BioC 3.1: CHECK report for DMRcaller on zin2
This page was generated on 2015-10-09 09:26:53 -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: /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 |
Command output
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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
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 | 0.004 | 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 |
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getWholeChromosomes | 0.438 | 0.004 | 0.522 |
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mergeDMRsIteratively | 4.442 | 0.004 | 6.844 |
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plotLocalMethylationProfile | 1.832 | 0.015 | 2.977 |
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plotMethylationDataCoverage | 1.349 | 0.004 | 2.052 |
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plotMethylationProfile | 1.579 | 0.008 | 1.965 |
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plotMethylationProfileFromData | 3.176 | 0.004 | 3.953 |
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plotOverlapProfile | 1.579 | 0.007 | 2.297 |
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poolMethylationDatasets | 1.604 | 0.008 | 2.203 |
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poolTwoMethylationDatasets | 1.240 | 0.000 | 1.608 |
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readBismark | 2.764 | 0.022 | 4.096 |
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readBismarkPool | 7.002 | 0.036 | 10.344 |
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saveBismark | 1.581 | 0.026 | 2.467 |
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