Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:37:09 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the TCGAutils package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1844/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TCGAutils 1.10.1 (landing page) Marcel Ramos
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: TCGAutils |
Version: 1.10.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCGAutils_1.10.1.tar.gz |
StartedAt: 2021-05-06 06:48:14 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 06:57:30 -0400 (Thu, 06 May 2021) |
EllapsedTime: 556.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TCGAutils.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TCGAutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TCGAutils_1.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/TCGAutils.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TCGAutils/DESCRIPTION’ ... OK * this is package ‘TCGAutils’ version ‘1.10.1’ * package encoding: UTF-8 * 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 ‘TCGAutils’ 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 ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘GenomicRanges:::.normarg_field’ See the note in ?`:::` about the use of this operator. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed simplifyTCGA 48.415 1.212 50.699 trimColData 33.279 1.029 35.336 TCGAprimaryTumors 32.303 0.972 34.661 imputeAssay 27.970 0.390 29.413 curatedTCGAData-helpers 24.802 0.344 26.114 oncoPrintTCGA 22.877 0.497 31.366 makeSummarizedExperimentFromGISTIC 8.374 0.650 9.946 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.12-bioc/meat/TCGAutils.Rcheck/00check.log’ for details.
TCGAutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TCGAutils ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘TCGAutils’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TCGAutils)
TCGAutils.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(TCGAutils) > > test_check("TCGAutils") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 42 ] > > proc.time() user system elapsed 15.693 0.649 19.549
TCGAutils.Rcheck/TCGAutils-Ex.timings
name | user | system | elapsed | |
ID-translation | 0.852 | 0.047 | 2.869 | |
TCGAbarcode | 0.001 | 0.001 | 0.001 | |
TCGAbiospec | 0.032 | 0.006 | 0.037 | |
TCGAprimaryTumors | 32.303 | 0.972 | 34.661 | |
TCGAsampleSelect | 0.009 | 0.002 | 0.010 | |
builds | 0.078 | 0.001 | 0.080 | |
curatedTCGAData-helpers | 24.802 | 0.344 | 26.114 | |
findGRangesCols | 0.002 | 0.000 | 0.002 | |
generateMap | 0.049 | 0.001 | 0.050 | |
getFileName | 0.061 | 0.004 | 0.283 | |
imputeAssay | 27.970 | 0.390 | 29.413 | |
makeGRangesListFromCopyNumber | 1.183 | 0.035 | 1.900 | |
makeGRangesListFromExonFiles | 0.263 | 0.006 | 0.270 | |
makeSummarizedExperimentFromGISTIC | 8.374 | 0.650 | 9.946 | |
mergeColData | 0.410 | 0.011 | 0.422 | |
oncoPrintTCGA | 22.877 | 0.497 | 31.366 | |
simplifyTCGA | 48.415 | 1.212 | 50.699 | |
trimColData | 33.279 | 1.029 | 35.336 | |