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CHECK report for trena on tokay2

This page was generated on 2018-10-17 08:44:00 -0400 (Wed, 17 Oct 2018).

Package 1503/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trena 1.2.0
Paul Shannon
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/trena
Branch: RELEASE_3_7
Last Commit: d75e0f5
Last Changed Date: 2018-04-30 10:35:46 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: trena
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:trena.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings trena_1.2.0.tar.gz
StartedAt: 2018-10-17 05:16:14 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:40:23 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1448.9 seconds
RetCode: 0
Status:  OK  
CheckDir: trena.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:trena.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings trena_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/trena.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'trena/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'trena' version '1.2.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... 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 ... 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 include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/trena.Rcheck/00check.log'
for details.



Installation output

trena.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL trena
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/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
  converting help for package 'trena'
    finding HTML links ... done
    BayesSpikeSolver-class                  html  
    BayesSpikeSolver                        html  
    CandidateFilter-class                   html  
    EnsembleSolver-class                    html  
    EnsembleSolver                          html  
    FootprintFilter-class                   html  
    FootprintFinder-class                   html  
    GeneOntologyFilter-class                html  
    HumanDHSFilter-class                    html  
    LassoPVSolver-class                     html  
    LassoPVSolver                           html  
    LassoSolver-class                       html  
    LassoSolver                             html  
    MotifMatcher-class                      html  
    finding level-2 HTML links ... done

    PearsonSolver-class                     html  
    PearsonSolver                           html  
    RandomForestSolver-class                html  
    RandomForestSolver                      html  
    RidgeSolver-class                       html  
    RidgeSolver                             html  
    Solver-class                            html  
    SpearmanSolver-class                    html  
    SpearmanSolver                          html  
    SqrtLassoSolver-class                   html  
    SqrtLassoSolver                         html  
    TReNA-package                           html  
    Trena-class                             html  
    VarianceFilter-class                    html  
    assessSnp                               html  
    closeDatabaseConnections                html  
    createGeneModel                         html  
    elasticNetSolver                        html  
    findMatchesByChromosomalRegion          html  
    getAssayData                            html  
    getAvailableSolvers                     html  
    getCandidates-FootprintFilter-method    html  
    getCandidates-GeneOntologyFilter-method
                                            html  
    getCandidates-HumanDHSFilter-method     html  
    getCandidates-VarianceFilter-method     html  
    getCandidates                           html  
    getChromLoc                             html  
    getEncodeRegulatoryTableNames-HumanDHSFilter
                                            html  
    getFootprintsForGene                    html  
    getFootprintsInRegion                   html  
    getGeneModelTableColumnNames            html  
    getGenePromoterRegion                   html  
    getGtfGeneBioTypes                      html  
    getGtfMoleculeTypes                     html  
    getPfms                                 html  
    getPromoterRegionsAllGenes              html  
    getProximalPromoter                     html  
    getRegulators                           html  
    getRegulatoryChromosomalRegions         html  
    getRegulatoryRegions                    html  
    getRegulatoryTableColumnNames           html  
    getSequence                             html  
    getSolverNames                          html  
    getTarget                               html  
    parseChromLocString                     html  
    parseDatabaseUri                        html  
    rescalePredictorWeights                 html  
    run                                     html  
    show-HumanDHSFilter-method              html  
    show.BayesSpikeSolver                   html  
    show.EnsembleSolver                     html  
    show.LassoPVSolver                      html  
    show.LassoSolver                        html  
    show.MotifMatcher                       html  
    show.PearsonSolver                      html  
    show.RandomForestSolver                 html  
    show.RidgeSolver                        html  
    show.SpearmanSolver                     html  
    show.SqrtLassoSolver                    html  
    solve.BayesSpike                        html  
    solve.Ensemble                          html  
    solve.Lasso                             html  
    solve.LassoPV                           html  
    solve.Pearson                           html  
    solve.RandomForest                      html  
    solve.Ridge                             html  
    solve.Spearman                          html  
    solve.SqrtLasso                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
See system.file("LICENSE", package="MotifDb") for use restrictions.
*** arch - x64
See system.file("LICENSE", package="MotifDb") for use restrictions.
* DONE (trena)
Making 'packages.html' ... done
In R CMD INSTALL

Tests output

trena.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

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

    windows

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
[1] --- test_constructor
[1] --- test_getChromLoc
[1] --- test_getFootprintsForGene
[1] --- test_getFootprintsInRegion
[1] --- test_getFootprintsInRegionWithVariants
Warning: call dbDisconnect() when finished working with a connection
[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_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_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] best$seq: ACCAGCATGCAAATTAGACAA
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByChromosomalRegion_contrastReferenceWithVariant
[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
[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
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
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See system.file("LICENSE", package="MotifDb") for use restrictions.
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See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
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See system.file("LICENSE", package="MotifDb") for use restrictions.
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          class
              <environment: namespace:flare>
            Y
            X
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
          class
          class
          class
          class
          class
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          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            time1
            time2
            tz
            units
          class
          class
          class
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          class
          class
          class
          class
          class
              <environment: namespace:base>
            x
            tz
            ...
          class
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          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
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          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
          class
          class
          class
              <environment: namespace:flare>
            Y
            X
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
          class
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          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
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          class
              <environment: namespace:base>
            time1
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            tz
            units
          class
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              <environment: namespace:base>
            x
            tz
            ...
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          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
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          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
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          class
              <environment: namespace:flare>
            Y
            X
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
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          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
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          class
              <environment: namespace:base>
            time1
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            tz
            units
          class
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              <environment: namespace:base>
            x
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            ...
          class
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          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              [1]
              [2]
              [3]
            names
              <environment: namespace:BiocParallel>
            node
          class
          class
              [1]
              [2]
              [3]
            names
                            [1]
<environment: namespace:parallel>
              [2]
                          [3]
node
                          <environment: namespace:BiocParallel>
                      class
names
                        [1]
node
              [2]
class
              [3]
                      class
          class
names
              <environment: namespace:BiocParallel>
            node
          class
          class
                            <environment: namespace:parallel>
<environment: namespace:BiocParallel>
                        node
node
                                  class
class
          <environment: namespace:parallel>
          class
            class
node
          class
          class
              <environment: namespace:parallel>
            node
          class
          class
              <environment: namespace:RSQLite>
            con_
          class
                            <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                                      con_
con_
<environment: namespace:RSQLite>
                                class
con_
class
                        <environment: namespace:RSQLite>
class
            con_
          class
                            <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                        con_
con_
          class
          class
              <environment: namespace:RSQLite>
            con_
          class
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d240>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6b0>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d3f0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b860>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d368>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b7d8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d238>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6a8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d240>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6b0>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
          class
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          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
          class
          class
          class
              <environment: namespace:flare>
            Y
            X
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
          class
          class
          class
          class
          class
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          class
          class
          class
          class
          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            time1
            time2
            tz
            units
          class
          class
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          class
              <environment: namespace:base>
            x
            tz
            ...
          class
          class
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          class
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          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
          class
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          class
          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
          class
          class
          class
              <environment: namespace:flare>
            Y
            X
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            time1
            time2
            tz
            units
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            x
            tz
            ...
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
          class
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          class
          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
          class
          class
          class
              <environment: namespace:flare>
            Y
            X
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
          class
          class
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          class
          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            time1
            time2
            tz
            units
          class
          class
          class
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          class
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          class
          class
              <environment: namespace:base>
            x
            tz
            ...
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
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              [2]
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class
              [3]
class
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names
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<environment: namespace:BiocParallel>
class
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<environment: namespace:BiocParallel>
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            con_
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con_
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<environment: namespace:RSQLite>
                                      con_
<environment: namespace:RSQLite>
con_
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          class
              class
con_
<environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                          <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                                    <environment: namespace:RSQLite>
con_
            con_
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          <environment: namespace:RSQLite>
class
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                          <environment: namespace:RSQLite>
                      con_
con_
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                      class
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con_
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                      con_
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            con_
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<environment: namespace:RSQLite>
            con_
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              con_
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[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d1c0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b630>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d240>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6b0>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d3f0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b860>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
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    class
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    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
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              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
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              <environment: namespace:flare>
            Y
            X
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            nlambda
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            d
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            rho
            max.ite
            prec
            intercept
            verbose
          class
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              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
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            [3]
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            time1
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              <environment: namespace:base>
            x
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            ...
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              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
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            elapsed
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              <environment: namespace:flare>
            X
            Y
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            rho
            method
            q
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            prec
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            verbose
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              <environment: namespace:base>
            x
            trim
            na.rm
            ...
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              <environment: namespace:flare>
            Y
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            lambda
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            n
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            rho
            max.ite
            prec
            intercept
            verbose
          class
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          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
          class
          class
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          class
              <environment: namespace:base>
            time1
            time2
            tz
            units
          class
          class
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              <environment: namespace:base>
            x
            tz
            ...
          class
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          class
          class
          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              [1]
              [2]
              [3]
            names
              [1]
              [2]
              [3]
            names
              <environment: namespace:BiocParallel>
            node
          class
              [1]
                            [2]
          <environment: namespace:BiocParallel>
              [3]
class
                                      [1]
              [2]
node
              [3]
names
                      names
class
          class
                            <environment: namespace:parallel>
<environment: namespace:BiocParallel>
            node
                      node
class
          class
                                      <environment: namespace:parallel>
class
<environment: namespace:BiocParallel>
                                    <environment: namespace:parallel>
            node
node
class
          class
                                class
class
node
          class
          class
          class
              <environment: namespace:parallel>
            node
          class
          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            con_
          class
                            <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                        con_
con_
                                  class
<environment: namespace:RSQLite>
class
            con_
          class
              <environment: namespace:RSQLite>
            con_
          class
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d2e8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b758>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d1c0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b630>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d3f0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b860>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d368>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b7d8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d240>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6b0>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d218>
lambda
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    as.error
    timeout
        <environment: 0x000000000518b688>
      ...
    class
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            [3]
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See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x000000000518d288>
lambda
    log
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    stop.immediate
    as.error
    timeout
        <environment: 0x000000000518b6f8>
      ...
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            [3]
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            x
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[1] --- test_basicConstructor
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.7-bioc/R/library/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://C:/Users/biocbuild/bbs-3.7-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.7-bioc/R/library/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://C:/Users/biocbuild/bbs-3.7-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.7-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.7-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Wed Oct 17 05:40:12 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 
 356.01   18.93 1079.06 

Example timings

trena.Rcheck/trena-Ex.timings

nameusersystemelapsed
BayesSpikeSolver0.010.010.20
CandidateFilter-class000
EnsembleSolver0.010.000.02
FootprintFilter-class000
GeneOntologyFilter-class0.070.020.15
HumanDHSFilter-class0.020.000.02
LassoPVSolver0.020.000.01
LassoSolver0.010.000.02
MotifMatcher-class0.270.000.26
PearsonSolver0.010.000.02
RandomForestSolver0.020.000.02
RidgeSolver000
Solver-class0.010.000.01
SpearmanSolver0.040.000.03
SqrtLassoSolver0.010.000.02
Trena-class000
VarianceFilter-class0.020.000.01
assessSnp000
createGeneModel000
findMatchesByChromosomalRegion000
getAssayData0.020.000.01
getAvailableSolvers000
getCandidates-FootprintFilter-method000
getCandidates-GeneOntologyFilter-method1.120.081.22
getCandidates-HumanDHSFilter-method000
getCandidates-VarianceFilter-method0.070.000.07
getChromLoc0.040.000.28
getEncodeRegulatoryTableNames-HumanDHSFilter000
getFootprintsForGene0.030.000.03
getFootprintsInRegion0.020.000.03
getGeneModelTableColumnNames000
getGenePromoterRegion0.030.000.03
getGtfGeneBioTypes0.020.000.02
getGtfMoleculeTypes0.010.000.01
getPfms0.200.010.22
getPromoterRegionsAllGenes0.070.020.08
getProximalPromoter000
getRegulators0.010.000.01
getRegulatoryChromosomalRegions1.080.033.74
getRegulatoryRegions000
getRegulatoryTableColumnNames000
getSequence000
getSolverNames0.020.000.01
getTarget0.010.000.02
parseChromLocString000
parseDatabaseUri000
rescalePredictorWeights0.020.000.02
show-HumanDHSFilter-method000
show.BayesSpikeSolver0.010.010.03
show.EnsembleSolver0.020.000.01
show.LassoPVSolver0.030.000.03
show.LassoSolver0.000.020.02
show.MotifMatcher0.020.000.02
show.PearsonSolver0.030.000.03
show.RandomForestSolver0.030.000.03
show.RidgeSolver0.010.000.01
show.SpearmanSolver0.040.000.03
show.SqrtLassoSolver0.000.020.02
solve.BayesSpike000
solve.Ensemble000
solve.Lasso2.890.103.00
solve.LassoPV0.240.020.25
solve.Pearson0.030.000.03
solve.RandomForest3.730.003.73
solve.Ridge4.720.034.75
solve.Spearman0.030.000.03
solve.SqrtLasso000