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

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### Running command:
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###   /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.

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### Running command:
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###   /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)

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

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