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CHECK report for PrecisionTrialDrawer on merida1

This page was generated on 2021-05-06 12:36:10 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the PrecisionTrialDrawer package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1379/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrecisionTrialDrawer 1.6.0  (landing page)
Giorgio Melloni
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/PrecisionTrialDrawer
Branch: RELEASE_3_12
Last Commit: 4d8e877
Last Changed Date: 2020-10-27 11:41:04 -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: PrecisionTrialDrawer
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrecisionTrialDrawer_1.6.0.tar.gz
StartedAt: 2021-05-06 04:52:33 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:57:02 -0400 (Thu, 06 May 2021)
EllapsedTime: 268.5 seconds
RetCode: 0
Status:   OK  
CheckDir: PrecisionTrialDrawer.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:PrecisionTrialDrawer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrecisionTrialDrawer_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/PrecisionTrialDrawer.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 ‘PrecisionTrialDrawer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PrecisionTrialDrawer’ version ‘1.6.0’
* 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 ‘PrecisionTrialDrawer’ 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 ... 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
newCancerPanel 7.157  0.128  21.154
panelDesigner  6.385  0.079  17.378
* 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: OK


Installation output

PrecisionTrialDrawer.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PrecisionTrialDrawer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘PrecisionTrialDrawer’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** testing if installed package can be loaded from final location
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** testing if installed package keeps a record of temporary installation path
* DONE (PrecisionTrialDrawer)

Tests output


Example timings

PrecisionTrialDrawer.Rcheck/PrecisionTrialDrawer-Ex.timings

nameusersystemelapsed
CancerPanel-class0.0010.0010.001
PrecisionTrialDrawer-package0.5210.0060.528
appendRepo0.3440.0190.366
coocMutexPlot1.7480.0471.796
coveragePlot0.1970.0130.212
coverageStackPlot0.2360.0230.260
cpArguments0.0260.0060.033
cpData0.0290.0040.034
cpDataSubset0.0120.0020.015
cpDesign0.0300.0050.034
cpFreq0.3000.0400.341
cpObj0.2570.0110.268
cpObj20.0700.0060.075
dataExtractor0.3970.0080.405
filterFusions0.3620.0160.378
filterMutations1.0970.0211.120
getAlterations0.1920.0060.426
newCancerPanel 7.157 0.12821.154
panelDesigner 6.385 0.07917.378
panelOptimizer0.0020.0000.002
panelexample0.0090.0030.012
propPowerSampleSize1.1970.0171.215
saturationPlot1.5770.0581.639
showCancerStudy0.0140.0010.037
showTumorType0.0530.0010.074
subsetAlterations0.5690.0230.593
survPowerSampleSize0.6700.0050.677
survPowerSampleSize1Arm0.7520.0050.759