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CHECK report for RTCGAToolbox on malbec1

This page was generated on 2020-11-23 12:14:32 -0500 (Mon, 23 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RTCGAToolbox PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1592/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGAToolbox 2.20.0
Marcel Ramos
Snapshot Date: 2020-11-22 14:42:09 -0500 (Sun, 22 Nov 2020)
URL: https://git.bioconductor.org/packages/RTCGAToolbox
Branch: RELEASE_3_12
Last Commit: 224bf4c
Last Changed Date: 2020-10-27 11:05:35 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCGAToolbox
Version: 2.20.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RTCGAToolbox_2.20.0.tar.gz
StartedAt: 2020-11-23 06:15:29 -0500 (Mon, 23 Nov 2020)
EndedAt: 2020-11-23 06:19:12 -0500 (Mon, 23 Nov 2020)
EllapsedTime: 223.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RTCGAToolbox.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RTCGAToolbox_2.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/RTCGAToolbox.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘2.20.0’
* 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 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
getGISTICPeaks 17.380  2.292  19.172
biocExtract     7.932  0.308  11.009
* 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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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL RTCGAToolbox
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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
biocExtract 7.932 0.30811.009
getBroadSubtypes0.0160.0000.208
getCNGECorrelation0.0000.0000.001
getData0.0240.0040.026
getDiffExpressedGenes0.0000.0000.001
getFirehoseAnalyzeDates0.0000.0040.001
getFirehoseData0.0000.0040.006
getFirehoseDatasets000
getFirehoseRunningDates0.0000.0000.001
getGISTICPeaks17.380 2.29219.172
getMutationRate0.0040.0000.005
getReport4.2760.2284.511
getSurvival0.0080.0000.007
showResults-CorResult0.0000.0000.001
showResults-DGEResult0.0040.0000.001
showResults0.0000.0000.001