Samuel Wieczorek
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/omXplore |
| git_branch: devel |
| git_last_commit: 8318898 |
| git_last_commit_date: 2025-06-10 09:31:05 -0400 (Tue, 10 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1475/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| omXplore 1.3.0 (landing page) Samuel Wieczorek
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the omXplore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/omXplore.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: omXplore |
| Version: 1.3.0 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omXplore.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings omXplore_1.3.0.tar.gz |
| StartedAt: 2025-08-15 06:01:53 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 06:08:31 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 397.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: omXplore.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omXplore.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings omXplore_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/omXplore.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'omXplore/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'omXplore' version '1.3.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 'omXplore' can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'boxPlot(dataIn = rv$data, ': unused argument (dataIn = rv$data)
Warning: replacing previous import 'bs4Dash::box' by 'graphics::box' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::column' by 'shiny::column' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::actionButton' by 'shiny::actionButton' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::tabsetPanel' by 'shiny::tabsetPanel' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::insertTab' by 'shiny::insertTab' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::navbarMenu' by 'shiny::navbarMenu' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::removePopover' by 'shinyBS::removePopover' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::addPopover' by 'shinyBS::addPopover' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::addTooltip' by 'shinyBS::addTooltip' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::createAlert' by 'shinyBS::createAlert' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::closeAlert' by 'shinyBS::closeAlert' when loading 'omXplore'
Warning: replacing previous import 'bs4Dash::removeTooltip' by 'shinyBS::removeTooltip' when loading 'omXplore'
Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'omXplore'
Warning: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'omXplore'
See 'F:/biocbuild/bbs-3.22-bioc/meat/omXplore.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 whether startup messages can be suppressed ... 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
Build_X_CC: no visible global function definition for 'metadata'
Build_X_CC: no visible global function definition for 'metadata<-'
Check_MSnSet_Consistency : <anonymous>: no visible global function
definition for 'experimentData'
MAE_Compatibility_with_Prostar_1x : <anonymous>: no visible binding for
global variable '.colData'
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for 'experimentData'
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for 'metadata'
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for 'metadata<-'
omXplore_intensity_server : <anonymous>: possible error in
boxPlot(dataIn = rv$data, conds = rv$conds, subset =
track.indices()): unused argument (dataIn = rv$data)
omXplore_pca_server : <anonymous>: no visible global function
definition for 'obj'
Undefined global functions or variables:
.colData experimentData metadata metadata<- obj
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
density-plot.Rd: RColorBrewer
intensity-plots.Rd: RColorBrewer
palette.Rd: RColorBrewer
plot-variance.Rd: RColorBrewer
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 ... 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 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
ds-pca 1.73 0.39 7.49
* 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: 1 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.22-bioc/meat/omXplore.Rcheck/00check.log'
for details.
omXplore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL omXplore ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'omXplore' ... ** this is package 'omXplore' version '1.3.0' ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'bs4Dash::box' by 'graphics::box' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::column' by 'shiny::column' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::actionButton' by 'shiny::actionButton' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::tabsetPanel' by 'shiny::tabsetPanel' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::insertTab' by 'shiny::insertTab' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::navbarMenu' by 'shiny::navbarMenu' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::removePopover' by 'shinyBS::removePopover' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::addPopover' by 'shinyBS::addPopover' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::addTooltip' by 'shinyBS::addTooltip' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::createAlert' by 'shinyBS::createAlert' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::closeAlert' by 'shinyBS::closeAlert' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::removeTooltip' by 'shinyBS::removeTooltip' when loading 'omXplore' Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'omXplore' Warning: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'omXplore' Note: possible error in 'boxPlot(dataIn = rv$data, ': unused argument (dataIn = rv$data) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'bs4Dash::box' by 'graphics::box' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::column' by 'shiny::column' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::actionButton' by 'shiny::actionButton' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::tabsetPanel' by 'shiny::tabsetPanel' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::insertTab' by 'shiny::insertTab' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::navbarMenu' by 'shiny::navbarMenu' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::removePopover' by 'shinyBS::removePopover' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::addPopover' by 'shinyBS::addPopover' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::addTooltip' by 'shinyBS::addTooltip' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::createAlert' by 'shinyBS::createAlert' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::closeAlert' by 'shinyBS::closeAlert' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::removeTooltip' by 'shinyBS::removeTooltip' when loading 'omXplore' Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'omXplore' Warning: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'omXplore' ** testing if installed package can be loaded from final location Warning: replacing previous import 'bs4Dash::box' by 'graphics::box' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::column' by 'shiny::column' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::actionButton' by 'shiny::actionButton' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::tabsetPanel' by 'shiny::tabsetPanel' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::insertTab' by 'shiny::insertTab' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::navbarMenu' by 'shiny::navbarMenu' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::removePopover' by 'shinyBS::removePopover' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::addPopover' by 'shinyBS::addPopover' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::addTooltip' by 'shinyBS::addTooltip' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::createAlert' by 'shinyBS::createAlert' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::closeAlert' by 'shinyBS::closeAlert' when loading 'omXplore' Warning: replacing previous import 'bs4Dash::removeTooltip' by 'shinyBS::removeTooltip' when loading 'omXplore' Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'omXplore' Warning: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'omXplore' ** testing if installed package keeps a record of temporary installation path * DONE (omXplore)
omXplore.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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)
>
> test_check("omXplore")
Loading required package: omXplore
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]
There were 14 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
15.76 1.50 17.25
omXplore.Rcheck/omXplore-Ex.timings
| name | user | system | elapsed | |
| GetPkgVersion | 2.20 | 1.41 | 3.61 | |
| Prostar-1x-compatible | 0 | 0 | 0 | |
| accessors | 0.05 | 0.01 | 0.06 | |
| color-legend | 0 | 0 | 0 | |
| converters | 0 | 0 | 0 | |
| corrmatrix | 0 | 0 | 0 | |
| customChart | 0 | 0 | 0 | |
| customExportMenu_HC | 0 | 0 | 0 | |
| density-plot | 0 | 0 | 0 | |
| ds-cc | 0 | 0 | 0 | |
| ds-pca | 1.73 | 0.39 | 7.49 | |
| ds-view | 0 | 0 | 0 | |
| external_app | 0 | 0 | 0 | |
| format_DT | 0 | 0 | 0 | |
| globals | 0 | 0 | 0 | |
| intensity-plots | 0 | 0 | 0 | |
| is.listOf | 0 | 0 | 0 | |
| omXplore-modules | 0.02 | 0.00 | 0.01 | |
| omXplore_heatmap | 0 | 0 | 0 | |
| omXplore_tabExplorer | 0 | 0 | 0 | |
| palette | 0 | 0 | 0 | |
| pep_prot_CC | 0.13 | 0.03 | 1.22 | |
| pkgs.require | 0 | 0 | 0 | |
| plot-variance | 0 | 0 | 0 | |
| plots_tracking | 0 | 0 | 0 | |
| q_metadata | 0.03 | 0.00 | 0.03 | |