package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GA4GHclient
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GA4GHclient.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GA4GHclient_1.26.0.tar.gz
StartedAt: 2024-02-28 20:37:10 -0500 (Wed, 28 Feb 2024)
EndedAt: 2024-02-28 20:43:06 -0500 (Wed, 28 Feb 2024)
EllapsedTime: 355.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GA4GHclient.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GA4GHclient.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GA4GHclient_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GA4GHclient.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GA4GHclient/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GA4GHclient’ version ‘1.26.0’
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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, aperm, 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 object is masked from 'package:utils':

    findMatches

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 (84) ══════════════════════════════════════════════════════════
• On Bioconductor (84): 'test-getBiosample.R:4:5', 'test-getCallSet.R:4:5',
  'test-getDataset.R:4:5', 'test-getExpressionLevel.R:4:5',
  'test-getFeature.R:4:5', 'test-getFeatureSet.R:4:5',
  'test-getIndividual.R:4:5', 'test-getReadGroupSet.R:4:5',
  'test-getReference.R:4:5', 'test-getReferenceSets.R:4:5',
  'test-getRnaQuantification.R:4:5', 'test-getRnaQuantificationSet.R:4:5',
  'test-getVariant.R:4:5', 'test-getVariant.R:15:5', 'test-getVariant.R:27:5',
  'test-getVariantAnnotationSet.R:4:5', 'test-getVariantSet.R:4:5',
  'test-listReferenceBases.R:4:5', 'test-makeVCFFromGA4GHResponse.R:4:5',
  'test-makeVCFHeaderFromGA4GHResponse.R:4:5', 'test-request.get.R:4:5',
  'test-request.get.R:12:5', 'test-request.post.R:4:5',
  'test-request.post.R:13:5', 'test-searchBiosamples.R:4:5',
  'test-searchBiosamples.R:13:5', 'test-searchBiosamples.R:22:5',
  'test-searchBiosamples.R:31:5', 'test-searchBiosamples.R:41:5',
  'test-searchCallSets.R:4:5', 'test-searchCallSets.R:14:5',
  'test-searchCallSets.R:23:5', 'test-searchCallSets.R:32:5',
  'test-searchCallSets.R:42:5', 'test-searchDatasets.R:6:5',
  'test-searchDatasets.R:14:5', 'test-searchDatasets.R:20:5',
  'test-searchExpressionLevels.R:4:5', 'test-searchExpressionLevels.R:15:5',
  'test-searchExpressionLevels.R:26:5', 'test-searchFeatureSets.R:6:5',
  'test-searchFeatureSets.R:14:5', 'test-searchFeatures.R:6:5',
  'test-searchFeatures.R:16:5', 'test-searchFeatures.R:25:5',
  'test-searchIndividuals.R:4:5', 'test-searchIndividuals.R:13:5',
  'test-searchIndividuals.R:22:5', 'test-searchIndividuals.R:31:5',
  'test-searchPhenotypeAssociationSets.R:4:5',
  'test-searchPhenotypeAssociations.R:4:5',
  'test-searchPhenotypeAssociations.R:14:5',
  'test-searchPhenotypeAssociations.R:24:5', 'test-searchReadGroupSets.R:4:5',
  'test-searchReads.R:4:5', 'test-searchReferenceSets.R:6:5',
  'test-searchReferenceSets.R:13:5', 'test-searchReferenceSets.R:19:5',
  'test-searchReferences.R:4:5', 'test-searchReferences.R:13:5',
  'test-searchReferences.R:21:5', 'test-searchReferences.R:29:5',
  'test-searchRnaQuantificationSets.R:4:5',
  'test-searchRnaQuantificationSets.R:13:5',
  'test-searchRnaQuantificationSets.R:22:5',
  'test-searchRnaQuantifications.R:4:5',
  'test-searchRnaQuantifications.R:14:5',
  'test-searchRnaQuantifications.R:24:5',
  'test-searchRnaQuantifications.R:34:5',
  'test-searchVariantAnnotationSets.R:6:5',
  'test-searchVariantAnnotationSets.R:15:5',
  'test-searchVariantAnnotationSets.R:24:5',
  'test-searchVariantAnnotations.R:4:5', 'test-searchVariantSets.R:4:5',
  'test-searchVariantSets.R:15:5', 'test-searchVariantSets.R:23:5',
  'test-searchVariants.R:4:5', 'test-searchVariants.R:15:5',
  'test-searchVariants.R:25:5', 'test-searchVariants.R:35:5',
  'test-searchVariants.R:47:5', 'test-searchVariants.R:59:5',
  'test-searchVariants.R:70:5', 'test-searchVariantsByGRanges.R:6:5'

[ FAIL 0 | WARN 0 | SKIP 84 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
 15.478   1.018  16.710 

Example timings

GA4GHclient.Rcheck/GA4GHclient-Ex.timings

nameusersystemelapsed
HGVSnames0.0010.0010.003
getBiosample0.0000.0000.032
getCallSet0.0000.0010.000
getDataset0.0000.0010.000
getExpressionLevel0.0000.0010.001
getFeature0.0000.0000.001
getFeatureSet0.0000.0000.001
getIndividual000
getReadGroupSet0.0000.0010.001
getReference0.0000.0010.000
getReferenceSet0.0010.0010.001
getRnaQuantification000
getRnaQuantificationSet0.0010.0000.001
getVariant000
getVariantAnnotationSet0.0000.0010.000
getVariantSet0.0000.0010.001
listReferenceBases000
makeVCFFromGA4GHResponse000
makeVCFHeaderFromGA4GHResponse0.0000.0000.001
searchBiosamples0.0010.0000.001
searchCallSets000
searchDatasets0.0000.0010.001
searchExpressionLevels0.0000.0010.001
searchFeatureSets0.0000.0010.000
searchFeatures0.0000.0000.001
searchIndividuals000
searchPhenotypeAssociationSets000
searchPhenotypeAssociations0.0000.0000.001
searchReadGroupSets0.0000.0000.001
searchReads0.0000.0000.001
searchReferenceSets000
searchReferences0.0010.0000.001
searchRnaQuantificationSets0.0000.0000.001
searchRnaQuantifications0.0000.0000.001
searchVariantAnnotationSets000
searchVariantAnnotations0.0000.0010.000
searchVariantSets0.0000.0010.000
searchVariants0.0000.0000.001
searchVariantsByGRanges0.0660.0090.076