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This page was generated on 2021-11-29 15:06:10 -0500 (Mon, 29 Nov 2021).

CHECK results for RTCGAToolbox on machv2

To the developers/maintainers of the RTCGAToolbox package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTCGAToolbox.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1669/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGAToolbox 2.24.0  (landing page)
Marcel Ramos
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/RTCGAToolbox
git_branch: RELEASE_3_14
git_last_commit: b1359f0
git_last_commit_date: 2021-10-26 12:20:48 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RTCGAToolbox
Version: 2.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTCGAToolbox_2.24.0.tar.gz
StartedAt: 2021-11-28 20:46:05 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 20:50:08 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 243.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RTCGAToolbox.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RTCGAToolbox_2.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/RTCGAToolbox.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGAToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCGAToolbox’ version ‘2.24.0’
* 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 ‘RTCGAToolbox’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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
biocExtract                        10.204  0.360  10.584
getGISTICPeaks                      9.333  0.654  11.979
makeSummarizedExperimentFromGISTIC  4.444  0.135   5.045
* 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


Installation output

RTCGAToolbox.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RTCGAToolbox
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘RTCGAToolbox’ ...
** 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 (RTCGAToolbox)

Tests output


Example timings

RTCGAToolbox.Rcheck/RTCGAToolbox-Ex.timings

nameusersystemelapsed
biocExtract10.204 0.36010.584
getBroadSubtypes0.0150.0040.384
getCNGECorrelation0.0010.0020.002
getData0.0200.0150.034
getDiffExpressedGenes0.0010.0010.001
getFirehoseAnalyzeDates0.0000.0000.001
getFirehoseData0.0040.0010.005
getFirehoseDatasets0.0000.0010.000
getFirehoseRunningDates0.0000.0000.001
getGISTICPeaks 9.333 0.65411.979
getMutationRate0.0040.0010.005
getReport4.6790.1124.795
getSurvival0.0070.0020.009
makeSummarizedExperimentFromGISTIC4.4440.1355.045
showResults-CorResult0.0020.0020.003
showResults-DGEResult0.0020.0010.002
showResults0.0010.0010.002