Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:42:56 -0400 (Tue, 09 Apr 2019).
Package 486/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ELMER 2.7.5 Tiago Chedraoui Silva
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
Package: ELMER |
Version: 2.7.5 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ELMER_2.7.5.tar.gz |
StartedAt: 2019-04-09 00:18:11 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 00:37:52 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 1180.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ELMER.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ELMER_2.7.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ELMER.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 ‘ELMER/DESCRIPTION’ ... OK * this is package ‘ELMER’ version ‘2.7.5’ * 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 ‘ELMER’ 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 ... NOTE addMutCol: no visible binding for global variable 'Hugo_Symbol' calcDistNearestTSS: no visible binding for global variable 'DistanceTSS' getRegionNearGenes : f: no visible binding for global variable 'Side' getRegionNearGenes: no visible binding for global variable 'ID' getTFtargets: no visible binding for global variable 'TF' Undefined global functions or variables: DistanceTSS Hugo_Symbol ID Side TF * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed TCGA.pipe 94.876 0.392 96.864 get.enriched.motif 28.309 0.312 30.798 getRandomPairs 22.872 0.100 29.313 schematic.plot 20.337 0.044 30.951 createMAE 17.365 0.240 30.911 scatter.plot 14.387 0.020 14.407 GetNearGenes 13.863 0.119 31.644 get.feature.probe 12.667 0.168 16.541 preAssociationProbeFiltering 9.600 0.096 13.688 get.pair 6.976 0.028 7.004 getRegionNearGenes 6.945 0.016 15.384 getTCGA 6.483 0.036 6.808 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: |=================================================== |99.03846% ˜0 s remaining |=================================================== |99.17582% ˜0 s remaining |=================================================== |99.31319% ˜0 s remaining |=================================================== |99.45055% ˜0 s remaining |=================================================== |99.58791% ˜0 s remaining |=================================================== |99.72527% ˜0 s remaining |=================================================== |99.86264% ˜0 s remaining |====================================================|100% ˜0 s remaining |====================================================|100% Completed after 1 s ══ testthat results ═══════════════════════════════════════════════════════════ OK: 116 SKIPPED: 0 FAILED: 1 1. Error: Gene expression is calculated (@test-get.pair.R#144) Error: testthat unit tests failed 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 ‘/home/biocbuild/bbs-3.9-bioc/meat/ELMER.Rcheck/00check.log’ for details.
ELMER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ELMER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘ELMER’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ELMER)
ELMER.Rcheck/tests/testthat.Rout.fail
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. 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Error: Gene expression is calculated (@test-get.pair.R#144) ───────────── undefined columns selected 1: get.pair(data = data, nearGenes = nearGenes, permu.size = 5, raw.pvalue = 0.001, Pe = 0.2, diffExp = TRUE, group.col = "definition", group1 = "Primary solid Tumor", group2 = "Solid Tissue Normal", dir.out = "./", permu.dir = "permu_test", label = "hypo") at testthat/test-get.pair.R:144 2: out[match(selected$GeneID, out$GeneID), c("log2FC", "diff.pvalue")] 3: `[.data.frame`(out, match(selected$GeneID, out$GeneID), c("log2FC", "diff.pvalue")) 4: stop("undefined columns selected") | | 0% |= |1.960784% ˜0 s remaining |== |3.921569% ˜0 s remaining |=== |5.882353% ˜0 s remaining |==== |7.843137% ˜0 s remaining |===== |9.803922% ˜0 s remaining |====== |11.76471% ˜0 s remaining |======= |13.72549% ˜0 s remaining |======== |15.68627% ˜0 s remaining |========= |17.64706% ˜0 s remaining |========== |19.60784% ˜0 s remaining |=========== |21.56863% ˜0 s remaining |============ |23.52941% ˜0 s 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═══════════════════════════════════════════════════════════ OK: 116 SKIPPED: 0 FAILED: 1 1. Error: Gene expression is calculated (@test-get.pair.R#144) Error: testthat unit tests failed Execution halted
ELMER.Rcheck/ELMER-Ex.timings
name | user | system | elapsed | |
GetNearGenes | 13.863 | 0.119 | 31.644 | |
TCGA.pipe | 94.876 | 0.392 | 96.864 | |
TF.rank.plot | 2.266 | 0.036 | 2.308 | |
addDistNearestTSS | 0.000 | 0.000 | 0.001 | |
addMutCol | 0 | 0 | 0 | |
calcDistNearestTSS | 0 | 0 | 0 | |
calculateEnrichement | 0.039 | 0.000 | 0.040 | |
createBigWigDNAmetArray | 0 | 0 | 0 | |
createIGVtrack | 0 | 0 | 0 | |
createMAE | 17.365 | 0.240 | 30.911 | |
createTSVTemplates | 0.014 | 0.000 | 0.014 | |
findMotifRegion | 0.000 | 0.001 | 0.001 | |
get.TFs | 2.130 | 0.027 | 2.157 | |
get.diff.meth | 2.877 | 0.020 | 2.898 | |
get.enriched.motif | 28.309 | 0.312 | 30.798 | |
get.feature.probe | 12.667 | 0.168 | 16.541 | |
get.pair | 6.976 | 0.028 | 7.004 | |
get.permu | 3.765 | 0.004 | 3.769 | |
get.tabs | 0.000 | 0.000 | 0.001 | |
getGeneID | 0.638 | 0.000 | 0.637 | |
getRandomPairs | 22.872 | 0.100 | 29.313 | |
getRegionNearGenes | 6.945 | 0.016 | 15.384 | |
getSymbol | 0.893 | 0.008 | 0.901 | |
getTCGA | 6.483 | 0.036 | 6.808 | |
getTFBindingSites | 0 | 0 | 0 | |
getTFtargets | 0.004 | 0.000 | 0.004 | |
getTSS | 0 | 0 | 0 | |
heatmapGene | 0.000 | 0.001 | 0.001 | |
heatmapPairs | 0 | 0 | 0 | |
metBoxPlot | 0 | 0 | 0 | |
motif.enrichment.plot | 0.653 | 0.002 | 0.656 | |
preAssociationProbeFiltering | 9.600 | 0.096 | 13.688 | |
promoterMeth | 0 | 0 | 0 | |
render_report | 0.000 | 0.000 | 0.001 | |
scatter.plot | 14.387 | 0.020 | 14.407 | |
schematic.plot | 20.337 | 0.044 | 30.951 | |