BioC 3.2: CHECK report for compcodeR on oaxaca

Package: compcodeR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compcodeR_1.6.0.tar.gz

StartedAt: 2016-04-22 23:03:30 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 23:07:57 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 266.1 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/compcodeR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.6.0’
* 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 ... [205s/211s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   54.133  2.783  56.972
NBPSeq.createRmd         35.510  2.382  39.434
DESeq.GLM.createRmd      14.777  1.115  15.767
convertcompDataToList     9.333  6.135  15.393
show-compData-method      9.857  5.486  15.268
EBSeq.createRmd           9.926  0.480  14.084
baySeq.createRmd          7.656  0.601   8.178
DESeq2.createRmd          7.371  0.795   8.118
NOISeq.prenorm.createRmd  5.920  0.555   6.400
* 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-3.2-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	14.777	1.115	15.767
DESeq.nbinom.createRmd	54.133	2.783	56.972
DESeq2.createRmd	7.371	0.795	8.118
DSS.createRmd	2.107	0.179	2.550
EBSeq.createRmd	9.926	0.480	14.084
NBPSeq.createRmd	35.510	2.382	39.434
NOISeq.prenorm.createRmd	5.920	0.555	6.400
SAMseq.createRmd	1.707	0.216	1.956
TCC.createRmd	2.584	0.208	2.982
baySeq.createRmd	7.656	0.601	8.178
checkDataObject	0.407	0.067	0.469
checkTableConsistency	1.355	0.133	1.475
check_compData	0.779	0.059	0.833
check_compData_results	0.896	0.097	1.387
compData	0.004	0.000	0.004
convertListTocompData	0.008	0.001	0.008
convertcompDataToList	9.333	6.135	15.393
edgeR.GLM.createRmd	1.519	0.133	1.636
edgeR.exact.createRmd	0.880	0.084	0.955
generateCodeHTMLs	0.899	0.103	1.059
generateSyntheticData	0.401	0.050	0.445
listcreateRmd	0.01	0.00	0.01
logcpm.limma.createRmd	0.617	0.075	0.686
runComparison	3.580	0.311	3.932
runComparisonGUI	0.001	0.000	0.001
runDiffExp	1.311	0.103	1.403
show-compData-method	9.857	5.486	15.268
sqrtcpm.limma.createRmd	0.670	0.077	0.746
summarizeSyntheticDataSet	2.192	0.187	2.407
ttest.createRmd	0.738	0.079	0.816
voom.limma.createRmd	0.863	0.082	0.936
voom.ttest.createRmd	0.746	0.078	0.821
vst.limma.createRmd	0.971	0.086	1.050
vst.ttest.createRmd	0.916	0.077	0.986