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CHECK report for DFP on merida2

This page was generated on 2018-10-17 08:47:51 -0400 (Wed, 17 Oct 2018).

Package 381/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DFP 1.38.0
Rodrigo Alvarez-Glez
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/DFP
Branch: RELEASE_3_7
Last Commit: 85f30ef
Last Changed Date: 2018-04-30 10:35:09 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DFP
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DFP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DFP_1.38.0.tar.gz
StartedAt: 2018-10-16 20:56:14 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:56:54 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 39.8 seconds
RetCode: 0
Status:  OK 
CheckDir: DFP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DFP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DFP_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/DFP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DFP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DFP’ version ‘1.38.0’
* 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 ‘DFP’ can be installed ... OK
* checking installed package size ... OK
* 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
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDiscriminantFuzzyPattern: warning in matrix(x, nr = ly, nc = lx,
  byrow = TRUE): partial argument match of 'nr' to 'nrow'
plotDiscriminantFuzzyPattern: warning in matrix(x, nr = ly, nc = lx,
  byrow = TRUE): partial argument match of 'nc' to 'ncol'
plotDiscriminantFuzzyPattern: warning in matrix(y, nr = ly, nc = lx):
  partial argument match of 'nr' to 'nrow'
plotDiscriminantFuzzyPattern: warning in matrix(y, nr = ly, nc = lx):
  partial argument match of 'nc' to 'ncol'
.plotGeneMF: no visible global function definition for ‘curve’
.plotGeneMF: no visible binding for global variable ‘x’
.plotGeneMF: no visible global function definition for ‘abline’
.plotGeneMF: no visible global function definition for ‘palette’
.plotGeneMF: no visible global function definition for ‘rainbow’
.plotGeneMF: no visible global function definition for ‘legend’
calculateFuzzyPatterns: no visible global function definition for
  ‘head’
discretizeExpressionValues: no visible global function definition for
  ‘head’
discriminantFuzzyPattern: no visible global function definition for
  ‘head’
plotDiscriminantFuzzyPattern: no visible global function definition for
  ‘image’
plotDiscriminantFuzzyPattern: no visible global function definition for
  ‘par’
plotDiscriminantFuzzyPattern: no visible global function definition for
  ‘axis’
plotDiscriminantFuzzyPattern: no visible global function definition for
  ‘text’
plotMembershipFunctions: no visible global function definition for
  ‘par’
readCSV: no visible global function definition for ‘read.table’
readCSV: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline axis curve head image legend palette par rainbow read.table
  text x
Consider adding
  importFrom("grDevices", "palette", "rainbow")
  importFrom("graphics", "abline", "axis", "curve", "image", "legend",
             "par", "text")
  importFrom("utils", "head", "read.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/DFP.Rcheck/00check.log’
for details.



Installation output

DFP.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DFP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘DFP’ ...
** 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
* DONE (DFP)

Tests output


Example timings

DFP.Rcheck/DFP-Ex.timings

nameusersystemelapsed
DFP-package1.5450.0961.655
ExpressionLevel-class0.0010.0010.002
HighExpressionLevel-class0.0020.0000.002
LowExpressionLevel-class0.0010.0010.001
MediumExpressionLevel-class0.0020.0000.001
discriminantFuzzyPattern1.3890.0201.425
readCSV0.1220.0030.129
rmadataset0.0100.0030.014