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BioC experimental data: CHECK report for DeSousa2013 on petty

This page was generated on 2014-10-04 17:43:38 -0700 (Sat, 04 Oct 2014).

Package 52/197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DeSousa2013 1.0.0
Xin Wang
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/DeSousa2013
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: DeSousa2013
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DeSousa2013_1.0.0.tar.gz
StartedAt: 2014-10-04 09:05:36 -0700 (Sat, 04 Oct 2014)
EndedAt: 2014-10-04 09:11:33 -0700 (Sat, 04 Oct 2014)
EllapsedTime: 356.6 seconds
RetCode: 0
Status:  OK 
CheckDir: DeSousa2013.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 --no-multiarch DeSousa2013_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-data-experiment/meat/DeSousa2013.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeSousa2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeSousa2013’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DeSousa2013’ can be installed ... [20s/22s] OK
* checking installed package size ... NOTE
  installed size is 44.7Mb
  sub-directories of 1Mb or more:
    data  43.7Mb
* 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
Namespaces in Imports field not imported from:
  ‘frmaTools’ ‘hgu133plus2frmavecs’ ‘rgl’
  All declared Imports should be used.
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [64s/70s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
compGapStats    23.983  0.688  25.873
selTopVarGenes   8.933  0.222   9.156
pbs2unigenes     7.488  1.009  10.082
buildClassifier  6.125  0.155   6.839
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-data-experiment/meat/DeSousa2013.Rcheck/00check.log’
for details.

DeSousa2013.Rcheck/00install.out:

* installing *source* package ‘DeSousa2013’ ...
** 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 (DeSousa2013)

DeSousa2013.Rcheck/DeSousa2013-Ex.timings:

nameusersystemelapsed
CRCPipeLine0.0010.0000.000
buildClassifier6.1250.1556.839
compGapStats23.983 0.68825.873
conClust1.2690.0742.433
data-AMC0.0050.0020.062
filterDiffGenes2.4630.0242.666
filterSamples0.3220.0200.357
findDiffGenes1.2670.1051.463
geneExpPre0.0000.0000.001
pamClassify0.1860.0250.260
pbs2unigenes 7.488 1.00910.082
progAMC0.1820.0070.238
selTopVarGenes8.9330.2229.156