| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 748/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GA4GHclient 1.24.0 (landing page) Welliton Souza
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the GA4GHclient package: - 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. |
| Package: GA4GHclient |
| Version: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2023-10-17 20:30:57 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 20:38:53 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 475.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GA4GHclient.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.24.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GA4GHclient.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GA4GHclient/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GA4GHclient’ version ‘1.24.0’
* 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
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-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)
GA4GHclient.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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
16.679 0.811 25.733
GA4GHclient.Rcheck/GA4GHclient-Ex.timings
| name | user | system | elapsed | |
| HGVSnames | 0.001 | 0.000 | 0.002 | |
| getBiosample | 0.000 | 0.000 | 0.001 | |
| getCallSet | 0 | 0 | 0 | |
| getDataset | 0.001 | 0.000 | 0.000 | |
| getExpressionLevel | 0 | 0 | 0 | |
| getFeature | 0 | 0 | 0 | |
| getFeatureSet | 0.001 | 0.000 | 0.000 | |
| getIndividual | 0 | 0 | 0 | |
| getReadGroupSet | 0 | 0 | 0 | |
| getReference | 0.000 | 0.001 | 0.000 | |
| getReferenceSet | 0.000 | 0.000 | 0.001 | |
| getRnaQuantification | 0 | 0 | 0 | |
| getRnaQuantificationSet | 0.000 | 0.001 | 0.000 | |
| getVariant | 0 | 0 | 0 | |
| getVariantAnnotationSet | 0.000 | 0.000 | 0.002 | |
| getVariantSet | 0 | 0 | 0 | |
| listReferenceBases | 0.000 | 0.000 | 0.001 | |
| makeVCFFromGA4GHResponse | 0.000 | 0.000 | 0.001 | |
| makeVCFHeaderFromGA4GHResponse | 0 | 0 | 0 | |
| searchBiosamples | 0 | 0 | 0 | |
| searchCallSets | 0 | 0 | 0 | |
| searchDatasets | 0.001 | 0.000 | 0.000 | |
| searchExpressionLevels | 0 | 0 | 0 | |
| searchFeatureSets | 0 | 0 | 0 | |
| searchFeatures | 0 | 0 | 0 | |
| searchIndividuals | 0 | 0 | 0 | |
| searchPhenotypeAssociationSets | 0.000 | 0.001 | 0.000 | |
| searchPhenotypeAssociations | 0 | 0 | 0 | |
| searchReadGroupSets | 0 | 0 | 0 | |
| searchReads | 0.001 | 0.000 | 0.001 | |
| searchReferenceSets | 0.000 | 0.000 | 0.001 | |
| searchReferences | 0.001 | 0.000 | 0.001 | |
| searchRnaQuantificationSets | 0 | 0 | 0 | |
| searchRnaQuantifications | 0 | 0 | 0 | |
| searchVariantAnnotationSets | 0 | 0 | 0 | |
| searchVariantAnnotations | 0 | 0 | 0 | |
| searchVariantSets | 0 | 0 | 0 | |
| searchVariants | 0.000 | 0.001 | 0.000 | |
| searchVariantsByGRanges | 0.071 | 0.006 | 0.102 | |