Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:49 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GenVisR on machv2


To the developers/maintainers of the GenVisR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenVisR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 762/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.26.0  (landing page)
Zachary Skidmore
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenVisR
git_branch: RELEASE_3_14
git_last_commit: 9bd43fb
git_last_commit_date: 2021-10-26 12:24:58 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GenVisR
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenVisR_1.26.0.tar.gz
StartedAt: 2022-01-20 13:25:21 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 13:39:52 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 870.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GenVisR.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenVisR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GenVisR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.26.0’
* 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 ‘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 LazyData ... 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 39.727  1.097  69.176
lolliplot       13.325  0.084  54.271
geneViz         11.500  0.231  11.748
genCov          10.213  0.458  10.689
cnFreq          10.367  0.036  10.417
cnSpec           6.321  0.029   6.356
lohSpec          5.329  0.096   5.430
* 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(GenVisR)
  > 
  > test_check("GenVisR")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On Bioconductor (54)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly ──
  `expected` not equivalent to `actual`.
  1/1 mismatches
  [1] 7 - 9 == -2
  
  [ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
  Error: Test failures
  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-3.14-bioc/meat/GenVisR.Rcheck/00check.log’
for details.


Installation output

GenVisR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenVisR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

GenVisR.Rcheck/tests/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (54)

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly ──
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 7 - 9 == -2

[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
Error: Test failures
Execution halted

Example timings

GenVisR.Rcheck/GenVisR-Ex.timings

nameusersystemelapsed
Lolliplot-class39.727 1.09769.176
TvTi2.9740.0213.002
Waterfall-class0.7840.0040.792
cnFreq10.367 0.03610.417
cnSpec6.3210.0296.356
cnView2.6990.0102.712
compIdent3.1480.1483.300
covBars1.1290.0111.145
genCov10.213 0.45810.689
geneViz11.500 0.23111.748
ideoView2.5160.0222.539
lohSpec5.3290.0965.430
lohView2.8550.0072.865
lolliplot13.325 0.08454.271
waterfall1.3720.0031.376