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CHECK report for bumphunter on merida2

This page was generated on 2019-04-09 13:27:46 -0400 (Tue, 09 Apr 2019).

Package 193/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bumphunter 1.25.4
Rafael A. Irizarry
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/bumphunter
Branch: master
Last Commit: ebf505e
Last Changed Date: 2019-04-03 17:29:15 -0400 (Wed, 03 Apr 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  WARNINGS  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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: bumphunter
Version: 1.25.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bumphunter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bumphunter_1.25.4.tar.gz
StartedAt: 2019-04-08 23:37:18 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:41:28 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 250.0 seconds
RetCode: 1
Status:  ERROR 
CheckDir: bumphunter.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bumphunter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bumphunter_1.25.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/bumphunter.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 ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.25.4’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'foreach',
  'iterators', 'parallel', 'locfit'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘bumphunter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bumphunterEngine: no visible binding for global variable ‘bootstraps’
Undefined global functions or variables:
  bootstraps
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 files with failing tests
  
     test_bumphunter.R 
       test_bumphunter 
       test_bumphunterParallel 
  
     test_smoothers.R 
       test_loessByCluster 
       test_runmedByCluster 
       test_smoother 
  
  
  Error in BiocGenerics:::testPackage("bumphunter") : 
    unit tests failed for package bumphunter
  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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/bumphunter.Rcheck/00check.log’
for details.

Installation output

bumphunter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bumphunter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘bumphunter’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (bumphunter)

Tests output

bumphunter.Rcheck/tests/runTests.Rout.fail


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.

> require("bumphunter") || stop("unable to load bumphunter")
Loading required package: bumphunter
Loading required package: S4Vectors
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


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
[1] TRUE
> BiocGenerics:::testPackage("bumphunter")
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.4.4).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
Loading required package: rngtools
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

The following object is masked from 'package:base':

    isFALSE

[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
Timing stopped at: 3.542 0.226 3.813
Error in checkEquals(bumps[nam], bumpsTest1[nam]) : 
  Component "table": Attributes: < Component "row.names": Mean relative difference: 0.6666667 >
Component "table": Component "start": Mean relative difference: 0.002954823
Component "table": Component "end": Mean relative difference: 0.003104456
Component "table": Component "value": Mean relative difference: 1.991512
Component "table": Component "area": Mean relative difference: 0.09979028
Component "table": Component "indexStart": Mean relative difference: 0.185567
Component "table": Component "indexEnd": Mean relative difference: 0.1792453
Component "table": Component "L": Mean relative difference: 0.1666667
Component "table": Component "p.value": Mean relative difference: 1.091837
Component "table": Component "fwer": Mean relative difference: 0.2857143
Component "table": Component "p.valueArea": Mean relative difference: 1.091837
Component "table": Component "fwerArea": Mean relative difference: 0.2857143
Component "coef": Mean relative difference: 0.678983
Component "fitted": Mean relative difference: 0.4064462
Component "pvaluesMarginal": Mean relative difference: 0.7381116
Component "null": Component "value": Component 3: Mean relative difference: 1
Component "null": Component "value": Component 5: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 14: Mean relative difference: 1
Component "null": Component "value": Component 16: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 24: Mean relative difference: 1
Component "null": Component "value": Component 34: Mean relative difference: 1
Component "null": Component "value": Component 39: Mean relative difference: 1
Component "null": Component "value": Component 51: Mean relative difference: 1
Component "null": Component "value": Component 66: Mean relative difference: 1
Component "null": Component "value": Component 75: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 87: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 98: Mean relative difference: 1
Component "null": Component "value": Component 99: Mean relative difference: 1
Component "null": Component "value": Component 115: Mean relative difference: 1
Component "null": Component "value": Component 121: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 132: Mean relative difference: 1
Component "null": Component "value": Component 141: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 156: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 223: Mean relative difference: 1
Component "null": Component "value": Component 248: Mean relative difference: 1
Component "null": Component "value": Component 276: Mean relative difference: 1
Component "null": Component "value": Component 287: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 304: Mean relative difference: 1
Component "null": Component "value": Component 307: Mean relative difference: 1
Component "null": Component "value": Component 317: Mean relative difference: 1
Component "null": Component "value": Component 325: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 342: Mean relative difference: 1
Component "null": Component "value": Component 351: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 355: Mean relative difference: 1
Component "null": Component "value": Component 358: Mean relative difference: 1
Component "null": Component "value": Component 370: Mean relative difference: 1
Component "null": Component "value": Component 378: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 379: Mean relative difference: 1
Component "null": Component "value": Component 385: Mean relative difference: 1
Component "null": Component "value": Component 387: Mean relative difference: 1
Component "null": Component "value": Component 389: Mean relative difference: 1
Component "null": Component "value": Component 390: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 430: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 463: Mean relative difference: 1
Component "null": Component "value": Component 464: Mean relative difference: 1
Component "null": Component "value": Component 480: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 492: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 495: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 3: Mean relative difference: 1
Component "null": Component "length": Component 5: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 14: Mean relative difference: 1
Component "null": Component "length": Component 16: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 24: Mean relative difference: 1
Component "null": Component "length": Component 34: Mean relative difference: 1
Component "null": Component "length": Component 39: Mean relative difference: 1
Component "null": Component "length": Component 51: Mean relative difference: 1
Component "null": Component "length": Component 66: Mean relative difference: 1
Component "null": Component "length": Component 75: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 87: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 98: Mean relative difference: 1
Component "null": Component "length": Component 99: Mean relative difference: 1
Component "null": Component "length": Component 115: Mean relative difference: 1
Component "null": Component "length": Component 121: Mean absolute difference: 1
Component "null": Component "length": Component 132: Mean relative difference: 1
Component "null": Component "length": Component 141: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 156: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 223: Mean relative difference: 1
Component "null": Component "length": Component 248: Mean relative difference: 1
Component "null": Component "length": Component 276: Mean relative difference: 1
Component "null": Component "length": Component 287: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 304: Mean relative difference: 1
Component "null": Component "length": Component 307: Mean relative difference: 1
Component "null": Component "length": Component 317: Mean relative difference: 1
Component "null": Component "length": Component 325: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 342: Mean relative difference: 1
Component "null": Component "length": Component 351: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 355: Mean relative difference: 1
Component "null": Component "length": Component 358: Mean relative difference: 1
Component "null": Component "length": Component 370: Mean relative difference: 1
Component "null": Component "length": Component 378: Mean absolute difference: 1
Component "null": Component "length": Component 379: Mean relative difference: 1
Component "null": Component "length": Component 385: Mean relative difference: 1
Component "null": Component "length": Component 387: Mean relative difference: 1
Component "null": Component "length": Component 389: Mean relative difference: 1
Component "null": Component "length": Component 390: Mean absolute difference: 1
Component "null": Component "length": Component 430: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 463: Mean relative difference: 1
Component "null": Component "length": Component 464: Mean relative difference: 1
Component "null": Component "length": Component 480: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 492: Mean absolute difference: 1
Component "null": Component "length": Component 495: Numeric: lengths (1, 2) differ

Loading required package: doParallel
[bumphunterEngine] Parallelizing using 2 workers/cores (backend: doParallelMC, version: 1.0.14).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
Timing stopped at: 4.029 1.875 3.332
Error in checkEquals(bumps[nam], bumpsTest1[nam]) : 
  Component "table": Attributes: < Component "row.names": Mean relative difference: 0.6666667 >
Component "table": Component "start": Mean relative difference: 0.002954823
Component "table": Component "end": Mean relative difference: 0.003104456
Component "table": Component "value": Mean relative difference: 1.991512
Component "table": Component "area": Mean relative difference: 0.09979028
Component "table": Component "indexStart": Mean relative difference: 0.185567
Component "table": Component "indexEnd": Mean relative difference: 0.1792453
Component "table": Component "L": Mean relative difference: 0.1666667
Component "table": Component "p.value": Mean relative difference: 1.091837
Component "table": Component "fwer": Mean relative difference: 0.2857143
Component "table": Component "p.valueArea": Mean relative difference: 1.091837
Component "table": Component "fwerArea": Mean relative difference: 0.2857143
Component "coef": Mean relative difference: 0.678983
Component "fitted": Mean relative difference: 0.4064462
Component "pvaluesMarginal": Mean relative difference: 0.7381116
Component "null": Component "value": Component 3: Mean relative difference: 1
Component "null": Component "value": Component 5: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 14: Mean relative difference: 1
Component "null": Component "value": Component 16: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 24: Mean relative difference: 1
Component "null": Component "value": Component 34: Mean relative difference: 1
Component "null": Component "value": Component 39: Mean relative difference: 1
Component "null": Component "value": Component 51: Mean relative difference: 1
Component "null": Component "value": Component 66: Mean relative difference: 1
Component "null": Component "value": Component 75: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 87: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 98: Mean relative difference: 1
Component "null": Component "value": Component 99: Mean relative difference: 1
Component "null": Component "value": Component 115: Mean relative difference: 1
Component "null": Component "value": Component 121: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 132: Mean relative difference: 1
Component "null": Component "value": Component 141: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 156: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 223: Mean relative difference: 1
Component "null": Component "value": Component 248: Mean relative difference: 1
Component "null": Component "value": Component 276: Mean relative difference: 1
Component "null": Component "value": Component 287: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 304: Mean relative difference: 1
Component "null": Component "value": Component 307: Mean relative difference: 1
Component "null": Component "value": Component 317: Mean relative difference: 1
Component "null": Component "value": Component 325: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 342: Mean relative difference: 1
Component "null": Component "value": Component 351: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 355: Mean relative difference: 1
Component "null": Component "value": Component 358: Mean relative difference: 1
Component "null": Component "value": Component 370: Mean relative difference: 1
Component "null": Component "value": Component 378: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 379: Mean relative difference: 1
Component "null": Component "value": Component 385: Mean relative difference: 1
Component "null": Component "value": Component 387: Mean relative difference: 1
Component "null": Component "value": Component 389: Mean relative difference: 1
Component "null": Component "value": Component 390: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 430: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 463: Mean relative difference: 1
Component "null": Component "value": Component 464: Mean relative difference: 1
Component "null": Component "value": Component 480: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 492: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 495: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 3: Mean relative difference: 1
Component "null": Component "length": Component 5: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 14: Mean relative difference: 1
Component "null": Component "length": Component 16: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 24: Mean relative difference: 1
Component "null": Component "length": Component 34: Mean relative difference: 1
Component "null": Component "length": Component 39: Mean relative difference: 1
Component "null": Component "length": Component 51: Mean relative difference: 1
Component "null": Component "length": Component 66: Mean relative difference: 1
Component "null": Component "length": Component 75: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 87: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 98: Mean relative difference: 1
Component "null": Component "length": Component 99: Mean relative difference: 1
Component "null": Component "length": Component 115: Mean relative difference: 1
Component "null": Component "length": Component 121: Mean absolute difference: 1
Component "null": Component "length": Component 132: Mean relative difference: 1
Component "null": Component "length": Component 141: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 156: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 223: Mean relative difference: 1
Component "null": Component "length": Component 248: Mean relative difference: 1
Component "null": Component "length": Component 276: Mean relative difference: 1
Component "null": Component "length": Component 287: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 304: Mean relative difference: 1
Component "null": Component "length": Component 307: Mean relative difference: 1
Component "null": Component "length": Component 317: Mean relative difference: 1
Component "null": Component "length": Component 325: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 342: Mean relative difference: 1
Component "null": Component "length": Component 351: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 355: Mean relative difference: 1
Component "null": Component "length": Component 358: Mean relative difference: 1
Component "null": Component "length": Component 370: Mean relative difference: 1
Component "null": Component "length": Component 378: Mean absolute difference: 1
Component "null": Component "length": Component 379: Mean relative difference: 1
Component "null": Component "length": Component 385: Mean relative difference: 1
Component "null": Component "length": Component 387: Mean relative difference: 1
Component "null": Component "length": Component 389: Mean relative difference: 1
Component "null": Component "length": Component 390: Mean absolute difference: 1
Component "null": Component "length": Component 430: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 463: Mean relative difference: 1
Component "null": Component "length": Component 464: Mean relative difference: 1
Component "null": Component "length": Component 480: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 492: Mean absolute difference: 1
Component "null": Component "length": Component 495: Numeric: lengths (1, 2) differ

Timing stopped at: 0.008 0.001 0.009
Error in checkEquals(smoothed, loessSmoothed) : 
  Component "fitted": Mean relative difference: 0.4823732

Timing stopped at: 0.006 0.001 0.008
Error in checkEquals(smoothed, runmedSmoothed) : 
  Component "fitted": Mean relative difference: 0.6813414

Timing stopped at: 0.037 0.042 0.064
Error in checkEquals(smoothed, loessSmoothed) : 
  Component "fitted": Mean relative difference: 0.4823732



RUNIT TEST PROTOCOL -- Mon Apr  8 23:41:23 2019 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 5 

 
1 Test Suite : 
bumphunter RUnit Tests - 5 test functions, 0 errors, 5 failures
FAILURE in test_bumphunter: Error in checkEquals(bumps[nam], bumpsTest1[nam]) : 
  Component "table": Attributes: < Component "row.names": Mean relative difference: 0.6666667 >
Component "table": Component "start": Mean relative difference: 0.002954823
Component "table": Component "end": Mean relative difference: 0.003104456
Component "table": Component "value": Mean relative difference: 1.991512
Component "table": Component "area": Mean relative difference: 0.09979028
Component "table": Component "indexStart": Mean relative difference: 0.185567
Component "table": Component "indexEnd": Mean relative difference: 0.1792453
Component "table": Component "L": Mean relative difference: 0.1666667
Component "table": Component "p.value": Mean relative difference: 1.091837
Component "table": Component "fwer": Mean relative difference: 0.2857143
Component "table": Component "p.valueArea": Mean relative difference: 1.091837
Component "table": Component "fwerArea": Mean relative difference: 0.2857143
Component "coef": Mean relative difference: 0.678983
Component "fitted": Mean relative difference: 0.4064462
Component "pvaluesMarginal": Mean relative difference: 0.7381116
Component "null": Component "value": Component 3: Mean relative difference: 1
Component "null": Component "value": Component 5: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 14: Mean relative difference: 1
Component "null": Component "value": Component 16: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 24: Mean relative difference: 1
Component "null": Component "value": Component 34: Mean relative difference: 1
Component "null": Component "value": Component 39: Mean relative difference: 1
Component "null": Component "value": Component 51: Mean relative difference: 1
Component "null": Component "value": Component 66: Mean relative difference: 1
Component "null": Component "value": Component 75: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 87: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 98: Mean relative difference: 1
Component "null": Component "value": Component 99: Mean relative difference: 1
Component "null": Component "value": Component 115: Mean relative difference: 1
Component "null": Component "value": Component 121: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 132: Mean relative difference: 1
Component "null": Component "value": Component 141: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 156: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 223: Mean relative difference: 1
Component "null": Component "value": Component 248: Mean relative difference: 1
Component "null": Component "value": Component 276: Mean relative difference: 1
Component "null": Component "value": Component 287: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 304: Mean relative difference: 1
Component "null": Component "value": Component 307: Mean relative difference: 1
Component "null": Component "value": Component 317: Mean relative difference: 1
Component "null": Component "value": Component 325: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 342: Mean relative difference: 1
Component "null": Component "value": Component 351: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 355: Mean relative difference: 1
Component "null": Component "value": Component 358: Mean relative difference: 1
Component "null": Component "value": Component 370: Mean relative difference: 1
Component "null": Component "value": Component 378: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 379: Mean relative difference: 1
Component "null": Component "value": Component 385: Mean relative difference: 1
Component "null": Component "value": Component 387: Mean relative difference: 1
Component "null": Component "value": Component 389: Mean relative difference: 1
Component "null": Component "value": Component 390: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 430: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 463: Mean relative difference: 1
Component "null": Component "value": Component 464: Mean relative difference: 1
Component "null": Component "value": Component 480: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 492: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 495: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 3: Mean relative difference: 1
Component "null": Component "length": Component 5: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 14: Mean relative difference: 1
Component "null": Component "length": Component 16: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 24: Mean relative difference: 1
Component "null": Component "length": Component 34: Mean relative difference: 1
Component "null": Component "length": Component 39: Mean relative difference: 1
Component "null": Component "length": Component 51: Mean relative difference: 1
Component "null": Component "length": Component 66: Mean relative difference: 1
Component "null": Component "length": Component 75: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 87: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 98: Mean relative difference: 1
Component "null": Component "length": Component 99: Mean relative difference: 1
Component "null": Component "length": Component 115: Mean relative difference: 1
Component "null": Component "length": Component 121: Mean absolute difference: 1
Component "null": Component "length": Component 132: Mean relative difference: 1
Component "null": Component "length": Component 141: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 156: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 223: Mean relative difference: 1
Component "null": Component "length": Component 248: Mean relative difference: 1
Component "null": Component "length": Component 276: Mean relative difference: 1
Component "null": Component "length": Component 287: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 304: Mean relative difference: 1
Component "null": Component "length": Component 307: Mean relative difference: 1
Component "null": Component "length": Component 317: Mean relative difference: 1
Component "null": Component "length": Component 325: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 342: Mean relative difference: 1
Component "null": Component "length": Component 351: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 355: Mean relative difference: 1
Component "null": Component "length": Component 358: Mean relative difference: 1
Component "null": Component "length": Component 370: Mean relative difference: 1
Component "null": Component "length": Component 378: Mean absolute difference: 1
Component "null": Component "length": Component 379: Mean relative difference: 1
Component "null": Component "length": Component 385: Mean relative difference: 1
Component "null": Component "length": Component 387: Mean relative difference: 1
Component "null": Component "length": Component 389: Mean relative difference: 1
Component "null": Component "length": Component 390: Mean absolute difference: 1
Component "null": Component "length": Component 430: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 463: Mean relative difference: 1
Component "null": Component "length": Component 464: Mean relative difference: 1
Component "null": Component "length": Component 480: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 492: Mean absolute difference: 1
Component "null": Component "length": Component 495: Numeric: lengths (1, 2) differ

FAILURE in test_bumphunterParallel: Error in checkEquals(bumps[nam], bumpsTest1[nam]) : 
  Component "table": Attributes: < Component "row.names": Mean relative difference: 0.6666667 >
Component "table": Component "start": Mean relative difference: 0.002954823
Component "table": Component "end": Mean relative difference: 0.003104456
Component "table": Component "value": Mean relative difference: 1.991512
Component "table": Component "area": Mean relative difference: 0.09979028
Component "table": Component "indexStart": Mean relative difference: 0.185567
Component "table": Component "indexEnd": Mean relative difference: 0.1792453
Component "table": Component "L": Mean relative difference: 0.1666667
Component "table": Component "p.value": Mean relative difference: 1.091837
Component "table": Component "fwer": Mean relative difference: 0.2857143
Component "table": Component "p.valueArea": Mean relative difference: 1.091837
Component "table": Component "fwerArea": Mean relative difference: 0.2857143
Component "coef": Mean relative difference: 0.678983
Component "fitted": Mean relative difference: 0.4064462
Component "pvaluesMarginal": Mean relative difference: 0.7381116
Component "null": Component "value": Component 3: Mean relative difference: 1
Component "null": Component "value": Component 5: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 14: Mean relative difference: 1
Component "null": Component "value": Component 16: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 24: Mean relative difference: 1
Component "null": Component "value": Component 34: Mean relative difference: 1
Component "null": Component "value": Component 39: Mean relative difference: 1
Component "null": Component "value": Component 51: Mean relative difference: 1
Component "null": Component "value": Component 66: Mean relative difference: 1
Component "null": Component "value": Component 75: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 87: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 98: Mean relative difference: 1
Component "null": Component "value": Component 99: Mean relative difference: 1
Component "null": Component "value": Component 115: Mean relative difference: 1
Component "null": Component "value": Component 121: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 132: Mean relative difference: 1
Component "null": Component "value": Component 141: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 156: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 223: Mean relative difference: 1
Component "null": Component "value": Component 248: Mean relative difference: 1
Component "null": Component "value": Component 276: Mean relative difference: 1
Component "null": Component "value": Component 287: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 304: Mean relative difference: 1
Component "null": Component "value": Component 307: Mean relative difference: 1
Component "null": Component "value": Component 317: Mean relative difference: 1
Component "null": Component "value": Component 325: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 342: Mean relative difference: 1
Component "null": Component "value": Component 351: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 355: Mean relative difference: 1
Component "null": Component "value": Component 358: Mean relative difference: 1
Component "null": Component "value": Component 370: Mean relative difference: 1
Component "null": Component "value": Component 378: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 379: Mean relative difference: 1
Component "null": Component "value": Component 385: Mean relative difference: 1
Component "null": Component "value": Component 387: Mean relative difference: 1
Component "null": Component "value": Component 389: Mean relative difference: 1
Component "null": Component "value": Component 390: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 430: Numeric: lengths (2, 1) differ
Component "null": Component "value": Component 463: Mean relative difference: 1
Component "null": Component "value": Component 464: Mean relative difference: 1
Component "null": Component "value": Component 480: Numeric: lengths (1, 2) differ
Component "null": Component "value": Component 492: Mean absolute difference: 0.2842654
Component "null": Component "value": Component 495: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 3: Mean relative difference: 1
Component "null": Component "length": Component 5: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 14: Mean relative difference: 1
Component "null": Component "length": Component 16: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 24: Mean relative difference: 1
Component "null": Component "length": Component 34: Mean relative difference: 1
Component "null": Component "length": Component 39: Mean relative difference: 1
Component "null": Component "length": Component 51: Mean relative difference: 1
Component "null": Component "length": Component 66: Mean relative difference: 1
Component "null": Component "length": Component 75: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 87: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 98: Mean relative difference: 1
Component "null": Component "length": Component 99: Mean relative difference: 1
Component "null": Component "length": Component 115: Mean relative difference: 1
Component "null": Component "length": Component 121: Mean absolute difference: 1
Component "null": Component "length": Component 132: Mean relative difference: 1
Component "null": Component "length": Component 141: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 156: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 223: Mean relative difference: 1
Component "null": Component "length": Component 248: Mean relative difference: 1
Component "null": Component "length": Component 276: Mean relative difference: 1
Component "null": Component "length": Component 287: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 304: Mean relative difference: 1
Component "null": Component "length": Component 307: Mean relative difference: 1
Component "null": Component "length": Component 317: Mean relative difference: 1
Component "null": Component "length": Component 325: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 342: Mean relative difference: 1
Component "null": Component "length": Component 351: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 355: Mean relative difference: 1
Component "null": Component "length": Component 358: Mean relative difference: 1
Component "null": Component "length": Component 370: Mean relative difference: 1
Component "null": Component "length": Component 378: Mean absolute difference: 1
Component "null": Component "length": Component 379: Mean relative difference: 1
Component "null": Component "length": Component 385: Mean relative difference: 1
Component "null": Component "length": Component 387: Mean relative difference: 1
Component "null": Component "length": Component 389: Mean relative difference: 1
Component "null": Component "length": Component 390: Mean absolute difference: 1
Component "null": Component "length": Component 430: Numeric: lengths (2, 1) differ
Component "null": Component "length": Component 463: Mean relative difference: 1
Component "null": Component "length": Component 464: Mean relative difference: 1
Component "null": Component "length": Component 480: Numeric: lengths (1, 2) differ
Component "null": Component "length": Component 492: Mean absolute difference: 1
Component "null": Component "length": Component 495: Numeric: lengths (1, 2) differ

FAILURE in test_loessByCluster: Error in checkEquals(smoothed, loessSmoothed) : 
  Component "fitted": Mean relative difference: 0.4823732

FAILURE in test_runmedByCluster: Error in checkEquals(smoothed, runmedSmoothed) : 
  Component "fitted": Mean relative difference: 0.6813414

FAILURE in test_smoother: Error in checkEquals(smoothed, loessSmoothed) : 
  Component "fitted": Mean relative difference: 0.4823732


Test files with failing tests

   test_bumphunter.R 
     test_bumphunter 
     test_bumphunterParallel 

   test_smoothers.R 
     test_loessByCluster 
     test_runmedByCluster 
     test_smoother 


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

Example timings

bumphunter.Rcheck/bumphunter-Ex.timings

nameusersystemelapsed
annotateNearest0.5820.0700.655
annotateTranscripts0.0010.0000.000
bumphunter3.4101.4762.783
clusterMaker0.0140.0040.018
dummyData0.0040.0010.005
getSegments0.0220.0040.026
locfitByCluster0.0630.0240.088
loessByCluster0.3020.0360.339
matchGenes000
regionFinder0.0350.0030.039
runmedByCluster0.0050.0000.006
smoother0.1420.0790.197