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This page was generated on 2021-12-06 13:05:55 -0500 (Mon, 06 Dec 2021).

CHECK results for DFP on machv2

To the developers/maintainers of the DFP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DFP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 501/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DFP 1.52.0  (landing page)
Rodrigo Alvarez-Glez
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/DFP
git_branch: RELEASE_3_14
git_last_commit: 7cc849a
git_last_commit_date: 2021-10-26 11:52:46 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DFP
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DFP_1.52.0.tar.gz
StartedAt: 2021-12-05 13:52:12 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 13:52:59 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 46.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DFP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DFP_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/DFP.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.52.0’
* 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-3.14-bioc/meat/DFP.Rcheck/00check.log’
for details.



Installation output

DFP.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DFP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘DFP’ ...
** 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 (DFP)

Tests output


Example timings

DFP.Rcheck/DFP-Ex.timings

nameusersystemelapsed
DFP-package1.7320.0961.832
ExpressionLevel-class0.0020.0010.002
HighExpressionLevel-class0.0000.0010.001
LowExpressionLevel-class0.0010.0010.001
MediumExpressionLevel-class0.0010.0010.001
discriminantFuzzyPattern1.6360.0231.664
readCSV0.1220.0040.128
rmadataset0.0190.0030.023