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This page was generated on 2022-01-22 11:11:11 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for RTCGAToolbox on merida1


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 1664/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGAToolbox 2.25.1  (landing page)
Marcel Ramos
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/RTCGAToolbox
git_branch: master
git_last_commit: 80c48ec
git_last_commit_date: 2021-10-27 11:01:30 -0500 (Wed, 27 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RTCGAToolbox
Version: 2.25.1
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_2.25.1.tar.gz
StartedAt: 2022-01-22 05:10:39 -0500 (Sat, 22 Jan 2022)
EndedAt: 2022-01-22 05:15:27 -0500 (Sat, 22 Jan 2022)
EllapsedTime: 287.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RTCGAToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running 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_2.25.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/RTCGAToolbox.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘2.25.1’
* 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                     11.392  0.600  13.524
biocExtract                        10.060  0.353  10.429
getReport                           5.331  0.145   5.484
makeSummarizedExperimentFromGISTIC  4.859  0.182   5.280
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RTCGAToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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
biocExtract10.060 0.35310.429
getBroadSubtypes0.0160.0040.249
getCNGECorrelation0.0010.0020.002
getData0.0250.0100.036
getDiffExpressedGenes0.0020.0010.002
getFirehoseAnalyzeDates000
getFirehoseData0.0060.0020.007
getFirehoseDatasets0.0000.0010.000
getFirehoseRunningDates0.0010.0000.001
getGISTICPeaks11.392 0.60013.524
getMutationRate0.0070.0020.009
getReport5.3310.1455.484
getSurvival0.0090.0020.010
makeSummarizedExperimentFromGISTIC4.8590.1825.280
showResults-CorResult0.0010.0010.002
showResults-DGEResult0.0020.0020.002
showResults0.0010.0010.002