BioC 3.1: CHECK report for DMRcaller on morelia
This page was generated on 2015-10-09 09:42:51 -0700 (Fri, 09 Oct 2015).
DMRcaller 1.0.0 Nicolae Radu Zabet
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/DMRcaller | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
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 |
Command output
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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
DMRcaller.Rcheck/00install.out:
* 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)
DMRcaller.Rcheck/DMRcaller-Ex.timings:
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 |
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computeMethylationDataCoverage | 0.934 | 0.205 | 1.140 |
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computeMethylationProfile | 2.400 | 0.244 | 2.659 |
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computeOverlapProfile | 1.172 | 0.093 | 1.265 |
|
filterDMRs | 3.281 | 0.312 | 3.594 |
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getWholeChromosomes | 0.501 | 0.097 | 0.598 |
|
mergeDMRsIteratively | 5.586 | 0.359 | 5.949 |
|
plotLocalMethylationProfile | 2.031 | 0.272 | 2.308 |
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plotMethylationDataCoverage | 1.323 | 0.261 | 1.591 |
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plotMethylationProfile | 1.869 | 0.189 | 2.220 |
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plotMethylationProfileFromData | 2.683 | 0.190 | 2.917 |
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plotOverlapProfile | 1.546 | 0.031 | 1.613 |
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poolMethylationDatasets | 1.725 | 0.361 | 2.088 |
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poolTwoMethylationDatasets | 1.220 | 0.296 | 1.518 |
|
readBismark | 4.158 | 0.336 | 4.558 |
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readBismarkPool | 9.777 | 0.795 | 10.796 |
|
saveBismark | 1.697 | 0.140 | 2.170 |
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