Package: trena

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:trena.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings trena_1.4.2.tar.gz

StartedAt: 2019-04-16 03:12:38 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:19:46 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 427.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: trena.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:trena.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings trena_1.4.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/trena.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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
* 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:
  Error: package or namespace load failed for 'trena':
   .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
    call: dbExistsTable(conn, "metadata")
    error: database disk image is malformed
  Error: unable to load trena Package
  In addition: Warning messages:
  1: Couldn't set cache size: database disk image is malformed
  Use `cache_size` = NULL to turn off this warning. 
  2: Couldn't set synchronous mode: database disk image is malformed
  Use `synchronous` = NULL to turn off this warning. 
  3: Couldn't set cache size: database disk image is malformed
  Use `cache_size` = NULL to turn off this warning. 
  4: Couldn't set synchronous mode: database disk image is malformed
  Use `synchronous` = NULL to turn off this warning. 
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/trena.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL trena
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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-apple-darwin15.6.0 (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.
Error: package or namespace load failed for 'trena':
 .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: dbExistsTable(conn, "metadata")
  error: database disk image is malformed
Error: unable to load trena Package
In addition: Warning messages:
1: Couldn't set cache size: database disk image is malformed
Use `cache_size` = NULL to turn off this warning. 
2: Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning. 
3: Couldn't set cache size: database disk image is malformed
Use `cache_size` = NULL to turn off this warning. 
4: Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning. 
Execution halted

name	user	system	elapsed
BayesSpikeSolver	0.018	0.001	0.021
CandidateFilter-class	0.001	0.000	0.001
EnsembleSolver	0.013	0.001	0.014
FootprintFilter-class	0.000	0.001	0.001
GeneOntologyFilter-class	0.050	0.002	0.052
HumanDHSFilter-class	0.003	0.001	0.003
LassoPVSolver	0.013	0.001	0.014
LassoSolver	0.014	0.002	0.015
MotifMatcher-class	0.232	0.005	0.243
PearsonSolver	0.014	0.002	0.016
RandomForestSolver	0.013	0.002	0.015
RidgeSolver	0.000	0.000	0.001
Solver-class	0.010	0.001	0.011
SpearmanSolver	0.016	0.002	0.018
SqrtLassoSolver	0.016	0.002	0.018
Trena-class	0.001	0.000	0.002
VarianceFilter-class	0.006	0.001	0.007
assessSnp	0	0	0
createGeneModelFromRegulatoryRegions	0.003	0.000	0.003
createGeneModelFromTfList	0.002	0.000	0.001
findMatchesByChromosomalRegion	0.001	0.000	0.000
getAssayData	0.011	0.001	0.013
getAvailableSolvers	0	0	0
getCandidates-FootprintFilter-method	0	0	0
getCandidates-GeneOntologyFilter-method	0.906	0.084	1.009
getCandidates-HumanDHSFilter-method	0.000	0.000	0.001
getCandidates-VarianceFilter-method	0.024	0.000	0.025
getChromLoc	0.019	0.001	0.020
getEncodeRegulatoryTableNames-HumanDHSFilter	0	0	0
getFootprintsForGene	0.017	0.001	0.018
getFootprintsInRegion	0.021	0.001	0.023
getGeneModelTableColumnNames	0.000	0.000	0.002
getGenePromoterRegion	0.015	0.001	0.016
getGtfGeneBioTypes	0.012	0.001	0.014
getGtfMoleculeTypes	0.012	0.001	0.014
getPfms	0.178	0.002	0.182
getPromoterRegionsAllGenes	0.058	0.001	0.060
getProximalPromoter	0.001	0.000	0.000
getRegulators	0.012	0.001	0.012
getRegulatoryChromosomalRegions	0.855	0.024	4.040
getRegulatoryRegions	0.001	0.000	0.000
getRegulatoryTableColumnNames	0.000	0.000	0.001
getSequence	0	0	0
getSolverNames	0.018	0.000	0.019
getTarget	0.010	0.001	0.011
parseChromLocString	0.000	0.000	0.001
parseDatabaseUri	0.001	0.000	0.002
rescalePredictorWeights	0.017	0.002	0.019
show-HumanDHSFilter-method	0	0	0
show.BayesSpikeSolver	0.018	0.002	0.020
show.EnsembleSolver	0.010	0.002	0.011
show.LassoPVSolver	0.020	0.002	0.022
show.LassoSolver	0.014	0.002	0.017
show.MotifMatcher	0.013	0.002	0.014
show.PearsonSolver	0.017	0.002	0.020
show.RandomForestSolver	0.019	0.002	0.021
show.RidgeSolver	0.016	0.002	0.018
show.SpearmanSolver	0.020	0.002	0.021
show.SqrtLassoSolver	0.018	0.002	0.020
solve.BayesSpike	0	0	0
solve.Lasso	3.361	0.247	3.698
solve.LassoPV	0.194	0.038	0.237
solve.Pearson	0.017	0.003	0.020
solve.RandomForest	3.668	0.092	3.820
solve.Ridge	4.611	0.235	4.881
solve.Spearman	0.027	0.003	0.029
solve.SqrtLasso	0.000	0.000	0.001