Jean-Philippe Villemin
| Snapshot Date: 2026-04-15 13:40 -0400 (Wed, 15 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/Battlefield |
| git_branch: devel |
| git_last_commit: 72e6883 |
| git_last_commit_date: 2026-02-27 06:29:35 -0400 (Fri, 27 Feb 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-16 11:36 -0400 (Thu, 16 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4928 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4659 |
| 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 152/2394 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Battlefield 0.99.1 (landing page) Jean-Philippe Villemin
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for Battlefield in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Battlefield package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Battlefield.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: Battlefield |
| Version: 0.99.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Battlefield.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Battlefield_0.99.1.tar.gz |
| StartedAt: 2026-04-15 18:32:27 -0400 (Wed, 15 Apr 2026) |
| EndedAt: 2026-04-15 18:33:41 -0400 (Wed, 15 Apr 2026) |
| EllapsedTime: 73.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Battlefield.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Battlefield.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Battlefield_0.99.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Battlefield.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-15 22:32:27 UTC
* using option ‘--no-vignettes’
* checking for file ‘Battlefield/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Battlefield’ version ‘0.99.1’
* 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 ‘Battlefield’ 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 ... OK
* 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 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: OK
Battlefield.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Battlefield ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘Battlefield’ ... ** this is package ‘Battlefield’ version ‘0.99.1’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (Battlefield)
Battlefield.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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(Battlefield)
> test_check("Battlefield")
Not enough core spots for pair(cluster=B, interface=A, mode=both). Requested:84, Available:3. Returning all available.
Not enough core spots for pair(cluster=A, interface=B, mode=both). Requested:100, Available:5. Returning all available.
Not enough core spots for pair(cluster=A, interface=B, mode=inner). Requested:50, Available:5. Returning all available.
---- Grid type detection ----
Estimated grid step: 1
Median distance ratio: 1.414
Detected grid type: square
--------------------------------
---- Neighborhood parameters ----
grid_type: square
connectivity: 4
radius: 1.01
k: 16
comment: Visium HD: 4-connectivity (square grid)
--------------------------------
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'core' layer detected. No cluster interfaces found.
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster 1: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'core' layer detected. No cluster interfaces found.
Cluster C: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster 1: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster 3: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster 2: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster C: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster 1: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster 3: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster 2: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster B: Only 'border' layer detected. All spots are at cluster interfaces.
Cluster A: Only 'core' layer detected. No cluster interfaces found.
Cluster B: Only 'core' layer detected. No cluster interfaces found.
Battlefield columns already exist: is_border, is_core, interface, border_mode. Set erase=TRUE to overwrite them.
Erasing pre-existing battlefield columns.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 187 ]
>
> proc.time()
user system elapsed
3.887 0.331 4.293
Battlefield.Rcheck/Battlefield-Ex.timings
| name | user | system | elapsed | |
| add_borders_to_spe | 0.646 | 0.021 | 0.671 | |
| add_layers_to_spe | 0.020 | 0.002 | 0.023 | |
| add_trajectories_to_spe | 0.039 | 0.003 | 0.042 | |
| adjacent_endpoint | 0.001 | 0.000 | 0.002 | |
| bresenham_line | 0.002 | 0.000 | 0.002 | |
| build_all_borders | 0.036 | 0.004 | 0.040 | |
| build_all_cores | 0.043 | 0.003 | 0.046 | |
| build_one_line | 0.003 | 0.000 | 0.004 | |
| build_one_trajectory | 0.003 | 0.000 | 0.003 | |
| build_similar_trajectories | 0.011 | 0.000 | 0.012 | |
| closest_spot | 0.001 | 0.000 | 0.000 | |
| compute_centroids | 0.001 | 0.000 | 0.000 | |
| count_all_inlaids | 0.026 | 0.000 | 0.026 | |
| count_all_neighborhoods | 0.061 | 0.002 | 0.062 | |
| count_inlaid | 0.009 | 0.000 | 0.010 | |
| count_neighborhood | 0.012 | 0.000 | 0.013 | |
| create_all_layers | 0.012 | 0.001 | 0.013 | |
| create_cluster_layers | 0.007 | 0.001 | 0.009 | |
| detect_grid_type | 0.003 | 0.001 | 0.004 | |
| directed_cluster_interface_pairs | 0.001 | 0.000 | 0.001 | |
| estimate_spot_spacing | 0.001 | 0.000 | 0.001 | |
| filter_out_by_endpoint_clusters | 0.007 | 0.001 | 0.008 | |
| get_inlaid_spots | 0.009 | 0.001 | 0.011 | |
| get_neighborhood_params | 0.001 | 0.001 | 0.001 | |
| get_neighborhood_spots | 0.012 | 0.000 | 0.012 | |
| point_segment_distance_vec | 0 | 0 | 0 | |
| remove_used_points | 0.001 | 0.000 | 0.001 | |
| select_border_spots | 0.004 | 0.000 | 0.004 | |
| select_core_spots | 0.038 | 0.000 | 0.038 | |
| shift_point | 0.000 | 0.000 | 0.001 | |
| unit_normal_left | 0.001 | 0.000 | 0.001 | |
| visiumHD_16um_simulated_spe | 0.034 | 0.001 | 0.037 | |
| visiumHD_8um_simulated_spe | 0.023 | 0.001 | 0.024 | |
| visium_simulated_spe | 0.022 | 0.002 | 0.024 | |