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BioC experimental data: CHECK report for Hiiragi2013 on perceval

This page was generated on 2015-08-22 17:44:51 -0700 (Sat, 22 Aug 2015).

Package 126/246HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Hiiragi2013 1.5.1
Andrzej Oles
Snapshot Date: 2015-08-22 06:15:25 -0700 (Sat, 22 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/Hiiragi2013
Last Changed Rev: 3341 / Revision: 3391
Last Changed Date: 2015-06-26 03:33:18 -0700 (Fri, 26 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
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: 1.5.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Hiiragi2013_1.5.1.tar.gz
StartedAt: 2015-08-22 09:27:03 -0700 (Sat, 22 Aug 2015)
EndedAt: 2015-08-22 09:32:26 -0700 (Sat, 22 Aug 2015)
EllapsedTime: 322.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Hiiragi2013.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Hiiragi2013_1.5.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/Hiiragi2013.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Hiiragi2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Hiiragi2013’ version ‘1.5.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Hiiragi2013’ can be installed ... [17s/32s] OK
* checking installed package size ... NOTE
  installed size is 139.3Mb
  sub-directories of 1Mb or more:
    data  136.3Mb
    doc     2.9Mb
* 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
* 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:
  ‘affy’ ‘boot’ ‘clue’ ‘geneplotter’ ‘gtools’ ‘KEGGREST’ ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/60s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
a         18.842  1.157  23.913
MDSplot    4.817  0.271   6.431
myHeatmap  4.012  0.537   5.278
* 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
  ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/Hiiragi2013.Rcheck/00check.log’
for details.


Hiiragi2013.Rcheck/00install.out:

* 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
* DONE (Hiiragi2013)

Hiiragi2013.Rcheck/Hiiragi2013-Ex.timings:

nameusersystemelapsed
MDSplot4.8170.2716.431
a18.842 1.15723.913
getDifferentialExpressedGenes3.6680.2714.841
myHeatmap4.0120.5375.278
myHeatmap20.0040.0000.004
pamCluster3.2500.2694.735
plotProjection0.0000.0000.001
x3.0990.1514.185
xq0.0220.0340.069
xql0.0110.0320.064