Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:30:11 -0400 (Wed, 17 Oct 2018).
Package 888/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
methylInheritance 1.4.0 Astrid Deschenes
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: methylInheritance |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings methylInheritance_1.4.0.tar.gz |
StartedAt: 2018-10-16 01:54:32 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 02:01:13 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 401.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methylInheritance.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings methylInheritance_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/methylInheritance.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methylInheritance/DESCRIPTION’ ... OK * this is package ‘methylInheritance’ version ‘1.4.0’ * package encoding: UTF-8 * 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 ‘methylInheritance’ 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed runPermutation 113.420 0.028 113.556 runObservation 50.956 0.040 51.029 samplesForTransgenerationalAnalysis 33.600 0.016 33.647 runOnePermutationOnAllGenerations 13.048 0.008 13.065 * 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: OK
methylInheritance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL methylInheritance ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘methylInheritance’ ... ** 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 (methylInheritance)
methylInheritance.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 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. > ## Run all tests presnt in the package > BiocGenerics:::testPackage("methylInheritance") Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb Permutation Analysis Number of Generations: 3 Number of Permutations: 20 Observation Results: SOURCE ELEMENT ANALYSIS TYPE RESULT 1 OBSERVATION SITES i2 HYPER1 4 2 OBSERVATION SITES i2 HYPER2 1 3 OBSERVATION SITES i2 HYPO1 2 4 OBSERVATION SITES i2 HYPO2 2 5 OBSERVATION SITES iAll HYPER 0 6 OBSERVATION SITES iAll HYPO 0 7 OBSERVATION TILES i2 HYPER1 1000 8 OBSERVATION TILES i2 HYPER2 0 9 OBSERVATION TILES i2 HYPO1 0 10 OBSERVATION TILES i2 HYPO2 0 11 OBSERVATION TILES iAll HYPER 0 12 OBSERVATION TILES iAll HYPO 0 RUNIT TEST PROTOCOL -- Tue Oct 16 02:01:11 2018 *********************************************** Number of test functions: 72 Number of errors: 0 Number of failures: 0 1 Test Suite : methylInheritance RUnit Tests - 72 test functions, 0 errors, 0 failures Number of test functions: 72 Number of errors: 0 Number of failures: 0 Warning messages: 1: In max(i) : no non-missing arguments to max; returning -Inf 2: In max(i) : no non-missing arguments to max; returning -Inf > > proc.time() user system elapsed 26.856 0.420 27.344
methylInheritance.Rcheck/methylInheritance-Ex.timings
name | user | system | elapsed | |
calculateSignificantLevel | 0.144 | 0.000 | 0.145 | |
createDataStructure | 0.040 | 0.008 | 0.062 | |
createOutputDir | 0.000 | 0.000 | 0.001 | |
demoForTransgenerationalAnalysis | 4.224 | 0.108 | 4.338 | |
extractInfo | 0.172 | 0.000 | 0.207 | |
formatInputMethylData | 0.204 | 0.032 | 0.237 | |
getGRangesFromMethylDiff | 0.080 | 0.000 | 0.081 | |
interGeneration | 0.812 | 0.004 | 0.815 | |
isInterGenerationResults | 0.000 | 0.000 | 0.002 | |
loadAllRDSResults | 0.132 | 0.000 | 0.132 | |
loadConvergenceData | 0.164 | 0.000 | 0.182 | |
mergePermutationAndObservation | 0.004 | 0.000 | 0.004 | |
methylInheritanceAllResults | 0.004 | 0.000 | 0.006 | |
methylInheritanceResults | 0.024 | 0.000 | 0.021 | |
plotConvergenceGraph | 0.472 | 0.000 | 0.476 | |
plotGraph | 0.436 | 0.004 | 0.442 | |
readInterGenerationResults | 0.032 | 0.000 | 0.030 | |
runObservation | 50.956 | 0.040 | 51.029 | |
runOnePermutationOnAllGenerations | 13.048 | 0.008 | 13.065 | |
runPermutation | 113.420 | 0.028 | 113.556 | |
samplesForTransgenerationalAnalysis | 33.600 | 0.016 | 33.647 | |
saveInterGenerationResults | 0.752 | 0.000 | 0.755 | |
validateExtractInfo | 0.004 | 0.000 | 0.003 | |
validateLoadConvergenceData | 0.004 | 0.000 | 0.001 | |
validateMergePermutationAndObservation | 0.000 | 0.000 | 0.002 | |
validateRunObservation | 0.108 | 0.004 | 0.113 | |
validateRunPermutation | 0.092 | 0.016 | 0.110 | |