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CHECK report for affyQCReport on merida1

This page was generated on 2020-04-15 12:34:26 -0400 (Wed, 15 Apr 2020).

Package 35/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyQCReport 1.64.0
Craig Parman
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/affyQCReport
Branch: RELEASE_3_10
Last Commit: c97d070
Last Changed Date: 2019-10-29 13:07:34 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: affyQCReport
Version: 1.64.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affyQCReport.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affyQCReport_1.64.0.tar.gz
StartedAt: 2020-04-15 00:18:10 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:20:42 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 152.5 seconds
RetCode: 0
Status:  OK 
CheckDir: affyQCReport.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affyQCReport.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affyQCReport_1.64.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/affyQCReport.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyQCReport/DESCRIPTION’ ... OK
* this is package ‘affyQCReport’ version ‘1.64.0’
* 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 ‘affyQCReport’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’ ‘Biobase’ ‘lattice’
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
borderQC1: warning in axis(1, label = ArrayIndex, at = seq(1 - 0.5,
  length(ArrayIndex) - 0.5), cex = 0.2): partial argument match of
  'label' to 'labels'
borderQC2: warning in axis(1, label = ArrayIndex, at = seq(1 - 0.5,
  length(ArrayIndex) - 0.5), cex = 0.2): partial argument match of
  'label' to 'labels'
correlationPlot: warning in axis(2, label = as.list(pretty(c, 10)), at
  = seq(0, 1, by = (1/(length(pretty(c, 10)) - 1)))): partial argument
  match of 'label' to 'labels'
correlationPlot: warning in axis(4, label =
  as.list(attr(object@phenoData, which = "varLabels")[1:phenodepth]),
  at = seq(1 - 0.5, phenodepth - 0.5), las = 1): partial argument match
  of 'label' to 'labels'
signalDist: warning in legend(((temppar$xaxp[2] -
  temppar$xaxp[1])/temppar$xaxp[3]) * (temppar$xaxp[3] - 1) +
  temppar$xaxp[1], temppar$yaxp[2], as.character(ArrayIndex), lt =
  1:length(ArrayIndex), col = 1:length(ArrayIndex), cex = 0.5): partial
  argument match of 'lt' to 'lty'
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/affyQCReport.Rcheck/00check.log’
for details.



Installation output

affyQCReport.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affyQCReport
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘affyQCReport’ ...
** 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 (affyQCReport)

Tests output


Example timings

affyQCReport.Rcheck/affyQCReport-Ex.timings

nameusersystemelapsed
QCReport000
affyQAReport000
borderQC10.5600.0300.591
borderQC20.6730.0050.679
correlationPlot2.4350.0772.521
signalDist2.3670.0822.463
titlePage0.3620.0140.378