Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).

CHECK results for Mfuzz on nebbiolo1

To the developers/maintainers of the Mfuzz package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Mfuzz.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 1120/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mfuzz 2.52.0  (landing page)
Matthias Futschik
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Mfuzz
git_branch: RELEASE_3_13
git_last_commit: 91496e8
git_last_commit_date: 2021-05-19 11:37:02 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: Mfuzz
Version: 2.52.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Mfuzz.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Mfuzz_2.52.0.tar.gz
StartedAt: 2021-10-14 10:34:49 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:35:21 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 32.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Mfuzz.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Mfuzz.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Mfuzz_2.52.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Mfuzz.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mfuzz/DESCRIPTION’ ... OK
* this is package ‘Mfuzz’ version ‘2.52.0’
* 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 ‘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 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/Mfuzz.Rcheck/00check.log’
for details.



Installation output

Mfuzz.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Mfuzz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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
Dmin0.0000.0000.001
acore000
cselection0.0010.0000.001
fill.NA0.0000.0010.001
filter.NA0.0000.0010.001
filter.std0.2640.0920.333
kmeans20.0000.0010.000
kmeans2.plot0.0000.0010.000
membership0.0000.0010.000
mestimate0.0000.0010.000
mfuzz0.0000.0010.001
mfuzz.plot0.0000.0000.001
mfuzz.plot20.0000.0020.003
mfuzzColorBar0.0000.0000.001
overlap0.0000.0010.001
overlap.plot0.0000.0010.001
partcoef0.0000.0010.001
randomise0.0460.0020.046
standardise000
standardise2000
top.count000