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CHECK report for methylInheritance on celaya2

This page was generated on 2019-10-16 13:00:06 -0400 (Wed, 16 Oct 2019).

Package 980/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylInheritance 1.8.0
Astrid Deschenes
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/methylInheritance
Branch: RELEASE_3_9
Last Commit: 3440afc
Last Changed Date: 2019-05-02 11:54:07 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: methylInheritance
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2019-10-16 04:31:56 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:45:53 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 837.1 seconds
RetCode: 0
Status:  OK 
CheckDir: methylInheritance.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylInheritance.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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                      288.184 44.786 234.807
samplesForTransgenerationalAnalysis 128.563 47.987  71.147
runObservation                      104.629  4.068 102.984
runOnePermutationOnAllGenerations    42.901 14.223  26.388
demoForTransgenerationalAnalysis     26.810 13.939  10.533
* 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:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylInheritance
###
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* 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)

Tests output

methylInheritance.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> ## 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
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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 -- Wed Oct 16 04:45:45 2019 
*********************************************** 
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 
104.208  37.221  59.919 

Example timings

methylInheritance.Rcheck/methylInheritance-Ex.timings

nameusersystemelapsed
calculateSignificantLevel0.4250.0560.481
createDataStructure0.1030.0150.119
createOutputDir0.0020.0010.003
demoForTransgenerationalAnalysis26.81013.93910.533
extractInfo0.1780.0030.183
formatInputMethylData0.3170.0640.381
getGRangesFromMethylDiff0.1100.0070.118
interGeneration1.1850.0071.192
isInterGenerationResults0.0020.0010.003
loadAllRDSResults0.1800.0030.183
loadConvergenceData0.2160.0030.220
mergePermutationAndObservation0.0040.0010.004
methylInheritanceAllResults0.0070.0150.023
methylInheritanceResults0.0490.0160.066
plotConvergenceGraph0.7930.0170.810
plotGraph0.7230.0350.757
readInterGenerationResults0.0570.0030.060
runObservation104.629 4.068102.984
runOnePermutationOnAllGenerations42.90114.22326.388
runPermutation288.184 44.786234.807
samplesForTransgenerationalAnalysis128.563 47.987 71.147
saveInterGenerationResults1.5320.0081.538
validateExtractInfo0.0030.0030.006
validateLoadConvergenceData0.0010.0010.002
validateMergePermutationAndObservation0.0020.0010.003
validateRunObservation0.1810.0460.227
validateRunPermutation0.1650.0260.192