Multiple platform build/check report for BioC 3.7 - CHECK report for trena on tokay2


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)

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> 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.
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[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
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        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
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    class
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        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
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        names
            [3]
          names
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              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
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            X
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            x
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              [1]
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              [1]
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                        [2]
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<environment: namespace:parallel>
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<environment: namespace:BiocParallel>
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names
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                        [2]
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                        [3]
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                        [1]
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              [2]
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              [1]
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              [1]
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              [2]
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                      <environment: namespace:parallel>
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              [3]
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                      node
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                          <environment: namespace:parallel>
<environment: namespace:BiocParallel>
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class
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            class
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                    class
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<environment: namespace:BiocParallel>
                                                        <environment: namespace:parallel>
class
            class
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                      class
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            class
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          <environment: namespace:parallel>
                          <environment: namespace:parallel>
class
node
                      node
class
                    class
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          class
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              <environment: namespace:RSQLite>
            con_
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                            <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                                        <environment: namespace:RSQLite>
            <environment: namespace:RSQLite>
con_
                        con_
con_
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                    class
          class
class
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                            <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                                      con_
<environment: namespace:RSQLite>
con_
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          class
              class
con_
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<environment: namespace:RSQLite>
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<environment: namespace:RSQLite>
                                    <environment: namespace:RSQLite>
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            con_
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          <environment: namespace:RSQLite>
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                      con_
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            con_
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                    class
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            con_
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              <environment: namespace:RSQLite>
                          <environment: namespace:RSQLite>
              con_
            <environment: namespace:RSQLite>
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                      con_
              class
                    <environment: namespace:RSQLite>
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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
    class
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        names
            [3]
          names
            names
              <environment: namespace:base>
            cpu
            elapsed
            transient
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              <environment: namespace:flare>
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              <environment: namespace:base>
            x
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              <environment: namespace:flare>
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          x
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            x
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            x
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            rho
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            x
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            na.rm
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            time1
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            xx
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            cl
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              [1]
              [2]
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              [1]
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              <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>
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class
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<environment: namespace:BiocParallel>
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node
class
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            con_
          class
                            <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                        con_
con_
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<environment: namespace:RSQLite>
class
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              <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
    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
              <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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              <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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              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
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          class
              <environment: namespace:base>
            time1
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            units
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              <environment: namespace:base>
            x
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            ...
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          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
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          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
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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
          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
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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
            max.ite
            verbose
          class
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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
name	user	system	elapsed
BayesSpikeSolver	0.01	0.01	0.20
CandidateFilter-class	0	0	0
EnsembleSolver	0.01	0.00	0.02
FootprintFilter-class	0	0	0
GeneOntologyFilter-class	0.07	0.02	0.15
HumanDHSFilter-class	0.02	0.00	0.02
LassoPVSolver	0.02	0.00	0.01
LassoSolver	0.01	0.00	0.02
MotifMatcher-class	0.27	0.00	0.26
PearsonSolver	0.01	0.00	0.02
RandomForestSolver	0.02	0.00	0.02
RidgeSolver	0	0	0
Solver-class	0.01	0.00	0.01
SpearmanSolver	0.04	0.00	0.03
SqrtLassoSolver	0.01	0.00	0.02
Trena-class	0	0	0
VarianceFilter-class	0.02	0.00	0.01
assessSnp	0	0	0
createGeneModel	0	0	0
findMatchesByChromosomalRegion	0	0	0
getAssayData	0.02	0.00	0.01
getAvailableSolvers	0	0	0
getCandidates-FootprintFilter-method	0	0	0
getCandidates-GeneOntologyFilter-method	1.12	0.08	1.22
getCandidates-HumanDHSFilter-method	0	0	0
getCandidates-VarianceFilter-method	0.07	0.00	0.07
getChromLoc	0.04	0.00	0.28
getEncodeRegulatoryTableNames-HumanDHSFilter	0	0	0
getFootprintsForGene	0.03	0.00	0.03
getFootprintsInRegion	0.02	0.00	0.03
getGeneModelTableColumnNames	0	0	0
getGenePromoterRegion	0.03	0.00	0.03
getGtfGeneBioTypes	0.02	0.00	0.02
getGtfMoleculeTypes	0.01	0.00	0.01
getPfms	0.20	0.01	0.22
getPromoterRegionsAllGenes	0.07	0.02	0.08
getProximalPromoter	0	0	0
getRegulators	0.01	0.00	0.01
getRegulatoryChromosomalRegions	1.08	0.03	3.74
getRegulatoryRegions	0	0	0
getRegulatoryTableColumnNames	0	0	0
getSequence	0	0	0
getSolverNames	0.02	0.00	0.01
getTarget	0.01	0.00	0.02
parseChromLocString	0	0	0
parseDatabaseUri	0	0	0
rescalePredictorWeights	0.02	0.00	0.02
show-HumanDHSFilter-method	0	0	0
show.BayesSpikeSolver	0.01	0.01	0.03
show.EnsembleSolver	0.02	0.00	0.01
show.LassoPVSolver	0.03	0.00	0.03
show.LassoSolver	0.00	0.02	0.02
show.MotifMatcher	0.02	0.00	0.02
show.PearsonSolver	0.03	0.00	0.03
show.RandomForestSolver	0.03	0.00	0.03
show.RidgeSolver	0.01	0.00	0.01
show.SpearmanSolver	0.04	0.00	0.03
show.SqrtLassoSolver	0.00	0.02	0.02
solve.BayesSpike	0	0	0
solve.Ensemble	0	0	0
solve.Lasso	2.89	0.10	3.00
solve.LassoPV	0.24	0.02	0.25
solve.Pearson	0.03	0.00	0.03
solve.RandomForest	3.73	0.00	3.73
solve.Ridge	4.72	0.03	4.75
solve.Spearman	0.03	0.00	0.03
solve.SqrtLasso	0	0	0
CHECK report for trena on tokay2

Summary

Command output

Installation output

Tests output

Example timings
