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This page was generated on 2022-01-21 13:05:51 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for trena on nebbiolo2


To the developers/maintainers of the trena package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/trena.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1998/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trena 1.16.0  (landing page)
Paul Shannon
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/trena
git_branch: RELEASE_3_14
git_last_commit: f742819
git_last_commit_date: 2021-10-26 12:35:29 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: trena
Version: 1.16.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:trena.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings trena_1.16.0.tar.gz
StartedAt: 2022-01-20 09:54:43 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 10:05:42 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 659.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: trena.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:trena.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings trena_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/trena.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.16.0’
* 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 ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    extdata   2.6Mb
* 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
  Found ‘inst/doc/makefile’: should be ‘Makefile’ and will be ignored
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/trena.Rcheck/00check.log’
for details.



Installation output

trena.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL trena
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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)

Tests output

trena.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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
Loaded glmnet 4.1-3
Loading required package: MotifDb
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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_BicorSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bicor
[1] --- test_BicorSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.bicor
[1] --- test_CandidateFilter
[1] --- test_CandidateFilter
[1] --- test_EnsembleSolverConstructor
[1] --- test_getSolverNames
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForestAndXGBoost
[1] --- test_selectedSolversOnly
[1] --- test_oneSolver
[1] --- test_invalidSolvers
[1] --- test_EnsembleSolverConstructor
[1] --- test_ampAD.mef2c.154tfs.278samples.ensemble
Warning in WGCNA::bicor(x = x, y = y, use = "pairwise.complete.obs") :
  bicor: zero MAD in variable 'x'. Pearson correlation was used for individual columns with zero (or missing) MAD.
[1] --- test_ampAD.mef2c.154tfs.278samples.randomForestAndXGBoost
[1] --- test_getSolverNames
[1] --- test_invalidSolvers
[1] --- test_oneSolver
[1] --- test_selectedSolversOnly
Warning in WGCNA::bicor(x = x, y = y, use = "pairwise.complete.obs") :
  bicor: zero MAD in variable 'x'. Pearson correlation was used for individual columns with zero (or missing) MAD.
[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
Warning: call dbDisconnect() when finished working with a connection
[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_getSequence
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_.injectSnp
[1] --- test_.getScoredMotifs
[1] --- test_noMatch
[1] --- test_findMatchesByChromosomalRegion
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByChromosomalRegion.yeast
[1] --- test_findMatchesByChromosomalRegion.athaliana
[1] --- test_.getScoredMotifs
[1] --- test_.injectSnp
[1] --- test_basicConstructor
[1] --- test_bugInStartEndOfMinusStrandHits
[1] --- test_findMatchesByChromosomalRegion
[1] --- test_findMatchesByChromosomalRegion.athaliana
[1] --- test_findMatchesByChromosomalRegion.twoAlternateAlleles
[1] --- test_findMatchesByChromosomalRegion.yeast
[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_VarianceFilter
[1] --- test_VarianceFilter
--- test_XGBoostSolverConstructor
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
--- test_ampAD.mef2c.154tfs.278samples.XGBoost
--- test_XGBoostSolverConstructor
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
--- test_ampAD.mef2c.154tfs.278samples.XGBoost


RUNIT TEST PROTOCOL -- Thu Jan 20 10:05:38 2022 
*********************************************** 
Number of test functions: 79 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
trena RUnit Tests - 79 test functions, 0 errors, 0 failures
Number of test functions: 79 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: 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
2: In WGCNA::bicor(x = x, y = y, use = "pairwise.complete.obs") :
  bicor: zero MAD in variable 'x'. Pearson correlation was used for individual columns with zero (or missing) MAD.
3: 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
4: In WGCNA::bicor(x = x, y = y, use = "pairwise.complete.obs") :
  bicor: zero MAD in variable 'x'. Pearson correlation was used for individual columns with zero (or missing) MAD.
5: In WGCNA::bicor(x = x, y = y, use = "pairwise.complete.obs") :
  bicor: zero MAD in variable 'x'. Pearson correlation was used for individual columns with zero (or missing) MAD.
6: In WGCNA::bicor(x = x, y = y, use = "pairwise.complete.obs") :
  bicor: zero MAD in variable 'x'. Pearson correlation was used for individual columns with zero (or missing) MAD.
> 
> proc.time()
   user  system elapsed 
320.355   3.913 323.276 

Example timings

trena.Rcheck/trena-Ex.timings

nameusersystemelapsed
BayesSpikeSolver0.0140.0010.015
BicorSolver0.0120.0000.013
CandidateFilter-class0.0000.0000.001
EnsembleSolver0.0070.0040.012
FootprintFilter-class000
GeneOntologyFilter-class0.0430.0000.043
HumanDHSFilter-class0.0000.0000.001
LassoPVSolver0.0110.0000.012
LassoSolver0.0380.0000.038
MotifMatcher-class0.1590.0000.158
PearsonSolver0.0110.0000.011
RandomForestSolver0.0110.0000.011
RidgeSolver000
Solver-class0.0050.0030.009
SpearmanSolver0.0100.0000.011
Trena-class0.0010.0000.000
VarianceFilter-class0.0050.0000.005
XGBoostSolver0.0120.0000.012
assessSnp0.0010.0000.000
createGeneModelFromRegulatoryRegions0.0010.0000.000
createGeneModelFromTfList0.0010.0000.000
findMatchesByChromosomalRegion000
getAssayData0.010.000.01
getAvailableSolvers000
getCandidates-FootprintFilter-method0.0000.0000.001
getCandidates-GeneOntologyFilter-method0.6100.0400.649
getCandidates-HumanDHSFilter-method000
getCandidates-VarianceFilter-method0.0070.0000.007
getChromLoc0.0090.0000.011
getEncodeRegulatoryTableNames-HumanDHSFilter0.0000.0000.001
getFootprintsForGene0.0070.0000.008
getFootprintsInRegion0.0110.0000.011
getGeneModelTableColumnNames0.0010.0000.000
getGenePromoterRegion0.0070.0000.007
getGtfGeneBioTypes0.0060.0000.007
getGtfMoleculeTypes0.0060.0000.007
getPfms0.1340.0120.145
getPromoterRegionsAllGenes0.0740.0000.075
getProximalPromoter0.0010.0000.000
getRegulators0.0870.0000.086
getRegulatoryChromosomalRegions0.0020.0000.002
getRegulatoryRegions000
getRegulatoryTableColumnNames0.0000.0000.001
getSequence0.0000.0000.001
getSolverNames0.0150.0040.019
getTarget0.0120.0000.012
parseChromLocString0.0010.0000.000
parseDatabaseUri0.0020.0000.002
rescalePredictorWeights0.0190.0000.020
show-HumanDHSFilter-method000
show.BayesSpikeSolver0.0190.0000.019
show.BicorSolver0.020.000.02
show.EnsembleSolver0.0160.0000.017
show.LassoPVSolver0.0140.0000.013
show.LassoSolver0.0110.0000.011
show.MotifMatcher0.010.000.01
show.PearsonSolver0.0150.0000.015
show.RandomForestSolver0.0140.0000.015
show.RidgeSolver0.0130.0000.012
show.SpearmanSolver0.0150.0000.014
show.XGBoostSolver0.0130.0040.017
solve.BayesSpike000
solve.Bicor0.0210.0000.022
solve.Ensemble000
solve.Lasso1.5350.0151.550
solve.LassoPV0.2810.0050.285
solve.Pearson1.1730.0161.190
solve.RandomForest2.9100.0282.938
solve.Ridge2.4240.0312.456
solve.Spearman0.0200.0010.020
solve.XGBoost0.8470.0040.448