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CHECK report for HD2013SGI on malbec2

This page was generated on 2021-01-21 16:01:11 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE HD2013SGI PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 163/386HostnameOS / ArchINSTALLBUILDCHECK
HD2013SGI 1.31.0
Bernd Fischer
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/HD2013SGI
Branch: master
Last Commit: 8971f18
Last Changed Date: 2020-10-27 10:01:22 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK 

Summary

Package: HD2013SGI
Version: 1.31.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HD2013SGI.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HD2013SGI_1.31.0.tar.gz
StartedAt: 2021-01-21 12:10:54 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 12:15:03 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 249.5 seconds
RetCode: 0
Status:  OK 
CheckDir: HD2013SGI.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HD2013SGI.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HD2013SGI_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/HD2013SGI.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HD2013SGI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HD2013SGI’ version ‘1.31.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'RColorBrewer', 'gplots', 'geneplotter', 'splots', 'limma', 'vcd',
  'LSD', 'EBImage'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HD2013SGI’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 525.2Mb
  sub-directories of 1Mb or more:
    data  524.1Mb
* 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
Packages in Depends field not imported from:
  ‘EBImage’ ‘LSD’ ‘RColorBrewer’ ‘geneplotter’ ‘gplots’ ‘limma’
  ‘splots’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘humanReadableNames’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HD2013SGIHeatmapHuman: no visible global function definition for ‘unit’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘pushViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘viewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.layout’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.rect’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.raster’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘popViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.text’
HD2013SGIHeatmapHuman: no visible global function definition for ‘gpar’
HD2013SGImaineffects: no visible binding for global variable ‘median’
HD2013SGImaineffects : <anonymous>: no visible binding for global
  variable ‘median’
HD2013SGImaineffects: no visible global function definition for
  ‘median’
HD2013SGIorderDim: no visible global function definition for ‘cor’
HD2013SGIorderDim: no visible global function definition for ‘hclust’
HD2013SGIorderDim: no visible global function definition for ‘as.dist’
HD2013SGIselectByStability: no visible global function definition for
  ‘lm’
HD2013SGIselectByStability : <anonymous>: no visible global function
  definition for ‘cor’
plotExampleInteractions: no visible binding for global variable ‘sd’
plotExampleInteractions: no visible global function definition for
  ‘par’
plotExampleInteractions: no visible global function definition for
  ‘barplot’
plotExampleInteractions: no visible global function definition for
  ‘abline’
plotExampleInteractions: no visible global function definition for
  ‘points’
plotExampleInteractions: no visible global function definition for
  ‘text’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘mad’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘par’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘barplot’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘abline’
plotExampleSingleGeneEffects: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  abline as.dist barplot cor gpar grid.layout grid.raster grid.rect
  grid.text hclust lm mad median par points popViewport pushViewport sd
  text unit viewport
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "points", "text")
  importFrom("stats", "as.dist", "cor", "hclust", "lm", "mad", "median",
             "sd")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
featuresPerWell 40.852  0.488  41.340
datamatrixfull   9.037  0.091   9.129
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/HD2013SGI.Rcheck/00check.log’
for details.



Installation output

HD2013SGI.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL HD2013SGI
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘HD2013SGI’ ...
** 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 (HD2013SGI)

Tests output


Example timings

HD2013SGI.Rcheck/HD2013SGI-Ex.timings

nameusersystemelapsed
HD2013SGI-package0.0510.0070.059
Interactions0.0510.0040.056
QueryAnnotation0.0010.0000.001
TargetAnnotation0.0030.0000.004
datamatrix0.0570.0000.058
datamatrixfull9.0370.0919.129
featuresPerWell40.852 0.48841.340
mainEffects0.3070.0080.315
nrOfInteractionsPerTarget0.0120.0010.012
stabilitySelection0.0140.0000.014