Package: trena

Version: 1.6.1

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_1.6.1.tar.gz

StartedAt: 2019-10-16 05:32:45 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:42:02 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 557.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: trena.Rcheck

Warnings: NA

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###
### 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_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/trena.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.1’
* package encoding: UTF-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 ... 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 ... ERROR
Running examples in ‘trena-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getRegulatoryChromosomalRegions,Trena-method
> ### Title: Get the regulatory chromosomal regions for a Trena object
> ### Aliases: getRegulatoryChromosomalRegions,Trena-method
> ###   getRegulatoryChromosomalRegions
> 
> ### ** Examples
> 
> # Get regulatory regions for MEF2C from a footprint database
> database.filename <- system.file(package="trena", "extdata", "mef2c.neigborhood.hg38.footprints.db")
> database.uri <- sprintf("sqlite://%s", database.filename)
> sources <- c(database.uri)
> 
> trena <- Trena("hg38")
> chromosome <- "chr5"
> mef2c.tss <- 88904257
> loc.start <- mef2c.tss - 1000
> loc.end   <- mef2c.tss + 1000
> 
> regions <- getRegulatoryChromosomalRegions(trena, chromosome, mef2c.tss-1000, mef2c.tss+1000,
+ sources, "MEF2C", mef2c.tss)
[1] calling footprintFilter with source = 'sqlite:///home/biocbuild/bbs-3.9-bioc/R/library/trena/extdata/mef2c.neigborhood.hg38.footprints.db', span: 2001
Error in postgresqlNewConnection(drv, ...) : 
  RS-DBI driver: (could not connect trena@bddsrds.globusgenomics.org:5432 on dbname "hg38": could not translate host name "bddsrds.globusgenomics.org" to address: Name or service not known
)
Calls: getRegulatoryChromosomalRegions ...  ->  -> postgresqlNewConnection
Execution halted
* 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:
  1 Test Suite : 
  trena RUnit Tests - 77 test functions, 1 error, 0 failures
  ERROR in /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_Trena.R: Error while sourcing  /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_Trena.R : Error in postgresqlNewConnection(drv, ...) : 
    RS-DBI driver: (could not connect trena@bddsrds.globusgenomics.org:5432 on dbname "hg38": could not translate host name "bddsrds.globusgenomics.org" to address: Name or service not known
  )
  
  Test files with failing tests
  
     test_Trena.R 
       /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_Trena.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
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/trena.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL trena
###
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* 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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 2.0-18

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

Attaching package: 'BiocGenerics'

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

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

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

    which

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand

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

    expand.grid

Loading required package: IRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

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

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

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

[1] --- test_directMode
[1] --- test_getOpenChromatinFastAndSimple
about to create RMySQL driver, getting regulatory regions
[1] --- test_getOpenChromatinFastAndSimple
about to create RMySQL driver, getting regulatory regions
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoPvSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.lassopv
[1] --- test_LassoSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_developAndFitDummyTestData
[1] --- test_fitDummyData
Warning: call dbDisconnect() when finished working with a connection
[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_findMatchesByMultipleChromosomalRegions
[1] --- test_getSequence
[1] --- test_noMatch
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_PearsonSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.pearson
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RandomForestSolverConstructor
[1] --- test_RandomForestSolverFewCandidates
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForest
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_alpha.ridge
[1] --- test_lambda.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_RidgeSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_alpha.ridge
[1] --- test_ampAD.mef2c.154tfs.278samples.ridge
[1] --- test_keep.metrics.ridge
[1] --- test_lambda.ridge
[1] --- test_getAssayData
[1] --- test_getTarget
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getRegulators
[1] --- test_eliminateSelfTFs
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_MatrixWarnings
[1] --- test_TargetAndRegulatorWarnings
[1] --- test_eliminateSelfTFs
[1] --- test_getAssayData
Warning in Solver(mtx, "gene1", c("gene2", "gene3")) :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_getRegulators
[1] --- test_getTarget
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SpearmanSolverConstructor
Warning in Solver(mtx.assay = mtx.assay, quiet = quiet, targetGene = targetGene,  :
  Target gene mean expression is in the bottom 10% of all genes in the assay matrix
[1] --- test_ampAD.mef2c.154tfs.278samples.spearman
[1] --- test_SqrtLassoSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.sqrtlasso
[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
Error in postgresqlNewConnection(drv, ...) : 
  RS-DBI driver: (could not connect trena@bddsrds.globusgenomics.org:5432 on dbname "hg38": could not translate host name "bddsrds.globusgenomics.org" to address: Name or service not known
)
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_VarianceFilter
[1] --- test_VarianceFilter


RUNIT TEST PROTOCOL -- Wed Oct 16 05:41:56 2019 
*********************************************** 
Number of test functions: 77 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 77 test functions, 1 error, 0 failures
ERROR in /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_Trena.R: Error while sourcing  /home/biocbuild/bbs-3.9-bioc/R/library/trena/unitTests/test_Trena.R : Error in postgresqlNewConnection(drv, ...) : 
  RS-DBI driver: (could not connect trena@bddsrds.globusgenomics.org:5432 on dbname "hg38": could not translate host name "bddsrds.globusgenomics.org" to address: Name or service not known
)

Test files with failing tests

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


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

name	user	system	elapsed
BayesSpikeSolver	0.021	0.000	0.077
CandidateFilter-class	0.001	0.000	0.001
EnsembleSolver	0.017	0.000	0.016
FootprintFilter-class	0.000	0.000	0.001
GeneOntologyFilter-class	0.065	0.000	0.072
HumanDHSFilter-class	0.002	0.000	0.002
LassoPVSolver	0.017	0.000	0.017
LassoSolver	0.017	0.000	0.016
MotifMatcher-class	0.221	0.003	0.226
PearsonSolver	0.017	0.000	0.016
RandomForestSolver	0.016	0.000	0.017
RidgeSolver	0.001	0.000	0.000
Solver-class	0.014	0.000	0.014
SpearmanSolver	0.015	0.000	0.015
SqrtLassoSolver	0.013	0.000	0.013
Trena-class	0.001	0.000	0.001
VarianceFilter-class	0.006	0.000	0.005
assessSnp	0	0	0
createGeneModelFromRegulatoryRegions	0.001	0.000	0.001
createGeneModelFromTfList	0.001	0.000	0.001
findMatchesByChromosomalRegion	0	0	0
getAssayData	0.01	0.00	0.01
getAvailableSolvers	0.001	0.000	0.000
getCandidates-FootprintFilter-method	0	0	0
getCandidates-GeneOntologyFilter-method	0.506	0.020	0.527
getCandidates-HumanDHSFilter-method	0	0	0
getCandidates-VarianceFilter-method	0.006	0.002	0.008
getChromLoc	0.011	0.000	0.011
getEncodeRegulatoryTableNames-HumanDHSFilter	0.001	0.000	0.000
getFootprintsForGene	0.008	0.000	0.008
getFootprintsInRegion	0.011	0.000	0.011
getGeneModelTableColumnNames	0	0	0
getGenePromoterRegion	0.007	0.000	0.007
getGtfGeneBioTypes	0.009	0.000	0.009
getGtfMoleculeTypes	0.008	0.000	0.007
getPfms	0.092	0.000	0.091
getPromoterRegionsAllGenes	0.032	0.000	0.032
getProximalPromoter	0	0	0
getRegulators	0.008	0.000	0.009