Package: AffyRNADegradation

Version: 1.28.0

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_1.28.0.tar.gz

StartedAt: 2019-04-15 22:18:25 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:20:01 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 95.9 seconds

RetCode: 0

Status:  OK

CheckDir: AffyRNADegradation.Rcheck

Warnings: 0

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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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/AffyRNADegradation.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.28.0’
* 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 ‘plot’
PlotDegradationHooks: no visible global function definition for ‘lines’
PlotDegradationHooks: no visible global function definition for
  ‘legend’
PlotDx: no visible global function definition for ‘plot’
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 ‘plot’
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 ‘plot’
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 plot
  points quantile rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "grid", "legend", "lines", "plot", "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 or elapsed time > 5s
                             user system elapsed
AffyDegradationBatch-class 17.735  0.452  18.277
AffyRNADegradation-package 15.079  0.306  15.522
AffyRNADegradation         14.741  0.286  15.135
GetTongs                   10.594  0.421  11.111
* 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-3.8-bioc/meat/AffyRNADegradation.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AffyRNADegradation
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘AffyRNADegradation’ ...
** 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
* DONE (AffyRNADegradation)

name	user	system	elapsed
AffyDegradationBatch-class	17.735	0.452	18.277
AffyRNADegradation-package	15.079	0.306	15.522
AffyRNADegradation	14.741	0.286	15.135
GetTongs	10.594	0.421	11.111