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This page was generated on 2024-03-01 11:36:20 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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

Package 1814/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGAToolbox 2.32.1  (landing page)
Marcel Ramos
Snapshot Date: 2024-02-29 14:05:06 -0500 (Thu, 29 Feb 2024)
git_url: https://git.bioconductor.org/packages/RTCGAToolbox
git_branch: RELEASE_3_18
git_last_commit: d05e55f
git_last_commit_date: 2023-10-25 18:09:17 -0500 (Wed, 25 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for RTCGAToolbox on nebbiolo2


To the developers/maintainers of the RTCGAToolbox package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RTCGAToolbox
Version: 2.32.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RTCGAToolbox_2.32.1.tar.gz
StartedAt: 2024-03-01 01:57:30 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 02:01:05 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 215.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RTCGAToolbox.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RTCGAToolbox_2.32.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RTCGAToolbox.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RTCGAToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCGAToolbox’ version ‘2.32.1’
* 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 loading without being on the library search path ... 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
makeSummarizedExperimentFromGISTIC 13.803  2.170  16.087
biocExtract                         6.661  0.356   7.018
getGISTICPeaks                      5.876  0.654   7.925
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘RTCGAToolbox-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

RTCGAToolbox.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL RTCGAToolbox
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘RTCGAToolbox’ ...
** using staged installation
** R
** data
** 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
biocExtract6.6610.3567.018
getBroadSubtypes0.1320.0000.285
getData0.0160.0040.020
getFirehoseAnalyzeDates000
getFirehoseData0.0080.0000.008
getFirehoseDatasets0.0010.0000.000
getFirehoseRunningDates0.0000.0000.001
getGISTICPeaks5.8760.6547.925
getLinks0.1230.0360.511
getMutationRate0.0070.0040.012
getReport0.0080.0000.007
makeSummarizedExperimentFromGISTIC13.803 2.17016.087
showResults-CorResult0.0080.0000.008
showResults-DGEResult0.0080.0000.007
showResults0.0120.0000.012