BioC 3.1: CHECK report for DMRcaller on moscato2
This page was generated on 2015-10-09 09:32:14 -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
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Version: 1.0.0
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Command: rm -rf DMRcaller.buildbin-libdir DMRcaller.Rcheck && mkdir DMRcaller.buildbin-libdir DMRcaller.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRcaller.buildbin-libdir DMRcaller_1.0.0.tar.gz >DMRcaller.Rcheck\00install.out 2>&1 && cp DMRcaller.Rcheck\00install.out DMRcaller-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=DMRcaller.buildbin-libdir --install="check:DMRcaller-install.out" --force-multiarch --no-vignettes --timings DMRcaller_1.0.0.tar.gz
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StartedAt: 2015-10-09 01:15:46 -0700 (Fri, 09 Oct 2015)
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EndedAt: 2015-10-09 01:20:46 -0700 (Fri, 09 Oct 2015)
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EllapsedTime: 300.1 seconds
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RetCode: 0
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Status: OK
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CheckDir: DMRcaller.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf DMRcaller.buildbin-libdir DMRcaller.Rcheck && mkdir DMRcaller.buildbin-libdir DMRcaller.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DMRcaller.buildbin-libdir DMRcaller_1.0.0.tar.gz >DMRcaller.Rcheck\00install.out 2>&1 && cp DMRcaller.Rcheck\00install.out DMRcaller-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=DMRcaller.buildbin-libdir --install="check:DMRcaller-install.out" --force-multiarch --no-vignettes --timings DMRcaller_1.0.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/DMRcaller.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'DMRcaller' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [72s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
readBismarkPool 14.09 0.30 14.38
computeDMRs 8.50 0.11 8.66
readBismark 6.49 0.11 6.63
mergeDMRsIteratively 5.18 0.02 5.19
plotMethylationProfileFromData 4.96 0.11 5.07
** running examples for arch 'x64' ... [71s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
readBismarkPool 12.54 0.50 13.09
computeDMRs 9.39 0.14 9.60
mergeDMRsIteratively 5.77 0.02 5.79
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [7s]
[7s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [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:
install for i386
* 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'
install for x64
* installing *source* package 'DMRcaller' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'DMRcaller' as DMRcaller_1.0.0.zip
* DONE (DMRcaller)
DMRcaller.Rcheck/examples_i386/DMRcaller-Ex.timings:
name | user | system | elapsed
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DMRcaller | 0.02 | 0.00 | 0.01 |
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analyseReadsInsideRegionsForCondition | 1.72 | 0.08 | 1.83 |
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computeDMRs | 8.50 | 0.11 | 8.66 |
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computeMethylationDataCoverage | 1.40 | 0.06 | 1.47 |
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computeMethylationProfile | 2.36 | 0.05 | 2.40 |
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computeOverlapProfile | 1.14 | 0.01 | 1.15 |
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filterDMRs | 3.32 | 0.05 | 3.37 |
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getWholeChromosomes | 0.51 | 0.03 | 0.55 |
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mergeDMRsIteratively | 5.18 | 0.02 | 5.19 |
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plotLocalMethylationProfile | 2.64 | 0.03 | 2.67 |
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plotMethylationDataCoverage | 2.48 | 0.03 | 2.53 |
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plotMethylationProfile | 1.92 | 0.00 | 1.92 |
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plotMethylationProfileFromData | 4.96 | 0.11 | 5.07 |
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plotOverlapProfile | 2.62 | 0.05 | 2.66 |
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poolMethylationDatasets | 2.39 | 0.14 | 2.53 |
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poolTwoMethylationDatasets | 1.56 | 0.09 | 1.66 |
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readBismark | 6.49 | 0.11 | 6.63 |
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readBismarkPool | 14.09 | 0.30 | 14.38 |
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saveBismark | 3.67 | 0.04 | 3.75 |
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DMRcaller.Rcheck/examples_x64/DMRcaller-Ex.timings:
name | user | system | elapsed
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DMRcaller | 0 | 0 | 0 |
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analyseReadsInsideRegionsForCondition | 1.92 | 0.05 | 1.97 |
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computeDMRs | 9.39 | 0.14 | 9.60 |
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computeMethylationDataCoverage | 1.00 | 0.03 | 1.03 |
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computeMethylationProfile | 2.40 | 0.06 | 2.47 |
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computeOverlapProfile | 1.33 | 0.00 | 1.33 |
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filterDMRs | 4.68 | 0.03 | 4.71 |
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getWholeChromosomes | 0.56 | 0.00 | 0.56 |
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mergeDMRsIteratively | 5.77 | 0.02 | 5.79 |
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plotLocalMethylationProfile | 2.67 | 0.06 | 2.73 |
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plotMethylationDataCoverage | 2.03 | 0.03 | 2.06 |
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plotMethylationProfile | 2.53 | 0.03 | 2.55 |
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plotMethylationProfileFromData | 4.54 | 0.08 | 4.62 |
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plotOverlapProfile | 2.14 | 0.00 | 2.14 |
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poolMethylationDatasets | 2.04 | 0.22 | 2.26 |
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poolTwoMethylationDatasets | 2.08 | 0.13 | 2.20 |
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readBismark | 4.65 | 0.18 | 4.86 |
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readBismarkPool | 12.54 | 0.50 | 13.09 |
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saveBismark | 2.93 | 0.06 | 3.00 |
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