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CHECK report for AffyRNADegradation on merida1

This page was generated on 2020-08-07 12:26:28 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AffyRNADegradation PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 35/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyRNADegradation 1.35.0
Mario Fasold
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/AffyRNADegradation
Branch: master
Last Commit: a30a663
Last Changed Date: 2020-04-27 14:28:04 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AffyRNADegradation
Version: 1.35.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AffyRNADegradation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AffyRNADegradation_1.35.0.tar.gz
StartedAt: 2020-08-06 23:38:41 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 23:40:29 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 107.9 seconds
RetCode: 0
Status:  OK 
CheckDir: AffyRNADegradation.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:AffyRNADegradation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AffyRNADegradation_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/AffyRNADegradation.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffyRNADegradation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AffyRNADegradation’ version ‘1.35.0’
* 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 ‘AffyRNADegradation’ 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 ... NOTE
Package in Depends field not imported from: ‘methods’
  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
ComputeTongs: no visible global function definition for ‘filter’
ComputeTongs: no visible global function definition for ‘na.omit’
EstimateHookParams: no visible global function definition for ‘loess’
EstimateHookParams: no visible global function definition for
  ‘quantile’
GetTongs: no visible global function definition for ‘ave’
PlotDegradationHooks: no visible global function definition for
  ‘rainbow’
PlotDegradationHooks: no visible global function definition for ‘lines’
PlotDegradationHooks: no visible global function definition for
  ‘legend’
PlotDx: no visible global function definition for ‘grid’
PlotDx: no visible global function definition for ‘points’
PlotDx: no visible global function definition for ‘lines’
PlotTongs: no visible global function definition for ‘grid’
PlotTongs: no visible global function definition for ‘lines’
PlotTongs: no visible global function definition for ‘legend’
RNADegradation: no visible global function definition for ‘ave’
RNADegradation: no visible global function definition for ‘loess’
RNADegradation: no visible global function definition for ‘approx’
RNADegradation: no visible global function definition for ‘new’
TryToFitDecayFunction: no visible global function definition for ‘nls’
TryToFitDecayFunction: no visible global function definition for ‘coef’
getProbeInfo.index: no visible global function definition for ‘ave’
Undefined global functions or variables:
  approx ave coef filter grid legend lines loess na.omit new nls points
  quantile rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "grid", "legend", "lines", "points")
  importFrom("methods", "new")
  importFrom("stats", "approx", "ave", "coef", "filter", "loess",
             "na.omit", "nls", "quantile")
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
AffyDegradationBatch-class 21.188  0.457  21.715
AffyRNADegradation-package 16.763  0.171  16.956
AffyRNADegradation         16.171  0.134  16.327
GetTongs                   10.952  0.184  11.152
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/AffyRNADegradation.Rcheck/00check.log’
for details.



Installation output

AffyRNADegradation.Rcheck/00install.out

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

Tests output


Example timings

AffyRNADegradation.Rcheck/AffyRNADegradation-Ex.timings

nameusersystemelapsed
AffyDegradationBatch-class21.188 0.45721.715
AffyRNADegradation-package16.763 0.17116.956
AffyRNADegradation16.171 0.13416.327
GetTongs10.952 0.18411.152