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This page was generated on 2023-10-16 11:37:05 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 818/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.32.0  (landing page)
Zachary Skidmore
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GenVisR
git_branch: RELEASE_3_17
git_last_commit: 8b1b564
git_last_commit_date: 2023-04-25 10:43:51 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for GenVisR on merida1


To the developers/maintainers of the GenVisR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GenVisR
Version: 1.32.0
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_1.32.0.tar.gz
StartedAt: 2023-10-16 02:07:15 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 02:31:45 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 1470.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GenVisR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GenVisR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.32.0’
* 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 35.346  1.879 144.931
geneViz         12.717  0.259  16.061
cnFreq          12.487  0.078  15.968
genCov          11.739  0.507  15.439
cnSpec           9.525  0.047  12.091
lohSpec          7.913  0.143  10.390
TvTi             3.989  0.035   5.120
compIdent        3.771  0.244   5.140
* 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:
  • MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
  • MutSpectra-class/mutspectra-frequency-plot.svg
  • MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
  • MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
  • MutSpectra-class/mutspectra-proportion-plot.svg
  • Rainfall-class/density-main-plot.svg
  • Rainfall-class/density-plot-add-layer.svg
  • Rainfall-class/drawplot-rainfall.svg
  • Rainfall-class/final-rainfall-alter-section-hieghts.svg
  • Rainfall-class/final-rainfall-base.svg
  • Rainfall-class/rainfall-main-plot.svg
  • Rainfall-class/rainfall-plot-add-layer.svg
  • Rainfall-class/rainfall-plot-aesthetic-options.svg
  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-3.17-bioc/meat/GenVisR.Rcheck/00check.log’
for details.


Installation output

GenVisR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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")
[ FAIL 1 | WARN 17 | SKIP 54 | PASS 601 ]

══ Skipped tests (54) ══════════════════════════════════════════════════════════
• On Bioconductor (54): 'test-Lolliplot-class.R:581:5',
  'test-Lolliplot-class.R:591:6', 'test-Lolliplot-class.R:619:5',
  'test-Lolliplot-class.R:631:5', 'test-Lolliplot-class.R:645:5',
  'test-Lolliplot-class.R:657:5', 'test-Lolliplot-class.R:673:5',
  'test-Lolliplot-class.R:756:5', 'test-Lolliplot-class.R:766:5',
  'test-Lolliplot-class.R:808:5', 'test-MutSpectra-class.R:284:5',
  'test-MutSpectra-class.R:294:5', 'test-MutSpectra-class.R:305:5',
  'test-MutSpectra-class.R:341:5', 'test-MutSpectra-class.R:351:5',
  'test-MutSpectra-class.R:362:5', 'test-MutSpectra-class.R:416:5',
  'test-MutSpectra-class.R:426:5', 'test-MutSpectra-class.R:456:5',
  'test-MutSpectra-class.R:464:5', 'test-Rainfall-class.R:246:5',
  'test-Rainfall-class.R:255:5', 'test-Rainfall-class.R:265:5',
  'test-Rainfall-class.R:302:5', 'test-Rainfall-class.R:311:5',
  'test-Rainfall-class.R:357:5', 'test-Rainfall-class.R:366:5',
  'test-Rainfall-class.R:403:5', 'test-Waterfall-class.R:661:5',
  'test-Waterfall-class.R:671:5', 'test-Waterfall-class.R:681:5',
  'test-Waterfall-class.R:691:5', 'test-Waterfall-class.R:728:5',
  'test-Waterfall-class.R:742:5', 'test-Waterfall-class.R:752:5',
  'test-Waterfall-class.R:762:5', 'test-Waterfall-class.R:772:5',
  'test-Waterfall-class.R:809:5', 'test-Waterfall-class.R:823:5',
  'test-Waterfall-class.R:836:5', 'test-Waterfall-class.R:849:5',
  'test-Waterfall-class.R:862:5', 'test-Waterfall-class.R:875:5',
  'test-Waterfall-class.R:888:5', 'test-Waterfall-class.R:932:5',
  'test-Waterfall-class.R:1023:5', 'test-Waterfall-class.R:1033:5',
  'test-Waterfall-class.R:1049:5', 'test-Waterfall-class.R:1065:5',
  'test-Waterfall-class.R:1081:5', 'test-Waterfall-class.R:1098:5',
  'test-Waterfall-class.R:1114:5', 'test-Waterfall-class.R:1152:5',
  'test-Waterfall-class.R:1159:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Lolliplot-class.R:526:5'): setDomainHeights domains are nested correctly ──
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 2 - 10 == -8

[ FAIL 1 | WARN 17 | SKIP 54 | PASS 601 ]
Deleting unused snapshots:
• Lolliplot-class/drawplot-lolliplot.svg
• Lolliplot-class/final-lolliplot-alter-section-height.svg
• Lolliplot-class/final-lolliplot-base.svg
• Lolliplot-class/lolliplot-density-plot-layer.svg
• Lolliplot-class/lolliplot-density-plot.svg
• Lolliplot-class/lolliplot-plot-base-add-domain-palette.svg
• Lolliplot-class/lolliplot-plot-base-add-labels.svg
• Lolliplot-class/lolliplot-plot-base-add-layer.svg
• Lolliplot-class/lolliplot-plot-base-add-mutation-palette.svg
• Lolliplot-class/lolliplot-plot-base.svg
• MutSpectra-class/drawplot-mutspectra.svg
• MutSpectra-class/final-mutspectra-alter-section-heights.svg
• MutSpectra-class/final-mutspectra-base.svg
• MutSpectra-class/mutspectra-clinical.svg
• MutSpectra-class/mutspectra-frequency-plot-add-layer.svg
• MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-frequency-plot.svg
• MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
• MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-proportion-plot.svg
• Rainfall-class/density-main-plot.svg
• Rainfall-class/density-plot-add-layer.svg
• Rainfall-class/drawplot-rainfall.svg
• Rainfall-class/final-rainfall-alter-section-hieghts.svg
• Rainfall-class/final-rainfall-base.svg
• Rainfall-class/rainfall-main-plot.svg
• Rainfall-class/rainfall-plot-add-layer.svg
• Rainfall-class/rainfall-plot-aesthetic-options.svg
Error: Test failures
Execution halted

Example timings

GenVisR.Rcheck/GenVisR-Ex.timings

nameusersystemelapsed
Lolliplot-class 35.346 1.879144.931
TvTi3.9890.0355.120
Waterfall-class1.2130.0101.549
cnFreq12.487 0.07815.968
cnSpec 9.525 0.04712.091
cnView1.6190.0172.110
compIdent3.7710.2445.140
covBars1.6640.0162.340
genCov11.739 0.50715.439
geneViz12.717 0.25916.061
ideoView0.8530.0061.103
lohSpec 7.913 0.14310.390
lohView1.4860.0201.940
waterfall2.3440.0232.996