R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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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, 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
Error in checkTrue(nrow(tbl.trimmed) == 12) : Test not TRUE

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

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

[1] --- test_directMode
[1] --- test_getOpenChromatinFastAndSimple
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getOpenChromatinFastAndSimple
about to create RMariaDB driver, getting regulatory regions
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_alpha.lasso
Warning: call dbDisconnect() when finished working with a connection
[1] --- test_lambda.lasso
[1] --- test_keep.metrics.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.lasso
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_keep.metrics.lasso
[1] --- test_lambda.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_.getScoredMotifs
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.03 0 0.06
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
In addition: Warning message:
In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_.injectSnp
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.05 0 0.17
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.38 0 0.94
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_findMatchesByChromosomalRegion
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.34 0 0.5
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.39 0 0.39
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_findMatchesByMultipleChromosomalRegions
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.25 0 0.25
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_getSequence
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.1 0 0.09
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_noMatch
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open C:/Users/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.26 0 0.27
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_alpha.ridge
[1] --- test_lambda.ridge
[1] --- test_keep.metrics.ridge
Error in checkTrue(tbl$lambda < 0.9) : Test not TRUE

[1] --- test_getAssayData
[1] --- test_getTarget
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.


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          class
          class
          class
          class
          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:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          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
          class
          class
          class
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          class
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          class
          class
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          class
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          class
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          class
          class
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          class
          class
          class
          class
          class
          class
          class
          class
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          class
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          class
          class
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          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          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
              [1]
            names
              [1]
            names
              [1]
              [1]
                        names
names
              <environment: namespace:parallel>
            node
          class
          class
              <environment: namespace:base>
            save
                          status
            <environment: namespace:parallel>
            runLast
node
          class
                    class
class
              <environment: namespace:base>
            save
            status
            runLast
          class
              <environment: namespace:parallel>
            node
          class
          class
              <environment: namespace:base>
            save
            status
            runLast
                        <environment: namespace:parallel>
            class
node
          class
          class
              <environment: namespace:methods>
            self
            field
            thisClass
            selfEnv
          class
          class
                        class
<environment: namespace:base>
                      class
          class
save
                                    class
<environment: namespace:methods>
status
                                  runLast
self
class
                      class
          field
class
                      class
thisClass
                      class
selfEnv
          class
          class
          class
          class
          class
          class
          class
                    class
class
                    class
class
          class
          class
          class
          class
          class
          class
                        <environment: namespace:methods>
class
                      def
class
                      self
class
                      me
            class
selfEnv
                      thisClass
class
          class
          class
          class
          class
                        <environment: namespace:methods>
class
                      class
          self
            class
          class
field
          class
                      class
thisClass
                      class
              <environment: namespace:methods>
                      selfEnv
class
def
                      class
          self
class
                      class
me
                                class
class
          selfEnv
                      class
class
thisClass
                    class
class
                    class
              class
          <environment: namespace:methods>
class
          class
                                self
class
          class
                      class
class
                              class
class
class
                    field
                      class
class
          class
class
          thisClass
class
                    class
                                selfEnv
class
class
class
                              class
class
                    class
class
          class
class
                                        class
class
class
                    class
                    class
class
class
                    class
          class
          class
class
          class
                    class
class
          class
                    class
class
          class
class
                              class
class
class
                    class
          class
class
                    class
          class
          class
                    class
class
class
                              class
class
          class
class
                    class
class
                                  class
class
          <environment: namespace:RSQLite>
                      class
class
                    con_
class
class
                              class
                        class
<environment: namespace:methods>
          class
class
class
                    class
class
                      def
class
                      class
self
                                                  <environment: namespace:RSQLite>
me
                        class
con_
<environment: namespace:methods>
                    selfEnv
            class
class
            thisClass
def
            self
            me
            selfEnv
            thisClass
          class
          class
          class
          class
          class
          class
                    class
          class
          class
          class
class
                        class
                    <environment: namespace:RSQLite>
class
            class
con_
                              class
class
class
                    class
class
                    class
class
                    class
class
                    class
class
                        class
<environment: namespace:RSQLite>
                                class
con_
          class
                    class
class
          class
class
          class
                    class
class
                    class
class
                    class
class
                    class
class
                    class
class
                    class
class
          class
                    class
class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:RSQLite>
            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.
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088f59a0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02189908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class

  <environment: 0x08872bd0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x08893bb8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088f4fa8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x08914e10>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021898e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x08883158>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088835a8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088e62c8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x08882e90>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a912ad0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a8f3da0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a974a00>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a923da0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a932ad0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02189a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: namespace 'trena' is not available and has been replaced
by .GlobalEnv when processing object ''
  <environment: 0x0a974a00>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.
class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
Warning: namespace 'trena' is not available and has been replaced
by .GlobalEnv when processing object ''
  <environment: 0x088b3948>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021898e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
Warning: namespace 'trena' is not available and has been replaced
by .GlobalEnv when processing object ''
  <environment: 0x088e56f8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.
Warning: namespace 'trena' is not available and has been replaced
by .GlobalEnv when processing object ''
  <environment: 0x088b2950>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021898e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
Warning: namespace 'trena' is not available and has been replaced
by .GlobalEnv when processing object ''
  <environment: 0x088a2a08>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021898e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088e4008>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x08872340>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class

  <environment: 0x088f5410>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169920>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088f4ce0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.


  <environment: 0x08915610>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02189a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
  <environment: 0x08905db0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088f5208>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class

  <environment: 0x08882a58>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169958>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088e47f0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169958>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
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[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0887c5d0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
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          class
          class
          class
          class
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              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
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            x
            what
            which
          class
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          class
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            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
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            success
            time
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            sout
          class
              <environment: namespace:parallel>
            node
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            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
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          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0888c5e0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
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    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
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            sout
          class
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            node
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            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088df8b0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169940>
      ...
    class
    class
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    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
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          class
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            names
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            success
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            sout
          class
              <environment: namespace:parallel>
            node
            data
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          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
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            lambda.min.value
            lambda.min.ratio
            rho
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            prec
            max.ite
            verbose
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          class
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              <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
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              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
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              <environment: namespace:base>
            time1
            time2
            tz
            units
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              <environment: namespace:base>
            x
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            ...
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              <environment: namespace:base>
            xx
            units
            cl
          class
  <environment: 0x088edcc0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
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    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          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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              <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
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          class
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          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
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          class
          class
          class
              <environment: namespace:base>
            time1
            time2
            tz
            units
          class
          class
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          class
              <environment: namespace:base>
            x
            tz
            ...
          class
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              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            file
            append
            type
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          class
          class
          class
          class
          class
              <environment: namespace:base>
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          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
          class
          class
          class
          class
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          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
          class
          class
          class
          class
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          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:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
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          class
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            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          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
          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
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          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
              [1]
                          [1]
names
            names
              [1]
            names
              [1]
            names
              <environment: namespace:parallel>
            node
          class
          class
              <environment: namespace:base>
            save
            status
            runLast
          class
              <environment: namespace:parallel>
            node
          class
          class
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            <environment: namespace:parallel>
node
            node
          class
                    class
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          class
              <environment: namespace:base>
            save
            status
            runLast
          class
              <environment: namespace:base>
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save
                        save
status
                                      status
runLast
<environment: namespace:methods>
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class
            field
runLast
            thisClass
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          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:methods>
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            me
            selfEnv
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          class
          class
          class
          class
          class
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                      class
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          class
          class
          class
          class
          class
                    class
class
                    class
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                    class
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                    class
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                    class
class
                    class
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                      class
                    class
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          class
          class
          class
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                              class
class
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                    class
class
                    class
class
                    class
class
                    class
class
                    class
class
                    class
class
                        <environment: namespace:RSQLite>
                                    con_
class
                    class
class
class
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                    class
                      class
class
          def
class
                      self
          class
                      class
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me
                      selfEnv
          class
                        class
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                      class
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                    class
                    class
class
class
                    class
class
          class
          class
          class
          class
          class
          class
          class
          class
          class
                        class
              <environment: namespace:methods>
            <environment: namespace:methods>
                      def
class
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                      class
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                      class
            me
me
                                  class
          selfEnv
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class
                      class
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          class
                      class
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class
          class
          class
          class
          class
                    class
class
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class
          class
                    class
class
          class
class
                    class
class
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class
                              class
class
class
                    class
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class
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class
                    class
class
          class
          class
                    class
class
                    class
class
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class
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class
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class
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class
                    class
class
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class
                    class
class
                    class
class
                    class
class
                    class
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                    class
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                    class
          class
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                    class
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                    class
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                                  class
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            con_
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          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            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: 0x088ef108>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088ce640>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0887d588>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0886c548>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class

  <environment: 0x088de640>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0887c968>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0888d020>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179958>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088ce9e0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021698e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a96f798>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a90b958>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a8fcbd0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a92cb38>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021898e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a91d718>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a91bc80>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02189908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0887c6b0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0886c8d0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02169948>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a8fd420>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088ff798>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a92cea8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02189a08>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088ff290>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179920>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0889dcd8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0887cc88>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x021798e0>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0a95fa90>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x02179908>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0889c788>
lambda
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        <environment: 0x02179908>
      ...
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  <environment: 0x0888d478>
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            x
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              [1]
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            object
            connection
            ascii
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            object
            ...
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x088dea08>
lambda
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        <environment: 0x02179920>
      ...
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            x
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            x
            what
            which
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          class
              [1]
            [1]
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              [2]
              [3]
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            ...
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0886c238>
lambda
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        <environment: 0x021698e0>
      ...
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            x
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              <environment: namespace:base>
            x
            what
            which
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              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
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            tag
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            object
            connection
            ascii
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          class
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            object
            ...
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See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0887d340>
lambda
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        <environment: 0x021798e0>
      ...
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            [3]
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              <environment: namespace:base>
            file
            append
            type
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              <environment: namespace:BiocParallel>
            x
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          class
              <environment: namespace:base>
            x
            what
            which
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              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
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            tag
            value
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            time
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            object
            connection
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  <environment: 0x088ad338>
lambda
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        <environment: 0x021898e0>
      ...
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            encoding
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              <environment: namespace:base>
            file
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            type
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          class
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          class
              <environment: namespace:BiocParallel>
            x
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          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
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            sout
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              <environment: namespace:parallel>
            node
            data
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              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0887d260>
lambda
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        <environment: 0x02169908>
      ...
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              <environment: namespace:base>
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            elapsed
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              <environment: namespace:flare>
            X
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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-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
about to create RMariaDB driver, getting regulatory regions
[1] calling HumanDHSFilter, span: 201
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_basicConstructor
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
about to create RMariaDB driver, getting regulatory regions
[1] calling HumanDHSFilter, span: 201
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Tue Apr 09 06:50:36 2019 
*********************************************** 
Number of test functions: 80 
Number of errors: 10 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 80 test functions, 10 errors, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R: Error while sourcing  C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R : Error in checkTrue(nrow(tbl.trimmed) == 12) : Test not TRUE

ERROR in test_.getScoredMotifs: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_.injectSnp: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_bugInStartEndOfMinusStrandHits: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_findMatchesByChromosomalRegion: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_findMatchesByChromosomalRegion.twoAlternateAlleles: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_findMatchesByMultipleChromosomalRegions: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_getSequence: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_noMatch: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R: Error while sourcing  C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R : Error in checkTrue(tbl$lambda < 0.9) : Test not TRUE


Test files with failing tests

   test_BayesSpikeSolver.R 
     C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R 

   test_MotifMatcher.R 
     test_.getScoredMotifs 
     test_.injectSnp 
     test_bugInStartEndOfMinusStrandHits 
     test_findMatchesByChromosomalRegion 
     test_findMatchesByChromosomalRegion.twoAlternateAlleles 
     test_findMatchesByMultipleChromosomalRegions 
     test_getSequence 
     test_noMatch 

   test_RidgeSolver.R 
     C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R 


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

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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, 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
Error in checkTrue(nrow(tbl.trimmed) == 12) : Test not TRUE

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

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

[1] --- test_directMode
[1] --- test_getOpenChromatinFastAndSimple
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getOpenChromatinFastAndSimple
about to create RMariaDB driver, getting regulatory regions
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
Warning: call dbDisconnect() when finished working with a connection
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_alpha.lasso
[1] --- test_lambda.lasso
[1] --- test_keep.metrics.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.lasso
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_keep.metrics.lasso
[1] --- test_lambda.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_.getScoredMotifs
[1] --- test_.injectSnp
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByMultipleChromosomalRegions
[1] --- test_getSequence
[1] --- test_noMatch
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_alpha.ridge
[1] --- test_lambda.ridge
[1] --- test_keep.metrics.ridge
Error in checkTrue(tbl$lambda < 0.9) : Test not TRUE

In addition: Warning message:
In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getAssayData
[1] --- test_getTarget
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000118011a8>
lambda
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x000000001180fc88>
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011811438>
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            x
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          x
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            xx
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            cl
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              <environment: namespace:base>
            cpu
            elapsed
            transient
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              <environment: namespace:flare>
            X
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            nlambda
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            lambda.min.ratio
            rho
            method
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            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
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
          class
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              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
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              <environment: namespace:base>
            time1
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              <environment: namespace:base>
            x
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              <environment: namespace:base>
            xx
            units
            cl
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              <environment: namespace:base>
            cpu
            elapsed
            transient
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              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
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            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
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              <environment: namespace:base>
            x
            trim
            na.rm
            ...
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              <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
            time2
            tz
            units
          class
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              <environment: namespace:base>
            x
            tz
            ...
          class
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          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          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
          class
          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
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            ...
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          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              [1]
            names
              [1]
            names
              [1]
                          [1]
            names
names
              <environment: namespace:parallel>
            node
          class
          class
              <environment: namespace:base>
            save
            status
            runLast
          class
              <environment: namespace:methods>
            self
            field
            thisClass
            selfEnv
          class
          class
          class
          class
          class
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          class
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          class
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          class
                        class
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                      class
          class
node
          class
          class
          class
          class
              <environment: namespace:methods>
            def
            self
                          me
<environment: namespace:parallel>
                          selfEnv
            <environment: namespace:parallel>
            node
thisClass
                      node
class
                        class
                    <environment: namespace:base>
            class
class
                    class
class
          class
save
                      class
          class
status
          class
          class
          class
          class
                      class
                        class
runLast
          class
<environment: namespace:base>
                                save
class
            class
status
                      class
runLast
                        class
<environment: namespace:base>
                                class
          class
save
class
                      class
          status
class
                      class
          class
          runLast
class
          class
                    class
class
          class
          class
          class
          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:methods>
            self
                          field
            thisClass
            selfEnv
<environment: namespace:methods>
            self
            field
                      thisClass
                          selfEnv
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            class
self
                      class
field
                      class
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                      selfEnv
          class
class
                    class
class
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class
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class
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class
                    class
class
          class
          class
                        <environment: namespace:methods>
            class
def
            self
            me
            selfEnv
            thisClass
              <environment: namespace:methods>
            def
            self
                          <environment: namespace:methods>
            me
def
                                  selfEnv
class
self
                        thisClass
          me
class
                      selfEnv
class
                      thisClass
class
          class
          class
          class
          class
                    class
class
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class
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          class
          class
          class
                    class
          class
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          class
          class
              <environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            con_
          class
                            <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                        con_
con_
                    class
class
                            <environment: namespace:RSQLite>
            con_
<environment: namespace:RSQLite>
                      con_
class
          class
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011810b58>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000118004c0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117ff430>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011801038>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x000000001180f560>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x000000001180f1b0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117ffb60>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44d20>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x000000001180f5b0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011810438>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011810748>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000019800698>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x000000001980fb60>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44d20>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x000000001980f9b8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x000000001980fd60>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000197ffd78>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000019800268>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000019810298>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000019810708>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000118109a8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011800bf0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000118018d8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011800bf0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011800c00>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000198100b8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
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            ascii
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            refhook
          class
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              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f1860>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
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            [3]
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            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000118103a8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
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            [3]
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          class
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            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011800348>
lambda
    log
    stop.on.error
    stop.immediate
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    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
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            [3]
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          class
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            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000118113b0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
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    class
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            [3]
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011810f10>
lambda
    log
    stop.on.error
    stop.immediate
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    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
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    class
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            [3]
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            version
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000118104c0>
lambda
    log
    stop.on.error
    stop.immediate
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    exportglobals
        <environment: 0x0000000004b44b70>
      ...
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            [3]
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[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f7a78>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44d20>
      ...
    class
    class
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            [3]
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011808b10>
lambda
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        <environment: 0x0000000004b44c40>
      ...
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011807fc8>
lambda
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        <environment: 0x0000000004b44b70>
      ...
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See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f8130>
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        <environment: 0x0000000004b44c40>
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                                              con_
class
<environment: namespace:RSQLite>
          class
class
                                          class
class
          con_
class
                    class
class
class
          class
          class
          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>
            con_
          class
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f7b28>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f7df8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011808f58>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117e8320>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011808b48>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011809648>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class

  <environment: 0x00000000117f81b8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011809648>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f88c0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000118095a8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011807ca0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class

  <environment: 0x00000000198091f8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000198081b8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000197f9cd8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000019806a30>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000197e85f8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000197f8a40>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000197f8848>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class

  <environment: 0x0000000019808b48>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000197f7ac8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c48>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000019808ff0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000011807b00>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class

  <environment: 0x00000000117f9310>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f7c38>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f8ef8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x0000000019807748>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f8068>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117e8178>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44b70>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          class
See system.file("LICENSE", package="MotifDb") for use restrictions.

  <environment: 0x00000000117f83a8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004b44c40>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            object
            open
            local
            encoding
          class
          class
          class
              <environment: namespace:base>
            file
            append
            type
            split
          class
          class
          class
          class
          class
              <environment: namespace:BiocParallel>
            x
          class
          class
          class
          class
              <environment: namespace:base>
            x
            what
            which
          class
              <environment: namespace:BiocParallel>
          class
              [1]
            [1]
          names
              [2]
              [3]
              [4]
              [5]
            names
              <environment: namespace:BiocParallel>
            tag
            value
            success
            time
            log
            sout
          class
              <environment: namespace:parallel>
            node
            data
          class
          class
          class
              <environment: namespace:base>
            object
            connection
            ascii
            xdr
            version
            refhook
          class
          class
              <environment: namespace:base>
            object
            ...
          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
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
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          class
          class
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          class
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          class
          class
          class
          class
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          class
          class
          class
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          class
          class
          class
          class
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          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
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          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            x
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            ...
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          class
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          class
          class
              <environment: namespace:flare>
            Y
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          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
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          class
              <environment: namespace:base>
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          class
              <environment: namespace:flare>
            X
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            lambda.min.value
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            q
            res.sd
            prec
            max.ite
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          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
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          class
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          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
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            ...
          class
          class
          class
          class
          class
              <environment: namespace:flare>
            Y
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            d
            maxdf
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          class
          class
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          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
          class
          class
          class
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          class
          class
          class
              <environment: namespace:base>
            time1
            time2
            tz
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          class
          class
          class
          class
          class
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          class
          class
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          class
          class
          class
              <environment: namespace:base>
            x
            tz
            ...
          class
          class
          class
          class
          class
          class
          class
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          class
          class
          class
              <environment: namespace:base>
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              <environment: namespace:base>
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            X
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          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
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          class
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[1] --- test_basicConstructor
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
about to create RMariaDB driver, getting regulatory regions
[1] calling HumanDHSFilter, span: 201
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_basicConstructor
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
about to create RMariaDB driver, getting regulatory regions
[1] calling HumanDHSFilter, span: 201
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Tue Apr 09 07:03:31 2019 
*********************************************** 
Number of test functions: 80 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 80 test functions, 2 errors, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R: Error while sourcing  C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R : Error in checkTrue(nrow(tbl.trimmed) == 12) : Test not TRUE

ERROR in C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R: Error while sourcing  C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R : Error in checkTrue(tbl$lambda < 0.9) : Test not TRUE


Test files with failing tests

   test_BayesSpikeSolver.R 
     C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R 

   test_RidgeSolver.R 
     C:/Users/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R 


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