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This page was generated on 2021-11-27 14:05:51 -0500 (Sat, 27 Nov 2021).

CHECK results for RadioGx on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RadioGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RadioGx_1.5.0.tar.gz
StartedAt: 2021-11-27 06:40:02 -0500 (Sat, 27 Nov 2021)
EndedAt: 2021-11-27 06:45:48 -0500 (Sat, 27 Nov 2021)
EllapsedTime: 345.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RadioGx.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RadioGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RadioGx_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/RadioGx.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* 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 ‘1.5.0’
* 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 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 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 12.892  0.301  13.208
* 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-3.15-bioc/meat/RadioGx.Rcheck/00check.log’
for details.



Installation output

RadioGx.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RadioGx
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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-class12.892 0.30113.208
availableRSets000
checkRSetStructure0.5420.0060.550
computeAUC0.0040.0000.005
computeD100.0010.0000.001
computeSF20.0000.0000.001
dim-RadioSet-method1.0760.0151.095
doseResponseCurve0.1170.0020.119
downloadRSet0.0010.0000.000
linearQuadraticModel0.0050.0000.005
mDataNames-RadioSet-method0.0000.0000.001
plotCurve0.0360.0000.037
radSensitivitySig0.9480.0330.984
radiationInfo-set000
radiationInfo0.0010.0000.001
radiationTypes-set0.0070.0000.008
radiationTypes0.4570.0070.464
show-RadioSet-method0.4750.0060.480
show-RadioSig-method0.8800.0240.907
showSigAnnot-RadioSig-method0.8280.0250.854
subsetTo-RadioSet-method0.2670.0090.276
summarizeMolecularProfiles-RadioSet-method0.6650.0040.669
summarizeSensitivityProfiles-RadioSet-method0.4640.0070.470