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This page was generated on 2023-10-12 14:51:35 -0400 (Thu, 12 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
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 92/421HostnameOS / ArchINSTALLBUILDCHECK
DeSousa2013 1.36.0  (landing page)
Xin Wang
Snapshot Date: 2023-10-12 07:30:02 -0400 (Thu, 12 Oct 2023)
git_url: https://git.bioconductor.org/packages/DeSousa2013
git_branch: RELEASE_3_17
git_last_commit: e74c27d
git_last_commit_date: 2023-04-25 10:33:07 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for DeSousa2013 on nebbiolo1


To the developers/maintainers of the DeSousa2013 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: DeSousa2013
Version: 1.36.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DeSousa2013.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DeSousa2013_1.36.0.tar.gz
StartedAt: 2023-10-12 11:13:38 -0400 (Thu, 12 Oct 2023)
EndedAt: 2023-10-12 11:18:26 -0400 (Thu, 12 Oct 2023)
EllapsedTime: 287.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DeSousa2013.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DeSousa2013.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings DeSousa2013_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/DeSousa2013.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘DeSousa2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeSousa2013’ version ‘1.36.0’
* 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 ‘DeSousa2013’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 44.0Mb
  sub-directories of 1Mb or more:
    data  43.8Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘frmaTools’ ‘hgu133plus2frmavecs’ ‘rgl’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CRCPipeLine: no visible global function definition for ‘data’
CRCPipeLine: no visible global function definition for ‘pdf’
CRCPipeLine: no visible global function definition for ‘graphics.off’
compGapStats: no visible binding for global variable ‘mad’
compGapStats : fun: no visible global function definition for ‘hclust’
compGapStats : fun: no visible global function definition for ‘as.dist’
compGapStats : fun: no visible global function definition for ‘cor’
compGapStats : fun: no visible global function definition for ‘cutree’
compGapStats: no visible binding for global variable ‘median’
figClassify: no visible global function definition for ‘layout’
figClassify: no visible global function definition for ‘par’
figClassify: no visible global function definition for ‘image’
figClassify: no visible global function definition for ‘axis’
figClassify: no visible global function definition for ‘box’
figClassify: no visible global function definition for ‘gray’
figClassify: no visible global function definition for ‘mtext’
figClassify: no visible global function definition for ‘barplot’
figClassify: no visible global function definition for ‘grid’
figGAP: no visible global function definition for ‘par’
figGAP: no visible global function definition for ‘lines’
figGAP: no visible global function definition for ‘title’
figKM: no visible global function definition for ‘axis’
figKM: no visible global function definition for ‘box’
figKM: no visible global function definition for ‘text’
figKM: no visible global function definition for ‘legend’
figPAMCV: no visible global function definition for ‘boxplot’
filterSamples: no visible global function definition for ‘as.dist’
filterSamples: no visible global function definition for ‘cor’
pamClassify: no visible global function definition for ‘hclust’
pamClassify: no visible global function definition for ‘as.dist’
pamClassify: no visible global function definition for ‘cor’
pbs2unigenes: no visible global function definition for ‘mappedkeys’
progAMC: no visible global function definition for ‘pchisq’
selTopVarGenes: no visible binding for global variable ‘mad’
selTopVarGenes: no visible binding for global variable ‘median’
Undefined global functions or variables:
  as.dist axis barplot box boxplot cor cutree data graphics.off gray
  grid hclust image layout legend lines mad mappedkeys median mtext par
  pchisq pdf text title
Consider adding
  importFrom("grDevices", "graphics.off", "gray", "pdf")
  importFrom("graphics", "axis", "barplot", "box", "boxplot", "grid",
             "image", "layout", "legend", "lines", "mtext", "par",
             "text", "title")
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "mad",
             "median", "pchisq")
  importFrom("utils", "data")
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
compGapStats 11.015  0.315  11.331
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘DeSousa2013-Vignette.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-data-experiment/meat/DeSousa2013.Rcheck/00check.log’
for details.



Installation output

DeSousa2013.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL DeSousa2013
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘DeSousa2013’ ...
** using staged installation
** R
** data
** 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 (DeSousa2013)

Tests output


Example timings

DeSousa2013.Rcheck/DeSousa2013-Ex.timings

nameusersystemelapsed
CRCPipeLine000
buildClassifier2.8150.2683.083
compGapStats11.015 0.31511.331
conClust0.5830.0240.607
data-AMC0.0020.0000.002
filterDiffGenes0.9640.0200.984
filterSamples0.1230.0000.123
findDiffGenes0.7050.0240.729
geneExpPre0.0000.0000.001
pamClassify0.1140.0040.117
pbs2unigenes3.8230.1413.965
progAMC0.0540.0070.062
selTopVarGenes4.5280.1204.648