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 02:09:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:20:28 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 682.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: methylInheritance.Rcheck

Warnings: NA

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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) (2018-11-27 r75683)
* 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                      239.460 55.442 186.180
samplesForTransgenerationalAnalysis 125.453 79.746  55.619
runObservation                      100.803  2.477 101.824
runOnePermutationOnAllGenerations    36.885 13.034  23.336
demoForTransgenerationalAnalysis     16.805  6.377   8.443
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
   test.runPermutation_good_001() - Valid parameters did not generated expected message.
  
  Test files with failing tests
  
     test_methylInheritanceInternalMethods.R 
       test.formatInputMethylData_good_01 
       test.validateRunPermutationUsingMethylKitInfo_sites_good_01 
  
     test_methylInheritanceMethods.R 
       test.runPermutation_good_001 
  
  
  Error in BiocGenerics:::testPackage("methylInheritance") : 
    unit tests failed for package methylInheritance
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylInheritance.Rcheck/00check.log’
for details.

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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’ ...
** 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)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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
Timing stopped at: 0.068 0.001 0.07
Error in checkEquals(obs, expGR, message) : 
  Component 1: Component 1: Attributes: < Component "sample.id": 1 string mismatch >
Component 1: Component 1: Component 2: Mean relative difference: 0.004950495
Component 1: Component 1: Component 3: Mean relative difference: 0.004950495
Component 1: Component 1: Component 5: Mean relative difference: 0.06772908
Component 1: Component 1: Component 6: Mean relative difference: 0.5
Component 1: Component 1: Component 7: Mean relative difference: 0.07692308
Component 2: Component 1: Attributes: < Component "sample.id": 1 string mismatch >
Component 2: Component 1: Component 2: Mean relative difference: 0.00199005
Component 2: Component 1: Component 3: Mean relative difference: 0.00199005
Component 2: Component 1: Component 5: Mean relative difference: 0.15625
Component 2: Component 1: Component 6: Mean relative difference: 1
Component 2: Component 1: Component 7: Mean relative difference: 0.1535433
Component 2: Component 2: Attributes: < Component "sample.id": 1 string mismatch >
Component 2: Component 2: Component 2: Mean relative difference: 0.0009910803
Component 2: Component 2: Component 3: Mean relative difference: 0.0009910803
Component 2: Component 2: Component 5: Mean relative difference: 0.08438819
Component 2: Component 2: Component 6: Mean relative difference: 3
Component 2: Component 2: Component 7: Mean relative difference: 0.0720339
Component 3: Component 1: Attributes: < Component "sample.id": 1 string mismatch >
Component 3: Component 1: Component 2: Mean relative difference: 0.002982107
Component 3: Component 1: Component 3: Mean relative difference: 0.002982107
Component 3: Component 1: Component 5: Mean relative difference: 0.147482
Component 3: Component 1: Component 6: Mean relative difference: 1.2
Component 3: Component 1: Component 7: Mean relative difference: 0.1355311
Component 3: Component 2: Attributes: < Component "sample.id": 1 string mismatch >
Component 3: Component 2: Component 2: Mean relative difference: 0.0009930487
Component 3: Component 2: Component 3: Mean relative difference: 0.0009930487
Component 3: Component 2: Component 5: Mean relative difference: 0.09448819
Component 3: Component 2: Component 6: Mean relative difference: 6
Component 3: Component 2: Component 7: Mean relative difference: 0.07905138
test.formatInputMethylData_good_01() - Function did not return expected values
Timing stopped at: 6.912 3.336 4.123
Error in checkEquals(obsV$PERMUTATION[[1]], exp, msg = message) : 
  Component "SITES": Component "i2": Component "HYPER": Component 1: Mean relative difference: 1
Component "SITES": Component "i2": Component "HYPO": Component 1: Mean absolute difference: 3
 test.validateRunPermutationUsingMethylKitInfo_sites_good_01() - Valid parameters did not generated expected results.
Timing stopped at: 59.46 38.86 21.23
Error in checkEquals(obsV$PERMUTATION, exp$PERMUTATION, msg = message) : 
  Component 1: Component 1: Component 1: Component 2: Component 1: Mean absolute difference: 1
Component 1: Component 1: Component 1: Component 2: Component 2: Mean relative difference: 2
Component 1: Component 1: Component 2: Component 2: Component 1: Mean absolute difference: 1
Component 1: Component 2: Component 1: Component 2: Component 1: Mean absolute difference: 1000
Component 2: Component 1: Component 1: Component 2: Component 2: Mean absolute difference: 1
 test.runPermutation_good_001() - Valid parameters did not generated expected message.
In addition: 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
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 02:20:22 2019 
*********************************************** 
Number of test functions: 72 
Number of errors: 0 
Number of failures: 3 

 
1 Test Suite : 
methylInheritance RUnit Tests - 72 test functions, 0 errors, 3 failures
FAILURE in test.formatInputMethylData_good_01: Error in checkEquals(obs, expGR, message) : 
  Component 1: Component 1: Attributes: < Component "sample.id": 1 string mismatch >
Component 1: Component 1: Component 2: Mean relative difference: 0.004950495
Component 1: Component 1: Component 3: Mean relative difference: 0.004950495
Component 1: Component 1: Component 5: Mean relative difference: 0.06772908
Component 1: Component 1: Component 6: Mean relative difference: 0.5
Component 1: Component 1: Component 7: Mean relative difference: 0.07692308
Component 2: Component 1: Attributes: < Component "sample.id": 1 string mismatch >
Component 2: Component 1: Component 2: Mean relative difference: 0.00199005
Component 2: Component 1: Component 3: Mean relative difference: 0.00199005
Component 2: Component 1: Component 5: Mean relative difference: 0.15625
Component 2: Component 1: Component 6: Mean relative difference: 1
Component 2: Component 1: Component 7: Mean relative difference: 0.1535433
Component 2: Component 2: Attributes: < Component "sample.id": 1 string mismatch >
Component 2: Component 2: Component 2: Mean relative difference: 0.0009910803
Component 2: Component 2: Component 3: Mean relative difference: 0.0009910803
Component 2: Component 2: Component 5: Mean relative difference: 0.08438819
Component 2: Component 2: Component 6: Mean relative difference: 3
Component 2: Component 2: Component 7: Mean relative difference: 0.0720339
Component 3: Component 1: Attributes: < Component "sample.id": 1 string mismatch >
Component 3: Component 1: Component 2: Mean relative difference: 0.002982107
Component 3: Component 1: Component 3: Mean relative difference: 0.002982107
Component 3: Component 1: Component 5: Mean relative difference: 0.147482
Component 3: Component 1: Component 6: Mean relative difference: 1.2
Component 3: Component 1: Component 7: Mean relative difference: 0.1355311
Component 3: Component 2: Attributes: < Component "sample.id": 1 string mismatch >
Component 3: Component 2: Component 2: Mean relative difference: 0.0009930487
Component 3: Component 2: Component 3: Mean relative difference: 0.0009930487
Component 3: Component 2: Component 5: Mean relative difference: 0.09448819
Component 3: Component 2: Component 6: Mean relative difference: 6
Component 3: Component 2: Component 7: Mean relative difference: 0.07905138
test.formatInputMethylData_good_01() - Function did not return expected values
FAILURE in test.validateRunPermutationUsingMethylKitInfo_sites_good_01: Error in checkEquals(obsV$PERMUTATION[[1]], exp, msg = message) : 
  Component "SITES": Component "i2": Component "HYPER": Component 1: Mean relative difference: 1
Component "SITES": Component "i2": Component "HYPO": Component 1: Mean absolute difference: 3
 test.validateRunPermutationUsingMethylKitInfo_sites_good_01() - Valid parameters did not generated expected results.
FAILURE in test.runPermutation_good_001: Error in checkEquals(obsV$PERMUTATION, exp$PERMUTATION, msg = message) : 
  Component 1: Component 1: Component 1: Component 2: Component 1: Mean absolute difference: 1
Component 1: Component 1: Component 1: Component 2: Component 2: Mean relative difference: 2
Component 1: Component 1: Component 2: Component 2: Component 1: Mean absolute difference: 1
Component 1: Component 2: Component 1: Component 2: Component 1: Mean absolute difference: 1000
Component 2: Component 1: Component 1: Component 2: Component 2: Mean absolute difference: 1
 test.runPermutation_good_001() - Valid parameters did not generated expected message.

Test files with failing tests

   test_methylInheritanceInternalMethods.R 
     test.formatInputMethylData_good_01 
     test.validateRunPermutationUsingMethylKitInfo_sites_good_01 

   test_methylInheritanceMethods.R 
     test.runPermutation_good_001 


Error in BiocGenerics:::testPackage("methylInheritance") : 
  unit tests failed for package methylInheritance
Execution halted

name	user	system	elapsed
calculateSignificantLevel	0.341	0.045	0.399
createDataStructure	0.099	0.006	0.105
createOutputDir	0.001	0.000	0.001
demoForTransgenerationalAnalysis	16.805	6.377	8.443
extractInfo	0.172	0.001	0.179
formatInputMethylData	0.391	0.049	0.453
getGRangesFromMethylDiff	0.122	0.004	0.129
interGeneration	1.379	0.003	1.424
isInterGenerationResults	0.002	0.001	0.002
loadAllRDSResults	0.166	0.002	0.176
loadConvergenceData	0.222	0.002	0.235
mergePermutationAndObservation	0.005	0.000	0.006
methylInheritanceAllResults	0.009	0.008	0.017
methylInheritanceResults	0.039	0.010	0.051
plotConvergenceGraph	0.687	0.005	0.704
plotGraph	0.721	0.015	0.765
readInterGenerationResults	0.045	0.002	0.048
runObservation	100.803	2.477	101.824
runOnePermutationOnAllGenerations	36.885	13.034	23.336
runPermutation	239.460	55.442	186.180
samplesForTransgenerationalAnalysis	125.453	79.746	55.619
saveInterGenerationResults	1.127	0.010	1.151
validateExtractInfo	0.002	0.002	0.003
validateLoadConvergenceData	0.001	0.000	0.001
validateMergePermutationAndObservation	0.002	0.001	0.002
validateRunObservation	0.161	0.025	0.189
validateRunPermutation	0.153	0.013	0.168