Package: Mfuzz

Version: 2.44.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mfuzz.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Mfuzz_2.44.0.tar.gz

StartedAt: 2019-10-16 05:10:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:11:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 63.8 seconds

RetCode: 0

Status:  OK

CheckDir: Mfuzz.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mfuzz.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Mfuzz_2.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Mfuzz.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
kmeans2.plot: no visible global function definition for 'X11'
mfuzz: no visible global function definition for 'cmeans'
mfuzz.plot: no visible global function definition for 'X11'
mfuzz.plot2: no visible global function definition for 'rgb'
mfuzz.plot2: no visible global function definition for 'X11'
mfuzzColorBar: no visible global function definition for 'rgb'
mfuzzColorBar: no visible global function definition for 'maColorBar'
Undefined global functions or variables:
  X11 cmeans maColorBar rgb
Consider adding
  importFrom("grDevices", "X11", "rgb")
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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Mfuzz.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Mfuzz_2.44.0.tar.gz && rm -rf Mfuzz.buildbin-libdir && mkdir Mfuzz.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Mfuzz.buildbin-libdir Mfuzz_2.44.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Mfuzz_2.44.0.zip && rm Mfuzz_2.44.0.tar.gz Mfuzz_2.44.0.zip
###
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install for i386

* installing *source* package 'Mfuzz' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Mfuzz'
    finding HTML links ... done
    Dmin                                    html  
    Mfuzzgui                                html  
    acore                                   html  
    cselection                              html  
    fill.NA                                 html  
    filter.NA                               html  
    filter.std                              html  
    kmeans2                                 html  
    kmeans2.plot                            html  
    membership                              html  
    mestimate                               html  
    mfuzz                                   html  
    mfuzz.plot                              html  
    mfuzz.plot2                             html  
    mfuzzColorBar                           html  
    overlap                                 html  
    overlap.plot                            html  
    partcoef                                html  
    randomise                               html  
    standardise                             html  
    standardise2                            html  
    table2eset                              html  
    top.count                               html  
    yeast                                   html  
    yeast.table                             html  
    yeast.table2                            html  
** 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

install for x64

* installing *source* package 'Mfuzz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Mfuzz' as Mfuzz_2.44.0.zip
* DONE (Mfuzz)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Mfuzz' successfully unpacked and MD5 sums checked