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CHECK report for PrecisionTrialDrawer on malbec2

This page was generated on 2020-10-16 11:56:29 -0400 (Fri, 16 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: 2020-10-15 14:40:03 -0400 (Thu, 15 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  OK [ OK ]UNNEEDED, same version exists in internal repository
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: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings PrecisionTrialDrawer_1.4.0.tar.gz
StartedAt: 2020-10-16 04:38:55 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 04:43:20 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 265.2 seconds
RetCode: 0
Status:  OK 
CheckDir: PrecisionTrialDrawer.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings PrecisionTrialDrawer_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/PrecisionTrialDrawer.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 5.323  0.064  11.226
panelDesigner  5.361  0.024  11.228
* 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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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL PrecisionTrialDrawer
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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-class0.0010.0000.002
PrecisionTrialDrawer-package0.2890.0060.295
appendRepo0.5560.0040.560
coocMutexPlot2.5370.0082.545
coveragePlot0.3570.0040.362
coverageStackPlot0.420.000.42
cpArguments0.0260.0000.027
cpData0.0310.0000.031
cpDataSubset0.0170.0000.016
cpDesign0.0380.0000.038
cpFreq0.3690.0120.393
cpObj0.3370.0000.338
cpObj20.0770.0000.077
dataExtractor0.6710.0040.674
filterFusions1.0520.0001.052
filterMutations1.3860.0001.387
getAlterations0.2680.0080.507
newCancerPanel 5.323 0.06411.226
panelDesigner 5.361 0.02411.228
panelOptimizer0.0010.0000.001
panelexample0.0060.0000.005
propPowerSampleSize0.7120.0000.712
saturationPlot1.7000.0161.716
showCancerStudy0.0150.0000.038
showTumorType0.0330.0000.054
subsetAlterations0.3970.0040.401
survPowerSampleSize0.5020.0040.506
survPowerSampleSize1Arm0.5670.0080.574