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CHECK report for rnaseqcomp on machv2

This page was generated on 2020-10-17 11:59:26 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE rnaseqcomp PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1514/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaseqcomp 1.18.0
Mingxiang Teng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/rnaseqcomp
Branch: RELEASE_3_11
Last Commit: 62cc381
Last Changed Date: 2020-04-27 14:49:58 -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: rnaseqcomp
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rnaseqcomp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rnaseqcomp_1.18.0.tar.gz
StartedAt: 2020-10-17 04:44:31 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:45:26 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 55.5 seconds
RetCode: 0
Status:  OK 
CheckDir: rnaseqcomp.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rnaseqcomp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rnaseqcomp_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rnaseqcomp.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaseqcomp/DESCRIPTION’ ... OK
* this is package ‘rnaseqcomp’ version ‘1.18.0’
* 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 ‘rnaseqcomp’ 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
plot2TX: no visible global function definition for ‘lines’
plot2TX: no visible global function definition for ‘box’
plot2TX: no visible global function definition for ‘legend’
plot2TX : <anonymous>: no visible binding for global variable ‘sd’
plot2TX : <anonymous>: no visible global function definition for ‘sd’
plotFC: no visible global function definition for ‘loess.smooth’
plotFC: no visible global function definition for ‘lines’
plotFC: no visible global function definition for ‘legend’
plotFC : <anonymous>: no visible global function definition for
  ‘median’
plotFC : <anonymous>: no visible global function definition for ‘sd’
plotNE: no visible global function definition for ‘lines’
plotNE: no visible global function definition for ‘points’
plotNE: no visible global function definition for ‘box’
plotNE: no visible global function definition for ‘legend’
plotROC: no visible global function definition for ‘median’
plotROC: no visible global function definition for ‘sd’
plotROC: no visible global function definition for ‘lines’
plotROC: no visible global function definition for ‘arrows’
plotROC: no visible global function definition for ‘abline’
plotROC: no visible global function definition for ‘legend’
plotSD : <anonymous>: no visible binding for global variable ‘sd’
plotSD: no visible global function definition for ‘loess.smooth’
plotSD: no visible global function definition for ‘lines’
plotSD: no visible global function definition for ‘box’
plotSD: no visible global function definition for ‘legend’
plotSD : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
plotSD : <anonymous> : <anonymous>: no visible global function
  definition for ‘mad’
signalCalibrate : <anonymous>: no visible binding for global variable
  ‘median’
signalCalibrate: no visible global function definition for ‘median’
Undefined global functions or variables:
  abline arrows box legend lines loess.smooth mad median points sd
Consider adding
  importFrom("graphics", "abline", "arrows", "box", "legend", "lines",
             "points")
  importFrom("stats", "loess.smooth", "mad", "median", "sd")
to your NAMESPACE file.
* 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
plotROC 9.406  2.640  12.054
plotNE  4.261  1.193   5.457
* 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/rnaseqcomp.Rcheck/00check.log’
for details.



Installation output

rnaseqcomp.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rnaseqcomp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘rnaseqcomp’ ...
** 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 (rnaseqcomp)

Tests output


Example timings

rnaseqcomp.Rcheck/rnaseqcomp-Ex.timings

nameusersystemelapsed
plot2TX0.7490.0780.828
plotFC0.3540.0270.381
plotNE4.2611.1935.457
plotROC 9.406 2.64012.054
plotSD2.3690.0262.400
signalCalibrate0.2390.0070.246