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BioC experimental data: CHECK report for Hiiragi2013 on moscato1

This page was generated on 2015-04-08 17:41:11 -0700 (Wed, 08 Apr 2015).

Package 113/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Hiiragi2013 1.1.3
Andrzej Oles
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/Hiiragi2013
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Hiiragi2013
Version: 1.1.3
Command: rm -rf Hiiragi2013.buildbin-libdir Hiiragi2013.Rcheck && mkdir Hiiragi2013.buildbin-libdir Hiiragi2013.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Hiiragi2013.buildbin-libdir Hiiragi2013_1.1.3.tar.gz >Hiiragi2013.Rcheck\00install.out 2>&1 && cp Hiiragi2013.Rcheck\00install.out Hiiragi2013-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Hiiragi2013.buildbin-libdir --install="check:Hiiragi2013-install.out" --force-multiarch --no-vignettes --timings Hiiragi2013_1.1.3.tar.gz
StartedAt: 2015-04-08 10:43:41 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 10:54:51 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 670.2 seconds
RetCode: 0
Status:  OK  
CheckDir: Hiiragi2013.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf Hiiragi2013.buildbin-libdir Hiiragi2013.Rcheck && mkdir Hiiragi2013.buildbin-libdir Hiiragi2013.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Hiiragi2013.buildbin-libdir Hiiragi2013_1.1.3.tar.gz >Hiiragi2013.Rcheck\00install.out 2>&1 && cp Hiiragi2013.Rcheck\00install.out Hiiragi2013-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Hiiragi2013.buildbin-libdir --install="check:Hiiragi2013-install.out" --force-multiarch --no-vignettes --timings Hiiragi2013_1.1.3.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-data-experiment/meat/Hiiragi2013.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.1.3'
* 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 138.3Mb
  sub-directories of 1Mb or more:
    data  136.3Mb
    doc     1.9Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* 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' ... [133s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
a                             21.94   0.67   62.16
MDSplot                        4.65   0.11   42.43
getDifferentialExpressedGenes  4.39   0.12    7.22
** running examples for arch 'x64' ... [59s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
a                             16.02   0.50   16.88
MDSplot                        5.21   0.08   10.45
getDifferentialExpressedGenes  4.14   0.22    6.98
myHeatmap                      3.91   0.06    7.70
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-data-experiment/meat/Hiiragi2013.Rcheck/00check.log'
for details.

Hiiragi2013.Rcheck/00install.out:


install for i386

* installing *source* package 'Hiiragi2013' ...
** 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 'Hiiragi2013' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Hiiragi2013' as Hiiragi2013_1.1.3.zip
* DONE (Hiiragi2013)

Hiiragi2013.Rcheck/examples_i386/Hiiragi2013-Ex.timings:

nameusersystemelapsed
MDSplot 4.65 0.1142.43
a21.94 0.6762.16
getDifferentialExpressedGenes4.390.127.22
myHeatmap4.230.054.27
myHeatmap2000
pamCluster3.680.034.58
plotProjection000
x3.560.013.58
xq0.020.000.01
xql0.000.020.02

Hiiragi2013.Rcheck/examples_x64/Hiiragi2013-Ex.timings:

nameusersystemelapsed
MDSplot 5.21 0.0810.45
a16.02 0.5016.88
getDifferentialExpressedGenes4.140.226.98
myHeatmap3.910.067.70
myHeatmap2000
pamCluster3.520.034.41
plotProjection000
x3.310.023.33
xq0.020.020.03
xql0.010.000.01