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This page was generated on 2024-06-11 14:51 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 186/425HostnameOS / ArchINSTALLBUILDCHECK
Hiiragi2013 1.41.0  (landing page)
Andrzej Oles
Snapshot Date: 2024-06-11 07:30 -0400 (Tue, 11 Jun 2024)
git_url: https://git.bioconductor.org/packages/Hiiragi2013
git_branch: devel
git_last_commit: 3911b68
git_last_commit_date: 2024-04-30 10:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Hiiragi2013 on nebbiolo2

To the developers/maintainers of the Hiiragi2013 package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Hiiragi2013
Version: 1.41.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Hiiragi2013.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Hiiragi2013_1.41.0.tar.gz
StartedAt: 2024-06-11 11:24:05 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 11:32:34 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 508.3 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-3.20-bioc/R/bin/R CMD check --install=check:Hiiragi2013.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Hiiragi2013_1.41.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/Hiiragi2013.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Hiiragi2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Hiiragi2013’ version ‘1.41.0’
* 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 code 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 loading without being on the library search path ... 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 24.969   1.37  27.336
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/Hiiragi2013.Rcheck/00check.log’
for details.


Installation output

Hiiragi2013.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Hiiragi2013
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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
MDSplot3.8900.1244.015
a24.969 1.37027.336
getDifferentialExpressedGenes3.3290.1343.463
myHeatmap3.7750.2324.007
myHeatmap2000
pamCluster2.9550.0723.026
plotProjection000
x2.9020.0402.942
xq0.010.000.01
xql0.0010.0040.004