BioC experimental data: CHECK report for DeSousa2013 on zin1

Package: DeSousa2013

Version: 1.5.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DeSousa2013_1.5.0.tar.gz

StartedAt: 2015-08-22 07:56:42 -0700 (Sat, 22 Aug 2015)

EndedAt: 2015-08-22 08:00:46 -0700 (Sat, 22 Aug 2015)

EllapsedTime: 243.8 seconds

RetCode: 0

Status:  OK

CheckDir: DeSousa2013.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DeSousa2013_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-data-experiment/meat/DeSousa2013.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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 ... [16s/18s] 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 ... [45s/45s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
compGapStats   18.519  0.116  18.707
selTopVarGenes  5.649  0.023   5.692
pbs2unigenes    5.304  0.040   5.598
* 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
  ‘/home/biocbuild/bbs-3.2-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	3.848	0.084	3.954
compGapStats	18.519	0.116	18.707
conClust	0.797	0.008	0.805
data-AMC	0.002	0.000	0.002
filterDiffGenes	1.448	0.000	1.451
filterSamples	0.152	0.000	0.158
findDiffGenes	0.882	0.000	0.925
geneExpPre	0.001	0.000	0.000
pamClassify	0.131	0.000	0.131
pbs2unigenes	5.304	0.040	5.598
progAMC	0.088	0.004	0.238
selTopVarGenes	5.649	0.023	5.692