BioC 3.2: CHECK report for compcodeR on perceval

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: 2015-11-10 03:36:56 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 03:42:10 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 314.3 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 Patched (2015-10-08 r69496)
* 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 ‘1.6.0’
* 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/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 ... [246s/251s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   71.688  3.532  75.276
NBPSeq.createRmd         46.819  3.116  50.012
show-compData-method     10.897  5.231  16.567
convertcompDataToList    10.649  5.411  16.527
DESeq.GLM.createRmd      13.587  1.095  15.469
EBSeq.createRmd          12.526  1.001  13.684
DESeq2.createRmd          8.044  1.004   9.513
baySeq.createRmd          7.374  0.650   8.445
NOISeq.prenorm.createRmd  7.090  0.771   8.115
* 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	13.587	1.095	15.469
DESeq.nbinom.createRmd	71.688	3.532	75.276
DESeq2.createRmd	8.044	1.004	9.513
DSS.createRmd	2.368	0.223	2.865
EBSeq.createRmd	12.526	1.001	13.684
NBPSeq.createRmd	46.819	3.116	50.012
NOISeq.prenorm.createRmd	7.090	0.771	8.115
SAMseq.createRmd	2.048	0.294	2.474
TCC.createRmd	3.970	0.260	4.434
baySeq.createRmd	7.374	0.650	8.445
checkDataObject	0.902	0.107	1.024
checkTableConsistency	1.556	0.185	1.786
check_compData	0.414	0.068	0.495
check_compData_results	0.970	0.129	1.132
compData	0.004	0.001	0.005
convertListTocompData	0.007	0.001	0.007
convertcompDataToList	10.649	5.411	16.527
edgeR.GLM.createRmd	1.808	0.169	2.048
edgeR.exact.createRmd	1.073	0.127	1.230
generateCodeHTMLs	1.012	0.127	1.222
generateSyntheticData	0.444	0.070	0.540
listcreateRmd	0.022	0.001	0.023
logcpm.limma.createRmd	0.785	0.096	0.913
runComparison	3.413	0.339	4.010
runComparisonGUI	0.000	0.000	0.001
runDiffExp	1.464	0.122	1.651
show-compData-method	10.897	5.231	16.567
sqrtcpm.limma.createRmd	0.774	0.089	0.911
summarizeSyntheticDataSet	2.000	0.189	2.352
ttest.createRmd	0.807	0.097	0.932
voom.limma.createRmd	0.994	0.110	1.129
voom.ttest.createRmd	0.836	0.081	0.939
vst.limma.createRmd	1.614	0.147	1.813
vst.ttest.createRmd	1.109	0.134	1.284