Multiple platform build/check report for BioC 3.10 - CHECK report for RTCGAToolbox on tokay1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.16.3.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RTCGAToolbox.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '2.16.3'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpEBkIa2/R.INSTALL2bc07f5825bc/RTCGAToolbox/man/biocExtract.Rd:32: file link 'RaggedExperiment' in package 'RaggedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/RTCGAToolbox.Rcheck/00install.out' for details.
* 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 ... NOTE
Namespace in Imports field not imported from: 'IRanges'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.setAnnoRows: no visible binding for global variable 'hugos'
Undefined global functions or variables:
  hugos
* 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 or elapsed time > 5s
               user system elapsed
getReport      7.84   0.60    8.43
getGISTICPeaks 0.56   0.05    6.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getReport      9.39   0.13    9.51
getGISTICPeaks 0.75   0.15    6.00
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/RTCGAToolbox.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/RTCGAToolbox_2.16.3.tar.gz && rm -rf RTCGAToolbox.buildbin-libdir && mkdir RTCGAToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGAToolbox.buildbin-libdir RTCGAToolbox_2.16.3.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL RTCGAToolbox_2.16.3.zip && rm RTCGAToolbox_2.16.3.tar.gz RTCGAToolbox_2.16.3.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 2540k  100 2540k    0     0  12.8M      0 --:--:-- --:--:-- --:--:-- 13.1M

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  
    RTCGASample                             html  
    RTCGAToolbox                            html  
    biocExtract                             html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpEBkIa2/R.INSTALL2bc07f5825bc/RTCGAToolbox/man/biocExtract.Rd:32: file link 'RaggedExperiment' in package 'RaggedExperiment' does not exist and so has been treated as a topic
    getBroadSubtypes                        html  
    getCNGECorrelation                      html  
    getData                                 html  
    getDiffExpressedGenes                   html  
    getFirehoseAnalyzeDates                 html  
    getFirehoseData                         html  
    getFirehoseDatasets                     html  
    getFirehoseRunningDates                 html  
    getGISTICPeaks                          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_2.16.3.zip
* DONE (RTCGAToolbox)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'RTCGAToolbox' successfully unpacked and MD5 sums checked

CHECK report for RTCGAToolbox on tokay1

Summary

Command output

Installation output

Tests output

Example timings