Multiple platform build/check report for BioC 3.21 - CHECK results for dyebias on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4396
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4110
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for dyebias on kjohnson3

To the developers/maintainers of the dyebias package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: dyebias

Version: 1.67.0

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_1.67.0.tar.gz

StartedAt: 2024-11-26 21:31:22 -0500 (Tue, 26 Nov 2024)

EndedAt: 2024-11-26 21:35:25 -0500 (Tue, 26 Nov 2024)

EllapsedTime: 242.3 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_1.67.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/dyebias.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebias/DESCRIPTION’ ... OK
* this is package ‘dyebias’ version ‘1.67.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 code 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 ... NOTE
checkRd: (-1) dyebias.apply.correction.Rd:33-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dyebias.apply.correction.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dyebias.apply.correction.Rd:41-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dyebias.apply.correction.Rd:134: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:136: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:137: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:139: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:141: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:150: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:151-152: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:153-154: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:155-156: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:157-161: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:162-163: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.apply.correction.Rd:164-166: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dyebias.trendplot.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dyebias.trendplot.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dyebias.trendplot.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dyebias.trendplot.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dyebias.trendplot.Rd:67-68: Lost braces in \itemize; meant \describe ?
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/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

name	user	system	elapsed
dyebias.application.subset	3.157	0.083	3.242
dyebias.apply.correction	0.663	0.020	0.684
dyebias.boxplot	0.517	0.036	0.558
dyebias.estimate.iGSDBs	0.359	0.006	0.366
dyebias.monotonicity	0.000	0.000	0.001
dyebias.monotonicityplot	0	0	0
dyebias.rgplot	1.020	0.049	1.070
dyebias.trendplot	1.326	0.035	1.362