BioC experimental data: CHECK report for DeSousa2013 on petty

Package: DeSousa2013

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeSousa2013_1.4.0.tar.gz

StartedAt: 2015-10-07 09:13:38 -0700 (Wed, 07 Oct 2015)

EndedAt: 2015-10-07 09:19:31 -0700 (Wed, 07 Oct 2015)

EllapsedTime: 353.1 seconds

RetCode: 0

Status:  OK

CheckDir: DeSousa2013.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeSousa2013_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-data-experiment/meat/DeSousa2013.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 ‘DeSousa2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeSousa2013’ version ‘1.4.0’
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pbs2unigenes: no visible global function definition for ‘mappedkeys’
* 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 ... [58s/69s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
compGapStats    21.792  0.688  25.648
pbs2unigenes     7.175  0.857  11.471
selTopVarGenes   7.159  0.185   7.345
buildClassifier  4.874  0.170   5.755
* 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-3.1-data-experiment/meat/DeSousa2013.Rcheck/00check.log’
for details.

* installing *source* package ‘DeSousa2013’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (DeSousa2013)

name	user	system	elapsed
CRCPipeLine	0	0	0
buildClassifier	4.874	0.170	5.755
compGapStats	21.792	0.688	25.648
conClust	1.20	0.06	2.57
data-AMC	0.003	0.001	0.023
filterDiffGenes	1.895	0.015	2.356
filterSamples	0.295	0.019	0.384
findDiffGenes	1.469	0.140	1.667
geneExpPre	0.001	0.000	0.000
pamClassify	0.164	0.017	0.284
pbs2unigenes	7.175	0.857	11.471
progAMC	0.122	0.005	0.684
selTopVarGenes	7.159	0.185	7.345