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This page was generated on 2024-03-01 11:36:34 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 831/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.35.0  (landing page)
Zachary Skidmore
Snapshot Date: 2024-02-28 14:00:14 -0500 (Wed, 28 Feb 2024)
git_url: https://git.bioconductor.org/packages/GenVisR
git_branch: devel
git_last_commit: fb3c43e
git_last_commit_date: 2023-10-24 10:47:14 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for GenVisR on nebbiolo1


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: 1.35.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenVisR_1.35.0.tar.gz
StartedAt: 2024-02-28 22:37:34 -0500 (Wed, 28 Feb 2024)
EndedAt: 2024-02-28 22:48:38 -0500 (Wed, 28 Feb 2024)
EllapsedTime: 663.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GenVisR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenVisR_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GenVisR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.35.0’
* 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 ... NOTE
Found the following non-portable file paths:
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
  GenVisR/tests/testthat/_snaps/Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* 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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘GenVisR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: waterfall
> ### Title: Construct a waterfall plot
> ### Aliases: waterfall
> 
> ### ** Examples
> 
> # Plot the data
> waterfall(brcaMAF, plotGenes=c("PIK3CA", "TP53", "USH2A", "MLL3", "BRCA1"))
Checking if input is properly formatted...
Calculating frequency of mutations...
Warning: The melt generic in data.table has been passed a table and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace, i.e. reshape2::melt(mutation_counts). In the next version, this warning will become an error.
Removing genes not in: PIK3CA, TP53, USH2A, MLL3, BRCA1
setting mutation hierarchy...
Warning: The dcast generic in data.table has been passed a data.frame and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is superseded and is no longer actively developed, and this redirection is now deprecated. Please do this redirection yourself like reshape2::dcast(x). In the next version, this warning will become an error.
Error in heatmap_grob[["grobs"]][[ind_legend]] : no such index at level 2
Calls: waterfall -> waterfall_align
Execution halted
* 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:
  • Waterfall-class/gene-plot-proportion-simple.svg
  • Waterfall-class/main-waterfall-add-layers.svg
  • Waterfall-class/main-waterfall-plot-base.svg
  • Waterfall-class/main-waterfall-plot-drop-true.svg
  • Waterfall-class/main-waterfall-plot-grid-true.svg
  • Waterfall-class/main-waterfall-plot-label.svg
  • Waterfall-class/main-waterfall-plot-samplenames-false.svg
  • Waterfall-class/main-waterfall-plot-xtitle-false.svg
  • Waterfall-class/mutation-plot-add-layers.svg
  • Waterfall-class/mutation-plot-burden-complex.svg
  • Waterfall-class/mutation-plot-burden-simple.svg
  • Waterfall-class/mutation-plot-frequency-complex.svg
  • Waterfall-class/mutation-plot-frequency-simple.svg
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/GenVisR.Rcheck/00check.log’
for details.


Installation output

GenVisR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GenVisR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 2 | WARN 19 | SKIP 54 | PASS 596 ]

══ Skipped tests (54) ══════════════════════════════════════════════════════════
• On Bioconductor (54): 'test-Lolliplot-class.R:564:5',
  'test-Lolliplot-class.R:574:6', 'test-Lolliplot-class.R:602:5',
  'test-Lolliplot-class.R:615:5', 'test-Lolliplot-class.R:626:5',
  'test-Lolliplot-class.R:641:5', 'test-Lolliplot-class.R:654:5',
  'test-Lolliplot-class.R:730:5', 'test-Lolliplot-class.R:740:5',
  'test-Lolliplot-class.R:778:5', 'test-MutSpectra-class.R:285:5',
  'test-MutSpectra-class.R:294:5', 'test-MutSpectra-class.R:303:5',
  'test-MutSpectra-class.R:336:5', 'test-MutSpectra-class.R:345:5',
  'test-MutSpectra-class.R:354:5', 'test-MutSpectra-class.R:405:5',
  'test-MutSpectra-class.R:413:5', 'test-MutSpectra-class.R:440:5',
  'test-MutSpectra-class.R:450:5', 'test-Rainfall-class.R:247:5',
  'test-Rainfall-class.R:255:5', 'test-Rainfall-class.R:263:5',
  'test-Rainfall-class.R:297:5', 'test-Rainfall-class.R:305:5',
  'test-Rainfall-class.R:348:5', 'test-Rainfall-class.R:355:5',
  'test-Rainfall-class.R:389:5', 'test-Waterfall-class.R:662:5',
  'test-Waterfall-class.R:670:5', 'test-Waterfall-class.R:678:5',
  'test-Waterfall-class.R:686:5', 'test-Waterfall-class.R:722:5',
  'test-Waterfall-class.R:733:5', 'test-Waterfall-class.R:741:5',
  'test-Waterfall-class.R:750:5', 'test-Waterfall-class.R:758:5',
  'test-Waterfall-class.R:794:5', 'test-Waterfall-class.R:808:5',
  'test-Waterfall-class.R:819:5', 'test-Waterfall-class.R:830:5',
  'test-Waterfall-class.R:841:5', 'test-Waterfall-class.R:852:5',
  'test-Waterfall-class.R:868:5', 'test-Waterfall-class.R:906:5',
  'test-Waterfall-class.R:991:5', 'test-Waterfall-class.R:1005:5',
  'test-Waterfall-class.R:1019:5', 'test-Waterfall-class.R:1033:5',
  'test-Waterfall-class.R:1048:5', 'test-Waterfall-class.R:1062:5',
  'test-Waterfall-class.R:1076:5', 'test-Waterfall-class.R:1105:5',
  'test-Waterfall-class.R:1122:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-deprecated.R:4:5'): waterfall levels data correctly and as such data aligns ──
Error in `heatmap_grob[["grobs"]][[ind_legend]]`: no such index at level 2

Backtrace:
    ▆
 1. └─GenVisR::waterfall(...) at test-deprecated.R:4:5
 2.   └─GenVisR:::waterfall_align(...)
── Error ('test-deprecated.R:10:5'): waterfall correctly counts mutations in a sample ──
Error in `heatmap_grob[["grobs"]][[ind_legend]]`: no such index at level 2

Backtrace:
    ▆
 1. └─GenVisR::waterfall(...) at test-deprecated.R:10:5
 2.   └─GenVisR:::waterfall_align(...)

[ FAIL 2 | WARN 19 | SKIP 54 | PASS 596 ]
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
• Waterfall-class/addgene-waterfall.svg
• Waterfall-class/drawplot-waterfall.svg
• Waterfall-class/final-waterfall-and-left-sub-plot-alter-sectionwidth.svg
• Waterfall-class/final-waterfall-and-left-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-and-left-and-bottom-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-and-left-sub-plot.svg
• Waterfall-class/final-waterfall-and-top-sub-plot-alter-sectionheights.svg
• Waterfall-class/final-waterfall-and-top-sub-plot.svg
• Waterfall-class/final-waterfall-base.svg
• Waterfall-class/gene-plot-add-layers.svg
• Waterfall-class/gene-plot-frequency-complex.svg
• Waterfall-class/gene-plot-frequency-simple.svg
• Waterfall-class/gene-plot-proportion-complex.svg
• Waterfall-class/gene-plot-proportion-simple.svg
• Waterfall-class/main-waterfall-add-layers.svg
• Waterfall-class/main-waterfall-plot-base.svg
• Waterfall-class/main-waterfall-plot-drop-true.svg
• Waterfall-class/main-waterfall-plot-grid-true.svg
• Waterfall-class/main-waterfall-plot-label.svg
• Waterfall-class/main-waterfall-plot-samplenames-false.svg
• Waterfall-class/main-waterfall-plot-xtitle-false.svg
• Waterfall-class/mutation-plot-add-layers.svg
• Waterfall-class/mutation-plot-burden-complex.svg
• Waterfall-class/mutation-plot-burden-simple.svg
• Waterfall-class/mutation-plot-frequency-complex.svg
• Waterfall-class/mutation-plot-frequency-simple.svg
Error: Test failures
Execution halted

Example timings

GenVisR.Rcheck/GenVisR-Ex.timings

nameusersystemelapsed
Lolliplot-class23.304 1.88133.545
TvTi1.5740.0281.602
Waterfall-class0.5110.0000.511
cnFreq5.4840.0765.559
cnSpec4.2740.0364.311
cnView0.4940.0040.498
compIdent1.7020.2081.910
covBars0.6950.0120.708
genCov7.2910.2447.534
geneViz6.9940.1567.150
ideoView0.2810.0080.289
lohSpec3.5780.1284.064
lohView0.5340.0120.545