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BioC experimental data: CHECK report for Hiiragi2013 on moscato2

This page was generated on 2014-10-04 17:42:02 -0700 (Sat, 04 Oct 2014).

Package 105/197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Hiiragi2013 1.0.0
Andrzej Oles
Snapshot Date: 2014-10-04 07:15:22 -0700 (Sat, 04 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_14/experiment/pkgs/Hiiragi2013
Last Changed Rev: 2799 / Revision: 3055
Last Changed Date: 2014-04-11 14:27:08 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Hiiragi2013
Version: 1.0.0
Command: rm -rf Hiiragi2013.buildbin-libdir && mkdir Hiiragi2013.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Hiiragi2013.buildbin-libdir Hiiragi2013_1.0.0.tar.gz >Hiiragi2013-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Hiiragi2013.buildbin-libdir --install="check:Hiiragi2013-install.out" --force-multiarch --no-vignettes --timings Hiiragi2013_1.0.0.tar.gz
StartedAt: 2014-10-04 10:19:40 -0700 (Sat, 04 Oct 2014)
EndedAt: 2014-10-04 10:27:56 -0700 (Sat, 04 Oct 2014)
EllapsedTime: 496.3 seconds
RetCode: 0
Status:  OK  
CheckDir: Hiiragi2013.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf Hiiragi2013.buildbin-libdir && mkdir Hiiragi2013.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Hiiragi2013.buildbin-libdir Hiiragi2013_1.0.0.tar.gz >Hiiragi2013-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Hiiragi2013.buildbin-libdir --install="check:Hiiragi2013-install.out" --force-multiarch --no-vignettes --timings Hiiragi2013_1.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-data-experiment/meat/Hiiragi2013.Rcheck'
* using R version 3.1.1 (2014-07-10)
* 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 '1.0.0'
* 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 138.2Mb
  sub-directories of 1Mb or more:
    data  136.3Mb
    doc     1.8Mb
* 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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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' ... [64s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
a                             24.35   0.67   29.07
MDSplot                        6.38   0.09    6.47
getDifferentialExpressedGenes  4.14   0.03    6.50
** running examples for arch 'x64' ... [74s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
a                             15.46   0.39   15.85
MDSplot                        4.80   0.08   23.79
getDifferentialExpressedGenes  3.90   0.13    6.39
myHeatmap                      3.88   0.09   14.34
* 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.14-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_1.0.0.zip
* DONE (Hiiragi2013)

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

nameusersystemelapsed
MDSplot6.380.096.47
a24.35 0.6729.07
getDifferentialExpressedGenes4.140.036.50
myHeatmap4.720.024.74
myHeatmap2000
pamCluster3.800.013.81
plotProjection000
x3.650.073.71
xq0.020.000.01
xql0.010.000.02

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

nameusersystemelapsed
MDSplot 4.80 0.0823.79
a15.46 0.3915.85
getDifferentialExpressedGenes3.900.136.39
myHeatmap 3.88 0.0914.34
myHeatmap2000
pamCluster3.340.063.40
plotProjection000
x3.040.113.15
xq0.030.000.03
xql0.000.020.02