Nicolae Radu Zabet
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DMRcaller |
| Branch: RELEASE_3_8 |
| Last Commit: bf03ca3 |
| Last Changed Date: 2019-02-15 13:16:10 -0400 (Fri, 15 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:31 -0400 (Tue, 16 Apr 2019).
| Package 420/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DMRcaller 1.14.2 Nicolae Radu Zabet
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: DMRcaller |
| Version: 1.14.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DMRcaller_1.14.2.tar.gz |
| StartedAt: 2019-04-15 23:34:01 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:40:06 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 365.1 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 --install=check:DMRcaller.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DMRcaller_1.14.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DMRcaller.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.2’
* 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 ... 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 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 ... NOTE
extractGC: no visible global function definition for ‘getSeq’
extractGC: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
getSeq seqlevels
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
readBismarkPool 7.458 0.615 8.203
mergeDMRsIteratively 7.712 0.112 7.891
computeDMRs 7.468 0.152 7.683
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.
DMRcaller.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DMRcaller ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘DMRcaller’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (DMRcaller)
DMRcaller.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("DMRcaller")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Calculating interpolations...
Identifying DMRs...
Analysed reads inside DMRs
Merge DMRs iteratively
Filter DMRs
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Selecting data...
Identifying DMRs...
Validating objects
Finding overlaps
Joining objects
Parameters checking ...
Extract methylation in the corresponding context
Computing DMRs at Chr1:1..4976
Count inside each bin...
Filter the bins...
Identifying DMRs...
Merge adjacent DMRs
Merge DMRs iteratively
Filter DMRs
Parameters checking ...
Merge DMRs iteratively ...
RUNIT TEST PROTOCOL -- Mon Apr 15 23:40:00 2019
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
DMRcaller RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
Warning message:
In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) :
'x' has been rounded to integer: Mean relative difference: 0.002857143
>
> proc.time()
user system elapsed
192.266 0.959 195.282
DMRcaller.Rcheck/DMRcaller-Ex.timings
| name | user | system | elapsed | |
| DMRcaller | 0.001 | 0.002 | 0.003 | |
| analyseReadsInsideRegionsForCondition | 1.298 | 0.097 | 1.409 | |
| computeDMRs | 7.468 | 0.152 | 7.683 | |
| computeDMRsReplicates | 0.001 | 0.000 | 0.001 | |
| computeMethylationDataCoverage | 0.824 | 0.107 | 0.939 | |
| computeMethylationDataSpatialCorrelation | 0.706 | 0.131 | 0.852 | |
| computeMethylationProfile | 1.358 | 0.143 | 1.524 | |
| computeOverlapProfile | 2.044 | 0.079 | 2.155 | |
| extractGC | 0 | 0 | 0 | |
| filterDMRs | 1.747 | 0.133 | 1.907 | |
| getWholeChromosomes | 0.606 | 0.067 | 0.677 | |
| joinReplicates | 0 | 0 | 0 | |
| mergeDMRsIteratively | 7.712 | 0.112 | 7.891 | |
| plotLocalMethylationProfile | 1.940 | 0.217 | 2.178 | |
| plotMethylationDataCoverage | 1.392 | 0.165 | 1.572 | |
| plotMethylationDataSpatialCorrelation | 0 | 0 | 0 | |
| plotMethylationProfile | 1.061 | 0.125 | 1.195 | |
| plotMethylationProfileFromData | 2.321 | 0.239 | 2.574 | |
| plotOverlapProfile | 2.021 | 0.041 | 2.078 | |
| poolMethylationDatasets | 1.375 | 0.245 | 1.637 | |
| poolTwoMethylationDatasets | 1.192 | 0.158 | 1.359 | |
| readBismark | 3.059 | 0.225 | 3.345 | |
| readBismarkPool | 7.458 | 0.615 | 8.203 | |
| saveBismark | 1.829 | 0.132 | 1.984 | |