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CHECK report for PrecisionTrialDrawer on machv2

This page was generated on 2020-10-17 11:59:14 -0400 (Sat, 17 Oct 2020).

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 1344/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrecisionTrialDrawer 1.4.0
Giorgio Melloni
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/PrecisionTrialDrawer
Branch: RELEASE_3_11
Last Commit: 7ded9c6
Last Changed Date: 2020-04-27 15:22:04 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PrecisionTrialDrawer
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2020-10-17 04:04:50 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:10:04 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 313.4 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PrecisionTrialDrawer.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.4.0’
* 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 7.532  0.112  13.452
panelDesigner  7.051  0.086  13.146
* 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-class0.0020.0000.002
PrecisionTrialDrawer-package0.3210.0100.332
appendRepo0.4870.0200.511
coocMutexPlot2.0930.0532.148
coveragePlot0.2540.0060.261
coverageStackPlot0.4150.0080.424
cpArguments0.0190.0030.023
cpData0.0360.0030.040
cpDataSubset0.0140.0020.016
cpDesign0.0310.0030.034
cpFreq0.2650.0340.300
cpObj0.3160.0110.328
cpObj20.0780.0070.085
dataExtractor0.6020.0120.639
filterFusions0.9410.0110.954
filterMutations1.3650.0271.397
getAlterations0.2700.0130.530
newCancerPanel 7.532 0.11213.452
panelDesigner 7.051 0.08613.146
panelOptimizer0.0010.0000.002
panelexample0.0110.0030.013
propPowerSampleSize1.4580.0181.478
saturationPlot2.0620.0612.125
showCancerStudy0.0170.0010.040
showTumorType0.0520.0020.077
subsetAlterations0.7550.0250.781
survPowerSampleSize0.8710.0080.880
survPowerSampleSize1Arm0.8880.0070.896