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CHECK report for trena on veracruz1

This page was generated on 2018-04-12 13:45:00 -0400 (Thu, 12 Apr 2018).

Package 1419/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trena 1.0.3
Paul Shannon
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/trena
Branch: RELEASE_3_6
Last Commit: a4c7bbb
Last Changed Date: 2018-03-03 14:58:28 -0400 (Sat, 03 Mar 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: trena
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings trena_1.0.3.tar.gz
StartedAt: 2018-04-12 10:29:14 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 10:43:32 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 858.2 seconds
RetCode: 0
Status:  OK 
CheckDir: trena.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings trena_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.3’
* 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 loading without being on the library search path ... 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 ... NOTE
.elasticNetSolver: no visible binding for global variable
  ‘cor.target.feature’
assessSnp,Trena: no visible binding for global variable ‘status’
assessSnp,Trena: no visible binding for global variable ‘assessed’
assessSnp,Trena: no visible binding for global variable
  ‘motifRelativeScore’
Undefined global functions or variables:
  assessed cor.target.feature motifRelativeScore status
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
FootprintFilter-class 0.386  0.011   5.465
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck/00check.log’
for details.



Installation output

trena.Rcheck/00install.out

* installing *source* package ‘trena’ ...
** R
** inst
** preparing 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


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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_pcaError
[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_pcaError
[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
Warning: call dbDisconnect() when finished working with a connection
[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_basicConstructor
[1] --- test_getEncodeRegulatoryTableNames
[1] --- test_checkSampleOfEncodeTables
[1] --- wgEncodeRegDnaseUwAg04449Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHmvecdneoPeak: 0 rows
[1] --- wgEncodeRegDnaseUwTh1Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHsmmtubePeak: 0 rows
[1] --- wgEncodeRegDnaseUwHcpepicPeak: 0 rows
[1] --- wgEncodeRegDnaseUwNhaPeak: 0 rows
[1] --- wgEncodeRegDnaseUwNb4Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHmvecdlyadPeak: 0 rows
[1] --- wgEncodeRegDnaseUwBonemarrowmscPeak: 0 rows
[1] --- wgEncodeRegDnaseUwGm06990Peak: 0 rows
[1] --- test_getRegulatoryRegions
[1] --- test_getCandidates.emptyRegion
[1] --- test_getCandidates.vrk2.twoRegions
[1] --- test_getCandidates.vrk2.rs13384219.variant
[1] --- test_basicConstructor
[1] --- test_checkSampleOfEncodeTables
[1] --- test_getCandidates.emptyRegion
[1] --- test_getCandidates.vrk2.rs13384219.variant
[1] --- test_getCandidates.vrk2.twoRegions
[1] --- test_getEncodeRegulatoryTableNames
[1] --- test_getRegulatoryRegions
[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
[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_.matchPwmForwardAndReverse
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
  chrom    start      end                   seq status
1  chr2 57907313 57907333 ACCAGCATGCAAATTAGACAA     wt
[1] 1 +
[1] 1 -
[1] 1 +
[1] 1 +
[1] 1 +
[1] --- about to check best$seq
$motifName
[1] "Hsapiens-jaspar2016-POU5F1B-MA0792.1"

$chrom
[1] "chr2"

$motifStart
[1] 57907318

$motifEnd
[1] 57907326

$strand
[1] "+"

$motifScore
[1] 6.707832

$motifRelativeScore
[1] 0.9208761

$match
[1] "CATGCAAAT"

$chromStart
[1] 57907313

$chromEnd
[1] 57907333

$seq
[1] "ACCAGCATGCAAATTAGACAA"

$status
[1] "wt"

[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByChromosomalRegion_contrastReferenceWithVariant
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
  chrom    start      end                   seq status
1  chr2 57907313 57907333 ACCAGCATGCAAATTAGACAA     wt
[1] 1 +
[1] 1 -
[1] 1 +
[1] 1 +
[1] 1 +
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
  chrom    start      end                   seq status
1  chr2 57907313 57907333 ACCAGCATGCGAATTAGACAA    mut
[1] 1 +
[1] 1 -
[1] 1 +
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
  chrom    start      end                   seq status
1  chr2 57907313 57907333 ACCAGCATGCAAATTAGACAA     wt
[1] 1 +
[1] 1 -
[1] 1 +
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[1] ---- MotifMatcher::findMatchesByChromosomalRegion
  chrom    start      end                   seq status
1  chr2 57907313 57907333 ACCAGCATGCGAATTAGACAA    mut
[1] 1 +
[1] 1 -
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[1] --- test_findMatchesByMultipleChromosomalRegions
[1] --- test_getSequence
[1] --- test_getSequenceWithVariants
[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
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_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RandomForestSolverConstructor
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_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:///Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
[1] calling HumanDHSFilter, span: 201
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite:///Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite:///Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_createGeneModel
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_assessSnp
[1] error, unrecognized variant name: 'rsBogus'
[1] --- test_assessSnp_allTypesWithDeltas
[1] --- test_basicConstructor
[1] --- test_createGeneModel
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
[1] calling HumanDHSFilter, span: 201
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite:///Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite:///Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite:///Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Thu Apr 12 10:43:24 2018 
*********************************************** 
Number of test functions: 85 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 85 test functions, 0 errors, 0 failures
Number of test functions: 85 
Number of errors: 0 
Number of failures: 0 
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
> 
> proc.time()
   user  system elapsed 
415.884  24.970 533.914 

Example timings

trena.Rcheck/trena-Ex.timings

nameusersystemelapsed
BayesSpikeSolver0.0220.0010.023
CandidateFilter-class0.0010.0000.001
EnsembleSolver0.0090.0010.010
FootprintFilter-class0.3860.0115.465
GeneOntologyFilter-class0.0290.0010.031
HumanDHSFilter-class0.9340.0084.318
LassoPVSolver0.0080.0010.008
LassoSolver0.0080.0000.008
MotifMatcher-class0.0640.0010.065
PearsonSolver0.0080.0010.009
RandomForestSolver0.0080.0010.009
RidgeSolver0.0080.0010.009
Solver-class0.0070.0010.008
SpearmanSolver0.0080.0010.009
SqrtLassoSolver0.0080.0000.009
Trena-class0.0010.0000.000
VarianceFilter-class0.0040.0000.004
assessSnp000
createGeneModel3.3780.0614.260
findMatchesByChromosomalRegion0.0010.0000.001
getAssayData0.0100.0000.012
getAvailableSolvers0.0010.0000.000
getCandidates-FootprintFilter-method0.2070.0083.472
getCandidates-GeneOntologyFilter-method1.0170.0701.142
getCandidates-HumanDHSFilter-method0.0010.0000.002
getCandidates-VarianceFilter-method0.0130.0010.014
getChromLoc0.0120.0010.012
getEncodeRegulatoryTableNames-HumanDHSFilter0.3110.0084.658
getFootprintsForGene0.0120.0000.013
getFootprintsInRegion0.0150.0000.015
getGeneModelTableColumnNames0.0010.0010.001
getGenePromoterRegion0.0290.0000.028
getGtfGeneBioTypes0.0110.0000.012
getGtfMoleculeTypes0.0110.0010.012
getPfms0.2040.0010.207
getPromoterRegionsAllGenes0.1590.0020.167
getProximalPromoter0.0920.0073.426
getRegulators0.0100.0010.013
getRegulatoryChromosomalRegions0.8690.0061.654
getRegulatoryRegions0.0010.0000.001
getRegulatoryTableColumnNames0.0010.0000.000
getSequence0.0010.0000.002
getSolverNames0.0080.0000.009
getTarget0.0070.0010.008
parseChromLocString0.010.000.01
parseDatabaseUri0.0020.0010.002
rescalePredictorWeights0.0110.0010.013
show-HumanDHSFilter-method0.2410.0094.127
show.BayesSpikeSolver0.0160.0000.016
show.EnsembleSolver0.0080.0010.009
show.LassoPVSolver0.0130.0010.014
show.LassoSolver0.0090.0020.010
show.MotifMatcher0.0120.0020.012
show.PearsonSolver0.0120.0010.013
show.RandomForestSolver0.0180.0020.020
show.RidgeSolver0.0090.0000.009
show.SpearmanSolver0.0160.0010.017
show.SqrtLassoSolver0.0160.0010.017
solve.BayesSpike0.0010.0000.001
solve.Ensemble0.0000.0000.001
solve.Lasso2.6600.1172.832
solve.LassoPV0.2260.0290.258
solve.Pearson0.0260.0020.027
solve.RandomForest3.1100.0153.165
solve.Ridge4.4270.1494.632
solve.Spearman0.0260.0010.032
solve.SqrtLasso0.0010.0000.001