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CHECK report for GenVisR on merida2

This page was generated on 2018-10-17 08:55:53 -0400 (Wed, 17 Oct 2018).

Package 605/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.12.1
Zachary Skidmore
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GenVisR
Branch: RELEASE_3_7
Last Commit: 1a07492
Last Changed Date: 2018-05-24 15:29:37 -0400 (Thu, 24 May 2018)
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 

Summary

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

Command output

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### 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
###
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* 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.


Installation output

GenVisR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GenVisR
###
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* 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)

Tests output

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

Example timings

GenVisR.Rcheck/GenVisR-Ex.timings

nameusersystemelapsed
Lolliplot-class30.140 5.58741.685
TvTi4.0350.0324.084
cnFreq8.8930.1849.194
cnSpec4.7540.0504.895
cnView0.9690.0030.978
compIdent2.0720.0542.130
covBars0.9470.0030.959
genCov6.8180.3897.297
geneViz3.9980.0904.116
ideoView0.5890.0030.596
lohSpec4.9090.0574.985
lohView0.8320.0020.840
lolliplot 3.437 0.03619.441
waterfall1.6140.0031.622