Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:55:53 -0400 (Wed, 17 Oct 2018).
Package 605/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GenVisR 1.12.1 Zachary Skidmore
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK |
Package: GenVisR |
Version: 1.12.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenVisR_1.12.1.tar.gz |
StartedAt: 2018-10-16 21:42:14 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 21:51:09 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 535.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenVisR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GenVisR_1.12.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GenVisR.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenVisR/DESCRIPTION’ ... OK * this is package ‘GenVisR’ version ‘1.12.1’ * 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 ‘GenVisR’ 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 ... NOTE Namespace in Imports field not imported from: ‘reshape2’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE setTierTwo,data.table : a: no visible binding for global variable ‘tmp’ toLolliplot,GMS: no visible binding for global variable ‘missingINdex’ toLolliplot,VEP: no visible binding for global variable ‘missingINdex’ Undefined global functions or variables: missingINdex tmp * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed Lolliplot-class 30.140 5.587 41.685 cnFreq 8.893 0.184 9.194 genCov 6.818 0.389 7.297 lolliplot 3.437 0.036 19.441 * 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: > library(testthat) > library(GenVisR) > > test_check("GenVisR") ── 1. Failure: setDomainHeights domains are nested correctly (@test-Lolliplot-cl `expected` not equivalent to `actual`. 1/1 mismatches [1] 6 - 8 == -2 ══ testthat results ═══════════════════════════════════════════════════════════ OK: 552 SKIPPED: 45 FAILED: 1 1. Failure: setDomainHeights domains are nested correctly (@test-Lolliplot-class.R#525) 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.7-bioc/meat/GenVisR.Rcheck/00check.log’ for details.
GenVisR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenVisR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘GenVisR’ ... ** R ** data *** moving datasets to lazyload DB ** 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 * DONE (GenVisR)
GenVisR.Rcheck/tests/testthat.Rout.fail
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 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. > library(testthat) > library(GenVisR) > > test_check("GenVisR") ── 1. Failure: setDomainHeights domains are nested correctly (@test-Lolliplot-cl `expected` not equivalent to `actual`. 1/1 mismatches [1] 6 - 8 == -2 ══ testthat results ═══════════════════════════════════════════════════════════ OK: 552 SKIPPED: 45 FAILED: 1 1. Failure: setDomainHeights domains are nested correctly (@test-Lolliplot-class.R#525) Error: testthat unit tests failed Execution halted
GenVisR.Rcheck/GenVisR-Ex.timings
name | user | system | elapsed | |
Lolliplot-class | 30.140 | 5.587 | 41.685 | |
TvTi | 4.035 | 0.032 | 4.084 | |
cnFreq | 8.893 | 0.184 | 9.194 | |
cnSpec | 4.754 | 0.050 | 4.895 | |
cnView | 0.969 | 0.003 | 0.978 | |
compIdent | 2.072 | 0.054 | 2.130 | |
covBars | 0.947 | 0.003 | 0.959 | |
genCov | 6.818 | 0.389 | 7.297 | |
geneViz | 3.998 | 0.090 | 4.116 | |
ideoView | 0.589 | 0.003 | 0.596 | |
lohSpec | 4.909 | 0.057 | 4.985 | |
lohView | 0.832 | 0.002 | 0.840 | |
lolliplot | 3.437 | 0.036 | 19.441 | |
waterfall | 1.614 | 0.003 | 1.622 | |