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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 834/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.38.0  (landing page)
Zachary Skidmore
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/GenVisR
git_branch: RELEASE_3_20
git_last_commit: 84e2b21
git_last_commit_date: 2024-10-29 10:06:37 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GenVisR on kjohnson1

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: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2024-12-20 20:45:36 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 20:54:24 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 528.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GenVisR.Rcheck
Warnings: 0

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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenVisR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.38.0’
* 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 code 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
buildWaterfallPlot,WaterfallData: no visible global function definition
  for ‘tail’
setTierTwo,data.table: no visible global function definition for ‘tail’
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 tail tmp
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) lohSpec.Rd:46: Lost braces; missing escapes or markup?
    46 | consisting of elements from the set {"M", "F"}. Used to suppress the plotting
       |                                     ^
* 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 26.728  1.223  28.806
geneViz          8.758  0.138   8.972
genCov           6.051  0.283   6.367
cnFreq           5.011  0.031   5.055
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/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


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 0 | WARN 9 | SKIP 54 | PASS 510 ]

══ 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'

[ FAIL 0 | WARN 9 | SKIP 54 | PASS 510 ]
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
> 
> proc.time()
   user  system elapsed 
125.047   5.906 130.621 

Example timings

GenVisR.Rcheck/GenVisR-Ex.timings

nameusersystemelapsed
Lolliplot-class26.728 1.22328.806
TvTi1.5230.0171.539
Waterfall-class0.5650.0050.573
cnFreq5.0110.0315.055
cnSpec4.1830.0444.248
cnView0.4810.0030.484
compIdent1.5190.1681.709
covBars0.7110.0060.722
genCov6.0510.2836.367
geneViz8.7580.1388.972
ideoView0.3820.0050.387
lohSpec3.1540.0603.235
lohView0.6060.0030.613