Paul Shannon
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/trena |
| Branch: RELEASE_3_6 |
| Last Commit: a4c7bbb |
| Last Changed Date: 2018-03-03 14:58:28 -0400 (Sat, 03 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:29:53 -0400 (Thu, 12 Apr 2018).
| Package 1419/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| trena 1.0.3 Paul Shannon
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ ERROR ] | OK | |||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: trena |
| Version: 1.0.3 |
| Command: rm -rf trena.buildbin-libdir trena.Rcheck && mkdir trena.buildbin-libdir trena.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trena.buildbin-libdir trena_1.0.3.tar.gz >trena.Rcheck\00install.out 2>&1 && cp trena.Rcheck\00install.out trena-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=trena.buildbin-libdir --install="check:trena-install.out" --force-multiarch --no-vignettes --timings trena_1.0.3.tar.gz |
| StartedAt: 2018-04-12 03:40:16 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 04:18:14 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 2277.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: trena.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### rm -rf trena.buildbin-libdir trena.Rcheck && mkdir trena.buildbin-libdir trena.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=trena.buildbin-libdir trena_1.0.3.tar.gz >trena.Rcheck\00install.out 2>&1 && cp trena.Rcheck\00install.out trena-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=trena.buildbin-libdir --install="check:trena-install.out" --force-multiarch --no-vignettes --timings trena_1.0.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'trena/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'trena' version '1.0.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'trena' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.elasticNetSolver: no visible binding for global variable
'cor.target.feature'
assessSnp,Trena: no visible binding for global variable 'status'
assessSnp,Trena: no visible binding for global variable 'assessed'
assessSnp,Trena: no visible binding for global variable
'motifRelativeScore'
Undefined global functions or variables:
assessed cor.target.feature motifRelativeScore status
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
createGeneModel 8.86 0.02 9.72
FootprintFilter-class 1.13 0.02 7.89
HumanDHSFilter-class 1.04 0.03 6.84
getCandidates-FootprintFilter-method 0.28 0.01 6.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
test_.parseVariantString
test_findMatchesByChromosomalRegion_contrastReferenceWithVariant
test_getSequenceWithVariants
test_RandomForestSolver.R
C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R
test_Trena.R
test_assessSnp
test_assessSnp_allTypesWithDeltas
Error in BiocGenerics:::testPackage("trena") :
unit tests failed for package trena
Execution halted
** running tests for arch 'x64' ...
Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64/R" CMD BATCH --vanilla "runTests.R" "runTests.Rout"' had status 1
ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
1 Test Suite :
trena RUnit Tests - 83 test functions, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R: Error while sourcing C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R : Error in checkEquals(rownames(tbl.10), c("HLF", "STAT4", "SATB2", "SATB1")) :
Lengths (3, 4) differ (string compare on first 3)
Test files with failing tests
test_RandomForestSolver.R
C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R
Error in BiocGenerics:::testPackage("trena") :
unit tests failed for package trena
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.Rcheck/00check.log'
for details.
trena.Rcheck/00install.out
install for i386
* installing *source* package 'trena' ...
** R
** inst
** preparing package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
converting help for package 'trena'
finding HTML links ... done
BayesSpikeSolver-class html
BayesSpikeSolver html
CandidateFilter-class html
EnsembleSolver-class html
EnsembleSolver html
FootprintFilter-class html
FootprintFinder-class html
GeneOntologyFilter-class html
HumanDHSFilter-class html
LassoPVSolver-class html
LassoPVSolver html
LassoSolver-class html
LassoSolver html
MotifMatcher-class html
finding level-2 HTML links ... done
PearsonSolver-class html
PearsonSolver html
RandomForestSolver-class html
RandomForestSolver html
RidgeSolver-class html
RidgeSolver html
Solver-class html
SpearmanSolver-class html
SpearmanSolver html
SqrtLassoSolver-class html
SqrtLassoSolver html
TReNA-package html
Trena-class html
VarianceFilter-class html
assessSnp html
closeDatabaseConnections html
createGeneModel html
findMatchesByChromosomalRegion html
getAssayData html
getAvailableSolvers html
getCandidates-FootprintFilter-method html
getCandidates-GeneOntologyFilter-method
html
getCandidates-HumanDHSFilter-method html
getCandidates-VarianceFilter-method html
getCandidates html
getChromLoc html
getEncodeRegulatoryTableNames-HumanDHSFilter
html
getFootprintsForGene html
getFootprintsInRegion html
getGeneModelTableColumnNames html
getGenePromoterRegion html
getGtfGeneBioTypes html
getGtfMoleculeTypes html
getPfms html
getPromoterRegionsAllGenes html
getProximalPromoter html
getRegulators html
getRegulatoryChromosomalRegions html
getRegulatoryRegions html
getRegulatoryTableColumnNames html
getSequence html
getSolverNames html
getTarget html
parseChromLocString html
parseDatabaseUri html
rescalePredictorWeights html
run html
show-HumanDHSFilter-method html
show.BayesSpikeSolver html
show.EnsembleSolver html
show.LassoPVSolver html
show.LassoSolver html
show.MotifMatcher html
show.PearsonSolver html
show.RandomForestSolver html
show.RidgeSolver html
show.SpearmanSolver html
show.SqrtLassoSolver html
solve.BayesSpike html
solve.Ensemble html
solve.Lasso html
solve.LassoPV html
solve.Pearson html
solve.RandomForest html
solve.Ridge html
solve.Spearman html
solve.SqrtLasso html
** building package indices
** installing vignettes
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
In R CMD INSTALL
install for x64
* installing *source* package 'trena' ...
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
* MD5 sums
packaged installation of 'trena' as trena_1.0.3.zip
* DONE (trena)
In R CMD INSTALL
In R CMD INSTALL
|
trena.Rcheck/tests_i386/runTests.Rout.fail
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, cbind, colMeans, colSums, colnames, 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
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
See system.file("LICENSE", package="MotifDb") for use restrictions.
[1] TRUE
> BiocGenerics:::testPackage('trena')
[1] --- test_BayesSpikeSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bayesSpike
[1] --- test_nOrderings
[1] --- test_BayesSpikeSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bayesSpike
[1] --- test_nOrderings
[1] --- test_CandidateFilter
[1] --- test_CandidateFilter
[1] --- test_EnsembleSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_selectedSolversOnly
[1] --- test_pcaError
[1] --- test_getSolverNames
[1] --- test_oneSolver
[1] --- test_invalidSolvers
[1] --- test_EnsembleSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_getSolverNames
[1] --- test_invalidSolvers
[1] --- test_oneSolver
[1] --- test_pcaError
[1] --- test_selectedSolversOnly
[1] --- test_FootprintFilter.byRegion
[1] --- test_FootprintFilter.byTwoRegions
[1] --- test_FootprintFilter.byRegion
[1] --- test_FootprintFilter.byTwoRegions
Loading required package: DBI
[1] --- test_parseDatabaseUri
[1] --- test_constructor
[1] --- test_getGtfGeneBioTypes
[1] --- test_getGtfMoleculeTypes
[1] --- test_getChromLoc
[1] --- test_getGenePromoterRegion
[1] --- test_getFootprintsInRegion
[1] --- test_getFootprintsInRegionWithVariants
[1] --- test_getFootprintsForGene
Warning: call dbDisconnect() when finished working with a connection
[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_basicConstructor
[1] --- test_getEncodeRegulatoryTableNames
[1] --- test_checkSampleOfEncodeTables
[1] --- wgEncodeRegDnaseUwAg04449Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHmvecdneoPeak: 0 rows
[1] --- wgEncodeRegDnaseUwTh1Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHsmmtubePeak: 0 rows
[1] --- wgEncodeRegDnaseUwHcpepicPeak: 0 rows
[1] --- wgEncodeRegDnaseUwNhaPeak: 0 rows
[1] --- wgEncodeRegDnaseUwNb4Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHmvecdlyadPeak: 0 rows
[1] --- wgEncodeRegDnaseUwBonemarrowmscPeak: 0 rows
[1] --- wgEncodeRegDnaseUwGm06990Peak: 0 rows
[1] --- test_getRegulatoryRegions
[1] --- test_getCandidates.emptyRegion
[1] --- test_getCandidates.vrk2.twoRegions
[1] --- test_getCandidates.vrk2.rs13384219.variant
Error in anyDuplicated.default(rowids) :
cannot allocate vector of length 1073741824
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_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_.matchPwmForwardAndReverse
Timing stopped at: 13.35 1.58 14.92
Error in anyDuplicated.default(rowids) :
cannot allocate vector of length 1073741824
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
chrom start end seq status
1 chr2 57907313 57907333 ACCAGCATGCAAATTAGACAA wt
[1] 1 +
[1] 1 -
[1] 1 +
[1] 1 +
[1] 1 +
[1] --- about to check best$seq
$motifName
[1] "Hsapiens-jaspar2016-POU5F1B-MA0792.1"
$chrom
[1] "chr2"
$motifStart
[1] 57907318
$motifEnd
[1] 57907326
$strand
[1] "+"
$motifScore
[1] 6.707832
$motifRelativeScore
[1] 0.9208761
$match
[1] "CATGCAAAT"
$chromStart
[1] 57907313
$chromEnd
[1] 57907333
$seq
[1] "ACCAGCATGCAAATTAGACAA"
$status
[1] "wt"
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByChromosomalRegion_contrastReferenceWithVariant
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
chrom start end seq status
1 chr2 57907313 57907333 ACCAGCATGCAAATTAGACAA wt
[1] 1 +
[1] 1 -
[1] 1 +
[1] 1 +
[1] 1 +
Timing stopped at: 14.7 0.75 15.47
Error in anyDuplicated.default(rowids) :
cannot allocate vector of length 1073741824
[1] --- test_findMatchesByMultipleChromosomalRegions
[1] --- test_getSequence
[1] --- test_getSequenceWithVariants
Timing stopped at: 11.98 1.31 13.3
Error in anyDuplicated.default(rowids) :
cannot allocate vector of length 1073741824
[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
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_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
Error in checkEquals(rownames(tbl.10), c("HLF", "STAT4", "SATB2", "SATB1")) :
2 string mismatches
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_alpha.ridge
[1] --- test_lambda.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.ridge
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_lambda.ridge
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getTarget
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bea850>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01bf035c>
...
warning
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb028>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x015d2774>
...
warning
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beab98>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a52804>
...
warning
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beacb0>
lambda
<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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
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nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
tz
...
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class
<environment: namespace:base>
xx
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class
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<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
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class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environme log
stop.on.error
stop.immediate
as.error
nt: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:compiler>
call
cond
body
cb
cntxt
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
timeout
<environment: 0x01a5277c>
...
warning
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
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class
class
class
class
class
class
class
<environment: namespace:base>
xx
units
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:compiler>
call
cond
body
cb
cntxt
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:base>
e1
e2
[1]
x
[2]
class
class
[3]
class
class
class
class
class
class
class
<environment: namespace:base>
time1
time2
tz
units
class
class
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class
class
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class
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class
class
class
class
class
<environment: namespace:base>
x
tz
...
class
class
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class
class
class
class
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class
<environment: namespace:base>
xx
units
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:compiler>
call
cond
body
cb
cntxt
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:compiler>
call
cond
body
cb
cntxt
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
[1]
[2]
[3]
names
[1]
<environment: namespace:BiocParallel>
[2]
[3]
[1]
node
[2]
[3]
[1]
[2]
[3]
names
names
names
<environment: namespace:parallel>
<environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
node
node
node
<environment: namespace:BiocParallel>
class
node
class
<environment: namespace:parallel>
node
class
<environment: namespace:parallel>
class
node
class
class
<environment: namespace:parallel>
node
class
class
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb0d0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a5280c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb6a8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01532ec4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb638>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a530ac>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb090>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a5284c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfae00>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a6275c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfaa10>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01c0020c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bebd50>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a53744>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb068>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a527a4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beaed8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a52834>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb300>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a627a4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beac48>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01bf0444>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb728>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01532f34>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb628>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a6301c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb068>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a627a4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb7d0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01532ffc>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb068>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a627a4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb650>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a530c4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb278>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01542834>
...
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: 0x01bfaa10>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01c0020c>
...
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:base>
cpu
elapsed
transient
class
<environment: namespace:flare>
X
Y
lambda
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[1]
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<environment: namespace:BiocParallel>
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<environment: namespace:BiocParallel>
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names
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[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfae00>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a6275c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb318>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a528bc>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x020c5ce8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01bf3424>
...
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
ncol
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length
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<environment: namespace:base>
x
trim
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...
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<environment: namespace:flare>
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<environment: namespace:base>
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[1]
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<environment: namespace:flare>
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<environment: namespace:flare>
Y
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<environment: namespace:flare>
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<environment: namespace:flare>
Y
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lambda
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max.ite
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PACKAGE
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<environment: namespace:base>
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elapsed
transient
class
<environment: namespace:flare>
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rho
method
q
res.sd
prec
max.ite
verbose
ncol
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nrow
ncol
byrow
length
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<environment: namespace:base>
x
trim
na.rm
...
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<environment: namespace:flare>
Y
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<environment: namespace:base>
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<environment: namespace:base>
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<environment: namespace:base>
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<environment: namespace:base>
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Y
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<environment: namespace:flare>
Y
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<environment: namespace:flare>
Y
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<environment: namespace:flare>
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<environment: namespace:flare>
Y
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PACKAGE
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<environment: 0x01bfb2b8>
lambda
log
stop.on.error
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<environment: 0x01a6275c>
...
class
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names
[3]
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<environment: namespace:base>
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<environment: namespace:base>
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...
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<environment: namespace:flare>
Y
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decreasing
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<environment: namespace:base>
e1
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[1]
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[2]
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[3]
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<environment: namespace:flare>
Y
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decreasing
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beta
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<environment: namespace:flare>
Y
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lambda
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max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
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byrow
ncol
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<environment: namespace:flare>
Y
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lambda
nlambda
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rho
max.ite
prec
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verbose
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decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
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q
lambda
nlambda
n
d
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rho
max.ite
prec
intercept
verbose
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PACKAGE
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ite
<environment: namespace:flare>
Y
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lambda
nlambda
n
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max.ite
prec
intercept
verbose
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decreasing
PACKAGE
beta
ite
<environment: namespace:base>
cpu
elapsed
transient
class
<environment: namespace:flare>
X
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lambda
nlambda
lambda.min.value
lambda.min.ratio
rho
method
q
res.sd
prec
max.ite
verbose
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
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<environment: namespace:base>
x
trim
na.rm
...
class
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<environment: namespace:flare>
Y
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lambda
nlambda
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max.ite
prec
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decreasing
PACKAGE
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<environment: namespace:base>
e1
e2
[1]
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[2]
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<environment: namespace:base>
time1
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<environment: namespace:base>
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<environment: namespace:base>
xx
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...
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inherits
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[1]
x
[2]
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[3]
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<environment: namespace:base>
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<environment: namespace:flare>
Y
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max.ite
prec
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verbose
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decreasing
PACKAGE
beta
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<environment: namespace:flare>
Y
X
lambda
nlambda
n
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rho
max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
byrow
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byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
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rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
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lambda
nlambda
n
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max.ite
prec
intercept
verbose
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decreasing
PACKAGE
beta
ite
[1]
[2]
[3]
names
[1]
[2]
[3]
<environment: namespace:BiocParallel>
[1]
[2]
[3]
node
[1]
[2]
[3]
names
names
names
<environment: namespace:parallel>
node
<environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
class
node
class
node
node
<environment: namespace:parallel>
node
<environment: namespace:parallel>
<environment: namespace:parallel>
class
class
node
node
class
class
class
class
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfafc0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a6277c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb068>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a627a4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb638>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a530ac>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfae58>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01542834>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb090>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a5284c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb628>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a5301c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb1e0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a62804>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb538>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a52f2c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bea4f0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01befcec>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb628>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a6301c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb5a0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a52f94>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb650>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a630c4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb500>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a52ef4>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb1b8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a5275c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01beb628>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a5301c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb0d0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a6280c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb0d0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a6280c>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x01bfb068>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a627a4>
...
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
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nrow
ncol
nrow
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<environment: namespace:base>
x
trim
na.rm
...
class
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<environment: namespace:flare>
Y
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lambda
nlambda
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max.ite
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decreasing
PACKAGE
beta
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<environment: namespace:base>
e1
e2
[1]
x
[2]
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[3]
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<environment: namespace:base>
time1
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<environment: namespace:base>
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<environment: namespace:flare>
Y
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lambda
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max.ite
prec
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nrow
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decreasing
PACKAGE
beta
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<environment: namespace:flare>
Y
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lambda
nlambda
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max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
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byrow
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<environment: namespace:flare>
Y
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lambda
nlambda
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max.ite
prec
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verbose
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decreasing
PACKAGE
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<environment: namespace:flare>
Y
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lambda
nlambda
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prec
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verbose
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PACKAGE
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<environment: namespace:flare>
Y
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lambda
nlambda
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max.ite
prec
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verbose
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decreasing
PACKAGE
beta
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<environment: 0x01beb050>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x01a5280c>
...
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
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nrow
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nrow
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nrow
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<environment: namespace:base>
x
trim
na.rm
...
class
class
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<environment: namespace:flare>
Y
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lambda
nlambda
n
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maxdf
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max.ite
prec
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nrow
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decreasing
PACKAGE
beta
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<environment: namespace:base>
e1
e2
[1]
x
[2]
class
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[3]
class
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<environment: namespace:base>
time1
time2
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units
class
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<environment: namespace:base>
x
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...
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<environment: namespace:base>
xx
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...
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class
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<environment: namespace:flare>
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<environment: namespace:BiocParallel>
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<environment: namespace:BiocParallel>
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[1] --- test_basicConstructor
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/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-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_createGeneModel
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_assessSnp
[1] error, unrecognized variant name: 'rsBogus'
[1] error, unrecognized variant name: 'rs3875089'
Timing stopped at: 11.06 0.78 11.85
Error in checkEquals(dim(tbl.assay), c(8, 12)) :
Mean absolute difference: 10
[1] --- test_assessSnp_allTypesWithDeltas
[1] error, unrecognized variant name: 'rs3763043'
Warning in is.na(x) :
is.na() applied to non-(list or vector) of type 'NULL'
Timing stopped at: 11.11 0.8 11.91
Error in checkEquals(sort(unique(tbl.assay$assessed)), c("in.both", "mut.only", :
target is NULL, current is character
[1] --- test_basicConstructor
[1] --- test_createGeneModel
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
[1] calling HumanDHSFilter, span: 201
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter
RUNIT TEST PROTOCOL -- Thu Apr 12 04:03:05 2018
***********************************************
Number of test functions: 77
Number of errors: 5
Number of failures: 2
1 Test Suite :
trena RUnit Tests - 77 test functions, 5 errors, 2 failures
ERROR in C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_HumanDHSFilter.R: Error while sourcing C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_HumanDHSFilter.R : Error in anyDuplicated.default(rowids) :
cannot allocate vector of length 1073741824
ERROR in test_.parseVariantString: Error in anyDuplicated.default(rowids) :
cannot allocate vector of length 1073741824
ERROR in test_findMatchesByChromosomalRegion_contrastReferenceWithVariant: Error in anyDuplicated.default(rowids) :
cannot allocate vector of length 1073741824
ERROR in test_getSequenceWithVariants: Error in anyDuplicated.default(rowids) :
cannot allocate vector of length 1073741824
ERROR in C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R: Error while sourcing C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R : Error in checkEquals(rownames(tbl.10), c("HLF", "STAT4", "SATB2", "SATB1")) :
2 string mismatches
FAILURE in test_assessSnp: Error in checkEquals(dim(tbl.assay), c(8, 12)) :
Mean absolute difference: 10
FAILURE in test_assessSnp_allTypesWithDeltas: Error in checkEquals(sort(unique(tbl.assay$assessed)), c("in.both", "mut.only", :
target is NULL, current is character
Test files with failing tests
test_HumanDHSFilter.R
C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_HumanDHSFilter.R
test_MotifMatcher.R
test_.parseVariantString
test_findMatchesByChromosomalRegion_contrastReferenceWithVariant
test_getSequenceWithVariants
test_RandomForestSolver.R
C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R
test_Trena.R
test_assessSnp
test_assessSnp_allTypesWithDeltas
Error in BiocGenerics:::testPackage("trena") :
unit tests failed for package trena
Execution halted
|
trena.Rcheck/tests_x64/runTests.Rout.fail
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require(trena) || stop("unable to load trena Package")
Loading required package: trena
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16
Loading required package: MotifDb
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:Matrix':
colMeans, colSums, rowMeans, rowSums, which
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, 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
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
See system.file("LICENSE", package="MotifDb") for use restrictions.
[1] TRUE
> BiocGenerics:::testPackage('trena')
[1] --- test_BayesSpikeSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bayesSpike
[1] --- test_nOrderings
[1] --- test_BayesSpikeSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bayesSpike
[1] --- test_nOrderings
[1] --- test_CandidateFilter
[1] --- test_CandidateFilter
[1] --- test_EnsembleSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_selectedSolversOnly
[1] --- test_pcaError
[1] --- test_getSolverNames
[1] --- test_oneSolver
[1] --- test_invalidSolvers
[1] --- test_EnsembleSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_getSolverNames
[1] --- test_invalidSolvers
[1] --- test_oneSolver
[1] --- test_pcaError
[1] --- test_selectedSolversOnly
[1] --- test_FootprintFilter.byRegion
[1] --- test_FootprintFilter.byTwoRegions
[1] --- test_FootprintFilter.byRegion
[1] --- test_FootprintFilter.byTwoRegions
Loading required package: DBI
[1] --- test_parseDatabaseUri
[1] --- test_constructor
[1] --- test_getGtfGeneBioTypes
[1] --- test_getGtfMoleculeTypes
[1] --- test_getChromLoc
[1] --- test_getGenePromoterRegion
[1] --- test_getFootprintsInRegion
[1] --- test_getFootprintsInRegionWithVariants
[1] --- test_getFootprintsForGene
Warning: call dbDisconnect() when finished working with a connection
[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_basicConstructor
[1] --- test_getEncodeRegulatoryTableNames
[1] --- test_checkSampleOfEncodeTables
[1] --- wgEncodeRegDnaseUwAg04449Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHmvecdneoPeak: 0 rows
[1] --- wgEncodeRegDnaseUwTh1Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHsmmtubePeak: 0 rows
[1] --- wgEncodeRegDnaseUwHcpepicPeak: 0 rows
[1] --- wgEncodeRegDnaseUwNhaPeak: 0 rows
[1] --- wgEncodeRegDnaseUwNb4Peak: 0 rows
[1] --- wgEncodeRegDnaseUwHmvecdlyadPeak: 0 rows
[1] --- wgEncodeRegDnaseUwBonemarrowmscPeak: 0 rows
[1] --- wgEncodeRegDnaseUwGm06990Peak: 0 rows
[1] --- test_getRegulatoryRegions
[1] --- test_getCandidates.emptyRegion
[1] --- test_getCandidates.vrk2.twoRegions
[1] --- test_getCandidates.vrk2.rs13384219.variant
[1] --- test_basicConstructor
[1] --- test_checkSampleOfEncodeTables
[1] --- test_getCandidates.emptyRegion
[1] --- test_getCandidates.vrk2.rs13384219.variant
[1] --- test_getCandidates.vrk2.twoRegions
[1] --- test_getEncodeRegulatoryTableNames
[1] --- test_getRegulatoryRegions
[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_.matchPwmForwardAndReverse
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
chrom start end seq status
1 chr2 57907313 57907333 ACCAGCATGCAAATTAGACAA wt
[1] 1 +
[1] 1 -
[1] 1 +
[1] 1 +
[1] 1 +
[1] --- about to check best$seq
$motifName
[1] "Hsapiens-jaspar2016-POU5F1B-MA0792.1"
$chrom
[1] "chr2"
$motifStart
[1] 57907318
$motifEnd
[1] 57907326
$strand
[1] "+"
$motifScore
[1] 6.707832
$motifRelativeScore
[1] 0.9208761
$match
[1] "CATGCAAAT"
$chromStart
[1] 57907313
$chromEnd
[1] 57907333
$seq
[1] "ACCAGCATGCAAATTAGACAA"
$status
[1] "wt"
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByChromosomalRegion_contrastReferenceWithVariant
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
chrom start end seq status
1 chr2 57907313 57907333 ACCAGCATGCAAATTAGACAA wt
[1] 1 +
[1] 1 -
[1] 1 +
[1] 1 +
[1] 1 +
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
chrom start end seq status
1 chr2 57907313 57907333 ACCAGCATGCGAATTAGACAA mut
[1] 1 +
[1] 1 -
[1] 1 +
[1] ---- MotifMatcher::findMatchesByChromosomalRegion
chrom start end seq status
1 chr2 57907313 57907333 ACCAGCATGCAAATTAGACAA wt
[1] 1 +
[1] 1 -
[1] 1 +
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[1] ---- MotifMatcher::findMatchesByChromosomalRegion
chrom start end seq status
1 chr2 57907313 57907333 ACCAGCATGCGAATTAGACAA mut
[1] 1 +
[1] 1 -
[1] 1 +
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[1] --- test_findMatchesByMultipleChromosomalRegions
[1] --- test_getSequence
[1] --- test_getSequenceWithVariants
[1] --- test_noMatch
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_RandomForestSolverConstructor
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_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
Error in checkEquals(rownames(tbl.10), c("HLF", "STAT4", "SATB2", "SATB1")) :
Lengths (3, 4) differ (string compare on first 3)
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_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_alpha.ridge
[1] --- test_lambda.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.ridge
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_lambda.ridge
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getTarget
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene, :
Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5be58>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a378>
...
warning
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6ba50>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b69f70>
...
warning
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5ba50>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59f70>
...
warning
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:compiler>
call
cond
body
cb
cntxt
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:compiler>
call
cond
body
cb
cntxt
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
<environment: 0x0000000006b5ba90>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59fb0>
...
warning
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:compiler>
call
cond
body
cb
cntxt
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:compiler>
call
cond
body
cb
cntxt
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
class
[1]
[2]
[3]
names
[1]
[2]
[3]
<environment: namespace:BiocParallel>
[1]
node
names
[2]
[3]
[1]
[2]
[3]
names
names
<environment: namespace:BiocParallel>
<environment: namespace:parallel>
node
node
<environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
node
class
node
class
<environment: namespace:parallel>
node
<environment: namespace:parallel>
<environment: namespace:parallel>
node
node
class
class
class
class
class
class
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b687c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c7d8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a3b8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b4c390>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b49f70>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b687c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c198>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59d78>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5b640>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59220>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c5c8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a1a8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6ae78>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b68a58>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b4abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b487c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b4c390>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b49f70>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6d628>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b6b208>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6c798>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b6a378>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c3d0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59fb0>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: 0x0000000006b6b460>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b69040>
...
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<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
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
class
class
class
<environment: namespace:base>
...
list
pos
envir
inherits
class
[1]
x
[2]
class
[3]
class
class
class
class
class
class
<environment: namespace:base>
verbose
reset
class
class
class
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
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<environment: namespace:flare>
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<environment: namespace:BiocParallel>
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[3]
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<environment: namespace:parallel>
<environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
[1]
<environment: namespace:BiocParallel>
node
[2]
node
[3]
<environment: namespace:BiocParallel>
names
node
class
[1]
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[2]
[3]
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<environment: namespace:parallel>
<environment: namespace:BiocParallel>
names
<environment: namespace:parallel>
<environment: namespace:BiocParallel>
[1]
names
<environment: namespace:parallel>
class
<environment: namespace:parallel>
[2]
node
<environment: namespace:parallel>
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<environment: namespace:parallel>
node
node
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[1]
[1]
[2]
<environment: namespace:BiocParallel>
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[3]
[2]
<environment: namespace:parallel>
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[3]
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[1]
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<environment: namespace:BiocParallel>
<environment: namespace:parallel>
[2]
[3]
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<environment: namespace:parallel>
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[3]
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<environment: namespace:parallel>
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<environment: namespace:parallel>
<environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
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<environment: namespace:BiocParallel>
<environment: namespace:parallel>
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<environment: namespace:parallel>
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<environment: namespace:parallel>
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[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c950>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a530>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6c7d8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b6a3b8>
...
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
ncol
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byrow
length
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<environment: namespace:base>
x
trim
na.rm
...
class
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<environment: namespace:flare>
Y
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lambda
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decreasing
PACKAGE
beta
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<environment: namespace:base>
e1
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[1]
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[2]
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<environment: namespace:base>
time1
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<environment: namespace:flare>
Y
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max.ite
prec
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<environment: namespace:flare>
Y
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prec
intercept
verbose
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PACKAGE
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<environment: namespace:flare>
Y
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decreasing
PACKAGE
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<environment: namespace:flare>
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max.ite
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verbose
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PACKAGE
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<environment: namespace:flare>
Y
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lambda
nlambda
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max.ite
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decreasing
PACKAGE
beta
ite
<environment: namespace:base>
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elapsed
transient
class
<environment: namespace:flare>
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rho
method
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res.sd
prec
max.ite
verbose
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byrow
length
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<environment: namespace:base>
x
trim
na.rm
...
class
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<environment: namespace:flare>
Y
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decreasing
PACKAGE
beta
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<environment: namespace:base>
e1
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[1]
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<environment: namespace:base>
time1
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<environment: namespace:base>
x
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<environment: namespace:base>
xx
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<environment: namespace:base>
...
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[1]
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<environment: namespace:base>
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<environment: namespace:flare>
Y
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lambda
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rho
max.ite
prec
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decreasing
PACKAGE
beta
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<environment: namespace:flare>
Y
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lambda
nlambda
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max.ite
prec
intercept
verbose
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decreasing
PACKAGE
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<environment: namespace:flare>
Y
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lambda
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<environment: namespace:flare>
Y
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<environment: namespace:flare>
Y
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lambda
nlambda
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prec
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verbose
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decreasing
PACKAGE
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<environment: 0x0000000006b5cd58>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a938>
...
class
class
class
class
class
class
names
[3]
names
names
<environment: namespace:base>
cpu
elapsed
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<environment: namespace:base>
x
trim
na.rm
...
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<environment: namespace:flare>
Y
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decreasing
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<environment: namespace:base>
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[1]
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[2]
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<environment: namespace:flare>
Y
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lambda
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max.ite
prec
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decreasing
PACKAGE
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<environment: namespace:flare>
Y
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lambda
nlambda
n
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rho
max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
nrow
ncol
<environment: namespace:base>
x
trim
na.rm
...
class
class
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class
<environment: namespace:flare>
Y
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lambda
nlambda
n
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max.ite
prec
intercept
verbose
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decreasing
PACKAGE
beta
ite
<environment: namespace:base>
e1
e2
[1]
x
[2]
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[3]
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<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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<environment: namespace:base>
...
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inherits
class
[1]
x
[2]
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[3]
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<environment: namespace:base>
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<environment: namespace:flare>
Y
X
lambda
nlambda
n
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rho
max.ite
prec
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verbose
nrow
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decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
byrow
ncol
byrow
ncol
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
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maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
[1]
[2]
[3]
names
[1]
[2]
[3]
<environment: namespace:BiocParallel>
[1]
node
[2]
[3]
names
[1]
[2]
[3]
names
names
<environment: namespace:BiocParallel>
<environment: namespace:parallel>
node
node
<environment: namespace:BiocParallel>
node
<environment: namespace:BiocParallel>
class
node
class
<environment: namespace:parallel>
<environment: namespace:parallel>
node
node
class
class
class
<environment: namespace:parallel>
class
node
class
class
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c390>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59f70>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c798>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a378>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c798>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a378>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6c390>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b69f70>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b4c798>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b4a378>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b4abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b487c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c3d0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59fb0>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5b640>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59220>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b6abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b687c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5b640>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b59220>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c798>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a378>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5ae78>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b58a58>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5c798>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b5a378>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b4c3d0>
lambda
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b49fb0>
...
class
class
class
class
class
class
names
[3]
names
names
See system.file("LICENSE", package="MotifDb") for use restrictions.
<environment: 0x0000000006b5abe8>
lambda
<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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
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nrow
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nrow
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<environment: namespace:base>
x
trim
na.rm
...
class
class
class
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class
<environment: namespace:flare>
Y
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lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:base>
e1
e2
[1]
x
[2]
class
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[3]
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<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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<environment: namespace:base>
...
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inherits
class
[1]
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[2]
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[3]
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<environment: namespace:base>
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class
class
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<environment: namespace:flare>
Y
X
lambda
nlambda
n
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maxdf
rho
max.ite
prec
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verbose
nrow
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decreasing
PACKAGE
beta
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<environment: namespace:flare>
Y
X
lambda
nlambda
n
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maxdf
rho
max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
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byrow
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beta
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<environment: namespace:flare>
Y
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lambda
nlambda
n
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maxdf
rho
max.ite
prec
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verbose
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decreasing
PACKAGE
beta
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<environment: namespace:flare>
Y
X
q
lambda
nlambda
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maxdf
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max.ite
prec
intercept
verbose
nrow
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decreasing
PACKAGE
beta
ite
<environme nt: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
log
stop.on.error
stop.immediate
as.error
timeout
<environment: 0x0000000006b587c8>
...
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
ncol
nrow
ncol
byrow
nrow
ncol
byrow
length
nrow
ncol
nrow
ncol
nrow
ncol
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X
q
lambda
nlambda
n
d
maxdf
rho
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
<environment: namespace:flare>
Y
X
lambda
nlambda
n
d
maxdf
max.ite
prec
intercept
verbose
nrow
ncol
decreasing
PACKAGE
beta
ite
[1]
[2]
[3]
[1]
[2]
[3]
names
[1]
[2]
[3]
[1]
[2]
[3]
[1]
names
[2]
[3]
[1]
[2]
names
[3]
names
[1]
<environment: namespace:BiocParallel>
[2]
[3]
node
[1]
[2]
[3]
names
[1]
names
[2]
[3]
names
<environment: namespace:BiocParallel>
[1]
names
[2]
[3]
names
node
<environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
[1]
node
[2]
node
[3]
names
<environment: namespace:parallel>
[1]
[2]
node
<environment: namespace:BiocParallel>
[3]
<environment: namespace:BiocParallel>
<environment: namespace:BiocParallel>
node
[1]
names
<environment: namespace:BiocParallel>
class
<environment: namespace:BiocParallel>
node
node
[2]
[1]
[3]
node
<environment: namespace:BiocParallel>
node
node
[2]
<environment: namespace:parallel>
[1]
[2]
<environment: namespace:parallel>
<environment: namespace:parallel>
[3]
names
<environment: namespace:BiocParallel>
class
[3]
<environment: namespace:parallel>
names
node
node
<environment: namespace:parallel>
[1]
names
node
<environment: namespace:parallel>
class
class
node
[2]
class
[3]
<environment: namespace:BiocParallel>
node
[1]
node
<environment: namespace:parallel>
node
class
[2]
[3]
node
<environment: namespace:BiocParallel>
<environment: namespace:parallel>
names
<environment: namespace:parallel>
node
class
node
[1]
[2]
<environment: namespace:BiocParallel>
class
names
class
[1]
node
class
names
class
class
class
[2]
<environment: namespace:parallel>
[3]
node
node
<environment: namespace:parallel>
[3]
<environment: namespace:BiocParallel>
class
class
names
node
<environment: namespace:parallel>
class
node
<environment: namespace:BiocParallel>
node
class
class
<environment: namespace:BiocParallel>
names
class
class
class
<environment: namespace:BiocParallel>
node
<environment: namespace:parallel>
class
node
class
class
node
class
node
<environment: namespace:BiocParallel>
node
class
node
<environment: namespace:parallel>
class
<environment: namespace:parallel>
<environment: namespace:parallel>
node
node
<environment: namespace:parallel>
class
node
class
node
class
class
class
<environment: namespace:parallel>
class
class
class
node
class
class
class
[1] --- test_basicConstructor
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/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-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_createGeneModel
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_assessSnp
[1] error, unrecognized variant name: 'rsBogus'
[1] --- test_assessSnp_allTypesWithDeltas
[1] --- test_basicConstructor
[1] --- test_createGeneModel
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
[1] calling HumanDHSFilter, span: 201
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite://C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter
RUNIT TEST PROTOCOL -- Thu Apr 12 04:18:04 2018
***********************************************
Number of test functions: 83
Number of errors: 1
Number of failures: 0
1 Test Suite :
trena RUnit Tests - 83 test functions, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R: Error while sourcing C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R : Error in checkEquals(rownames(tbl.10), c("HLF", "STAT4", "SATB2", "SATB1")) :
Lengths (3, 4) differ (string compare on first 3)
Test files with failing tests
test_RandomForestSolver.R
C:/Users/biocbuild/bbs-3.6-bioc/meat/trena.buildbin-libdir/trena/unitTests/test_RandomForestSolver.R
Error in BiocGenerics:::testPackage("trena") :
unit tests failed for package trena
Execution halted
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trena.Rcheck/examples_i386/trena-Ex.timings
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trena.Rcheck/examples_x64/trena-Ex.timings
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