BioC 3.1: CHECK report for DMRcaller on zin2

Package: DMRcaller

Version: 1.0.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DMRcaller_1.0.0.tar.gz

StartedAt: 2015-10-09 00:36:39 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:39:47 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 187.9 seconds

RetCode: 0

Status:  OK

CheckDir: DMRcaller.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DMRcaller_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/DMRcaller.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [6s/10s] 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 ... [47s/68s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
computeDMRs          7.135  0.033  10.082
readBismarkPool      7.002  0.036  10.344
mergeDMRsIteratively 4.442  0.004   6.844
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/9s]
 [6s/10s] 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	0.004	0.000	0.004
analyseReadsInsideRegionsForCondition	1.507	0.020	2.165
computeDMRs	7.135	0.033	10.082
computeMethylationDataCoverage	0.792	0.007	1.249
computeMethylationProfile	2.092	0.008	3.121
computeOverlapProfile	1.002	0.004	1.461
filterDMRs	2.756	0.002	4.018
getWholeChromosomes	0.438	0.004	0.522
mergeDMRsIteratively	4.442	0.004	6.844
plotLocalMethylationProfile	1.832	0.015	2.977
plotMethylationDataCoverage	1.349	0.004	2.052
plotMethylationProfile	1.579	0.008	1.965
plotMethylationProfileFromData	3.176	0.004	3.953
plotOverlapProfile	1.579	0.007	2.297
poolMethylationDatasets	1.604	0.008	2.203
poolTwoMethylationDatasets	1.240	0.000	1.608
readBismark	2.764	0.022	4.096
readBismarkPool	7.002	0.036	10.344
saveBismark	1.581	0.026	2.467