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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1458/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omXplore 1.0.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/omXplore
git_branch: RELEASE_3_20
git_last_commit: a23afb8
git_last_commit_date: 2024-10-29 11:34:04 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for omXplore on lconway

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.

raw results


Summary

Package: omXplore
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omXplore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omXplore_1.0.0.tar.gz
StartedAt: 2024-11-20 00:47:12 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 00:55:09 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 477.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: omXplore.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omXplore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omXplore_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/omXplore.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omXplore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omXplore’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘omXplore’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'plots_tracking_server("tracker", ': unused argument (reset = reactive({
  Note: possible error in 'omXplore_intensity_server("iplot", ': unused argument (reset = reactive({
See ‘/Users/biocbuild/bbs-3.20-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: possible error in
  plots_tracking_server("tracker", obj = reactive({: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in obj: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in }), i = reactive({:
  unused argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in i: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in }), reset = reactive({:
  unused argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in input$reset: unused
  argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in }), is.enabled =
  reactive({: unused argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in TRUE: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in })): unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in
  omXplore_intensity_server("iplot", obj = reactive({: unused argument
  (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in }), track.indices =
  reactive({: unused argument (reset = reactive({ input$reset }))
omXplore_intensity : server: possible error in indices(): unused
  argument (reset = reactive({ input$reset }))
Undefined global functions or variables:
  .colData experimentData metadata metadata<-
* 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 ... WARNING
Undocumented arguments in Rd file 'intensity-plots.Rd'
  ‘remoteReset’ ‘is.enabled’

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 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
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/omXplore.Rcheck/00check.log’
for details.


Installation output

omXplore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL omXplore
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘omXplore’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'plots_tracking_server("tracker", ': unused argument (reset = reactive({
    input$reset
})) 
Note: possible error in 'omXplore_intensity_server("iplot", ': unused argument (reset = reactive({
    input$reset
})) 
** 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 (omXplore)

Tests output

omXplore.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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)
> 
> test_check("omXplore")
Loading required package: omXplore
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 10.423   0.693  11.208 

Example timings

omXplore.Rcheck/omXplore-Ex.timings

nameusersystemelapsed
GetPkgVersion1.1620.6931.901
Prostar-1x-compatible0.0030.0020.005
accessors0.0670.0050.073
color-legend000
converters000
corrmatrix000
customChart000
customExportMenu_HC000
density-plot0.7700.0832.387
ds-cc0.0000.0000.001
ds-pca0.5030.0580.564
ds-view000
external_app000
format_DT000
globals0.0010.0000.000
intensity-plots0.0010.0010.001
is.listOf000
omXplore-modules0.0010.0000.001
omXplore_heatmap000
omXplore_tabExplorer000
palette0.0050.0010.006
pep_prot_CC0.0920.0200.582
pkgs.require0.0000.0000.001
plot-variance0.0010.0000.000
plots_tracking0.0000.0000.001
q_metadata0.0240.0020.026