Package: Mfuzz

Version: 2.44.0

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_2.44.0.tar.gz

StartedAt: 2019-10-16 04:34:54 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:36:10 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 75.8 seconds

RetCode: 0

Status:  OK

CheckDir: Mfuzz.Rcheck

Warnings: 0

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### Running command:
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###   /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_2.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Mfuzz.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mfuzz/DESCRIPTION’ ... OK
* this is package ‘Mfuzz’ version ‘2.44.0’
* 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’
Dmin: no visible global function definition for ‘plot’
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 ‘plot’
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’
filter.std: no visible global function definition for ‘plot’
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 ‘plot’
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 plot.default points prcomp rgb sd text write.exprs
Consider adding
  importFrom("grDevices", "X11", "rgb")
  importFrom("graphics", "axis", "lines", "par", "plot", "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-3.9-bioc/meat/Mfuzz.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Mfuzz
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

name	user	system	elapsed
Dmin	0.003	0.001	0.004
acore	0.002	0.000	0.002
cselection	0.004	0.001	0.004
fill.NA	0.001	0.001	0.001
filter.NA	0.001	0.000	0.001
filter.std	0.764	0.639	1.388
kmeans2	0.001	0.000	0.001
kmeans2.plot	0.001	0.001	0.001
membership	0.002	0.001	0.003
mestimate	0.002	0.001	0.003
mfuzz	0.003	0.000	0.003
mfuzz.plot	0.003	0.000	0.003
mfuzz.plot2	0.015	0.001	0.016
mfuzzColorBar	0.001	0.000	0.001
overlap	0.002	0.000	0.003
overlap.plot	0.005	0.000	0.005
partcoef	0.005	0.001	0.005
randomise	0.111	0.030	0.140
standardise	0.001	0.001	0.002
standardise2	0.001	0.000	0.002
top.count	0.002	0.000	0.002