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CHECK report for arrayMvout on malbec1

This page was generated on 2020-08-12 11:14:45 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE arrayMvout PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 77/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayMvout 1.47.0
V. Carey
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/arrayMvout
Branch: master
Last Commit: 972577c
Last Changed Date: 2020-04-27 14:18:24 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: arrayMvout
Version: 1.47.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:arrayMvout.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings arrayMvout_1.47.0.tar.gz
StartedAt: 2020-08-11 23:56:55 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-12 00:03:25 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 390.7 seconds
RetCode: 0
Status:  OK 
CheckDir: arrayMvout.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:arrayMvout.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings arrayMvout_1.47.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/arrayMvout.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘arrayMvout/DESCRIPTION’ ... OK
* this is package ‘arrayMvout’ version ‘1.47.0’
* 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 ‘arrayMvout’ 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 ... 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘lumi’ ‘methods’ ‘parody’
  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
.affyArrayOutliers: no visible global function definition for
  ‘sampleNames’
.affyArrayOutliers: no visible global function definition for ‘fitPLM’
.affyArrayOutliers: no visible global function definition for ‘boxplot’
.affyArrayOutliers: no visible global function definition for ‘Mbox’
.affyArrayOutliers: no visible global function definition for
  ‘AffyRNAdeg’
.affyArrayOutliers: no visible global function definition for ‘prcomp’
.affyArrayOutliers : <anonymous>: no visible global function definition
  for ‘mv.calout.detect’
.affyArrayOutliers: no visible global function definition for
  ‘mv.calout.detect’
.lumiArrayOutliers: no visible global function definition for ‘lumiQ’
.lumiArrayOutliers: no visible global function definition for ‘prcomp’
.lumiArrayOutliers: no visible global function definition for
  ‘mv.calout.detect’
.lumiArrayOutliers : <anonymous>: no visible global function definition
  for ‘mv.calout.detect’
ArrayOutliers,data.frame-numeric-ANY: no visible global function
  definition for ‘prcomp’
ArrayOutliers,data.frame-numeric-ANY: no visible global function
  definition for ‘mv.calout.detect’
ArrayOutliers,data.frame-numeric-ANY : <anonymous>: no visible global
  function definition for ‘mv.calout.detect’
plot,arrOutStruct-ANY: no visible global function definition for
  ‘biplot’
plot,arrOutStruct-ANY: no visible global function definition for
  ‘prcomp’
Undefined global functions or variables:
  AffyRNAdeg Mbox biplot boxplot fitPLM lumiQ mv.calout.detect prcomp
  sampleNames
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "biplot", "prcomp")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
ArrayOutliers-methods 25.036  0.376  25.672
ArrayOutliers         21.244  0.152  21.454
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/arrayMvout.Rcheck/00check.log’
for details.



Installation output

arrayMvout.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL arrayMvout
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘arrayMvout’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (arrayMvout)

Tests output


Example timings

arrayMvout.Rcheck/arrayMvout-Ex.timings

nameusersystemelapsed
ArrayOutliers-methods25.036 0.37625.672
ArrayOutliers21.244 0.15221.454
arrOutStruct-class0.0640.0000.064