Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-09-30 12:06 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 2062/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialOmicsOverlay 1.9.2  (landing page)
Maddy Griswold
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 Sep 2025)
git_url: https://git.bioconductor.org/packages/SpatialOmicsOverlay
git_branch: devel
git_last_commit: 9c1b7c8
git_last_commit_date: 2025-09-29 11:27:47 -0400 (Mon, 29 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    TIMEOUT  skipped


CHECK results for SpatialOmicsOverlay on kjohnson3

To the developers/maintainers of the SpatialOmicsOverlay package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialOmicsOverlay.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: SpatialOmicsOverlay
Version: 1.9.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialOmicsOverlay_1.9.2.tar.gz
StartedAt: 2025-09-29 21:49:19 -0400 (Mon, 29 Sep 2025)
EndedAt: 2025-09-29 21:52:22 -0400 (Mon, 29 Sep 2025)
EllapsedTime: 183.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SpatialOmicsOverlay.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialOmicsOverlay_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpatialOmicsOverlay.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ version ‘1.9.2’
* package encoding: UTF-8
* 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 ‘SpatialOmicsOverlay’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
plotSpatialOverlay: no visible binding for global variable ‘xcoor’
plotSpatialOverlay: no visible binding for global variable ‘ycoor’
plotSpatialOverlay: no visible binding for global variable ‘sampleID’
plotSpatialOverlay: no visible binding for global variable ‘Target’
scaleBarPrinting: no visible binding for global variable ‘X’
scaleBarPrinting: no visible binding for global variable ‘Y’
Undefined global functions or variables:
  Target X Y sampleID xcoor ycoor
* 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 ... OK
* 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
add4ChannelImage    6.837  0.561   5.232
readSpatialOverlay  4.927  0.449   4.777
changeImageColoring 4.682  0.368   4.474
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpatialOmicsOverlay.Rcheck/00check.log’
for details.


Installation output

SpatialOmicsOverlay.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SpatialOmicsOverlay’ ...
** this is package ‘SpatialOmicsOverlay’ version ‘1.9.2’
** 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 (SpatialOmicsOverlay)

Tests output

SpatialOmicsOverlay.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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)
> library(vdiffr)
> 
> options( java.parameters = "-Xmx4g" )
> library( "RBioFormats" )
BioFormats library version 7.3.0
> 
> library(SpatialOmicsOverlay)
> 
> # #run tests
> test_check("SpatialOmicsOverlay")
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: NanoStringNCTools
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ggplot2
Extracting XML
Parsing XML - scan metadata
Parsing XML - overlay data
Generating Coordinates
Extracting XML
Parsing XML - scan metadata
Parsing XML - overlay data
Generating Coordinates
Calculating and scaling coordinates
Calculating and scaling coordinates
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 422 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 422 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 51.858   4.632  52.739 

Example timings

SpatialOmicsOverlay.Rcheck/SpatialOmicsOverlay-Ex.timings

nameusersystemelapsed
add4ChannelImage6.8370.5615.232
addImageOmeTiff4.4480.3544.148
addPlottingFactor0.1740.0060.181
bookendStr0.0010.0000.001
changeColoringIntensity4.4760.3444.027
changeImageColoring4.6820.3684.474
checkValidRes0.9780.0900.850
createCoordFile0.9600.0130.973
createMask3.0950.1233.247
cropSamples4.6530.3324.429
cropTissue4.3080.3834.167
downloadMouseBrainImage0.0410.0030.044
flipX3.8350.3123.716
flipY3.8680.3553.729
fluorLegend0.8910.0690.961
moveCoords0.0770.0060.084
parseOverlayAttrs1.1840.1361.115
parseScanMetadata1.3500.1461.107
plotSpatialOverlay0.7250.0760.802
readLabWorksheet0.0020.0000.001
readSpatialOverlay4.9270.4494.777
recolor3.9420.3433.777
removeSample0.0870.0030.091
xmlExtraction1.1140.1251.093