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This page was generated on 2021-10-25 14:06:48 -0400 (Mon, 25 Oct 2021).

CHECK results for AffyRNADegradation on merida1

To the developers/maintainers of the AffyRNADegradation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AffyRNADegradation.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 33/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyRNADegradation 1.39.0  (landing page)
Mario Fasold
Snapshot Date: 2021-10-24 14:50:04 -0400 (Sun, 24 Oct 2021)
git_url: https://git.bioconductor.org/packages/AffyRNADegradation
git_branch: master
git_last_commit: e8a0b74
git_last_commit_date: 2021-05-19 11:51:02 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: AffyRNADegradation
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AffyRNADegradation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AffyRNADegradation_1.39.0.tar.gz
StartedAt: 2021-10-25 00:26:19 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 00:28:34 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 134.1 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/Resources/bin/R CMD check --install=check:AffyRNADegradation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AffyRNADegradation_1.39.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AffyRNADegradation.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.39.0’
* 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 23.514  0.522  24.077
AffyRNADegradation-package 18.072  0.209  18.309
AffyRNADegradation         17.111  0.137  17.271
GetTongs                   12.265  0.208  12.505
* 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-3.14-bioc/meat/AffyRNADegradation.Rcheck/00check.log’
for details.



Installation output

AffyRNADegradation.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AffyRNADegradation
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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-class23.514 0.52224.077
AffyRNADegradation-package18.072 0.20918.309
AffyRNADegradation17.111 0.13717.271
GetTongs12.265 0.20812.505