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CHECK report for Polyfit on merida1

This page was generated on 2021-05-06 12:36:09 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the Polyfit package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1367/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Polyfit 1.24.0  (landing page)
Conrad Burden
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Polyfit
Branch: RELEASE_3_12
Last Commit: 68c011d
Last Changed Date: 2020-10-27 10:57:27 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Polyfit
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Polyfit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Polyfit_1.24.0.tar.gz
StartedAt: 2021-05-06 04:49:58 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:52:51 -0400 (Thu, 06 May 2021)
EllapsedTime: 172.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Polyfit.Rcheck
Warnings: 1

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:Polyfit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Polyfit_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/Polyfit.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Polyfit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Polyfit’ version ‘1.24.0’
* 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 ‘Polyfit’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/Polyfit.Rcheck/00install.out’ for details.
* 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
levelPValues: no visible global function definition for ‘hist’
levelPValues: no visible global function definition for ‘lm’
levelPValues: no visible global function definition for ‘nlm’
levelPValues: no visible global function definition for ‘density’
levelPValues: no visible global function definition for ‘p.adjust’
levelPValues: no visible global function definition for ‘par’
levelPValues: no visible global function definition for ‘mtext’
levelPValues: no visible global function definition for ‘abline’
levelPValues: no visible global function definition for ‘points’
pfNbinomTest: no visible global function definition for ‘is’
pfNbinomTest: no visible global function definition for ‘fData’
pfNbinomTest: no visible global function definition for ‘p.adjust’
pfNbinomTestForMatrices : <anonymous>: no visible global function
  definition for ‘dnbinom’
twoSidedPValueFromDiscrete: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  abline density dnbinom fData hist is lm mtext nlm p.adjust par points
  runif
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "par", "points")
  importFrom("methods", "is")
  importFrom("stats", "density", "dnbinom", "lm", "nlm", "p.adjust",
             "runif")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
pfNbinomTest    23.425  0.166  23.618
Polyfit-package 13.099  0.163  13.280
levelPValues    12.833  0.147  13.002
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/Polyfit.Rcheck/00check.log’
for details.



Installation output

Polyfit.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Polyfit
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Polyfit’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
** testing if installed package can be loaded from final location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
** testing if installed package keeps a record of temporary installation path
* DONE (Polyfit)

Tests output


Example timings

Polyfit.Rcheck/Polyfit-Ex.timings

nameusersystemelapsed
Polyfit-package13.099 0.16313.280
levelPValues12.833 0.14713.002
pfNbinomTest23.425 0.16623.618
twoSidedPValueFromDiscrete0.410.140.55