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CHECK report for RadioGx on merida1

This page was generated on 2021-05-06 12:36:17 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RadioGx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RadioGx_1.0.0.tar.gz
StartedAt: 2021-05-06 05:08:54 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:13:09 -0400 (Thu, 06 May 2021)
EllapsedTime: 255.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RadioGx.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RadioGx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RadioGx_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/RadioGx.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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 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 10.594  0.406  11.021
* 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
  ‘/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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RadioGx
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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
** 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
* DONE (RadioGx)

Tests output


Example timings

RadioGx.Rcheck/RadioGx-Ex.timings

nameusersystemelapsed
RadioSet-class10.594 0.40611.021
availableRSets000
checkRSetStructure0.3830.0120.396
computeAUC0.0040.0000.005
computeD10000
computeSF20.0000.0010.001
dim-RadioSet-method0.3490.0050.355
doseResponseCurve0.0920.0050.097
downloadRSet0.0000.0010.001
linearQuadraticModel0.0060.0020.007
mDataNames-RadioSet-method0.0030.0000.004
plotCurve0.0320.0090.041
radSensitivitySig2.0990.1322.232
radiationInfo-set0.0010.0010.000
radiationInfo0.0010.0010.002
radiationTypes-set0.0070.0010.008
radiationTypes0.3130.0030.317
show-RadioSet-method0.3530.0090.363
show-RadioSig-method0.7330.0770.816
showSigAnnot-RadioSig-method0.6640.0680.732
subsetTo-RadioSet-method0.1610.0170.177
summarizeMolecularProfiles-RadioSet-method0.5240.0330.557
summarizeSensitivityProfiles-RadioSet-method0.3410.0050.347