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CHECK report for Hiiragi2013 on riesling1

This page was generated on 2021-01-21 16:01:30 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE Hiiragi2013 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 175/386HostnameOS / ArchINSTALLBUILDCHECK
Hiiragi2013 1.27.0
Andrzej Oles
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/Hiiragi2013
Branch: master
Last Commit: b179cf6
Last Changed Date: 2020-10-27 10:01:36 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: Hiiragi2013
Version: 1.27.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Hiiragi2013.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Hiiragi2013_1.27.0.tar.gz
StartedAt: 2021-01-21 11:27:37 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:30:34 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 177.8 seconds
RetCode: 0
Status:  OK  
CheckDir: Hiiragi2013.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Hiiragi2013.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Hiiragi2013_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/Hiiragi2013.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Hiiragi2013/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Hiiragi2013' version '1.27.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'affy', 'Biobase', 'boot', 'clue', 'cluster', 'genefilter',
  'geneplotter', 'gplots', 'gtools', 'KEGGREST', 'MASS',
  'mouse4302.db', 'RColorBrewer', 'xtable'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'Hiiragi2013' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 136.5Mb
  sub-directories of 1Mb or more:
    data  136.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Packages in Depends field not imported from:
  'KEGGREST' 'affy' 'boot' 'clue' 'geneplotter' 'gtools' 'mouse4302.db'
  'xtable'
  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
MDSplot: no visible global function definition for 'dist'
MDSplot: no visible global function definition for 'par'
MDSplot: no visible global function definition for 'points'
MDSplot: no visible global function definition for 'grey'
MDSplot: no visible global function definition for 'text'
getDifferentialExpressedGenes: no visible global function definition
  for 'quantile'
getDifferentialExpressedGenes: no visible global function definition
  for 'p.adjust'
myHeatmap: no visible global function definition for 'as.dendrogram'
myHeatmap: no visible global function definition for 'hclust'
myHeatmap: no visible global function definition for 'dist'
myHeatmap: no visible global function definition for 'order.dendrogram'
myHeatmap2: no visible global function definition for
  'colorRampPalette'
ordermat : <anonymous>: no visible global function definition for
  'order.dendrogram'
ordermat : <anonymous>: no visible global function definition for
  'as.dendrogram'
ordermat : <anonymous>: no visible global function definition for
  'hclust'
ordermat : <anonymous>: no visible global function definition for
  'dist'
pamCluster: no visible global function definition for 'dist'
Undefined global functions or variables:
  as.dendrogram colorRampPalette dist grey hclust order.dendrogram
  p.adjust par points quantile text
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "par", "points", "text")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "p.adjust", "quantile")
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
Examples with CPU (user + system) or elapsed time > 5s
   user system elapsed
a 10.97    0.3   11.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
  user system elapsed
a 8.81   0.28    9.09
* 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/Hiiragi2013.Rcheck/00check.log'
for details.



Installation output

Hiiragi2013.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/Hiiragi2013_1.27.0.tar.gz && rm -rf Hiiragi2013.buildbin-libdir && mkdir Hiiragi2013.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Hiiragi2013.buildbin-libdir Hiiragi2013_1.27.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Hiiragi2013_1.27.0.zip && rm Hiiragi2013_1.27.0.tar.gz Hiiragi2013_1.27.0.zip
###
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##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 18  136M   18 25.3M    0     0  27.0M      0  0:00:05 --:--:--  0:00:05 27.0M
 69  136M   69 95.4M    0     0  49.3M      0  0:00:02  0:00:01  0:00:01 49.3M
100  136M  100  136M    0     0  58.9M      0  0:00:02  0:00:02 --:--:-- 58.9M

install for i386

* installing *source* package 'Hiiragi2013' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Hiiragi2013'
    finding HTML links ... done
    MDSplot                                 html  
REDIRECT:topic	 MDSplot -> MDSplot.html [ SUCCESS ]
    a                                       html  
REDIRECT:topic	 a -> a.html [ SUCCESS ]
    getDifferentialExpressedGenes           html  
REDIRECT:topic	 getDifferentialExpressedGenes -> getDifferentialExpressedGenes.html [ SUCCESS ]
    myHeatmap                               html  
REDIRECT:topic	 myHeatmap -> myHeatmap.html [ SUCCESS ]
    myHeatmap2                              html  
REDIRECT:topic	 myHeatmap2 -> myHeatmap2.html [ SUCCESS ]
    pamCluster                              html  
REDIRECT:topic	 pamCluster -> pamCluster.html [ SUCCESS ]
    plotProjection                          html  
REDIRECT:topic	 plotProjection -> plotProjection.html [ SUCCESS ]
    x                                       html  
REDIRECT:topic	 x -> x.html [ SUCCESS ]
    xq                                      html  
REDIRECT:topic	 xq -> xq.html [ SUCCESS ]
    xql                                     html  
REDIRECT:topic	 xql -> xql.html [ SUCCESS ]
** 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 'Hiiragi2013' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Hiiragi2013' as Hiiragi2013_1.27.0.zip
* DONE (Hiiragi2013)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'Hiiragi2013' successfully unpacked and MD5 sums checked

Tests output


Example timings

Hiiragi2013.Rcheck/examples_i386/Hiiragi2013-Ex.timings

nameusersystemelapsed
MDSplot3.250.013.27
a10.97 0.3011.26
getDifferentialExpressedGenes2.970.053.01
myHeatmap3.280.203.48
myHeatmap2000
pamCluster2.610.092.71
plotProjection000
x2.620.042.66
xq0.000.010.01
xql000

Hiiragi2013.Rcheck/examples_x64/Hiiragi2013-Ex.timings

nameusersystemelapsed
MDSplot2.780.062.84
a8.810.289.09
getDifferentialExpressedGenes2.390.112.50
myHeatmap2.910.173.08
myHeatmap20.010.000.01
pamCluster2.100.052.14
plotProjection000
x2.040.052.09
xq0.000.020.02
xql000