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This page was generated on 2021-10-15 15:05:51 -0400 (Fri, 15 Oct 2021).

CHECK results for RTCGAToolbox on nebbiolo1

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 1644/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGAToolbox 2.22.1  (landing page)
Marcel Ramos
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/RTCGAToolbox
git_branch: RELEASE_3_13
git_last_commit: adc18d9
git_last_commit_date: 2021-06-14 16:46:27 -0400 (Mon, 14 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 2.22.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RTCGAToolbox_2.22.1.tar.gz
StartedAt: 2021-10-14 11:26:08 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:29:01 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 172.7 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-3.13-bioc/R/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RTCGAToolbox_2.22.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RTCGAToolbox.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.22.1’
* 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 ‘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
getGISTICPeaks 16.107  3.216  23.055
biocExtract     6.041  0.212   6.256
* 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-3.13-bioc/R/bin/R CMD INSTALL RTCGAToolbox
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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
biocExtract6.0410.2126.256
getBroadSubtypes0.0160.0000.136
getCNGECorrelation0.0020.0000.002
getData0.020.020.04
getDiffExpressedGenes0.0020.0000.002
getFirehoseAnalyzeDates0.0010.0000.001
getFirehoseData0.0060.0000.005
getFirehoseDatasets0.0000.0010.001
getFirehoseRunningDates0.0000.0010.002
getGISTICPeaks16.107 3.21623.055
getMutationRate0.0020.0030.006
getReport3.8270.4084.236
getSurvival0.0060.0000.006
makeSummarizedExperimentFromGISTIC3.9430.3523.896
showResults-CorResult0.0010.0000.001
showResults-DGEResult0.0010.0000.001
showResults0.0010.0000.001