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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 Oct 2021).

CHECK results for Hiiragi2013 on nebbiolo2

To the developers/maintainers of the Hiiragi2013 package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 177/404HostnameOS / ArchINSTALLBUILDCHECK
Hiiragi2013 1.29.0  (landing page)
Andrzej Oles
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/Hiiragi2013
git_branch: master
git_last_commit: 2607674
git_last_commit_date: 2021-05-19 11:39:59 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Hiiragi2013
Version: 1.29.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Hiiragi2013.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Hiiragi2013_1.29.0.tar.gz
StartedAt: 2021-10-16 12:18:38 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 12:21:06 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 147.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Hiiragi2013.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Hiiragi2013.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Hiiragi2013_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/Hiiragi2013.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Hiiragi2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Hiiragi2013’ version ‘1.29.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'affy', 'Biobase', 'boot', 'clue', 'cluster', 'genefilter',
  'geneplotter', 'gplots', 'gtools', 'KEGGREST', 'MASS',
  'mouse4302.db', 'RColorBrewer', 'xtable'
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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Hiiragi2013’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 136.5Mb
  sub-directories of 1Mb or more:
    data  136.3Mb
* 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:
  ‘KEGGREST’ ‘affy’ ‘boot’ ‘clue’ ‘geneplotter’ ‘gtools’ ‘mouse4302.db’
  ‘xtable’
  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
MDSplot: no visible global function definition for ‘dist’
MDSplot: no visible global function definition for ‘par’
MDSplot: no visible global function definition for ‘points’
MDSplot: no visible global function definition for ‘grey’
MDSplot: no visible global function definition for ‘text’
getDifferentialExpressedGenes: no visible global function definition
  for ‘quantile’
getDifferentialExpressedGenes: no visible global function definition
  for ‘p.adjust’
myHeatmap: no visible global function definition for ‘as.dendrogram’
myHeatmap: no visible global function definition for ‘hclust’
myHeatmap: no visible global function definition for ‘dist’
myHeatmap: no visible global function definition for ‘order.dendrogram’
myHeatmap2: no visible global function definition for
  ‘colorRampPalette’
ordermat : <anonymous>: no visible global function definition for
  ‘order.dendrogram’
ordermat : <anonymous>: no visible global function definition for
  ‘as.dendrogram’
ordermat : <anonymous>: no visible global function definition for
  ‘hclust’
ordermat : <anonymous>: no visible global function definition for
  ‘dist’
pamCluster: no visible global function definition for ‘dist’
Undefined global functions or variables:
  as.dendrogram colorRampPalette dist grey hclust order.dendrogram
  p.adjust par points quantile text
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "par", "points", "text")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "p.adjust", "quantile")
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
a 11.746  0.559  12.306
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/Hiiragi2013.Rcheck/00check.log’
for details.



Installation output

Hiiragi2013.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Hiiragi2013
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘Hiiragi2013’ ...
** 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 (Hiiragi2013)

Tests output


Example timings

Hiiragi2013.Rcheck/Hiiragi2013-Ex.timings

nameusersystemelapsed
MDSplot3.1420.0993.242
a11.746 0.55912.306
getDifferentialExpressedGenes2.7120.1252.836
myHeatmap3.1120.1963.309
myHeatmap2000
pamCluster2.2450.0752.321
plotProjection000
x2.3180.0432.361
xq0.0050.0030.008
xql0.0030.0010.003