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CHECK report for RTCGAToolbox on tokay1

This page was generated on 2019-04-13 11:25:25 -0400 (Sat, 13 Apr 2019).

Package 1361/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGAToolbox 2.12.1
Marcel Ramos
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/RTCGAToolbox
Branch: RELEASE_3_8
Last Commit: 46aedee
Last Changed Date: 2018-10-30 14:51:40 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCGAToolbox
Version: 2.12.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.12.1.tar.gz
StartedAt: 2019-04-13 05:14:19 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:18:54 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 275.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCGAToolbox.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGAToolbox.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.12.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RTCGAToolbox.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.12.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-bioc/tmpdir/Rtmpa6cDfH/R.INSTALL101c2ea965f5/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-3.8-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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getGISTIC: no visible global function definition for 'mcols<-'
Undefined global functions or variables:
  mcols<-
* 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      6.66   0.19    6.84
getGISTICPeaks 0.76   0.11   10.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getReport      7.36   0.30    7.66
getGISTICPeaks 0.78   0.06    5.63
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/RTCGAToolbox.Rcheck/00check.log'
for details.



Installation output

RTCGAToolbox.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RTCGAToolbox_2.12.1.tar.gz && rm -rf RTCGAToolbox.buildbin-libdir && mkdir RTCGAToolbox.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGAToolbox.buildbin-libdir RTCGAToolbox_2.12.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RTCGAToolbox_2.12.1.zip && rm RTCGAToolbox_2.12.1.tar.gz RTCGAToolbox_2.12.1.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 2539k  100 2539k    0     0  38.5M      0 --:--:-- --:--:-- --:--:-- 41.3M

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'RTCGAToolbox' ...
** 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-3.8-bioc/tmpdir/Rtmpa6cDfH/R.INSTALL101c2ea965f5/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
In R CMD INSTALL

install for x64

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'RTCGAToolbox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGAToolbox' as RTCGAToolbox_2.12.1.zip
* DONE (RTCGAToolbox)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RTCGAToolbox' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

RTCGAToolbox.Rcheck/examples_i386/RTCGAToolbox-Ex.timings

nameusersystemelapsed
biocExtract000
getBroadSubtypes0.050.000.27
getCNGECorrelation0.670.050.72
getData0.330.080.41
getDiffExpressedGenes0.190.030.21
getFirehoseAnalyzeDates0.000.000.25
getFirehoseData0.050.000.05
getFirehoseDatasets0.000.000.05
getFirehoseRunningDates0.000.000.09
getGISTICPeaks 0.76 0.1110.06
getMutationRate0.080.010.10
getReport6.660.196.84
getSurvival0.110.000.11
showResults-CorResult0.670.090.76
showResults-DGEResult0.220.020.24
showResults0.170.000.17

RTCGAToolbox.Rcheck/examples_x64/RTCGAToolbox-Ex.timings

nameusersystemelapsed
biocExtract000
getBroadSubtypes0.100.020.21
getCNGECorrelation1.500.041.55
getData0.310.050.36
getDiffExpressedGenes0.240.000.23
getFirehoseAnalyzeDates0.000.000.05
getFirehoseData0.030.000.03
getFirehoseDatasets0.000.000.05
getFirehoseRunningDates0.000.000.09
getGISTICPeaks0.780.065.63
getMutationRate0.050.020.06
getReport7.360.307.66
getSurvival0.110.010.13
showResults-CorResult0.770.050.81
showResults-DGEResult0.20.00.2
showResults0.170.010.19