Package: methylInheritance

Version: 1.7.2

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_1.7.2.tar.gz

StartedAt: 2019-04-09 03:28:42 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:42:50 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 847.6 seconds

RetCode: 0

Status:  OK

CheckDir: methylInheritance.Rcheck

Warnings: 0

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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_1.7.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylInheritance.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.7.2’
* 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                      285.844 56.283 224.413
samplesForTransgenerationalAnalysis 147.264 69.415  69.217
runObservation                      121.715  3.507 129.705
runOnePermutationOnAllGenerations    37.972 11.080  27.841
demoForTransgenerationalAnalysis     23.159  7.876  11.040
* 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

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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)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, colMeans, colSums, 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, 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 Apr  9 03:42:42 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 
104.868  41.648  56.440 

name	user	system	elapsed
calculateSignificantLevel	0.461	0.070	0.618
createDataStructure	0.120	0.005	0.134
createOutputDir	0.001	0.000	0.002
demoForTransgenerationalAnalysis	23.159	7.876	11.040
extractInfo	0.228	0.004	0.239
formatInputMethylData	0.448	0.097	0.566
getGRangesFromMethylDiff	0.110	0.008	0.122
interGeneration	1.585	0.011	1.726
isInterGenerationResults	0.002	0.000	0.002
loadAllRDSResults	0.240	0.004	0.259
loadConvergenceData	0.297	0.005	0.312
mergePermutationAndObservation	0.006	0.001	0.008
methylInheritanceAllResults	0.011	0.023	0.036
methylInheritanceResults	0.064	0.021	0.090
plotConvergenceGraph	0.811	0.010	0.906
plotGraph	0.822	0.030	0.883
readInterGenerationResults	0.056	0.004	0.060
runObservation	121.715	3.507	129.705
runOnePermutationOnAllGenerations	37.972	11.080	27.841
runPermutation	285.844	56.283	224.413
samplesForTransgenerationalAnalysis	147.264	69.415	69.217
saveInterGenerationResults	1.457	0.006	1.464
validateExtractInfo	0.004	0.003	0.007
validateLoadConvergenceData	0.002	0.001	0.002
validateMergePermutationAndObservation	0.002	0.001	0.003
validateRunObservation	0.139	0.035	0.174
validateRunPermutation	0.120	0.024	0.145