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CHECK report for DeSousa2013 on malbec2

This page was generated on 2018-10-16 14:18:22 -0400 (Tue, 16 Oct 2018).

Package 77/342HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeSousa2013 1.16.0
Xin Wang
Snapshot Date: 2018-10-16 07:35:22 -0400 (Tue, 16 Oct 2018)
URL: https://git.bioconductor.org/packages/DeSousa2013
Branch: RELEASE_3_7
Last Commit: 6cabf7a
Last Changed Date: 2018-04-30 10:31:27 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: DeSousa2013
Version: 1.16.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DeSousa2013.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DeSousa2013_1.16.0.tar.gz
StartedAt: 2018-10-16 10:50:15 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 10:54:24 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 249.0 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-3.7-bioc/R/bin/R CMD check --install=check:DeSousa2013.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DeSousa2013_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/DeSousa2013.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.16.0’
* 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 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 ‘plot’
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’
figSilh: no visible global function definition for ‘plot’
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 plot text title
Consider adding
  importFrom("grDevices", "graphics.off", "gray", "pdf")
  importFrom("graphics", "axis", "barplot", "box", "boxplot", "grid",
             "image", "layout", "legend", "lines", "mtext", "par",
             "plot", "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 or elapsed time > 5s
                 user system elapsed
compGapStats   12.412  0.124  13.245
selTopVarGenes  5.008  0.044   5.060
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-data-experiment/meat/DeSousa2013.Rcheck/00check.log’
for details.



Installation output

DeSousa2013.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL DeSousa2013
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘DeSousa2013’ ...
** 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
* DONE (DeSousa2013)

Tests output


Example timings

DeSousa2013.Rcheck/DeSousa2013-Ex.timings

nameusersystemelapsed
CRCPipeLine000
buildClassifier2.6440.0522.944
compGapStats12.412 0.12413.245
conClust0.6080.0080.655
data-AMC0.0040.0000.020
filterDiffGenes0.8800.0041.058
filterSamples0.1040.0120.122
findDiffGenes0.7120.0160.729
geneExpPre0.0000.0000.001
pamClassify0.1040.0000.108
pbs2unigenes4.4520.0724.699
progAMC0.0680.0000.100
selTopVarGenes5.0080.0445.060