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: 2015-10-27 02:35:52 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:40:24 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 272.1 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 3.2.2 (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 ‘1.6.0’
* 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 ... [5s/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 ... 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 ... [204s/208s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   51.902  2.912  54.987
NBPSeq.createRmd         34.049  2.328  38.263
show-compData-method     10.636  5.373  15.956
convertcompDataToList     9.851  5.311  15.094
DESeq.GLM.createRmd      13.013  0.794  14.234
EBSeq.createRmd          10.601  0.560  11.231
baySeq.createRmd          8.678  0.698   9.295
DESeq2.createRmd          7.852  0.865   9.482
NOISeq.prenorm.createRmd  6.181  0.571   7.947
* 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	13.013	0.794	14.234
DESeq.nbinom.createRmd	51.902	2.912	54.987
DESeq2.createRmd	7.852	0.865	9.482
DSS.createRmd	2.476	0.222	2.944
EBSeq.createRmd	10.601	0.560	11.231
NBPSeq.createRmd	34.049	2.328	38.263
NOISeq.prenorm.createRmd	6.181	0.571	7.947
SAMseq.createRmd	1.766	0.227	2.062
TCC.createRmd	3.074	0.228	3.511
baySeq.createRmd	8.678	0.698	9.295
checkDataObject	0.415	0.067	0.478
checkTableConsistency	1.428	0.150	1.571
check_compData	0.407	0.053	0.461
check_compData_results	0.897	0.105	0.993
compData	0.005	0.001	0.005
convertListTocompData	0.008	0.001	0.007
convertcompDataToList	9.851	5.311	15.094
edgeR.GLM.createRmd	1.763	0.170	1.919
edgeR.exact.createRmd	0.923	0.096	1.013
generateCodeHTMLs	0.934	0.106	1.071
generateSyntheticData	0.436	0.066	0.497
listcreateRmd	0.011	0.000	0.012
logcpm.limma.createRmd	0.689	0.084	0.766
runComparison	3.422	0.308	3.795
runComparisonGUI	0.001	0.000	0.001
runDiffExp	0.922	0.100	1.013
show-compData-method	10.636	5.373	15.956
sqrtcpm.limma.createRmd	0.683	0.085	0.761
summarizeSyntheticDataSet	1.939	0.169	2.122
ttest.createRmd	0.715	0.078	0.791
voom.limma.createRmd	0.915	0.102	1.014
voom.ttest.createRmd	0.760	0.092	0.861
vst.limma.createRmd	1.036	0.094	1.130
vst.ttest.createRmd	0.999	0.096	1.108