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CHECK report for trena on merida2

This page was generated on 2019-04-09 13:35:06 -0400 (Tue, 09 Apr 2019).

Package 1636/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trena 1.5.8
Paul Shannon
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/trena
Branch: master
Last Commit: 6f670e4
Last Changed Date: 2018-11-28 13:55:59 -0400 (Wed, 28 Nov 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: trena
Version: 1.5.8
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:trena.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings trena_1.5.8.tar.gz
StartedAt: 2019-04-09 04:12:07 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:22:51 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 644.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: trena.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:trena.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings trena_1.5.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/trena.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 ‘trena/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trena’ version ‘1.5.8’
* 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 ‘trena’ 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 ... WARNING
Missing link or links in documentation object 'Trena-class.Rd':
  ‘createGeneModel’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'normalizeModel,PCAMax-method'
  ‘normalizing.max’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
solve.Ridge 5.045  0.237   5.326
* 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:
  ERROR in test_findMatchesByChromosomalRegion.twoAlternateAlleles: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
  
  Test files with failing tests
  
     test_MotifMatcher.R 
       test_.getScoredMotifs 
       test_.injectSnp 
       test_bugInStartEndOfMinusStrandHits 
       test_findMatchesByChromosomalRegion 
       test_findMatchesByChromosomalRegion.twoAlternateAlleles 
  
  
  Error in BiocGenerics:::testPackage("trena") : 
    unit tests failed for package trena
  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, 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/trena.Rcheck/00check.log’
for details.

Installation output

trena.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘trena’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
* DONE (trena)

Tests output

trena.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(trena) || stop("unable to load trena Package")
Loading required package: trena
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Loading required package: MotifDb
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:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand

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

    expand.grid

Loading required package: IRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

See system.file("LICENSE", package="MotifDb") for use restrictions.

[1] TRUE
> BiocGenerics:::testPackage('trena')
[1] --- test_BayesSpikeSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bayesSpike
[1] --- test_nOrderings
[1] --- test_BayesSpikeSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bayesSpike
[1] --- test_nOrderings
[1] --- test_CandidateFilter
[1] --- test_CandidateFilter
[1] --- test_EnsembleSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_selectedSolversOnly
[1] --- test_getSolverNames
[1] --- test_oneSolver
[1] --- test_invalidSolvers
[1] --- test_EnsembleSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_getSolverNames
[1] --- test_invalidSolvers
[1] --- test_oneSolver
[1] --- test_selectedSolversOnly
[1] --- test_FootprintFilter.byRegion
[1] --- test_FootprintFilter.byTwoRegions
[1] --- test_FootprintFilter.byRegion
[1] --- test_FootprintFilter.byTwoRegions
Loading required package: DBI
[1] --- test_parseDatabaseUri
[1] --- test_constructor
[1] --- test_getGtfGeneBioTypes
[1] --- test_getGtfMoleculeTypes
[1] --- test_getChromLoc
[1] --- test_getGenePromoterRegion
[1] --- test_getFootprintsInRegion
[1] --- test_getFootprintsInRegionWithVariants
[1] --- test_getFootprintsForGene
[1] --- test_constructor
[1] --- test_getChromLoc
[1] --- test_getFootprintsForGene
[1] --- test_getFootprintsInRegion
[1] --- test_getFootprintsInRegionWithVariants
[1] --- test_getGenePromoterRegion
[1] --- test_getGtfGeneBioTypes
[1] --- test_getGtfMoleculeTypes
[1] --- test_parseDatabaseUri
[1] --- test_directMode
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1] --- test_directMode
[1] --- test_getOpenChromatinFastAndSimple
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getOpenChromatinFastAndSimple
about to create RMariaDB driver, getting regulatory regions
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
Warning: call dbDisconnect() when finished working with a connection
[1] --- test_alpha.lasso
[1] --- test_lambda.lasso
[1] --- test_keep.metrics.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.lasso
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_keep.metrics.lasso
[1] --- test_lambda.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_.getScoredMotifs
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 0.043 0 0.046
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
In addition: Warning messages:
1: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
2: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
3: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_.injectSnp
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 0.041 0 0.042
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 0.244 0.001 0.247
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_findMatchesByChromosomalRegion
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 0.249 0.001 0.251
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 0.289 0.002 0.291
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_findMatchesByMultipleChromosomalRegions
[1] --- test_getSequence
[1] --- test_noMatch
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_alpha.ridge
[1] --- test_lambda.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.ridge
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_lambda.ridge
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getTarget
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
[1] --- test_basicConstructor
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite:///Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
about to create RMariaDB driver, getting regulatory regions
[1] calling HumanDHSFilter, span: 201
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite:///Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite:///Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_basicConstructor
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
about to create RMariaDB driver, getting regulatory regions
[1] calling HumanDHSFilter, span: 201
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite:///Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite:///Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite:///Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Tue Apr  9 04:22:36 2019 
*********************************************** 
Number of test functions: 86 
Number of errors: 5 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 86 test functions, 5 errors, 0 failures
ERROR in test_.getScoredMotifs: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_.injectSnp: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_bugInStartEndOfMinusStrandHits: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_findMatchesByChromosomalRegion: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_findMatchesByChromosomalRegion.twoAlternateAlleles: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed

Test files with failing tests

   test_MotifMatcher.R 
     test_.getScoredMotifs 
     test_.injectSnp 
     test_bugInStartEndOfMinusStrandHits 
     test_findMatchesByChromosomalRegion 
     test_findMatchesByChromosomalRegion.twoAlternateAlleles 


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

Example timings

trena.Rcheck/trena-Ex.timings

nameusersystemelapsed
BayesSpikeSolver0.0170.0010.018
CandidateFilter-class0.0010.0000.001
EnsembleSolver0.0140.0020.017
FootprintFilter-class0.0010.0000.001
GeneOntologyFilter-class0.0570.0030.061
HumanDHSFilter-class0.0020.0000.003
LassoPVSolver0.0110.0020.013
LassoSolver0.0100.0020.012
MotifMatcher-class0.2140.0040.220
PearsonSolver0.0100.0010.011
RandomForestSolver0.0110.0010.013
RidgeSolver000
Solver-class0.0090.0010.010
SpearmanSolver0.0140.0020.017
SqrtLassoSolver0.0120.0010.013
Trena-class0.0010.0010.001
VarianceFilter-class0.0070.0010.007
assessSnp000
createGeneModelFromRegulatoryRegions0.0040.0010.005
createGeneModelFromTfList0.0020.0000.001
findMatchesByChromosomalRegion0.0010.0000.000
getAssayData0.0300.0040.034
getAvailableSolvers0.0000.0010.000
getCandidates-FootprintFilter-method0.0000.0000.001
getCandidates-GeneOntologyFilter-method0.8920.1601.072
getCandidates-HumanDHSFilter-method0.0010.0000.001
getCandidates-VarianceFilter-method0.0160.0010.016
getChromLoc0.0160.0010.018
getEncodeRegulatoryTableNames-HumanDHSFilter0.0000.0010.000
getFootprintsForGene0.0130.0010.015
getFootprintsInRegion0.0200.0020.021
getGeneModelTableColumnNames0.0010.0000.001
getGenePromoterRegion0.0160.0010.017
getGtfGeneBioTypes0.0120.0010.014
getGtfMoleculeTypes0.0090.0000.009
getPfms0.1630.0020.168
getPromoterRegionsAllGenes0.0580.0020.060
getProximalPromoter0.0010.0010.000
getRegulators0.0100.0010.012
getRegulatoryChromosomalRegions0.8410.0404.168
getRegulatoryRegions0.0010.0000.000
getRegulatoryTableColumnNames000
getSequence000
getSolverNames0.0180.0030.021
getTarget0.0110.0010.013
parseChromLocString0.0000.0010.000
parseDatabaseUri0.0010.0000.002
rescalePredictorWeights0.0360.0020.039
show-HumanDHSFilter-method0.0000.0010.000
show.BayesSpikeSolver0.0130.0000.013
show.EnsembleSolver0.0100.0010.011
show.LassoPVSolver0.0140.0010.015
show.LassoSolver0.0100.0010.011
show.MotifMatcher0.0100.0010.011
show.PearsonSolver0.0130.0010.015
show.RandomForestSolver0.0140.0020.015
show.RidgeSolver0.0130.0010.013
show.SpearmanSolver0.0200.0020.021
show.SqrtLassoSolver0.0160.0010.018
solve.BayesSpike000
solve.Lasso2.9390.1843.137
solve.LassoPV0.1950.0440.241
solve.Pearson0.0130.0020.014
solve.RandomForest3.4540.0273.505
solve.Ridge5.0450.2375.326
solve.Spearman0.0320.0030.035
solve.SqrtLasso000