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This page was generated on 2021-11-27 14:05:18 -0500 (Sat, 27 Nov 2021).

CHECK results for RadioGx on riesling1

To the developers/maintainers of the RadioGx package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RadioGx.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1507/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RadioGx 1.5.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-11-26 14:50:14 -0500 (Fri, 26 Nov 2021)
git_url: https://git.bioconductor.org/packages/RadioGx
git_branch: master
git_last_commit: a981039
git_last_commit_date: 2021-10-26 13:00:29 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'CoreGx' which is not available

Summary

Package: RadioGx
Version: 1.5.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RadioGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RadioGx_1.5.0.tar.gz
StartedAt: 2021-11-27 03:29:33 -0500 (Sat, 27 Nov 2021)
EndedAt: 2021-11-27 03:34:33 -0500 (Sat, 27 Nov 2021)
EllapsedTime: 300.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RadioGx.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RadioGx.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RadioGx_1.5.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RadioGx.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.5.0'
* 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
* 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 LazyData ... 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
RadioSet-class 5.43   0.57    6.01
* 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
  'D:/biocbuild/bbs-3.15-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://155.52.207.165/BBS/3.15/bioc/src/contrib/RadioGx_1.5.0.tar.gz && rm -rf RadioGx.buildbin-libdir && mkdir RadioGx.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RadioGx.buildbin-libdir RadioGx_1.5.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RadioGx_1.5.0.zip && rm RadioGx_1.5.0.tar.gz RadioGx_1.5.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 94 2232k   94 2110k    0     0  3589k      0 --:--:-- --:--:-- --:--:-- 3583k
100 2232k  100 2232k    0     0  3744k      0 --:--:-- --:--:-- --:--:-- 3738k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'RadioGx' as RadioGx_1.5.0.zip
* DONE (RadioGx)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'RadioGx' successfully unpacked and MD5 sums checked

Tests output


Example timings

RadioGx.Rcheck/RadioGx-Ex.timings

nameusersystemelapsed
RadioSet-class5.430.576.01
availableRSets000
checkRSetStructure0.640.040.68
computeAUC000
computeD10000
computeSF2000
dim-RadioSet-method0.160.030.18
doseResponseCurve0.050.000.05
downloadRSet000
linearQuadraticModel000
mDataNames-RadioSet-method000
plotCurve0.040.000.05
radSensitivitySig0.430.010.43
radiationInfo-set000
radiationInfo000
radiationTypes-set000
radiationTypes0.230.020.25
show-RadioSet-method0.190.010.21
show-RadioSig-method0.340.040.37
showSigAnnot-RadioSig-method0.350.040.39
subsetTo-RadioSet-method0.070.020.10
summarizeMolecularProfiles-RadioSet-method0.270.030.29
summarizeSensitivityProfiles-RadioSet-method0.160.030.19