Package: trena

Version: 1.4.2

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:trena.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings trena_1.4.2.tar.gz

StartedAt: 2019-04-16 03:30:35 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:43:08 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 753.4 seconds

RetCode: 0

Status:  OK

CheckDir: trena.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:trena.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings trena_1.4.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/trena.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trena/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trena’ version ‘1.4.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 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 ... OK
* 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
getRegulatoryChromosomalRegions 0.852  0.008   5.264
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/trena.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL trena
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘trena’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
* DONE (trena)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

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

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

Attaching package: 'BiocGenerics'

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

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

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

    colMeans, colSums, rowMeans, rowSums, which

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, 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_getSolverNames
[1] --- test_oneSolver
[1] --- test_invalidSolvers
[1] --- test_EnsembleSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_getSolverNames
[1] --- test_invalidSolvers
[1] --- test_oneSolver
[1] --- test_selectedSolversOnly
[1] --- test_FootprintFilter.byRegion
[1] --- test_FootprintFilter.byTwoRegions
[1] --- test_FootprintFilter.byRegion
[1] --- test_FootprintFilter.byTwoRegions
Loading required package: DBI
[1] --- test_parseDatabaseUri
[1] --- test_constructor
[1] --- test_getGtfGeneBioTypes
[1] --- test_getGtfMoleculeTypes
[1] --- test_getChromLoc
[1] --- test_getGenePromoterRegion
[1] --- test_getFootprintsInRegion
[1] --- test_getFootprintsForGene
[1] --- test_constructor
[1] --- test_getChromLoc
[1] --- test_getFootprintsForGene
[1] --- test_getFootprintsInRegion
[1] --- test_getGenePromoterRegion
[1] --- test_getGtfGeneBioTypes
[1] --- test_getGtfMoleculeTypes
[1] --- test_parseDatabaseUri
[1] --- test_directMode
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

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

[1] --- test_directMode
[1] --- test_getOpenChromatinFastAndSimple
[1] --- test_getOpenChromatinFastAndSimple
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_alpha.lasso
[1] --- test_lambda.lasso
[1] --- test_keep.metrics.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.lasso
[1] --- test_ampAD.mef2c.154tfs.278samples.lasso
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
[1] --- test_keep.metrics.lasso
[1] --- test_lambda.lasso
[1] --- test_scalePredictorPenalties.lasso
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_.getScoredMotifs
[1] --- test_.injectSnp
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByChromosomalRegion_contrastReferenceWithVariant
[1] --- test_findMatchesByMultipleChromosomalRegions
[1] --- test_getSequence
[1] --- test_getSequenceWithVariants
[1] --- test_noMatch
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_alpha.ridge
[1] --- test_lambda.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.ridge
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_lambda.ridge
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getTarget
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
[1] --- test_lambda.sqrtlasso
[1] --- test_nCores.sqrtlasso
[1] --- test_basicConstructor
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
[1] calling HumanDHSFilter, span: 201
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_assessSnp
[1] error, unrecognized variant name: 'rsBogus'
[1] --- test_assessSnp_allTypesWithDeltas
[1] --- test_basicConstructor
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
[1] calling HumanDHSFilter, span: 201
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.8-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Tue Apr 16 03:43:03 2019 
*********************************************** 
Number of test functions: 85 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 85 test functions, 0 errors, 0 failures
Number of test functions: 85 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
2: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
3: In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
> 
> proc.time()
   user  system elapsed 
383.148  23.692 424.084 

name	user	system	elapsed
BayesSpikeSolver	0.748	0.000	0.762
CandidateFilter-class	0.000	0.000	0.001
EnsembleSolver	0.016	0.000	0.016
FootprintFilter-class	0.000	0.000	0.001
GeneOntologyFilter-class	0.076	0.000	0.113
HumanDHSFilter-class	0.000	0.000	0.001
LassoPVSolver	0.016	0.000	0.017
LassoSolver	0.016	0.000	0.017
MotifMatcher-class	0.252	0.000	0.250
PearsonSolver	0.016	0.000	0.018
RandomForestSolver	0.016	0.000	0.017
RidgeSolver	0	0	0
Solver-class	0.012	0.000	0.014
SpearmanSolver	0.020	0.000	0.018
SqrtLassoSolver	0.016	0.000	0.018
Trena-class	0.000	0.000	0.001
VarianceFilter-class	0.004	0.004	0.007
assessSnp	0.000	0.000	0.001
createGeneModelFromRegulatoryRegions	0.000	0.000	0.002
createGeneModelFromTfList	0.004	0.000	0.001
findMatchesByChromosomalRegion	0	0	0
getAssayData	0.016	0.000	0.014
getAvailableSolvers	0.000	0.000	0.001
getCandidates-FootprintFilter-method	0.000	0.000	0.001
getCandidates-GeneOntologyFilter-method	0.916	0.036	0.950
getCandidates-HumanDHSFilter-method	0	0	0
getCandidates-VarianceFilter-method	0.02	0.00	0.02
getChromLoc	0.012	0.000	0.012
getEncodeRegulatoryTableNames-HumanDHSFilter	0	0	0
getFootprintsForGene	0.008	0.000	0.010
getFootprintsInRegion	0.012	0.000	0.012
getGeneModelTableColumnNames	0.004	0.000	0.000
getGenePromoterRegion	0.008	0.000	0.009
getGtfGeneBioTypes	0.008	0.000	0.009
getGtfMoleculeTypes	0.008	0.000	0.009
getPfms	0.104	0.008	0.111
getPromoterRegionsAllGenes	0.052	0.004	0.057
getProximalPromoter	0	0	0
getRegulators	0.012	0.000	0.009
getRegulatoryChromosomalRegions	0.852	0.008	5.264
getRegulatoryRegions	0.000	0.000	0.001
getRegulatoryTableColumnNames	0.000	0.000	0.001
getSequence	0	0	0
getSolverNames	0.020	0.000	0.022
getTarget	0.012	0.000	0.013
parseChromLocString	0	0	0
parseDatabaseUri	0.000	0.000	0.002
rescalePredictorWeights	0.016	0.004	0.020
show-HumanDHSFilter-method	0.000	0.000	0.001
show.BayesSpikeSolver	0.020	0.000	0.022
show.EnsembleSolver	0.016	0.000	0.016
show.LassoPVSolver	0.020	0.000	0.021
show.LassoSolver	0.016	0.000	0.016
show.MotifMatcher	0.012	0.000	0.015
show.PearsonSolver	0.020	0.000	0.022
show.RandomForestSolver	0.024	0.000	0.021
show.RidgeSolver	0.016	0.000	0.018
show.SpearmanSolver	0.04	0.00	0.04
show.SqrtLassoSolver	0.016	0.000	0.018
solve.BayesSpike	0.000	0.000	0.001
solve.Lasso	2.760	0.056	2.825
solve.LassoPV	0.204	0.000	0.226
solve.Pearson	0.020	0.000	0.018
solve.RandomForest	3.892	0.000	3.902
solve.Ridge	4.084	0.004	4.091
solve.Spearman	0.020	0.000	0.021
solve.SqrtLasso	0.000	0.000	0.001