BioC 3.1: CHECK report for DMRcaller on petty

Package: DMRcaller

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DMRcaller_1.0.0.tar.gz

StartedAt: 2015-10-08 22:39:46 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:44:07 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 261.3 seconds

RetCode: 0

Status:  OK

CheckDir: DMRcaller.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 DMRcaller_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/DMRcaller.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 ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘DMRcaller’ can be installed ... [14s/14s] 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [91s/91s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
computeDMRs                    14.102  0.271  14.381
readBismarkPool                11.613  1.047  12.855
mergeDMRsIteratively            8.575  0.166   8.745
plotMethylationProfileFromData  6.712  0.405   7.122
filterDMRs                      4.987  0.312   5.305
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [12s/12s]
 [13s/13s] OK
* 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: OK

* installing *source* package ‘DMRcaller’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (DMRcaller)

name	user	system	elapsed
DMRcaller	0.008	0.002	0.009
analyseReadsInsideRegionsForCondition	2.618	0.158	2.775
computeDMRs	14.102	0.271	14.381
computeMethylationDataCoverage	1.192	0.220	1.413
computeMethylationProfile	3.158	0.230	3.388
computeOverlapProfile	2.382	0.074	2.460
filterDMRs	4.987	0.312	5.305
getWholeChromosomes	0.724	0.136	0.861
mergeDMRsIteratively	8.575	0.166	8.745
plotLocalMethylationProfile	3.032	0.437	3.468
plotMethylationDataCoverage	2.601	0.397	3.004
plotMethylationProfile	2.943	0.269	3.213
plotMethylationProfileFromData	6.712	0.405	7.122
plotOverlapProfile	3.316	0.088	3.411
poolMethylationDatasets	3.094	0.468	3.571
poolTwoMethylationDatasets	1.980	0.392	2.373
readBismark	4.241	0.335	4.661
readBismarkPool	11.613	1.047	12.855
saveBismark	1.918	0.173	2.208