BioC 2.14: CHECK report for compcodeR on morelia

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 22:08:44 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:13:21 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 276.6 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.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 --no-multiarch compcodeR_1.0.0.tar.gz
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* 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-darwin13.1.0 (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 ... [6s/6s] 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 ... [177s/192s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   54.726  2.706  64.996
DESeq.GLM.createRmd      18.855  1.285  20.329
show-compData-method     11.630  2.754  14.406
convertcompDataToList    10.596  2.901  14.380
EBSeq.createRmd          10.039  0.372  10.986
baySeq.createRmd          8.230  0.620  10.042
DESeq2.createRmd          6.769  0.812   8.743
NOISeq.prenorm.createRmd  5.448  0.485   6.361
HTSDiff.createRmd         3.356  0.528   5.483
* 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	18.855	1.285	20.329
DESeq.nbinom.createRmd	54.726	2.706	64.996
DESeq2.createRmd	6.769	0.812	8.743
DSS.createRmd	1.741	0.165	1.909
EBSeq.createRmd	10.039	0.372	10.986
HTSDiff.createRmd	3.356	0.528	5.483
NBPSeq.createRmd	0.897	0.096	1.149
NOISeq.prenorm.createRmd	5.448	0.485	6.361
SAMseq.createRmd	1.954	0.187	2.138
TCC.createRmd	2.952	0.210	3.140
baySeq.createRmd	8.230	0.620	10.042
checkDataObject	0.457	0.059	0.510
checkTableConsistency	1.730	0.150	2.812
check_compData	0.454	0.057	0.507
check_compData_results	0.981	0.091	1.063
compData	0.004	0.000	0.005
convertListTocompData	0.007	0.001	0.008
convertcompDataToList	10.596	2.901	14.380
edgeR.GLM.createRmd	2.199	0.164	2.345
edgeR.exact.createRmd	1.063	0.102	1.175
generateCodeHTMLs	1.088	0.108	1.204
generateSyntheticData	0.447	0.055	0.497
listcreateRmd	0.012	0.000	0.013
logcpm.limma.createRmd	0.807	0.084	0.885
runComparison	3.769	0.306	4.091
runComparisonGUI	0.001	0.000	0.001
runDiffExp	1.087	0.106	1.182
show-compData-method	11.630	2.754	14.406
sqrtcpm.limma.createRmd	0.863	0.083	0.944
summarizeSyntheticDataSet	2.120	0.152	2.323
ttest.createRmd	0.795	0.087	0.873
voom.limma.createRmd	1.031	0.096	1.115
voom.ttest.createRmd	0.853	0.090	0.933
vst.limma.createRmd	1.146	0.092	1.229
vst.ttest.createRmd	1.118	0.094	1.215