BioC 3.1: CHECK report for DMRcaller on morelia

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: 2015-10-09 01:20:15 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:23:12 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 176.9 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 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [8s/8s] 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 ... [61s/63s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
readBismarkPool      9.777  0.795  10.796
computeDMRs          9.192  0.490   9.712
mergeDMRsIteratively 5.586  0.359   5.949
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/8s] 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	0.005	0.001	0.553
analyseReadsInsideRegionsForCondition	1.496	0.153	1.709
computeDMRs	9.192	0.490	9.712
computeMethylationDataCoverage	0.934	0.205	1.140
computeMethylationProfile	2.400	0.244	2.659
computeOverlapProfile	1.172	0.093	1.265
filterDMRs	3.281	0.312	3.594
getWholeChromosomes	0.501	0.097	0.598
mergeDMRsIteratively	5.586	0.359	5.949
plotLocalMethylationProfile	2.031	0.272	2.308
plotMethylationDataCoverage	1.323	0.261	1.591
plotMethylationProfile	1.869	0.189	2.220
plotMethylationProfileFromData	2.683	0.190	2.917
plotOverlapProfile	1.546	0.031	1.613
poolMethylationDatasets	1.725	0.361	2.088
poolTwoMethylationDatasets	1.220	0.296	1.518
readBismark	4.158	0.336	4.558
readBismarkPool	9.777	0.795	10.796
saveBismark	1.697	0.140	2.170