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BioC 3.4: CHECK report for Mfuzz on moscato1

This page was generated on 2016-09-21 03:41:44 -0700 (Wed, 21 Sep 2016).

Package 741/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mfuzz 2.33.0
Matthias Futschik
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Mfuzz
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Mfuzz
Version: 2.33.0
Command: rm -rf Mfuzz.buildbin-libdir Mfuzz.Rcheck && mkdir Mfuzz.buildbin-libdir Mfuzz.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Mfuzz.buildbin-libdir Mfuzz_2.33.0.tar.gz >Mfuzz.Rcheck\00install.out 2>&1 && cp Mfuzz.Rcheck\00install.out Mfuzz-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Mfuzz.buildbin-libdir --install="check:Mfuzz-install.out" --force-multiarch --no-vignettes --timings Mfuzz_2.33.0.tar.gz
StartedAt: 2016-09-20 12:10:32 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:11:37 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 65.4 seconds
RetCode: 0
Status:  OK  
CheckDir: Mfuzz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Mfuzz.buildbin-libdir Mfuzz.Rcheck && mkdir Mfuzz.buildbin-libdir Mfuzz.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Mfuzz.buildbin-libdir Mfuzz_2.33.0.tar.gz >Mfuzz.Rcheck\00install.out 2>&1 && cp Mfuzz.Rcheck\00install.out Mfuzz-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Mfuzz.buildbin-libdir --install="check:Mfuzz-install.out" --force-multiarch --no-vignettes --timings Mfuzz_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Mfuzz.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.33.0'
* 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 installed files from 'inst/doc' ... 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
  'D:/biocbld/bbs-3.4-bioc/meat/Mfuzz.Rcheck/00check.log'
for details.


Mfuzz.Rcheck/00install.out:


install for i386

* installing *source* package 'Mfuzz' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Mfuzz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Mfuzz' as Mfuzz_2.33.0.zip
* DONE (Mfuzz)

Mfuzz.Rcheck/examples_i386/Mfuzz-Ex.timings:

nameusersystemelapsed
Dmin000
acore000
cselection000
fill.NA000
filter.NA000
filter.std0.310.000.31
kmeans2000
kmeans2.plot000
membership000
mestimate000
mfuzz0.010.000.02
mfuzz.plot000
mfuzz.plot2000
mfuzzColorBar0.020.000.01
overlap000
overlap.plot000
partcoef000
randomise0.050.020.06
standardise000
standardise2000
top.count000

Mfuzz.Rcheck/examples_x64/Mfuzz-Ex.timings:

nameusersystemelapsed
Dmin000
acore000
cselection000
fill.NA000
filter.NA000
filter.std0.570.000.57
kmeans2000
kmeans2.plot000
membership000
mestimate000
mfuzz0.020.000.01
mfuzz.plot000
mfuzz.plot20.020.000.02
mfuzzColorBar000
overlap000
overlap.plot000
partcoef000
randomise0.110.000.11
standardise000
standardise20.020.000.02
top.count000