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CHECK report for RmiR on merida1

This page was generated on 2021-05-06 12:36:30 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RmiR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1542/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RmiR 1.46.0  (landing page)
Francesco Favero
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RmiR
Branch: RELEASE_3_12
Last Commit: 6facff2
Last Changed Date: 2020-10-27 10:35:51 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RmiR
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RmiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RmiR_1.46.0.tar.gz
StartedAt: 2021-05-06 05:31:13 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:33:01 -0400 (Thu, 06 May 2021)
EllapsedTime: 107.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RmiR.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:RmiR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RmiR_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/RmiR.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 ‘RmiR/DESCRIPTION’ ... OK
* this is package ‘RmiR’ version ‘1.46.0’
* 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 ‘RmiR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to ‘RSVGTipsDevice’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RSVGTipsDevice’ ‘RmiR.Hs.miRNA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRmiRtc: no visible global function definition for ‘devSVGTips’
plotRmiRtc: no visible global function definition for
  ‘setSVGShapeToolTip’
plotRmiRtc: no visible global function definition for ‘setSVGShapeURL’
plotRmiRtc: no visible global function definition for ‘points’
plotRmiRtc: no visible global function definition for ‘lines’
plotRmiRtc: no visible global function definition for ‘legend’
plotRmiRtc: no visible global function definition for ‘dev.off’
readRmiRtc: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dev.off devSVGTips legend lines points setSVGShapeToolTip
  setSVGShapeURL write.table
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "legend", "lines", "points")
  importFrom("utils", "write.table")
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 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
RmiR       14.734  0.642  15.974
RmiRtc      6.458  0.120   6.590
plotRmiRtc  6.467  0.085   6.602
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/RmiR.Rcheck/00check.log’
for details.



Installation output

RmiR.Rcheck/00install.out

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

Tests output


Example timings

RmiR.Rcheck/RmiR-Ex.timings

nameusersystemelapsed
RmiR14.734 0.64215.974
RmiRtc6.4580.1206.590
data0.0230.0010.026
plotRmiRtc6.4670.0856.602