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This page was generated on 2021-10-15 15:06:47 -0400 (Fri, 15 Oct 2021).

CHECK results for PrecisionTrialDrawer on machv2

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: /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_1.8.0.tar.gz
StartedAt: 2021-10-14 22:29:36 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:33:33 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 237.6 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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/PrecisionTrialDrawer.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 7.095  0.119  11.503
panelDesigner  7.077  0.087  10.665
* 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-3.13-bioc/meat/PrecisionTrialDrawer.Rcheck/00check.log’
for details.



Installation output

PrecisionTrialDrawer.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PrecisionTrialDrawer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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-class0.0020.0010.003
PrecisionTrialDrawer-package0.3410.0080.349
appendRepo0.9380.0200.958
coocMutexPlot1.7710.0601.832
coveragePlot0.2470.0110.259
coverageStackPlot0.3050.0070.313
cpArguments0.0200.0030.024
cpData0.0180.0020.020
cpDataSubset0.0100.0010.012
cpDesign0.0290.0040.033
cpFreq0.3240.0520.377
cpObj0.2580.0110.270
cpObj20.0450.0050.051
dataExtractor0.4640.0030.468
filterFusions0.4610.0150.477
filterMutations1.3880.0161.404
getAlterations0.2440.0080.705
newCancerPanel 7.095 0.11911.503
panelDesigner 7.077 0.08710.665
panelOptimizer0.0010.0010.002
panelexample0.0060.0020.009
propPowerSampleSize0.9610.0150.977
saturationPlot2.1400.0712.214
showCancerStudy0.0190.0010.062
showTumorType0.0530.0020.099
subsetAlterations0.7250.0240.750
survPowerSampleSize0.6820.0080.691
survPowerSampleSize1Arm0.7210.0060.730