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: 2015-10-27 06:45:52 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:51:07 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 315.3 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/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 ... [246s/252s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   69.520  3.581  73.137
NBPSeq.createRmd         46.821  3.235  50.133
convertcompDataToList    10.554  6.763  17.787
show-compData-method     10.737  6.484  17.648
DESeq.GLM.createRmd      13.823  1.128  15.105
EBSeq.createRmd          12.191  1.048  14.900
DESeq2.createRmd          7.878  0.985   9.492
baySeq.createRmd          7.420  0.637   8.541
NOISeq.prenorm.createRmd  7.161  0.828   8.371
* 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	13.823	1.128	15.105
DESeq.nbinom.createRmd	69.520	3.581	73.137
DESeq2.createRmd	7.878	0.985	9.492
DSS.createRmd	2.776	0.250	3.551
EBSeq.createRmd	12.191	1.048	14.900
NBPSeq.createRmd	46.821	3.235	50.133
NOISeq.prenorm.createRmd	7.161	0.828	8.371
SAMseq.createRmd	2.025	0.283	2.391
TCC.createRmd	3.976	0.283	4.432
baySeq.createRmd	7.420	0.637	8.541
checkDataObject	0.429	0.084	0.541
checkTableConsistency	1.609	0.179	1.857
check_compData	0.438	0.067	0.537
check_compData_results	1.027	0.137	1.208
compData	0.004	0.000	0.004
convertListTocompData	0.006	0.000	0.008
convertcompDataToList	10.554	6.763	17.787
edgeR.GLM.createRmd	1.834	0.184	2.103
edgeR.exact.createRmd	1.089	0.135	1.273
generateCodeHTMLs	1.028	0.126	1.220
generateSyntheticData	0.444	0.061	0.532
listcreateRmd	0.018	0.001	0.019
logcpm.limma.createRmd	0.770	0.114	0.928
runComparison	3.496	0.365	4.094
runComparisonGUI	0.000	0.000	0.001
runDiffExp	1.009	0.117	1.180
show-compData-method	10.737	6.484	17.648
sqrtcpm.limma.createRmd	0.748	0.083	0.862
summarizeSyntheticDataSet	2.019	0.202	2.395
ttest.createRmd	0.796	0.113	0.955
voom.limma.createRmd	1.001	0.117	1.172
voom.ttest.createRmd	0.820	0.103	0.958
vst.limma.createRmd	1.190	0.123	1.354
vst.ttest.createRmd	1.133	0.109	1.293