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This page was generated on 2021-10-26 14:08:34 -0400 (Tue, 26 Oct 2021).

CHECK results for dyebias on machv2

To the developers/maintainers of the dyebias package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dyebias.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 552/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dyebias 1.53.0  (landing page)
Philip Lijnzaad
Snapshot Date: 2021-10-25 14:50:11 -0400 (Mon, 25 Oct 2021)
git_url: https://git.bioconductor.org/packages/dyebias
git_branch: master
git_last_commit: 7a8d4aa
git_last_commit_date: 2021-05-19 11:42:55 -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: dyebias
Version: 1.53.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dyebias.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dyebias_1.53.0.tar.gz
StartedAt: 2021-10-26 02:56:12 -0400 (Tue, 26 Oct 2021)
EndedAt: 2021-10-26 02:57:18 -0400 (Tue, 26 Oct 2021)
EllapsedTime: 66.0 seconds
RetCode: 0
Status:   OK  
CheckDir: dyebias.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dyebias.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dyebias_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/dyebias.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebias/DESCRIPTION’ ... OK
* this is package ‘dyebias’ version ‘1.53.0’
* 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 ‘dyebias’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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' calls in package code:
  ‘limma’ ‘methods’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘marray’
  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
.check.reporter.labels: no visible global function definition for
  ‘maLabels’
.check.reporter.labels: no visible global function definition for
  ‘maGnames’
.check.reporter.labels: no visible global function definition for
  ‘maNspots’
.check.slide.labels: no visible global function definition for
  ‘maNsamples’
.check.slide.labels: no visible global function definition for
  ‘maLabels’
.check.slide.labels: no visible global function definition for
  ‘maTargets’
.find.estimators: no visible global function definition for ‘quantile’
.limma.to.dataframe: no visible global function definition for ‘is’
.limma.to.dataframe: no visible global function definition for ‘eBayes’
.limma.to.dataframe: no visible global function definition for
  ‘p.adjust’
.mann.kendall: no visible global function definition for ‘cor.test’
.merge.dyebias: no visible global function definition for ‘maLabels’
.merge.dyebias: no visible global function definition for ‘maGnames’
.monotonicity: no visible global function definition for ‘maNsamples’
.monotonicity : <anonymous>: no visible global function definition for
  ‘maM’
.monotonicity : slope: no visible global function definition for
  ‘lsfit’
.rg.subsets: no visible global function definition for ‘quantile’
.set.design: no visible global function definition for ‘modelMatrix’
.set.design : <anonymous>: no visible global function definition for
  ‘modelMatrix’
.set.output: no visible global function definition for ‘X11’
.set.output: no visible global function definition for ‘quartz’
.set.output: no visible global function definition for ‘pdf’
.set.output: no visible global function definition for ‘png’
.set.output: no visible global function definition for ‘postscript’
.slide.bias: no visible global function definition for ‘maNsamples’
.slide.bias: no visible global function definition for ‘maLabels’
.slide.bias: no visible global function definition for ‘maTargets’
.slide.bias: no visible global function definition for ‘maM’
.slide.bias.order: no visible binding for global variable ‘median’
dyebias.application.subset: no visible global function definition for
  ‘maInfo’
dyebias.application.subset: no visible global function definition for
  ‘maTargets’
dyebias.application.subset: no visible global function definition for
  ‘maNspots’
dyebias.application.subset: no visible global function definition for
  ‘maNsamples’
dyebias.application.subset: no visible global function definition for
  ‘maRb’
dyebias.application.subset: no visible global function definition for
  ‘maGb’
dyebias.application.subset: no visible global function definition for
  ‘maRf’
dyebias.application.subset: no visible global function definition for
  ‘maGf’
dyebias.apply.correction: no visible global function definition for
  ‘maM’
dyebias.apply.correction: no visible global function definition for
  ‘maNspots’
dyebias.apply.correction: no visible global function definition for
  ‘maNsamples’
dyebias.apply.correction: no visible global function definition for
  ‘maLabels’
dyebias.apply.correction: no visible global function definition for
  ‘maGnames’
dyebias.apply.correction: no visible global function definition for
  ‘maInfo’
dyebias.apply.correction: no visible global function definition for
  ‘maTargets’
dyebias.apply.correction: no visible global function definition for
  ‘median’
dyebias.apply.correction: no visible global function definition for
  ‘sd’
dyebias.apply.correction: no visible global function definition for
  ‘var.test’
dyebias.apply.correction: no visible global function definition for
  ‘maA’
dyebias.apply.correction: no visible global function definition for
  ‘maM<-’
dyebias.apply.correction: no visible global function definition for
  ‘maA<-’
dyebias.apply.correction: no visible global function definition for
  ‘is’
dyebias.apply.correction: no visible global function definition for
  ‘maR<-’
dyebias.apply.correction: no visible global function definition for
  ‘maG<-’
dyebias.boxplot: no visible global function definition for ‘maNsamples’
dyebias.boxplot: no visible global function definition for ‘par’
dyebias.boxplot: no visible global function definition for ‘boxplot’
dyebias.boxplot: no visible global function definition for ‘abline’
dyebias.boxplot: no visible global function definition for ‘dev.off’
dyebias.estimate.iGSDBs: no visible global function definition for ‘is’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maLabels’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maGnames’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maNspots’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maNsamples’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maM’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maA’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maInfo’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘maTargets’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘new’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘lmFit’
dyebias.estimate.iGSDBs: no visible global function definition for
  ‘eBayes’
dyebias.maplot: no visible global function definition for ‘maM’
dyebias.maplot: no visible global function definition for ‘maA’
dyebias.maplot: no visible global function definition for ‘box’
dyebias.maplot: no visible global function definition for ‘abline’
dyebias.maplot: no visible global function definition for ‘points’
dyebias.maplot: no visible global function definition for ‘dev.off’
dyebias.monotonicityplot: no visible global function definition for
  ‘points’
dyebias.monotonicityplot: no visible global function definition for
  ‘dev.off’
dyebias.rgplot: no visible global function definition for ‘maA’
dyebias.rgplot: no visible global function definition for ‘maM’
dyebias.rgplot: no visible global function definition for ‘axis’
dyebias.rgplot: no visible global function definition for ‘box’
dyebias.rgplot: no visible global function definition for ‘abline’
dyebias.rgplot: no visible global function definition for ‘points’
dyebias.rgplot: no visible global function definition for ‘dev.off’
dyebias.trendplot: no visible global function definition for ‘quantile’
dyebias.trendplot: no visible global function definition for
  ‘maNsamples’
dyebias.trendplot : <anonymous>: no visible global function definition
  for ‘maM’
dyebias.trendplot: no visible binding for global variable ‘median’
dyebias.trendplot: no visible global function definition for ‘matplot’
dyebias.trendplot: no visible global function definition for ‘axis’
dyebias.trendplot: no visible global function definition for ‘matlines’
dyebias.trendplot: no visible global function definition for ‘abline’
dyebias.trendplot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  X11 abline axis box boxplot cor.test dev.off eBayes is lmFit lsfit
  maA maA<- maG<- maGb maGf maGnames maInfo maLabels maM maM<-
  maNsamples maNspots maR<- maRb maRf maTargets matlines matplot median
  modelMatrix new p.adjust par pdf png points postscript quantile
  quartz sd var.test
Consider adding
  importFrom("grDevices", "X11", "dev.off", "pdf", "png", "postscript",
             "quartz")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "matlines",
             "matplot", "par", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "cor.test", "lsfit", "median", "p.adjust",
             "quantile", "sd", "var.test")
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
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/dyebias.Rcheck/00check.log’
for details.



Installation output

dyebias.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dyebias
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘dyebias’ ...
** 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 (dyebias)

Tests output


Example timings

dyebias.Rcheck/dyebias-Ex.timings

nameusersystemelapsed
dyebias.application.subset3.0320.1443.184
dyebias.apply.correction2.0640.1062.172
dyebias.boxplot2.0890.0982.188
dyebias.estimate.iGSDBs1.4620.0331.495
dyebias.monotonicity0.0000.0010.001
dyebias.monotonicityplot0.0000.0010.001
dyebias.rgplot3.2310.1613.400
dyebias.trendplot4.0440.0904.139