Laure Cougnaud
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/esetVis |
| git_branch: RELEASE_3_21 |
| git_last_commit: 66c9cd7 |
| git_last_commit_date: 2025-04-15 11:02:52 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 692/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| esetVis 1.34.0 (landing page) Laure Cougnaud
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: esetVis |
| Version: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:esetVis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings esetVis_1.34.0.tar.gz |
| StartedAt: 2025-04-21 19:20:57 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 19:22:05 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 67.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: esetVis.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:esetVis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings esetVis_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/esetVis.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘esetVis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esetVis’ version ‘1.34.0’
* 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 for sufficient/correct file permissions ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
esetLda.Rd: eSet-class
esetPlotWrapper.Rd: eSet-class
esetSpectralMap.Rd: eSet-class
esetTsne.Rd: eSet-class
getGeneSetsForPlot.Rd: eSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 18.742 2.111 20.952
* 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-3.21-bioc/meat/esetVis.Rcheck/00check.log’
for details.
esetVis.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL esetVis ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘esetVis’ ... ** this is package ‘esetVis’ version ‘1.34.0’ ** 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)
esetVis.Rcheck/esetVis-Ex.timings
| name | user | system | elapsed | |
| esetLda | 2.320 | 0.048 | 2.373 | |
| esetPlotWrapper | 1.919 | 0.053 | 1.979 | |
| esetSpectralMap | 1.779 | 0.058 | 1.839 | |
| esetTsne | 1.303 | 0.036 | 1.345 | |
| getGeneSetsForPlot | 18.742 | 2.111 | 20.952 | |