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trena.Rcheck/tests_i386/runTests.Rout.fail
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 2.0-18
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 object is masked from 'package:Matrix':
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, 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, 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_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 RMySQL driver, getting regulatory regions
[1] --- test_getOpenChromatinFastAndSimple
about to create RMySQL 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
[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
[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
[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
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[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
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tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
See system.file("LICENSE", package="MotifDb") for use restrictions.
See system.file("LICENSE", package="MotifDb") for use restrictions.
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
class
[1]
[1]
names
[2]
[3]
[4]
[5]
names
tag
value
success
time
log
sout
class
node
data
class
class
class
object
connection
ascii
xdr
version
refhook
class
class
object
...
class
lambda
log
stop.on.error
stop.immediate
as.error
timeout
exportglobals
...
class
class
class
class
class
class
class
names
[3]
names
names
object
open
local
encoding
class
class
class
file
append
type
split
class
class
class
class
class
x
class
class
class
class
x
what
which
class
|