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This page was generated on 2021-12-01 17:17:29 -0500 (Wed, 01 Dec 2021).

CHECK results for methylInheritance on nebbiolo2

To the developers/maintainers of the methylInheritance package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylInheritance.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1121/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylInheritance 1.18.0  (landing page)
Astrid Deschênes
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/methylInheritance
git_branch: RELEASE_3_14
git_last_commit: 0387c10
git_last_commit_date: 2021-10-26 12:34:47 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: methylInheritance
Version: 1.18.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings methylInheritance_1.18.0.tar.gz
StartedAt: 2021-11-30 09:52:48 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 10:00:56 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 488.1 seconds
RetCode: 0
Status:   OK  
CheckDir: methylInheritance.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:methylInheritance.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings methylInheritance_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/methylInheritance.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.18.0’
* 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 (user + system) or elapsed time > 5s
                                       user system elapsed
runPermutation                      118.194  0.635 118.300
runObservation                       47.484  0.843  48.050
samplesForTransgenerationalAnalysis  40.395  0.204  38.915
runOnePermutationOnAllGenerations    14.106  0.049  13.581
demoForTransgenerationalAnalysis      7.611  0.164   7.775
* 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


Installation output

methylInheritance.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL methylInheritance
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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)

Tests output

methylInheritance.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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.

> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("methylInheritance")
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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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 Nov 30 10:00:53 2021 
*********************************************** 
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
methylInheritance RUnit Tests - 75 test functions, 0 errors, 0 failures
Number of test functions: 75 
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 
 41.197   0.933  42.118 

Example timings

methylInheritance.Rcheck/methylInheritance-Ex.timings

nameusersystemelapsed
calculateSignificantLevel0.0160.0000.016
createDataStructure0.0620.0000.062
createOutputDir0.0010.0000.001
demoForTransgenerationalAnalysis7.6110.1647.775
extractInfo0.2240.0000.224
formatInputMethylData0.2340.0350.269
getGRangesFromMethylDiff0.1230.0070.132
interGeneration1.3910.3871.779
isInterGenerationResults0.0020.0000.001
loadAllRDSResults0.2170.0590.277
loadConvergenceData0.2470.0830.333
mergePermutationAndObservation0.0030.0000.004
methylInheritanceAllResults0.0020.0030.007
methylInheritanceResults0.0080.0080.017
plotConvergenceGraph0.4700.0550.526
plotGraph0.2980.0290.325
readInterGenerationResults0.0480.0280.075
runObservation47.484 0.84348.050
runOnePermutationOnAllGenerations14.106 0.04913.581
runPermutation118.194 0.635118.300
samplesForTransgenerationalAnalysis40.395 0.20438.915
saveInterGenerationResults1.1930.0001.193
validateExtractInfo0.0000.0020.002
validateLoadConvergenceData0.0000.0010.001
validateMergePermutationAndObservation0.0000.0000.001
validateRunObservation0.1120.0000.113
validateRunPermutation0.1090.0040.114