Package: GenVisR

Version: 1.19.2

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_1.19.2.tar.gz

StartedAt: 2020-01-16 04:54:47 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 05:10:18 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 931.3 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_1.19.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GenVisR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.19.2’
* 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’
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 (user + system) or elapsed time > 5s
                  user system elapsed
Lolliplot-class 44.003 10.309  70.521
genCov          12.960  0.904  14.881
cnFreq          10.980  0.071  11.555
lohSpec          7.710  0.180   8.812
geneViz          7.023  0.255   8.077
cnSpec           5.904  0.057   6.348
lolliplot        5.498  0.101  78.062
* 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:
  subscript out of bounds
  Backtrace:
   1. GenVisR:::constructTranscriptData(...)
   2. GenVisR:::constructTranscriptData(...)
   3. GenVisR:::.local(object, ...)
   4. biomaRt::getBM(...)
   5. biomaRt:::.createHash(...)
   6. biomaRt::listEnsemblArchives()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 607 | SKIPPED: 44 | WARNINGS: 11 | FAILED: 1 ]
  1. Error: (unknown) (@test-Lolliplot-class.R#376) 
  
  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-3.11-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/4.0/Resources/library’
* installing *source* package ‘GenVisR’ ...
** using staged installation
** 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 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 (GenVisR)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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. Error: (unknown) (@test-Lolliplot-class.R#376)  ──────────────────────────
subscript out of bounds
Backtrace:
 1. GenVisR:::constructTranscriptData(...)
 2. GenVisR:::constructTranscriptData(...)
 3. GenVisR:::.local(object, ...)
 4. biomaRt::getBM(...)
 5. biomaRt:::.createHash(...)
 6. biomaRt::listEnsemblArchives()

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 607 | SKIPPED: 44 | WARNINGS: 11 | FAILED: 1 ]
1. Error: (unknown) (@test-Lolliplot-class.R#376) 

Error: testthat unit tests failed
Execution halted

name	user	system	elapsed
Lolliplot-class	44.003	10.309	70.521
TvTi	3.588	0.040	3.628
Waterfall-class	3.240	0.653	1.140
cnFreq	10.980	0.071	11.555
cnSpec	5.904	0.057	6.348
cnView	1.380	0.012	1.504
compIdent	4.196	0.153	4.653
covBars	1.223	0.011	1.280
genCov	12.960	0.904	14.881
geneViz	7.023	0.255	8.077
ideoView	0.867	0.014	0.944
lohSpec	7.710	0.180	8.812
lohView	1.397	0.013	1.585
lolliplot	5.498	0.101	78.062
waterfall	2.330	0.016	2.623