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CHECK report for RadioGx on tokay1

This page was generated on 2021-05-06 12:33:06 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RadioGx package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1445/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RadioGx 1.0.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RadioGx
Branch: RELEASE_3_12
Last Commit: 54fe743
Last Changed Date: 2020-10-27 11:58:11 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RadioGx
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RadioGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RadioGx_1.0.0.tar.gz
StartedAt: 2021-05-06 05:58:02 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:02:55 -0400 (Thu, 06 May 2021)
EllapsedTime: 293.4 seconds
RetCode: 0
Status:   OK   
CheckDir: RadioGx.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:RadioGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RadioGx_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RadioGx.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RadioGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RadioGx' version '1.0.0'
* 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 'RadioGx' 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 ... NOTE
  Note: found 14 marked UTF-8 strings
* 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
RadioSet-class 11.55   0.75    12.3
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
RadioSet-class 10.87    0.5   11.38
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/RadioGx.Rcheck/00check.log'
for details.



Installation output

RadioGx.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/RadioGx_1.0.0.tar.gz && rm -rf RadioGx.buildbin-libdir && mkdir RadioGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RadioGx.buildbin-libdir RadioGx_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RadioGx_1.0.0.zip && rm RadioGx_1.0.0.tar.gz RadioGx_1.0.0.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 2237k  100 2237k    0     0  48.2M      0 --:--:-- --:--:-- --:--:-- 49.6M

install for i386

* installing *source* package 'RadioGx' ...
** 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 'RadioGx'
    finding HTML links ... done
    RadioSet-class                          html  
    RadioSet                                html  
    RadioSig                                html  
    availableRSets                          html  
    checkRSetStructure                      html  
    clevelandSmall                          html  
    computeAUC                              html  
    computeD10                              html  
    computeSF2                              html  
    dim-RadioSet-method                     html  
    doseResponseCurve                       html  
    downloadRSet                            html  
    linearQuadraticModel                    html  
    mDataNames-RadioSet-method              html  
    plotCurve                               html  
    radSensitivitySig                       html  
    radiationInfo-set                       html  
    radiationInfo                           html  
    radiationTypes-set                      html  
    radiationTypes                          html  
    show-RadioSet-method                    html  
    show-RadioSig-method                    html  
    showSigAnnot-RadioSig-method            html  
    sub-RadioSet-ANY-ANY-ANY-method         html  
    subsetTo-RadioSet-method                html  
    summarizeMolecularProfiles-RadioSet-method
                                            html  
    summarizeSensitivityProfiles-RadioSet-method
                                            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 'RadioGx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RadioGx' as RadioGx_1.0.0.zip
* DONE (RadioGx)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RadioGx' successfully unpacked and MD5 sums checked

Tests output


Example timings

RadioGx.Rcheck/examples_i386/RadioGx-Ex.timings

nameusersystemelapsed
RadioSet-class11.55 0.7512.30
availableRSets000
checkRSetStructure0.420.040.46
computeAUC000
computeD10000
computeSF2000
dim-RadioSet-method0.310.080.39
doseResponseCurve0.080.000.08
downloadRSet000
linearQuadraticModel000
mDataNames-RadioSet-method000
plotCurve0.070.000.07
radSensitivitySig1.280.041.33
radiationInfo-set000
radiationInfo000
radiationTypes-set000
radiationTypes0.280.020.29
show-RadioSet-method0.360.000.36
show-RadioSig-method0.500.090.60
showSigAnnot-RadioSig-method0.530.050.57
subsetTo-RadioSet-method0.110.000.11
summarizeMolecularProfiles-RadioSet-method0.420.040.47
summarizeSensitivityProfiles-RadioSet-method0.310.020.33

RadioGx.Rcheck/examples_x64/RadioGx-Ex.timings

nameusersystemelapsed
RadioSet-class10.87 0.5011.38
availableRSets000
checkRSetStructure0.290.030.33
computeAUC0.020.000.02
computeD10000
computeSF2000
dim-RadioSet-method0.280.030.31
doseResponseCurve0.110.000.11
downloadRSet000
linearQuadraticModel0.010.000.02
mDataNames-RadioSet-method000
plotCurve0.130.000.12
radSensitivitySig1.610.081.69
radiationInfo-set000
radiationInfo000
radiationTypes-set0.010.000.01
radiationTypes0.360.000.36
show-RadioSet-method0.320.030.35
show-RadioSig-method0.540.050.59
showSigAnnot-RadioSig-method0.530.010.55
subsetTo-RadioSet-method0.130.020.14
summarizeMolecularProfiles-RadioSet-method0.470.010.48
summarizeSensitivityProfiles-RadioSet-method0.310.050.36