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CHECK report for synergyfinder on celaya2

This page was generated on 2020-01-16 13:46:10 -0500 (Thu, 16 Jan 2020).

Package 1694/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
synergyfinder 2.1.4
Shuyu Zheng
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/synergyfinder
Branch: master
Last Commit: afe68a9
Last Changed Date: 2020-01-13 10:46:49 -0500 (Mon, 13 Jan 2020)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: synergyfinder
Version: 2.1.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings synergyfinder_2.1.4.tar.gz
StartedAt: 2020-01-16 09:23:05 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 09:24:14 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 69.5 seconds
RetCode: 0
Status:  OK 
CheckDir: synergyfinder.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings synergyfinder_2.1.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/synergyfinder.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synergyfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synergyfinder’ version ‘2.1.4’
* package encoding: UTF-8
* 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 ‘synergyfinder’ 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 ... NOTE
FitDoseResponse: no visible global function definition for ‘is’
PlotDoseResponse: no visible binding for global variable ‘conc_c’
PlotDoseResponse: no visible binding for global variable ‘conc_r’
PlotDoseResponse: no visible binding for global variable ‘Inhibition’
ZIP: no visible global function definition for ‘predict’
Undefined global functions or variables:
  Inhibition conc_c conc_r is predict
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.11-bioc/meat/synergyfinder.Rcheck/00check.log’
for details.



Installation output

synergyfinder.Rcheck/00install.out

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

Tests output


Example timings

synergyfinder.Rcheck/synergyfinder-Ex.timings

nameusersystemelapsed
AddNoise0.1440.0150.158
Bliss0.0170.0050.021
CalculateSynergy3.6800.3344.300
CorrectBaseLine0.1770.0030.181
ExtractSingleDrug0.0140.0020.016
FindModelType0.0390.0010.040
FitDoseResponse0.0360.0010.040
HSA0.0130.0010.014
ImputeNA0.0150.0020.017
Loewe0.2650.0070.446
PlotDoseResponse1.0840.0261.121
PlotSynergy1.2580.0271.290
ReshapeData0.0130.0020.015
ZIP1.9450.1342.080