Multiple platform build/check report for BioC 3.20 - CHECK results for esetVis on palomino4

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
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 esetVis on palomino4

To the developers/maintainers of the esetVis package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/esetVis.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: esetVis

Version: 1.31.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:esetVis.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings esetVis_1.31.0.tar.gz

StartedAt: 2024-06-10 02:31:51 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 02:36:53 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 302.4 seconds

RetCode: 0

Status: OK

CheckDir: esetVis.Rcheck

Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:esetVis.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings esetVis_1.31.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/esetVis.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'esetVis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'esetVis' version '1.31.0'
* 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 whether package 'esetVis' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ggvisPlotEset: no visible global function definition for ':='
ggvisPlotEset: no visible binding for global variable 'fill'
ggvisPlotEset: no visible binding for global variable 'shape'
ggvisPlotEset: no visible binding for global variable 'size'
ggvisPlotEset: no visible binding for global variable 'opacity'
Undefined global functions or variables:
  := fill opacity shape size
* checking Rd files ... NOTE
checkRd: (-1) esetLda.Rd:122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetLda.Rd:123: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetLda.Rd:124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetLda.Rd:242: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetLda.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetLda.Rd:264-265: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetLda.Rd:267: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetLda.Rd:268: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetLda.Rd:269: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetLda.Rd:271: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetLda.Rd:272: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetPlot-class.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetPlot-class.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetPlot-class.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetPlotWrapper.Rd:127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetPlotWrapper.Rd:128: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetPlotWrapper.Rd:129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetPlotWrapper.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetPlotWrapper.Rd:244: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetPlotWrapper.Rd:272: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetPlotWrapper.Rd:273: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetPlotWrapper.Rd:277-278: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetSpectralMap.Rd:131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetSpectralMap.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetSpectralMap.Rd:133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetSpectralMap.Rd:251: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetSpectralMap.Rd:252: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetSpectralMap.Rd:273: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetSpectralMap.Rd:275: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetSpectralMap.Rd:276: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetSpectralMap.Rd:277: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetSpectralMap.Rd:278: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetSpectralMap.Rd:281: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetSpectralMap.Rd:282: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetTsne.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetTsne.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetTsne.Rd:113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetTsne.Rd:157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetTsne.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) esetTsne.Rd:179-180: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetTsne.Rd:182: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetTsne.Rd:183: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetTsne.Rd:185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) esetTsne.Rd:186: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGeneSetsForPlot.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGeneSetsForPlot.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getMethodsInputObjectEsetVis.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getMethodsInputObjectEsetVis.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getMethodsInputObjectEsetVis.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getMethodsInputObjectEsetVis.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getMethodsInputObjectEsetVis.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getMethodsInputObjectEsetVis.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getMethodsInputObjectEsetVis.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotTopElements.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotTopElements.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotTopElements.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotTopElements.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'getCoordGeneSets.Rd':
  '...'

Documented arguments not in \usage in Rd file 'getTopElements.Rd':
  'returnTopElements'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
getGeneSetsForPlot 55.14   7.32   65.85
esetLda             6.82   1.32    8.30
esetSpectralMap     4.86   0.64    5.82
esetPlotWrapper     4.91   0.50    5.72
esetTsne            4.00   0.33    5.14
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/esetVis.Rcheck/00check.log'
for details.

Installation output

esetVis.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL esetVis
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'esetVis' ...
** using staged installation
** R
** 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 (esetVis)

Tests output

Example timings

esetVis.Rcheck/esetVis-Ex.timings

name	user	system	elapsed
esetLda	6.82	1.32	8.30
esetPlotWrapper	4.91	0.50	5.72
esetSpectralMap	4.86	0.64	5.82
esetTsne	4.00	0.33	5.14
getGeneSetsForPlot	55.14	7.32	65.85