BioC 2.14: CHECK report for compcodeR on petty

Package: compcodeR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch compcodeR_1.0.0.tar.gz

StartedAt: 2014-10-07 21:28:53 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:37:02 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 489.6 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch compcodeR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/compcodeR.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 ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rpanel’
* 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 ‘compcodeR’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [312s/342s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   98.053  5.511 108.794
DESeq.GLM.createRmd      30.834  1.999  33.376
show-compData-method     20.066  6.130  28.412
convertcompDataToList    19.263  6.318  29.771
EBSeq.createRmd          18.424  0.648  23.463
DESeq2.createRmd         11.407  1.296  13.916
baySeq.createRmd         10.851  0.724  12.184
NOISeq.prenorm.createRmd  9.719  0.846  13.621
runComparison             6.741  0.541   9.102
HTSDiff.createRmd         5.226  0.761   6.858
TCC.createRmd             5.297  0.350   6.529
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/compcodeR.Rcheck/00check.log’
for details.

* installing *source* package ‘compcodeR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (compcodeR)

name	user	system	elapsed
DESeq.GLM.createRmd	30.834	1.999	33.376
DESeq.nbinom.createRmd	98.053	5.511	108.794
DESeq2.createRmd	11.407	1.296	13.916
DSS.createRmd	3.585	0.285	4.771
EBSeq.createRmd	18.424	0.648	23.463
HTSDiff.createRmd	5.226	0.761	6.858
NBPSeq.createRmd	1.611	0.176	2.441
NOISeq.prenorm.createRmd	9.719	0.846	13.621
SAMseq.createRmd	3.982	0.348	4.441
TCC.createRmd	5.297	0.350	6.529
baySeq.createRmd	10.851	0.724	12.184
checkDataObject	0.851	0.089	0.941
checkTableConsistency	3.028	0.229	3.434
check_compData	0.835	0.076	0.917
check_compData_results	1.908	0.169	2.092
compData	0.008	0.001	0.009
convertListTocompData	0.013	0.001	0.014
convertcompDataToList	19.263	6.318	29.771
edgeR.GLM.createRmd	3.476	0.268	4.826
edgeR.exact.createRmd	1.941	0.143	2.110
generateCodeHTMLs	1.971	0.179	2.220
generateSyntheticData	0.854	0.085	0.955
listcreateRmd	0.03	0.00	0.03
logcpm.limma.createRmd	1.586	0.144	1.765
runComparison	6.741	0.541	9.102
runComparisonGUI	0.002	0.000	0.002
runDiffExp	2.445	0.178	2.722
show-compData-method	20.066	6.130	28.412
sqrtcpm.limma.createRmd	1.532	0.144	1.694
summarizeSyntheticDataSet	3.268	0.249	3.677
ttest.createRmd	1.549	0.127	1.667
voom.limma.createRmd	2.319	0.151	2.469
voom.ttest.createRmd	1.617	0.158	3.575
vst.limma.createRmd	2.210	0.173	2.432
vst.ttest.createRmd	2.104	0.186	2.405