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CHECK report for RTCGAToolbox on tokay1

This page was generated on 2020-11-25 11:56:01 -0500 (Wed, 25 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: 2020-11-24 14:40:26 -0500 (Tue, 24 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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.20.0.tar.gz
StartedAt: 2020-11-25 06:58:11 -0500 (Wed, 25 Nov 2020)
EndedAt: 2020-11-25 07:03:23 -0500 (Wed, 25 Nov 2020)
EllapsedTime: 311.4 seconds
RetCode: 0
Status:  OK  
CheckDir: RTCGAToolbox.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RTCGAToolbox.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
biocExtract    6.45   0.60   10.35
getGISTICPeaks 5.29   0.62   23.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
biocExtract    8.58   0.22   12.09
getGISTICPeaks 7.73   0.30   25.80
getReport      5.22   0.15    5.37
* 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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/RTCGAToolbox_2.20.0.tar.gz && rm -rf RTCGAToolbox.buildbin-libdir && mkdir RTCGAToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGAToolbox.buildbin-libdir RTCGAToolbox_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RTCGAToolbox_2.20.0.zip && rm RTCGAToolbox_2.20.0.tar.gz RTCGAToolbox_2.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2173k  100 2173k    0     0  13.6M      0 --:--:-- --:--:-- --:--:-- 13.9M

install for i386

* 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
  converting help for package 'RTCGAToolbox'
    finding HTML links ... done
    CorResult-class                         html  
    DGEResult-class                         html  
    FirehoseCGHArray-class                  html  
    FirehoseData-class                      html  
    FirehoseGISTIC-class                    html  
    FirehoseMethylationArray-class          html  
    FirehosemRNAArray-class                 html  
    RTCGAToolbox                            html  
    accmini                                 html  
    biocExtract                             html  
    finding level-2 HTML links ... done

    getBroadSubtypes                        html  
    getCNGECorrelation                      html  
    getData                                 html  
    getDiffExpressedGenes                   html  
    getFirehoseAnalyzeDates                 html  
    getFirehoseData                         html  
    getFirehoseDatasets                     html  
    getFirehoseRunningDates                 html  
    getGISTICPeaks                          html  
    getLinks                                html  
    getMutationRate                         html  
    getReport                               html  
    getSurvival                             html  
    hg19.ucsc.gene.locations                html  
    selectType                              html  
    showResults-CorResult                   html  
    showResults-DGEResult                   html  
    showResults                             html  
** 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

install for x64

* installing *source* package 'RTCGAToolbox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGAToolbox' as RTCGAToolbox_2.20.0.zip
* DONE (RTCGAToolbox)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RTCGAToolbox' successfully unpacked and MD5 sums checked

Tests output


Example timings

RTCGAToolbox.Rcheck/examples_i386/RTCGAToolbox-Ex.timings

nameusersystemelapsed
biocExtract 6.45 0.6010.35
getBroadSubtypes0.040.000.17
getCNGECorrelation000
getData0.000.010.01
getDiffExpressedGenes000
getFirehoseAnalyzeDates000
getFirehoseData000
getFirehoseDatasets000
getFirehoseRunningDates0.020.000.02
getGISTICPeaks 5.29 0.6223.11
getMutationRate0.000.020.01
getReport4.390.224.61
getSurvival000
showResults-CorResult0.010.000.01
showResults-DGEResult000
showResults000

RTCGAToolbox.Rcheck/examples_x64/RTCGAToolbox-Ex.timings

nameusersystemelapsed
biocExtract 8.58 0.2212.09
getBroadSubtypes0.040.030.14
getCNGECorrelation000
getData0.030.000.03
getDiffExpressedGenes000
getFirehoseAnalyzeDates000
getFirehoseData0.020.000.01
getFirehoseDatasets000
getFirehoseRunningDates000
getGISTICPeaks 7.73 0.3025.80
getMutationRate0.020.000.02
getReport5.220.155.37
getSurvival0.020.000.01
showResults-CorResult000
showResults-DGEResult000
showResults000