Back to Multiple platform build/check report for BioC 3.7
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for Mfuzz on tokay2

This page was generated on 2018-10-17 08:32:44 -0400 (Wed, 17 Oct 2018).

Package 897/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mfuzz 2.40.0
Matthias Futschik
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Mfuzz
Branch: RELEASE_3_7
Last Commit: 540462d
Last Changed Date: 2018-04-30 10:35:04 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Mfuzz
Version: 2.40.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mfuzz.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Mfuzz_2.40.0.tar.gz
StartedAt: 2018-10-17 03:18:07 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:19:06 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 58.5 seconds
RetCode: 0
Status:  OK  
CheckDir: Mfuzz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mfuzz.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Mfuzz_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Mfuzz.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.40.0'
* 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-3.7-bioc/meat/Mfuzz.Rcheck/00check.log'
for details.



Installation output

Mfuzz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Mfuzz_2.40.0.tar.gz && rm -rf Mfuzz.buildbin-libdir && mkdir Mfuzz.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Mfuzz.buildbin-libdir Mfuzz_2.40.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Mfuzz_2.40.0.zip && rm Mfuzz_2.40.0.tar.gz Mfuzz_2.40.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  418k  100  418k    0     0  6179k      0 --:--:-- --:--:-- --:--:-- 6856k

install for i386

* installing *source* package 'Mfuzz' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'Mfuzz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Mfuzz' as Mfuzz_2.40.0.zip
* DONE (Mfuzz)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Mfuzz' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

Mfuzz.Rcheck/examples_i386/Mfuzz-Ex.timings

nameusersystemelapsed
Dmin000
acore000
cselection000
fill.NA000
filter.NA000
filter.std0.300.010.32
kmeans2000
kmeans2.plot000
membership000
mestimate000
mfuzz000
mfuzz.plot000
mfuzz.plot20.000.020.02
mfuzzColorBar000
overlap000
overlap.plot000
partcoef0.010.000.01
randomise0.050.000.05
standardise000
standardise2000
top.count000

Mfuzz.Rcheck/examples_x64/Mfuzz-Ex.timings

nameusersystemelapsed
Dmin000
acore0.020.000.02
cselection000
fill.NA000
filter.NA000
filter.std0.410.020.43
kmeans2000
kmeans2.plot000
membership000
mestimate000
mfuzz000
mfuzz.plot000
mfuzz.plot20.010.000.02
mfuzzColorBar000
overlap000
overlap.plot000
partcoef000
randomise0.030.020.05
standardise000
standardise2000
top.count000