Astrid Deschenes
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/methylInheritance |
| Branch: RELEASE_3_10 |
| Last Commit: 6822d45 |
| Last Changed Date: 2019-10-29 13:10:24 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:45:19 -0400 (Wed, 15 Apr 2020).
| Package 1023/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| methylInheritance 1.10.0 Astrid Deschenes
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: methylInheritance |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylInheritance_1.10.0.tar.gz |
| StartedAt: 2020-04-15 03:47:28 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:59:40 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 732.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylInheritance.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylInheritance_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/methylInheritance.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylInheritance/DESCRIPTION’ ... OK
* this is package ‘methylInheritance’ version ‘1.10.0’
* 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 261.307 91.814 195.291
samplesForTransgenerationalAnalysis 134.376 98.996 61.014
runObservation 108.592 0.873 111.246
runOnePermutationOnAllGenerations 45.371 30.431 21.917
demoForTransgenerationalAnalysis 31.123 27.450 10.435
* 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: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylInheritance ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘methylInheritance’ ... ** 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 (methylInheritance)
methylInheritance.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
> ## 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, 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, 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
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
uniting...
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 -- Wed Apr 15 03:59:33 2020
***********************************************
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: Use of `formatForGraphDataFrame$RESULT` is discouraged. Use `RESULT` instead.
2: In max(i) : no non-missing arguments to max; returning -Inf
3: In max(i) : no non-missing arguments to max; returning -Inf
>
> proc.time()
user system elapsed
108.970 56.940 53.976
methylInheritance.Rcheck/methylInheritance-Ex.timings
| name | user | system | elapsed | |
| calculateSignificantLevel | 0.309 | 0.027 | 0.338 | |
| createDataStructure | 0.079 | 0.008 | 0.088 | |
| createOutputDir | 0.000 | 0.001 | 0.001 | |
| demoForTransgenerationalAnalysis | 31.123 | 27.450 | 10.435 | |
| extractInfo | 0.200 | 0.001 | 0.210 | |
| formatInputMethylData | 0.283 | 0.036 | 0.321 | |
| getGRangesFromMethylDiff | 0.097 | 0.003 | 0.100 | |
| interGeneration | 1.418 | 0.006 | 1.444 | |
| isInterGenerationResults | 0.001 | 0.000 | 0.002 | |
| loadAllRDSResults | 0.249 | 0.002 | 0.255 | |
| loadConvergenceData | 0.283 | 0.002 | 0.286 | |
| mergePermutationAndObservation | 0.003 | 0.000 | 0.004 | |
| methylInheritanceAllResults | 0.009 | 0.016 | 0.024 | |
| methylInheritanceResults | 0.034 | 0.016 | 0.051 | |
| plotConvergenceGraph | 0.781 | 0.006 | 0.793 | |
| plotGraph | 0.823 | 0.019 | 0.863 | |
| readInterGenerationResults | 0.071 | 0.002 | 0.077 | |
| runObservation | 108.592 | 0.873 | 111.246 | |
| runOnePermutationOnAllGenerations | 45.371 | 30.431 | 21.917 | |
| runPermutation | 261.307 | 91.814 | 195.291 | |
| samplesForTransgenerationalAnalysis | 134.376 | 98.996 | 61.014 | |
| saveInterGenerationResults | 1.178 | 0.007 | 1.195 | |
| validateExtractInfo | 0.003 | 0.001 | 0.005 | |
| validateLoadConvergenceData | 0.001 | 0.000 | 0.001 | |
| validateMergePermutationAndObservation | 0.000 | 0.000 | 0.002 | |
| validateRunObservation | 0.139 | 0.021 | 0.160 | |
| validateRunPermutation | 0.144 | 0.013 | 0.160 | |