BioC experimental data: CHECK report for DeSousa2013 on morelia

Package: DeSousa2013

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DeSousa2013_1.7.0.tar.gz

StartedAt: 2015-11-25 10:22:45 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 10:29:59 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 433.6 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/DeSousa2013.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.0’
* 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 ... [15s/33s] 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’
Undefined global functions or variables:
  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 ... [38s/82s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
compGapStats    11.925  0.438  15.804
pbs2unigenes     5.822  0.591  31.959
selTopVarGenes   5.430  0.200   5.966
buildClassifier  3.278  0.159   5.882
* 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-3.3-data-experiment/meat/DeSousa2013.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
CRCPipeLine	0.001	0.000	0.001
buildClassifier	3.278	0.159	5.882
compGapStats	11.925	0.438	15.804
conClust	1.045	0.073	3.937
data-AMC	0.003	0.000	0.154
filterDiffGenes	1.406	0.019	2.239
filterSamples	0.103	0.011	0.352
findDiffGenes	0.787	0.068	0.856
geneExpPre	0	0	0
pamClassify	0.104	0.009	0.287
pbs2unigenes	5.822	0.591	31.959
progAMC	0.079	0.004	1.596
selTopVarGenes	5.430	0.200	5.966