Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:59:53 -0400 (Wed, 16 Oct 2019).
Package 597/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GA4GHclient 1.8.0 Welliton Souza
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: GA4GHclient |
Version: 1.8.0 |
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_1.8.0.tar.gz |
StartedAt: 2019-10-16 02:56:04 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 03:02:11 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 367.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GA4GHclient.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GA4GHclient.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.0’ * 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/Versions/Current/Resources/bin/R CMD INSTALL GA4GHclient ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid No methods found in package 'BiocGenerics' for request: 'lengths' when loading 'GA4GHclient' > > test_check("GA4GHclient") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 10 | SKIPPED: 84 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 19.193 1.590 20.901
GA4GHclient.Rcheck/GA4GHclient-Ex.timings
name | user | system | elapsed | |
HGVSnames | 0.002 | 0.000 | 0.002 | |
getBiosample | 0.001 | 0.000 | 0.001 | |
getCallSet | 0.000 | 0.000 | 0.001 | |
getDataset | 0.000 | 0.001 | 0.000 | |
getExpressionLevel | 0.001 | 0.001 | 0.000 | |
getFeature | 0 | 0 | 0 | |
getFeatureSet | 0.001 | 0.000 | 0.001 | |
getIndividual | 0 | 0 | 0 | |
getReadGroupSet | 0 | 0 | 0 | |
getReference | 0.000 | 0.000 | 0.001 | |
getReferenceSet | 0.001 | 0.000 | 0.000 | |
getRnaQuantification | 0.001 | 0.000 | 0.000 | |
getRnaQuantificationSet | 0.000 | 0.000 | 0.001 | |
getVariant | 0 | 0 | 0 | |
getVariantAnnotationSet | 0.000 | 0.000 | 0.001 | |
getVariantSet | 0.000 | 0.000 | 0.001 | |
listReferenceBases | 0.000 | 0.000 | 0.001 | |
makeVCFFromGA4GHResponse | 0.001 | 0.000 | 0.001 | |
makeVCFHeaderFromGA4GHResponse | 0.000 | 0.000 | 0.001 | |
searchBiosamples | 0 | 0 | 0 | |
searchCallSets | 0.000 | 0.001 | 0.001 | |
searchDatasets | 0.000 | 0.001 | 0.001 | |
searchExpressionLevels | 0.000 | 0.001 | 0.000 | |
searchFeatureSets | 0.001 | 0.001 | 0.000 | |
searchFeatures | 0.000 | 0.001 | 0.001 | |
searchIndividuals | 0.000 | 0.001 | 0.000 | |
searchPhenotypeAssociationSets | 0.001 | 0.000 | 0.001 | |
searchPhenotypeAssociations | 0.001 | 0.000 | 0.000 | |
searchReadGroupSets | 0 | 0 | 0 | |
searchReads | 0.000 | 0.000 | 0.001 | |
searchReferenceSets | 0 | 0 | 0 | |
searchReferences | 0.000 | 0.000 | 0.001 | |
searchRnaQuantificationSets | 0 | 0 | 0 | |
searchRnaQuantifications | 0.000 | 0.000 | 0.001 | |
searchVariantAnnotationSets | 0.001 | 0.000 | 0.001 | |
searchVariantAnnotations | 0.001 | 0.000 | 0.001 | |
searchVariantSets | 0.000 | 0.000 | 0.001 | |
searchVariants | 0.000 | 0.000 | 0.001 | |
searchVariantsByGRanges | 0.074 | 0.011 | 0.085 | |