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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).

CHECK results for PrecisionTrialDrawer on nebbiolo1

To the developers/maintainers of the PrecisionTrialDrawer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PrecisionTrialDrawer.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 1426/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PrecisionTrialDrawer 1.8.0  (landing page)
Giorgio Melloni
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/PrecisionTrialDrawer
git_branch: RELEASE_3_13
git_last_commit: 8690c66
git_last_commit_date: 2021-05-19 12:39:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PrecisionTrialDrawer
Version: 1.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings PrecisionTrialDrawer_1.8.0.tar.gz
StartedAt: 2021-10-14 11:05:12 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:08:57 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 224.7 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-3.13-bioc/R/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings PrecisionTrialDrawer_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/PrecisionTrialDrawer.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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 4.578  0.100  39.023
panelDesigner  3.873  0.063  31.001
* 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-3.13-bioc/R/bin/R CMD INSTALL PrecisionTrialDrawer
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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-class0.0020.0000.001
PrecisionTrialDrawer-package0.1670.0080.176
appendRepo0.3490.0040.354
coocMutexPlot1.910.021.93
coveragePlot0.1570.0040.160
coverageStackPlot0.1810.0200.201
cpArguments0.0090.0040.013
cpData0.0160.0000.015
cpDataSubset0.0060.0040.009
cpDesign0.0180.0000.019
cpFreq0.1870.0320.220
cpObj0.1520.0120.164
cpObj20.0340.0040.037
dataExtractor0.3090.0120.322
filterFusions0.3550.0040.358
filterMutations0.8040.0040.808
getAlterations0.1990.0040.490
newCancerPanel 4.578 0.10039.023
panelDesigner 3.873 0.06331.001
panelOptimizer0.0010.0000.000
panelexample0.0050.0000.005
propPowerSampleSize0.6050.0080.613
saturationPlot1.2330.0161.248
showCancerStudy0.0230.0000.058
showTumorType0.0330.0040.078
subsetAlterations0.3830.0190.402
survPowerSampleSize0.4990.0000.499
survPowerSampleSize1Arm0.5760.0080.584