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CHECK report for DeSousa2013 on malbec2

This page was generated on 2021-01-14 15:58:59 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE DeSousa2013 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 92/385HostnameOS / ArchINSTALLBUILDCHECK
DeSousa2013 1.27.0
Xin Wang
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/DeSousa2013
Branch: master
Last Commit: bb7af97
Last Changed Date: 2020-10-27 10:02:18 -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: DeSousa2013
Version: 1.27.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DeSousa2013.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DeSousa2013_1.27.0.tar.gz
StartedAt: 2021-01-14 11:59:05 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:02:58 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 233.5 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-3.13-bioc/R/bin/R CMD check --install=check:DeSousa2013.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DeSousa2013_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/DeSousa2013.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 ‘DeSousa2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeSousa2013’ version ‘1.27.0’
* 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 ... 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 ‘DeSousa2013’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 43.9Mb
  sub-directories of 1Mb or more:
    data  43.7Mb
* 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
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   12.950  0.176  13.237
selTopVarGenes  5.264  0.024   5.288
* 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-3.13-data-experiment/meat/DeSousa2013.Rcheck/00check.log’
for details.



Installation output

DeSousa2013.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DeSousa2013
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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
buildClassifier3.1660.0523.218
compGapStats12.950 0.17613.237
conClust1.2930.0121.306
data-AMC0.0010.0000.001
filterDiffGenes1.0340.0001.034
filterSamples0.1170.0000.117
findDiffGenes0.8570.0360.893
geneExpPre000
pamClassify0.1180.0080.126
pbs2unigenes3.3460.0563.546
progAMC0.0540.0000.054
selTopVarGenes5.2640.0245.288