Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 13:02:27 -0400 (Wed, 16 Oct 2019).
Package 1633/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
TCGAutils 1.4.0 Marcel Ramos
| 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: TCGAutils |
Version: 1.4.0 |
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_1.4.0.tar.gz |
StartedAt: 2019-10-16 07:19:02 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 07:26:27 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 445.4 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_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TCGAutils.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 ‘TCGAutils/DESCRIPTION’ ... OK * this is package ‘TCGAutils’ version ‘1.4.0’ * 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 or elapsed time > 5s user system elapsed simplifyTCGA 52.295 4.970 58.227 makeSummarizedExperimentFromGISTIC 24.661 8.535 21.098 trimColData 19.706 2.166 22.400 imputeAssay 18.943 1.318 21.054 * 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-3.9-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/3.6/Resources/library’ * installing *source* package ‘TCGAutils’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 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(TCGAutils) > > #test_check("TCGAutils") > > proc.time() user system elapsed 0.453 0.172 0.569
TCGAutils.Rcheck/TCGAutils-Ex.timings
name | user | system | elapsed | |
ID-translation | 1.012 | 0.065 | 2.798 | |
TCGAbarcode | 0.001 | 0.001 | 0.001 | |
TCGAbiospec | 0.135 | 0.004 | 0.140 | |
TCGAsampleSelect | 0.014 | 0.002 | 0.017 | |
builds | 0.064 | 0.003 | 0.067 | |
curatedTCGAData-helpers | 0.012 | 0.002 | 0.014 | |
findGRangesCols | 0.004 | 0.000 | 0.005 | |
generateMap | 0.096 | 0.003 | 0.099 | |
getFileName | 0.571 | 0.007 | 0.745 | |
imputeAssay | 18.943 | 1.318 | 21.054 | |
makeGRangesListFromCopyNumber | 0.566 | 0.032 | 1.367 | |
makeGRangesListFromExonFiles | 0.175 | 0.004 | 0.180 | |
makeSummarizedExperimentFromGISTIC | 24.661 | 8.535 | 21.098 | |
mergeColData | 0.548 | 0.014 | 0.564 | |
simplifyTCGA | 52.295 | 4.970 | 58.227 | |
trimColData | 19.706 | 2.166 | 22.400 | |