Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:27:21 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the DMRcaller package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 493/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DMRcaller 1.22.0 (landing page) Nicolae Radu Zabet
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: DMRcaller |
Version: 1.22.0 |
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DMRcaller_1.22.0.tar.gz |
StartedAt: 2021-05-06 01:01:19 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 01:06:59 -0400 (Thu, 06 May 2021) |
EllapsedTime: 339.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DMRcaller.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DMRcaller.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DMRcaller_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/DMRcaller.Rcheck’ * using R version 4.0.5 (2021-03-31) * 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 ‘1.22.0’ * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mergeDMRsIteratively 16.552 0.008 16.587 computeDMRs 14.932 0.016 14.961 readBismarkPool 7.872 0.120 8.015 * 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 ‘/home/biocbuild/bbs-3.12-bioc/meat/DMRcaller.Rcheck/00check.log’ for details.
DMRcaller.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL DMRcaller ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘DMRcaller’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DMRcaller)
DMRcaller.Rcheck/tests/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, 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 -- Thu May 6 01:06:55 2021 *********************************************** 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 158.080 0.776 159.142
DMRcaller.Rcheck/DMRcaller-Ex.timings
name | user | system | elapsed | |
DMRcaller | 0 | 0 | 0 | |
analyseReadsInsideRegionsForCondition | 0.944 | 0.032 | 0.974 | |
computeDMRs | 14.932 | 0.016 | 14.961 | |
computeDMRsReplicates | 0.000 | 0.000 | 0.001 | |
computeMethylationDataCoverage | 0.468 | 0.012 | 0.480 | |
computeMethylationDataSpatialCorrelation | 0.476 | 0.040 | 0.517 | |
computeMethylationProfile | 1.320 | 0.012 | 1.334 | |
computeOverlapProfile | 2.648 | 0.012 | 2.663 | |
extractGC | 0 | 0 | 0 | |
filterDMRs | 2.112 | 0.016 | 2.128 | |
getWholeChromosomes | 0.200 | 0.008 | 0.209 | |
joinReplicates | 0 | 0 | 0 | |
mergeDMRsIteratively | 16.552 | 0.008 | 16.587 | |
plotLocalMethylationProfile | 1.876 | 0.016 | 1.893 | |
plotMethylationDataCoverage | 1.524 | 0.016 | 1.544 | |
plotMethylationDataSpatialCorrelation | 0 | 0 | 0 | |
plotMethylationProfile | 1.536 | 0.004 | 1.542 | |
plotMethylationProfileFromData | 3.600 | 0.020 | 3.627 | |
plotOverlapProfile | 3.176 | 0.012 | 3.196 | |
poolMethylationDatasets | 1.156 | 0.028 | 1.186 | |
poolTwoMethylationDatasets | 0.936 | 0.016 | 0.950 | |
readBismark | 3.036 | 0.024 | 3.063 | |
readBismarkPool | 7.872 | 0.120 | 8.015 | |
saveBismark | 1.992 | 0.024 | 2.018 | |