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CHECK report for Mfuzz on machv2

This page was generated on 2020-10-17 11:58:57 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Mfuzz PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1071/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mfuzz 2.48.0
Matthias Futschik
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Mfuzz
Branch: RELEASE_3_11
Last Commit: 7f20e30
Last Changed Date: 2020-04-27 14:12:53 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Mfuzz
Version: 2.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mfuzz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mfuzz_2.48.0.tar.gz
StartedAt: 2020-10-17 02:59:29 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:00:32 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 63.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Mfuzz.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mfuzz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mfuzz_2.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Mfuzz.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mfuzz/DESCRIPTION’ ... OK
* this is package ‘Mfuzz’ version ‘2.48.0’
* 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 ‘Mfuzz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ‘marray’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Biobase’ ‘e1071’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Dmin: warning in mfuzz(eset, c = i, m = m): partial argument match of
  'c' to 'centers'
Mfuzzgui : objectBrowser2 : viewEnv: warning in ls(env = env, all =
  TRUE): partial argument match of 'env' to 'envir'
Mfuzzgui : objectBrowser2 : viewEnv: warning in ls(env = env, all =
  TRUE): partial argument match of 'all' to 'all.names'
Dmin: no visible global function definition for ‘dist’
Mfuzzgui : browseObject: no visible global function definition for
  ‘exprs’
Mfuzzgui : browseFile: no visible global function definition for
  ‘exprs’
Mfuzzgui : filter1: no visible global function definition for ‘exprs’
Mfuzzgui : export.eset: no visible global function definition for
  ‘write.exprs’
Mfuzzgui : export.eset: no visible global function definition for
  ‘exprs’
acore: no visible global function definition for ‘exprs’
cselection: no visible global function definition for ‘points’
cselection: no visible global function definition for ‘lines’
fill.NA: no visible global function definition for ‘exprs’
fill.NA: no visible global function definition for ‘median’
fill.NA: no visible global function definition for ‘exprs<-’
filter.NA: no visible global function definition for ‘exprs’
filter.std: no visible global function definition for ‘exprs’
filter.std: no visible global function definition for ‘sd’
kmeans2: no visible global function definition for ‘kmeans’
kmeans2: no visible global function definition for ‘exprs’
kmeans2.plot: no visible global function definition for ‘exprs’
kmeans2.plot: no visible global function definition for ‘X11’
kmeans2.plot: no visible global function definition for ‘par’
kmeans2.plot: no visible global function definition for ‘plot.default’
kmeans2.plot: no visible global function definition for ‘lines’
membership: no visible global function definition for ‘dist’
mestimate: no visible global function definition for ‘exprs’
mfuzz: no visible global function definition for ‘cmeans’
mfuzz: no visible global function definition for ‘exprs’
mfuzz.plot: no visible global function definition for ‘exprs’
mfuzz.plot: no visible global function definition for ‘X11’
mfuzz.plot: no visible global function definition for ‘par’
mfuzz.plot: no visible global function definition for ‘plot.default’
mfuzz.plot: no visible global function definition for ‘axis’
mfuzz.plot: no visible global function definition for ‘lines’
mfuzz.plot2: no visible global function definition for ‘exprs’
mfuzz.plot2: no visible global function definition for ‘rgb’
mfuzz.plot2: no visible global function definition for ‘X11’
mfuzz.plot2: no visible global function definition for ‘par’
mfuzz.plot2: no visible global function definition for ‘plot.default’
mfuzz.plot2: no visible global function definition for ‘axis’
mfuzz.plot2: no visible global function definition for ‘lines’
mfuzzColorBar: no visible global function definition for ‘rgb’
mfuzzColorBar: no visible global function definition for ‘par’
mfuzzColorBar: no visible global function definition for ‘maColorBar’
overlap.plot: no visible global function definition for ‘prcomp’
overlap.plot: no visible global function definition for ‘lines’
overlap.plot: no visible global function definition for ‘points’
overlap.plot: no visible global function definition for ‘text’
randomise: no visible global function definition for ‘exprs’
randomise: no visible global function definition for ‘exprs<-’
standardise: no visible global function definition for ‘exprs’
standardise: no visible global function definition for ‘sd’
standardise: no visible global function definition for ‘exprs<-’
standardise2: no visible global function definition for ‘exprs’
standardise2: no visible global function definition for ‘sd’
standardise2: no visible global function definition for ‘exprs<-’
Undefined global functions or variables:
  X11 axis cmeans dist exprs exprs<- kmeans lines maColorBar median par
  plot.default points prcomp rgb sd text write.exprs
Consider adding
  importFrom("grDevices", "X11", "rgb")
  importFrom("graphics", "axis", "lines", "par", "plot.default",
             "points", "text")
  importFrom("stats", "dist", "kmeans", "median", "prcomp", "sd")
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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/Mfuzz.Rcheck/00check.log’
for details.



Installation output

Mfuzz.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Mfuzz
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Mfuzz’ ...
** 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 (Mfuzz)

Tests output


Example timings

Mfuzz.Rcheck/Mfuzz-Ex.timings

nameusersystemelapsed
Dmin0.0010.0000.002
acore0.0010.0010.002
cselection0.0010.0010.001
fill.NA0.0000.0000.001
filter.NA000
filter.std0.5640.2950.820
kmeans20.0010.0000.001
kmeans2.plot0.0010.0000.002
membership0.0020.0010.003
mestimate0.0010.0010.002
mfuzz0.0010.0000.002
mfuzz.plot0.0020.0010.003
mfuzz.plot20.0120.0010.013
mfuzzColorBar0.0010.0000.001
overlap0.0010.0000.001
overlap.plot0.0010.0010.003
partcoef0.0030.0010.003
randomise0.0950.0160.110
standardise0.0010.0010.002
standardise20.0020.0010.001
top.count0.0010.0000.002