Multiple platform build/check report for BioC 3.8 - CHECK report for trena on tokay1


R version 3.5.1 Patched (2018-07-24 r75008) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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> require(trena) || stop("unable to load trena Package")
Loading required package: trena
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Loading required package: MotifDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

See system.file("LICENSE", package="MotifDb") for use restrictions.

[1] TRUE
> BiocGenerics:::testPackage('trena')
[1] --- test_BayesSpikeSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bayesSpike
[1] --- test_nOrderings
[1] --- test_BayesSpikeSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bayesSpike
[1] --- test_nOrderings
[1] --- test_CandidateFilter
[1] --- test_CandidateFilter
[1] --- test_EnsembleSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_selectedSolversOnly
[1] --- test_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_getFootprintsForGene
[1] --- test_constructor
[1] --- test_getChromLoc
[1] --- test_getFootprintsForGene
[1] --- test_getFootprintsInRegion
[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
[1] --- test_getOpenChromatinFastAndSimple
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_alpha.lasso
[1] --- test_lambda.lasso
[1] --- test_keep.metrics.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.lasso
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_keep.metrics.lasso
[1] --- test_lambda.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_.getScoredMotifs
[1] --- test_.injectSnp
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByChromosomalRegion_contrastReferenceWithVariant
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 13.42 0.57 14
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
In addition: Warning messages:
1: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
2: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
3: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_findMatchesByMultipleChromosomalRegions
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 0.22 0 0.22
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_getSequence
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 0.06 0 0.07
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_getSequenceWithVariants
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
Timing stopped at: 0.05 0 0.04
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
[1] --- test_noMatch
Warning in .seqlengths_TwoBitFile(x) : End of file reading 4 bytes
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
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.ridge
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_lambda.ridge
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getTarget
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
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              [3]
            names
              <environment: namespace:BiocParallel>
            node
              [1]
          class
              [2]
                        [3]
class
            names
              [1]
                            [2]
<environment: namespace:parallel>
              [3]
                        node
              [1]
names
                        [2]
class
              [3]
                                    <environment: namespace:BiocParallel>
class
            names
node
          class
                        class
              <environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
                        node
node
                    class
class
                    class
              class
<environment: namespace:parallel>
            node
>               
<environment: namespace:parallel>
                      node
class
                                  <environment: namespace:parallel>
class
class
                      node
class
          class
          class
> 
> 
> 
              <environment: namespace:methods>
            self
            field
            thisClass
            selfEnv
                        class
<environment: namespace:methods>
                      class
          class
self
                      class
          field
class
                      class
thisClass
          class
          class
                      selfEnv
              class
<environment: namespace:methods>
                      class
self
                      class
field
                      class
thisClass
                    class
class
                    class
                      class
                        class
class
          <environment: namespace:methods>
selfEnv
          class
class
                                class
class
                    self
class
            class
                    class
                    field
class
class
          class
class
                                class
class
                    class
thisClass
class
                                class
class
          selfEnv
          class
class
                    class
                        class
class
          <environment: namespace:methods>
          class
class
                                class
def
          class
class
                                class
                    self
class
class
                    class
class
          class
          class
class
                                class
me
class
                      class
selfEnv
                      class
                    thisClass
class
class
                    class
class
                    class
class
                    class
class
                        class
          <environment: namespace:methods>
class
                                class
def
          class
class
                                class
class
self
                      class
me
                                              selfEnv
class
class
<environment: namespace:methods>
                                            class
def
                      class
self
thisClass
class
                      me
class
                                selfEnv
class
class
                      thisClass
class
          class
          class
          class
          class
                    class
class
                    class
class
                    class
          class
          class
                    class
class
class
                                            class
class
<environment: namespace:methods>
          class
          class
            class
          def
                      class
          self
class
                      me
class
class
                                class
class
selfEnv
                              class
class
          class
class
                                class
class
                    thisClass
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
                              class
class
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
                                      <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
            class
            con_
con_
                    class
                                  class
<environment: namespace:RSQLite>
class
class
                      con_
class
          class
                            <environment: namespace:RSQLite>
<environment: namespace:RSQLite>
                        con_
con_
                    class
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: 0x0000000011c631e0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c53b30>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c639d0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c54808>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c536d0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
  <environment: 0x0000000011c53f70>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c53168>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c631a8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c531a8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
  <environment: 0x0000000011c43618>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c638c0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
  <environment: 0x0000000019c539d0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c53a68>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c53c80>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c645b0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c54478>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c64828>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c43370>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc1b8>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
              <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
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          class
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          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
  <environment: 0x0000000019c63f78>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc1e8>
      ...
    class
    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
          class
          class
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          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
class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
          class
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          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
          class
          class
          class
              <environment: namespace:flare>
            Y
            X
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
          class
          class
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          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
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              <environment: namespace:base>
            x
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            ...
          class
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          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
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          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
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          class
              <environment: namespace:flare>
            Y
            X
            lambda
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            rho
            max.ite
            prec
            intercept
            verbose
          class
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          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
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      class
            [3]
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          class
              <environment: namespace:base>
            time1
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            units
          class
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              <environment: namespace:base>
            x
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            ...
          class
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          class
          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
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            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          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: 0x0000000011c4d4b0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
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        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c5d538>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
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        names
            [3]
          names
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See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c4d6e8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
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        names
            [3]
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See system.file("LICENSE", package="MotifDb") for use restrictions.
              <environment: namespace:base>
            cpu
            elapsed
            transient
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              <environment: namespace:flare>
            X
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            rho
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  <environment: 0x0000000011c5db70>
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            X
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              <environment: namespace:base>
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            [1]
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            time1
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              <environment: namespace:base>
            xx
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    log
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    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
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        names
            [3]
          names
            names
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
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            lambda.min.ratio
            rho
            method
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            res.sd
            prec
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            verbose
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              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
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              <environment: namespace:flare>
            Y
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            prec
            intercept
            verbose
          class
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              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
          class
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          class
              <environment: namespace:base>
            time1
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              <environment: namespace:base>
            x
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            ...
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              <environment: namespace:base>
            xx
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          class
              <environment: namespace:flare>
            X
            Y
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            lambda.min.ratio
            rho
            method
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            prec
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            verbose
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          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
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            [3]
          class
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            time2
            tz
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              <environment: namespace:base>
            x
            tz
            ...
          class
          class
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          class
          class
          class
          class
          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              [1]
              [2]
              [3]
            names
              [1]
                            [2]
              [3]
<environment: namespace:BiocParallel>
                        node
names
          class
          class
              [1]
              [2]
              [3]
                          names
<environment: namespace:BiocParallel>
            node
              [1]
                                      [2]
class
              [3]
<environment: namespace:parallel>
                      class
            node
names
                        class
<environment: namespace:BiocParallel>
                      class
node
              <environment: namespace:parallel>
                          node
          <environment: namespace:BiocParallel>
                      class
class
node
                    class
class
          class
          class
> 
              <environment: namespace:parallel>
                          <environment: namespace:parallel>
            node
node
          >           class

          class
class
          class
> 
> 
              <environment: namespace:methods>
            self
            field
            thisClass
                          <environment: namespace:methods>
selfEnv
            self
                          field
<environment: namespace:methods>
                        self
thisClass
                      class
            field
                      selfEnv
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            selfEnv
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          class
          class
          class
                        class
<environment: namespace:methods>
                    class
class
                                self
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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                                        class
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          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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                                            <environment: namespace:methods>
            class
class
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                                class
self
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                      me
            class
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                      class
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                        class
          <environment: namespace:methods>
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                      def
            class
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                                    class
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          <environment: namespace:methods>
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                        selfEnv
def
                                  thisClass
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                      me
class
                      selfEnv
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                      thisClass
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          class
                        <environment: namespace:methods>
class
                      def
          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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                              class
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                    class
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                                        class
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          class
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                    class
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                    class
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                    class
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          class
          class
          class
          class
          class
                        class
<environment: namespace:RSQLite>
            con_
          class
              <environment: namespace:RSQLite>
            con_
                                      <environment: namespace:RSQLite>
            class
con_
<environment: namespace:RSQLite>
                      con_
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.
  <environment: 0x0000000011c4c7f8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c5d1d0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
  <environment: 0x0000000011c4cf90>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c4d050>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c4ce10>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c5cd18>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc140>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c5d540>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c5c7d0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c5d118>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc258>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c4d668>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c4cba0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c3c8b0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c4d890>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc178>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019bea898>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c5c560>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c5c7d0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000019c5b240>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c3d0f8>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
    exportglobals
        <environment: 0x0000000004ccc168>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
See system.file("LICENSE", package="MotifDb") for use restrictions.
  <environment: 0x0000000011c4ccb0>
lambda
    log
    stop.on.error
    stop.immediate
    as.error
    timeout
              <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
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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
    exportglobals
        <environment: 0x0000000004ccc238>
      ...
    class
    class
    class
    class
    class
    class
    class
        names
            [3]
          names
            names
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
          class
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          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
          class
          class
          class
              <environment: namespace:flare>
            Y
            X
            lambda
            nlambda
            n
            d
            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
            [3]
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            time1
            time2
            tz
            units
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            x
            tz
            ...
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
          class
              <environment: namespace:base>
            xx
            units
            cl
          class
              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
            Y
            lambda
            nlambda
            lambda.min.value
            lambda.min.ratio
            rho
            method
            q
            res.sd
            prec
            max.ite
            verbose
          class
          class
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          class
              <environment: namespace:base>
            x
            trim
            na.rm
            ...
          class
          class
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              <environment: namespace:flare>
            Y
            X
            lambda
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            n
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            maxdf
            rho
            max.ite
            prec
            intercept
            verbose
          class
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          class
              <environment: namespace:base>
            e1
            e2
            [1]
          x
            [2]
      class
      class
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          class
          class
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          class
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          class
          class
              <environment: namespace:base>
            time1
            time2
            tz
            units
          class
          class
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              <environment: namespace:base>
            x
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            ...
          class
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              <environment: namespace:base>
            xx
            units
            cl
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              <environment: namespace:base>
            cpu
            elapsed
            transient
          class
              <environment: namespace:flare>
            X
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            rho
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            prec
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              <environment: namespace:base>
            x
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            ...
          class
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              <environment: namespace:flare>
            Y
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            intercept
            verbose
          class
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              <environment: namespace:base>
            e1
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            [1]
          x
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[1] --- test_basicConstructor
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
[1] calling HumanDHSFilter, span: 201
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.8-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_assessSnp
[1] error, unrecognized variant name: 'rsBogus'
[1] --- test_assessSnp_allTypesWithDeltas
[1] --- test_basicConstructor
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
[1] calling HumanDHSFilter, span: 201
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.8-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-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Sun Nov 18 06:06:42 2018 
*********************************************** 
Number of test functions: 85 
Number of errors: 5 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 85 test functions, 5 errors, 0 failures
ERROR in test_findMatchesByChromosomalRegion_contrastReferenceWithVariant: 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_getSequenceWithVariants: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_noMatch: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed

Test files with failing tests

   test_MotifMatcher.R 
     test_findMatchesByChromosomalRegion_contrastReferenceWithVariant 
     test_findMatchesByMultipleChromosomalRegions 
     test_getSequence 
     test_getSequenceWithVariants 
     test_noMatch 


Error in BiocGenerics:::testPackage("trena") : 
  unit tests failed for package trena
Execution halted
name	user	system	elapsed
BayesSpikeSolver	0.02	0.01	0.11
CandidateFilter-class	0	0	0
EnsembleSolver	0.01	0.00	0.02
FootprintFilter-class	0	0	0
GeneOntologyFilter-class	0.03	0.00	0.05
HumanDHSFilter-class	0	0	0
LassoPVSolver	0.02	0.00	0.01
LassoSolver	0.01	0.00	0.02
MotifMatcher-class	0.18	0.00	0.17
PearsonSolver	0.01	0.00	0.02
RandomForestSolver	0.01	0.00	0.02
RidgeSolver	0	0	0
Solver-class	0.02	0.00	0.01
SpearmanSolver	0.01	0.00	0.02
SqrtLassoSolver	0.02	0.00	0.01
Trena-class	0	0	0
VarianceFilter-class	0	0	0
assessSnp	0.02	0.00	0.01
createGeneModelFromRegulatoryRegions	0	0	0
createGeneModelFromTfList	0	0	0
findMatchesByChromosomalRegion	0.02	0.00	0.02
getAssayData	0.01	0.00	0.02
getAvailableSolvers	0	0	0
getCandidates-FootprintFilter-method	0	0	0
getCandidates-GeneOntologyFilter-method	0.85	0.13	0.96
getCandidates-HumanDHSFilter-method	0.01	0.00	0.02
getCandidates-VarianceFilter-method	0.02	0.00	0.02
getChromLoc	0.03	0.00	0.11
getEncodeRegulatoryTableNames-HumanDHSFilter	0	0	0
getFootprintsForGene	0.00	0.00	0.03
getFootprintsInRegion	0.01	0.00	0.07
getGeneModelTableColumnNames	0.02	0.00	0.02
getGenePromoterRegion	0	0	0
getGtfGeneBioTypes	0.01	0.00	0.02
getGtfMoleculeTypes	0.02	0.00	0.01
getPfms	0.11	0.00	0.11
getPromoterRegionsAllGenes	0.03	0.01	0.05
getProximalPromoter	0	0	0
getRegulators	0.02	0.00	0.01
getRegulatoryChromosomalRegions	0.93	0.03	4.99
getRegulatoryRegions	0	0	0
getRegulatoryTableColumnNames	0.02	0.00	0.01
getSequence	0	0	0
getSolverNames	0.02	0.00	0.02
getTarget	0	0	0
parseChromLocString	0	0	0
parseDatabaseUri	0	0	0
rescalePredictorWeights	0.02	0.00	0.02
show-HumanDHSFilter-method	0	0	0
show.BayesSpikeSolver	0.01	0.00	0.02
show.EnsembleSolver	0.00	0.02	0.01
show.LassoPVSolver	0.02	0.00	0.02
show.LassoSolver	0.01	0.00	0.01
show.MotifMatcher	0.00	0.01	0.02
show.PearsonSolver	0.02	0.00	0.01
show.RandomForestSolver	0.00	0.02	0.02
show.RidgeSolver	0.01	0.00	0.02
show.SpearmanSolver	0.00	0.02	0.01
show.SqrtLassoSolver	0.02	0.00	0.02
solve.BayesSpike	0	0	0
solve.Lasso	2.77	0.12	2.89
solve.LassoPV	0.14	0.03	0.22
solve.Pearson	0.04	0.00	0.04
solve.RandomForest	3.27	0.00	3.27
solve.Ridge	5.14	0.00	5.14
solve.Spearman	0.03	0.00	0.03
solve.SqrtLasso	0.02	0.00	0.02
CHECK report for trena on tokay1

Summary

Command output

Installation output

Tests output

Example timings
