BioC 3.1: CHECK report for compcodeR on morelia

Package: compcodeR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compcodeR_1.4.0.tar.gz

StartedAt: 2015-10-09 00:37:41 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:41:30 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 229.1 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 compcodeR_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/compcodeR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* 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 ... [4s/5s] 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 ... NOTE
'library' or 'require' call to ‘rpanel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... [166s/171s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   47.441  4.578  52.152
DESeq.GLM.createRmd      13.408  1.326  15.049
convertcompDataToList    10.009  4.008  13.972
show-compData-method      9.980  3.941  13.848
baySeq.createRmd         12.598  1.312  13.981
EBSeq.createRmd          10.168  0.835  11.115
NOISeq.prenorm.createRmd  7.622  0.929   8.624
DESeq2.createRmd          6.484  0.974   8.097
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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	13.408	1.326	15.049
DESeq.nbinom.createRmd	47.441	4.578	52.152
DESeq2.createRmd	6.484	0.974	8.097
DSS.createRmd	1.775	0.207	2.132
EBSeq.createRmd	10.168	0.835	11.115
NBPSeq.createRmd	0.715	0.101	0.875
NOISeq.prenorm.createRmd	7.622	0.929	8.624
SAMseq.createRmd	1.484	0.182	3.240
TCC.createRmd	2.456	0.252	3.023
baySeq.createRmd	12.598	1.312	13.981
checkDataObject	0.414	0.074	0.482
checkTableConsistency	1.421	0.175	1.593
check_compData	0.444	0.052	0.491
check_compData_results	0.904	0.097	0.991
compData	0.003	0.000	0.004
convertListTocompData	0.004	0.001	0.005
convertcompDataToList	10.009	4.008	13.972
edgeR.GLM.createRmd	1.688	0.200	1.871
edgeR.exact.createRmd	0.952	0.102	1.057
generateCodeHTMLs	0.963	0.107	1.166
generateSyntheticData	0.420	0.041	0.456
listcreateRmd	0.011	0.000	0.011
logcpm.limma.createRmd	0.734	0.101	0.827
runComparison	3.224	0.382	4.517
runComparisonGUI	0.001	0.000	0.001
runDiffExp	0.944	0.102	1.042
show-compData-method	9.980	3.941	13.848
sqrtcpm.limma.createRmd	0.723	0.105	0.821
summarizeSyntheticDataSet	2.150	0.246	2.679
ttest.createRmd	0.736	0.116	0.932
voom.limma.createRmd	0.908	0.127	1.028
voom.ttest.createRmd	0.699	0.095	0.801
vst.limma.createRmd	1.008	0.129	1.131
vst.ttest.createRmd	0.945	0.102	1.039