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###
### 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GA4GHclient.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GA4GHclient/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GA4GHclient’ version ‘1.30.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 ... 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GA4GHclient
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, saveRDS, setdiff, 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 
  4.714   0.180   4.891