Package: trena

Version: 1.5.8

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:trena.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings trena_1.5.8.tar.gz

StartedAt: 2019-04-09 04:08:19 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:18:19 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 600.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: trena.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:trena.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings trena_1.5.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/trena.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.5.8’
* 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 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 ... WARNING
Missing link or links in documentation object 'Trena-class.Rd':
  ‘createGeneModel’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'normalizeModel,PCAMax-method'
  ‘normalizing.max’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 0.724  0.009   6.113
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  Test files with failing tests
  
     test_BayesSpikeSolver.R 
       /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R 
  
     test_MotifMatcher.R 
       test_.injectSnp 
  
     test_RidgeSolver.R 
       /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R 
  
  
  Error in BiocGenerics:::testPackage("trena") : 
    unit tests failed for package trena
  Execution halted
* 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 ERROR, 2 WARNINGs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/trena.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL trena
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘trena’ ...
** using staged installation
** 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 from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path
* DONE (trena)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, 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
Error in checkTrue(nrow(tbl.trimmed) == 12) : Test not TRUE

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

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

[1] --- test_directMode
[1] --- test_getOpenChromatinFastAndSimple
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getOpenChromatinFastAndSimple
about to create RMariaDB driver, getting regulatory regions
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
Warning: call dbDisconnect() when finished working with a connection
[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
Warning in .seqlengths_TwoBitFile(x) :
  mustOpen: Can't open /home/biocbuild/bbs-3.9-bioc/R/library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit to read: No such file or directory
Timing stopped at: 0.038 0 0.037
Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
In addition: Warning message:
In Solver(mtx.assay = mtx.assay, targetGene = targetGene, candidateRegulators = candidateRegulators,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByMultipleChromosomalRegions
[1] --- test_getSequence
[1] --- test_noMatch
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_alpha.ridge
[1] --- test_lambda.ridge
[1] --- test_keep.metrics.ridge
Error in checkTrue(tbl$lambda < 0.9) : Test not TRUE

[1] --- test_getAssayData
[1] --- test_getTarget
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
[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-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
about to create RMariaDB driver, getting regulatory regions
[1] calling HumanDHSFilter, span: 201
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_basicConstructor
[1] --- test_createGeneModelFromRegulatoryRegions
[1] --- test_createGeneModelFromTfList
[1] --- test_getProximalPromoterHuman
[1] --- test_getProximalPromoterMouse
[1] --- test_getRegulatoryRegions_encodeDHS
[1] calling HumanDHSFilter, span: 5
about to create RMariaDB driver, getting regulatory regions
[1] calling HumanDHSFilter, span: 201
about to create RMariaDB driver, getting regulatory regions
[1] --- test_getRegulatoryRegions_oneFootprintSource
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_getRegulatoryRegions_twoFootprintSources
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
[1] --- test_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Tue Apr  9 04:18:14 2019 
*********************************************** 
Number of test functions: 80 
Number of errors: 3 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 80 test functions, 3 errors, 0 failures
ERROR in /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R: Error while sourcing  /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R : Error in checkTrue(nrow(tbl.trimmed) == 12) : Test not TRUE

ERROR in test_.injectSnp: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R: Error while sourcing  /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R : Error in checkTrue(tbl$lambda < 0.9) : Test not TRUE


Test files with failing tests

   test_BayesSpikeSolver.R 
     /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_BayesSpikeSolver.R 

   test_MotifMatcher.R 
     test_.injectSnp 

   test_RidgeSolver.R 
     /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_RidgeSolver.R 


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

name	user	system	elapsed
BayesSpikeSolver	0.022	0.000	0.034
CandidateFilter-class	0.001	0.000	0.001
EnsembleSolver	0.017	0.000	0.017
FootprintFilter-class	0.000	0.000	0.001
GeneOntologyFilter-class	0.070	0.000	0.071
HumanDHSFilter-class	0.002	0.000	0.001
LassoPVSolver	0.017	0.000	0.018
LassoSolver	0.017	0.000	0.017
MotifMatcher-class	0.205	0.000	0.204
PearsonSolver	0.012	0.004	0.017
RandomForestSolver	0.053	0.000	0.053
RidgeSolver	0	0	0
Solver-class	0.013	0.000	0.012
SpearmanSolver	0.015	0.000	0.016
SqrtLassoSolver	0.016	0.000	0.015
Trena-class	0.001	0.000	0.001
VarianceFilter-class	0.006	0.000	0.007
assessSnp	0	0	0
createGeneModelFromRegulatoryRegions	0.002	0.000	0.002
createGeneModelFromTfList	0.001	0.000	0.001
findMatchesByChromosomalRegion	0	0	0
getAssayData	0.009	0.004	0.012
getAvailableSolvers	0.000	0.000	0.001
getCandidates-FootprintFilter-method	0.000	0.000	0.001
getCandidates-GeneOntologyFilter-method	0.988	0.029	1.018
getCandidates-HumanDHSFilter-method	0.000	0.000	0.001
getCandidates-VarianceFilter-method	0.011	0.000	0.012
getChromLoc	0.016	0.000	0.016
getEncodeRegulatoryTableNames-HumanDHSFilter	0.000	0.000	0.001
getFootprintsForGene	0.014	0.000	0.014
getFootprintsInRegion	0.019	0.000	0.019
getGeneModelTableColumnNames	0.001	0.000	0.000
getGenePromoterRegion	0.008	0.004	0.012
getGtfGeneBioTypes	0.012	0.000	0.013
getGtfMoleculeTypes	0.012	0.000	0.012
getPfms	0.154	0.000	0.153
getPromoterRegionsAllGenes	0.051	0.000	0.051
getProximalPromoter	0	0	0
getRegulators	0.011	0.000	0.012
getRegulatoryChromosomalRegions	0.724	0.009	6.113
getRegulatoryRegions	0	0	0
getRegulatoryTableColumnNames	0.000	0.000	0.001
getSequence	0	0	0
getSolverNames	0.016	0.003	0.019
getTarget	0.047	0.000	0.047
parseChromLocString	0.001	0.000	0.001
parseDatabaseUri	0.002	0.000	0.001
rescalePredictorWeights	0.021	0.000	0.022
show-HumanDHSFilter-method	0.001	0.000	0.000
show.BayesSpikeSolver	0.022	0.000	0.022
show.EnsembleSolver	0.016	0.000	0.016
show.LassoPVSolver	0.014	0.000	0.014
show.LassoSolver	0.011	0.000	0.011
show.MotifMatcher	0.01	0.00	0.01
show.PearsonSolver	0.014	0.000	0.014
show.RandomForestSolver	0.014	0.000	0.014
show.RidgeSolver	0.013	0.000	0.013
show.SpearmanSolver	0.011	0.004	0.015
show.SqrtLassoSolver	0.009	0.008	0.017
solve.BayesSpike	0	0	0
solve.Lasso	2.262	0.004	2.266
solve.LassoPV	0.151	0.000	0.150
solve.Pearson	0.011	0.000	0.011
solve.RandomForest	3.872	0.000	3.872
solve.Ridge	3.844	0.000	3.844
solve.Spearman	0.021	0.000	0.021
solve.SqrtLasso	0	0	0