BioC 3.3: CHECK report for compcodeR on morelia

Package: compcodeR

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compcodeR_1.7.1.tar.gz

StartedAt: 2015-10-22 04:49:42 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 04:53:07 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 205.1 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_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/compcodeR.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.7.1’
* 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 ... [3s/4s] 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 ... [152s/153s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   43.756  2.289  46.212
NBPSeq.createRmd         28.775  1.930  30.933
convertcompDataToList     7.105  3.422  10.508
show-compData-method      7.072  3.215  10.271
DESeq.GLM.createRmd       9.325  0.670  10.043
EBSeq.createRmd           7.083  0.512   7.783
baySeq.createRmd          5.327  0.480   5.861
NOISeq.prenorm.createRmd  5.096  0.527   5.573
* 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-3.3-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	9.325	0.670	10.043
DESeq.nbinom.createRmd	43.756	2.289	46.212
DESeq2.createRmd	4.359	0.492	4.833
DSS.createRmd	1.449	0.118	1.728
EBSeq.createRmd	7.083	0.512	7.783
NBPSeq.createRmd	28.775	1.930	30.933
NOISeq.prenorm.createRmd	5.096	0.527	5.573
SAMseq.createRmd	1.182	0.176	1.423
TCC.createRmd	1.737	0.154	2.130
baySeq.createRmd	5.327	0.480	5.861
checkDataObject	0.267	0.041	0.303
checkTableConsistency	0.980	0.115	1.088
check_compData	0.277	0.034	0.307
check_compData_results	0.600	0.079	0.673
compData	0.002	0.000	0.003
convertListTocompData	0.004	0.001	0.005
convertcompDataToList	7.105	3.422	10.508
edgeR.GLM.createRmd	1.160	0.121	1.270
edgeR.exact.createRmd	0.661	0.069	0.724
generateCodeHTMLs	0.617	0.069	0.712
generateSyntheticData	0.513	0.036	0.547
listcreateRmd	0.008	0.000	0.008
logcpm.limma.createRmd	0.424	0.063	0.484
runComparison	2.040	0.184	2.220
runComparisonGUI	0.001	0.000	0.000
runDiffExp	0.552	0.064	0.612
show-compData-method	7.072	3.215	10.271
sqrtcpm.limma.createRmd	0.461	0.065	0.521
summarizeSyntheticDataSet	1.338	0.132	1.472
ttest.createRmd	0.489	0.064	0.548
voom.limma.createRmd	0.632	0.071	0.698
voom.ttest.createRmd	0.509	0.058	0.561
vst.limma.createRmd	0.723	0.068	0.786
vst.ttest.createRmd	0.673	0.070	0.740