Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:58 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 affycomp on lconway


To the developers/maintainers of the affycomp package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affycomp.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 23/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycomp 1.74.0  (landing page)
Rafael A. Irizarry
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/affycomp
git_branch: RELEASE_3_16
git_last_commit: 1160d63
git_last_commit_date: 2022-11-01 10:35:39 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: affycomp
Version: 1.74.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affycomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affycomp_1.74.0.tar.gz
StartedAt: 2023-04-10 18:44:06 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 18:44:50 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 43.8 seconds
RetCode: 0
Status:   OK  
CheckDir: affycomp.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affycomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affycomp_1.74.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/affycomp.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affycomp/DESCRIPTION’ ... OK
* this is package ‘affycomp’ version ‘1.74.0’
* 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 ‘affycomp’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
* 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
'library' or 'require' call to ‘splines’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘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
affycomp.figure2b: warning in affycomp.compfig2b(list(l), method.name =
  l$method.name, add.legend = FALSE, main = main): partial argument
  match of 'method.name' to 'method.names'
affycompPlot: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableAll: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableOverallSNR: warning in vector(mode = "character", len = N):
  partial argument match of 'len' to 'length'
tableRanks: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
affycomp.compfig2: no visible global function definition for ‘lines’
affycomp.compfig2: no visible global function definition for ‘legend’
affycomp.compfig2b: no visible global function definition for ‘lines’
affycomp.compfig2b: no visible global function definition for ‘legend’
affycomp.compfig3: no visible global function definition for ‘boxplot’
affycomp.compfig4a: no visible global function definition for ‘lines’
affycomp.compfig4a: no visible global function definition for ‘legend’
affycomp.compfig4b: no visible global function definition for ‘lines’
affycomp.compfig4b: no visible global function definition for ‘legend’
affycomp.compfig4b: no visible global function definition for ‘abline’
affycomp.compfig4c: no visible global function definition for ‘lines’
affycomp.compfig4c: no visible global function definition for ‘legend’
affycomp.compfig4c: no visible global function definition for ‘abline’
affycomp.compfig5a: no visible global function definition for ‘lines’
affycomp.compfig5a: no visible global function definition for ‘legend’
affycomp.compfig5b: no visible global function definition for ‘lines’
affycomp.compfig5b: no visible global function definition for ‘legend’
affycomp.compfig5cde: no visible global function definition for ‘lines’
affycomp.compfig5cde: no visible global function definition for
  ‘legend’
affycomp.compfig7: no visible global function definition for ‘boxplot’
affycomp.compfigs: no visible global function definition for ‘par’
affycomp.compfigs: no visible global function definition for
  ‘dev.interactive’
affycomp.figure1: no visible global function definition for
  ‘topo.colors’
affycomp.figure1: no visible global function definition for
  ‘heat.colors’
affycomp.figure1: no visible global function definition for ‘points’
affycomp.figure1: no visible global function definition for ‘text’
affycomp.figure1b: no visible global function definition for
  ‘topo.colors’
affycomp.figure1b: no visible global function definition for
  ‘heat.colors’
affycomp.figure1b: no visible global function definition for ‘points’
affycomp.figure1b: no visible global function definition for ‘text’
affycomp.figure3: no visible global function definition for ‘abline’
affycomp.figure3: no visible global function definition for ‘points’
affycomp.figure4a: no visible global function definition for ‘lines’
affycomp.figure4b: no visible global function definition for ‘abline’
affycomp.figure6a: no visible global function definition for ‘matplot’
affycomp.figure6a: no visible global function definition for ‘lines’
affycomp.figure6a: no visible global function definition for ‘abline’
affycomp.figure6b: no visible global function definition for ‘lines’
affycomp.figure6b: no visible global function definition for ‘abline’
affycomp.figure7: no visible global function definition for ‘lm’
affycomp.figure7: no visible global function definition for ‘lines’
affycomp.figure7: no visible global function definition for ‘abline’
affycomp.figures: no visible global function definition for ‘par’
affycomp.figures: no visible global function definition for
  ‘dev.interactive’
assessDilution: no visible global function definition for ‘exprs’
assessDilution: no visible global function definition for ‘pData’
assessDilution : <anonymous>: no visible global function definition for
  ‘cor’
assessDilution : <anonymous>: no visible binding for global variable
  ‘sd’
assessDilution: no visible global function definition for ‘lm’
assessDilution: no visible global function definition for ‘median’
assessDilution: no visible global function definition for ‘cor’
assessFC: no visible global function definition for ‘exprs’
assessFC: no visible global function definition for ‘pData’
assessFC: no visible global function definition for ‘quantile’
assessFC: no visible global function definition for ‘lm’
assessFC2: no visible global function definition for ‘exprs’
assessFC2: no visible global function definition for ‘pData’
assessLS: no visible global function definition for ‘exprs’
assessLS: no visible global function definition for ‘pData’
assessLS: no visible global function definition for ‘featureNames’
assessLS: no visible global function definition for ‘lm’
assessLS: no visible global function definition for ‘cor’
assessMA: no visible global function definition for ‘exprs’
assessMA: no visible global function definition for ‘pData’
assessMA2: no visible global function definition for ‘exprs’
assessMA2: no visible global function definition for ‘pData’
assessMA2: no visible global function definition for ‘featureNames’
assessMA2: no visible binding for global variable ‘median’
assessSD: no visible global function definition for ‘exprs’
assessSD: no visible global function definition for ‘assayDataElement’
assessSD: no visible global function definition for ‘pData’
assessSD : <anonymous>: no visible binding for global variable ‘sd’
assessSD: no visible global function definition for ‘cor’
assessSignal: no visible global function definition for ‘exprs’
assessSignal: no visible global function definition for ‘pData’
assessSignal: no visible global function definition for ‘featureNames’
assessSignal: no visible global function definition for ‘lm’
assessSpikeIn2: no visible global function definition for ‘exprs’
assessSpikeInSD: no visible global function definition for ‘pData’
assessSpikeInSD: no visible global function definition for
  ‘featureNames’
assessSpikeInSD: no visible global function definition for ‘esApply’
assessSpikeInSD: no visible binding for global variable ‘sd’
assessSpikeInSD: no visible global function definition for ‘loess’
exprset.log: no visible global function definition for ‘exprs’
exprset.log: no visible global function definition for ‘exprs<-’
getData: no visible global function definition for ‘data’
read.dilution: no visible global function definition for ‘read.csv’
read.dilution: no visible global function definition for ‘sampleNames’
read.dilution: no visible global function definition for ‘new’
read.spikein: no visible global function definition for ‘read.csv’
read.spikein: no visible global function definition for ‘sampleNames’
read.spikein: no visible global function definition for ‘new’
remove.hgu133a.xhyb: no visible global function definition for
  ‘featureNames’
tableMA2 : myauc: no visible global function definition for ‘approx’
tableMA2: no visible global function definition for ‘IQR’
tableMA2: no visible global function definition for ‘quantile’
tableOverallSNR: no visible global function definition for ‘median’
tableOverallSNR: no visible global function definition for ‘IQR’
tableOverallSNR: no visible global function definition for ‘quantile’
tableSD: no visible global function definition for ‘IQR’
tableSpikeInSD: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  IQR abline addVigs2WinMenu approx assayDataElement boxplot cor data
  dev.interactive esApply exprs exprs<- featureNames heat.colors legend
  lines lm loess matplot median new pData par points quantile read.csv
  sampleNames sd text topo.colors
Consider adding
  importFrom("grDevices", "dev.interactive", "heat.colors",
             "topo.colors")
  importFrom("graphics", "abline", "boxplot", "legend", "lines",
             "matplot", "par", "points", "text")
  importFrom("methods", "new")
  importFrom("stats", "IQR", "approx", "cor", "lm", "loess", "median",
             "quantile", "sd")
  importFrom("utils", "data", "read.csv")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/affycomp.Rcheck/00check.log’
for details.



Installation output

affycomp.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘affycomp’ ...
** using staged installation
** R
** data
** 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 (affycomp)

Tests output


Example timings

affycomp.Rcheck/affycomp-Ex.timings

nameusersystemelapsed
SD0.4780.0290.514
affycomp.compfigs.auxiliary0.2650.0290.301
affycomp.figures.auxiliary0.3310.0360.372
affycomp.table0.2550.0180.276
affycompPlot0.5030.0540.564