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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1450/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
omXplore 1.1.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/omXplore
git_branch: devel
git_last_commit: 89d574c
git_last_commit_date: 2024-10-29 11:34:04 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: omXplore
Version: 1.1.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:omXplore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings omXplore_1.1.0.tar.gz
StartedAt: 2024-12-24 09:28:55 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:35:25 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 389.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: omXplore.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:omXplore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings omXplore_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omXplore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omXplore’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 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 ‘/home/biocbuild/bbs-3.21-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 ...Warning: program compiled against libxml 212 using older 211
 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 loading without being on the library search path ... 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 ... 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 ... 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck/00check.log’
for details.


Installation output

omXplore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL omXplore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> 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 
 17.022   0.520  17.592 

Example timings

omXplore.Rcheck/omXplore-Ex.timings

nameusersystemelapsed
GetPkgVersion0.0770.0040.081
Prostar-1x-compatible0.0040.0000.004
accessors0.0600.0000.059
color-legend000
converters000
corrmatrix000
customChart000
customExportMenu_HC000
density-plot2.3780.1022.568
ds-cc000
ds-pca0.8570.0880.947
ds-view0.0010.0000.000
external_app000
format_DT000
globals0.0000.0000.001
intensity-plots0.0000.0000.001
is.listOf0.0000.0000.001
omXplore-modules0.0020.0000.002
omXplore_heatmap000
omXplore_tabExplorer000
palette0.0030.0040.008
pep_prot_CC0.1780.0200.198
pkgs.require0.0010.0000.001
plot-variance000
plots_tracking000
q_metadata0.0420.0000.042