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This page was generated on 2021-12-01 17:18:11 -0500 (Wed, 01 Dec 2021).

CHECK results for arrayMvout on machv2

To the developers/maintainers of the arrayMvout package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/arrayMvout.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 80/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayMvout 1.52.0  (landing page)
V. Carey
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/arrayMvout
git_branch: RELEASE_3_14
git_last_commit: 963b432
git_last_commit_date: 2021-10-26 11:53:12 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: arrayMvout
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:arrayMvout.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings arrayMvout_1.52.0.tar.gz
StartedAt: 2021-11-30 13:45:08 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 13:51:28 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 379.4 seconds
RetCode: 0
Status:   OK  
CheckDir: arrayMvout.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:arrayMvout.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings arrayMvout_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/arrayMvout.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘arrayMvout/DESCRIPTION’ ... OK
* this is package ‘arrayMvout’ version ‘1.52.0’
* 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 ... OK
* 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 ‘qc’
.affyArrayOutliers: no visible global function definition for ‘avbg’
.affyArrayOutliers: no visible global function definition for ‘sfs’
.affyArrayOutliers: no visible global function definition for
  ‘percent.present’
.affyArrayOutliers: no visible global function definition for ‘ratios’
.affyArrayOutliers: no visible global function definition for ‘fitPLM’
.affyArrayOutliers: no visible global function definition for ‘prcomp’
.lumiArrayOutliers: no visible global function definition for ‘prcomp’
ArrayOutliers,data.frame-numeric-ANY: no visible global function
  definition for ‘prcomp’
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:
  avbg biplot fitPLM percent.present prcomp qc ratios sfs
Consider adding
  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 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-3.14-bioc/meat/arrayMvout.Rcheck/00check.log’
for details.



Installation output

arrayMvout.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL arrayMvout
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘arrayMvout’ ...
** using staged installation
** R
** data
** inst
** 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-methods0.0220.0020.024
ArrayOutliers0.0000.0010.001
arrOutStruct-class0.1390.0120.151