BioC 3.1: CHECK report for compcodeR on petty

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: 2015-10-08 22:16:13 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:22:27 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 374.1 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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [7s/7s] 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 ... [273s/289s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   86.336  4.925  94.769
show-compData-method     17.022  7.207  24.053
convertcompDataToList    16.678  7.464  24.841
DESeq.GLM.createRmd      20.465  1.498  21.734
EBSeq.createRmd          17.390  1.025  21.255
baySeq.createRmd         16.145  1.138  18.409
NOISeq.prenorm.createRmd 12.509  1.097  14.728
DESeq2.createRmd         10.362  1.277  14.872
runComparison             5.182  0.431   5.664
TCC.createRmd             4.847  0.298   5.518
* 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	20.465	1.498	21.734
DESeq.nbinom.createRmd	86.336	4.925	94.769
DESeq2.createRmd	10.362	1.277	14.872
DSS.createRmd	3.132	0.276	3.510
EBSeq.createRmd	17.390	1.025	21.255
NBPSeq.createRmd	1.225	0.133	1.389
NOISeq.prenorm.createRmd	12.509	1.097	14.728
SAMseq.createRmd	3.058	0.332	3.435
TCC.createRmd	4.847	0.298	5.518
baySeq.createRmd	16.145	1.138	18.409
checkDataObject	0.712	0.087	2.158
checkTableConsistency	2.340	0.210	2.521
check_compData	0.680	0.079	0.746
check_compData_results	1.469	0.141	1.587
compData	0.007	0.001	0.008
convertListTocompData	0.011	0.001	0.012
convertcompDataToList	16.678	7.464	24.841
edgeR.GLM.createRmd	2.831	0.271	3.060
edgeR.exact.createRmd	1.587	0.159	1.729
generateCodeHTMLs	1.501	0.148	1.629
generateSyntheticData	0.714	0.095	0.794
listcreateRmd	0.030	0.001	0.030
logcpm.limma.createRmd	1.201	0.147	1.328
runComparison	5.182	0.431	5.664
runComparisonGUI	0.001	0.000	0.002
runDiffExp	1.608	0.145	1.733
show-compData-method	17.022	7.207	24.053
sqrtcpm.limma.createRmd	1.186	0.118	1.285
summarizeSyntheticDataSet	3.028	0.257	3.293
ttest.createRmd	1.174	0.130	1.287
voom.limma.createRmd	1.493	0.138	1.609
voom.ttest.createRmd	1.807	0.132	1.925
vst.limma.createRmd	1.682	0.152	2.321
vst.ttest.createRmd	1.283	0.128	2.511