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CHECK report for trena on celaya2

This page was generated on 2019-04-09 13:18:21 -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 06:05:09 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:21:20 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 971.0 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) (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 ‘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                     5.029  0.389   5.419
getRegulatoryChromosomalRegions 1.033  0.052  32.674
* 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:
       /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_BayesSpikeSolver.R 
  
     test_FootprintFinder.R 
       /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_FootprintFinder.R 
  
     test_HumanDHSFilter.R 
       /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_HumanDHSFilter.R 
  
     test_RidgeSolver.R 
       /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_RidgeSolver.R 
  
  
  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’ ...
** using staged installation
** 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 from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path
* DONE (trena)

Tests output

trena.Rcheck/tests/runTests.Rout.fail


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.

> 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
Error in checkTrue(nrow(tbl.trimmed) == 12) : Test not TRUE

In addition: Warning message:
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_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
Error in loadNamespace(name) : 
  there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
In addition: Warning message:
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_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
Error in loadNamespace(name) : 
  there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
[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
Warning: call dbDisconnect() when finished working with a connection
[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
[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
[1] --- test_.injectSnp
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[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
Error in checkTrue(tbl$lambda < 0.9) : Test not TRUE

[1] --- test_getAssayData
[1] --- test_getTarget
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_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[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_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 06:21:10 2019 
*********************************************** 
Number of test functions: 65 
Number of errors: 4 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 65 test functions, 4 errors, 0 failures
ERROR in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_BayesSpikeSolver.R: Error while sourcing  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_BayesSpikeSolver.R : Error in checkTrue(nrow(tbl.trimmed) == 12) : Test not TRUE

ERROR in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_FootprintFinder.R: Error while sourcing  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_FootprintFinder.R : Error in loadNamespace(name) : 
  there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
ERROR in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_HumanDHSFilter.R: Error while sourcing  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_HumanDHSFilter.R : Error in loadNamespace(name) : 
  there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
ERROR in /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_RidgeSolver.R: Error while sourcing  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_RidgeSolver.R : Error in checkTrue(tbl$lambda < 0.9) : Test not TRUE


Test files with failing tests

   test_BayesSpikeSolver.R 
     /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_BayesSpikeSolver.R 

   test_FootprintFinder.R 
     /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_FootprintFinder.R 

   test_HumanDHSFilter.R 
     /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_HumanDHSFilter.R 

   test_RidgeSolver.R 
     /Library/Frameworks/R.framework/Versions/3.6/Resources/library/trena/unitTests/test_RidgeSolver.R 


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

Example timings

trena.Rcheck/trena-Ex.timings

nameusersystemelapsed
BayesSpikeSolver0.0170.0010.020
CandidateFilter-class0.0020.0000.002
EnsembleSolver0.0120.0020.013
FootprintFilter-class000
GeneOntologyFilter-class0.0560.0030.060
HumanDHSFilter-class0.0030.0000.004
LassoPVSolver0.0150.0030.018
LassoSolver0.0120.0030.015
MotifMatcher-class0.2490.0040.252
PearsonSolver0.0120.0030.014
RandomForestSolver0.0170.0030.021
RidgeSolver0.0010.0000.000
Solver-class0.0130.0030.016
SpearmanSolver0.0180.0030.020
SqrtLassoSolver0.0170.0030.021
Trena-class0.0010.0000.002
VarianceFilter-class0.0060.0020.007
assessSnp0.0000.0000.001
createGeneModelFromRegulatoryRegions0.0050.0010.005
createGeneModelFromTfList0.0020.0010.003
findMatchesByChromosomalRegion0.0010.0000.000
getAssayData0.0120.0030.016
getAvailableSolvers0.0000.0000.001
getCandidates-FootprintFilter-method0.0000.0010.001
getCandidates-GeneOntologyFilter-method1.0090.1531.167
getCandidates-HumanDHSFilter-method0.0000.0010.001
getCandidates-VarianceFilter-method0.0470.0060.053
getChromLoc0.0170.0020.020
getEncodeRegulatoryTableNames-HumanDHSFilter0.0010.0000.000
getFootprintsForGene0.0110.0020.014
getFootprintsInRegion0.0190.0020.022
getGeneModelTableColumnNames0.0000.0000.001
getGenePromoterRegion0.0150.0020.016
getGtfGeneBioTypes0.0170.0010.018
getGtfMoleculeTypes0.0150.0010.016
getPfms0.1210.0010.122
getPromoterRegionsAllGenes0.0690.0070.076
getProximalPromoter0.0010.0000.001
getRegulators0.0120.0020.014
getRegulatoryChromosomalRegions 1.033 0.05232.674
getRegulatoryRegions0.0000.0010.001
getRegulatoryTableColumnNames0.0010.0010.001
getSequence0.0010.0000.001
getSolverNames0.0160.0040.020
getTarget0.0090.0030.013
parseChromLocString0.0010.0010.001
parseDatabaseUri0.0010.0010.002
rescalePredictorWeights0.0170.0040.020
show-HumanDHSFilter-method0.0000.0000.001
show.BayesSpikeSolver0.0180.0040.022
show.EnsembleSolver0.0130.0030.016
show.LassoPVSolver0.0170.0040.022
show.LassoSolver0.0120.0040.016
show.MotifMatcher0.0380.0050.043
show.PearsonSolver0.0140.0010.015
show.RandomForestSolver0.0150.0020.016
show.RidgeSolver0.0150.0030.017
show.SpearmanSolver0.0170.0020.020
show.SqrtLassoSolver0.0180.0030.020
solve.BayesSpike0.0000.0000.001
solve.Lasso3.4140.3223.738
solve.LassoPV0.2930.0920.386
solve.Pearson0.0150.0030.018
solve.RandomForest3.2560.0323.289
solve.Ridge5.0290.3895.419
solve.Spearman0.0360.0060.042
solve.SqrtLasso0.0000.0000.001