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

This page was generated on 2025-08-12 12:06 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 2057/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPIAT 1.11.0  (landing page)
Yuzhou Feng
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/SPIAT
git_branch: devel
git_last_commit: 6b188b4
git_last_commit_date: 2025-04-15 12:56:43 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SPIAT on nebbiolo2

To the developers/maintainers of the SPIAT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPIAT.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: SPIAT
Version: 1.11.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SPIAT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SPIAT_1.11.0.tar.gz
StartedAt: 2025-08-12 06:01:49 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 06:10:28 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 519.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SPIAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SPIAT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SPIAT_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SPIAT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SPIAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPIAT’ version ‘1.11.0’
* 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 ‘SPIAT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  Artistic-2.0 + file LICENSE
* 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 loading without being on the library search path ... 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 LazyData ... 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
dimensionality_reduction_plot 20.725  0.100  20.826
calculate_percentage_of_grids  7.246  0.048   7.293
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SPIAT.Rcheck/00check.log’
for details.


Installation output

SPIAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SPIAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SPIAT’ ...
** this is package ‘SPIAT’ version ‘1.11.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SPIAT)

Tests output

SPIAT.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(SPIAT)
Loading required package: SpatialExperiment
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

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: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

> 
> test_check("SPIAT")
[1] "Markers had been selected in minimum distance calculation: "
[1] "Immune1" "Tumour" 
[1] "Crossing of cross K function is detected for this image, indicating a potential immune ring."
[1] "The crossing happens at the 50% of the specified distance."
[1] "The alpha of Polygon is: 63.24375"
[1] "Markers had been selected in minimum distance calculation: "
[1] "Non-border" "Border"    
[1] "Tumour_marker"
[1] "Immune_marker1"
[1] "Immune_marker2"
[1] "Immune_marker3"
[1] "Immune_marker4"
[1] "Tumour_marker"
[1] "Immune_marker1"
[1] "Immune_marker2"
[1] "Immune_marker3"
[1] "Immune_marker4"
[1] "Tumour_marker  threshold intensity:  0.445450443784465"
[1] "Immune_marker1  threshold intensity:  0.116980867970434"
[1] "Immune_marker2  threshold intensity:  0.124283809517202"
[1] "Immune_marker3  threshold intensity:  0.0166413130263845"
[1] "Immune_marker4  threshold intensity:  0.00989731350898589"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 80 ]
> 
> proc.time()
   user  system elapsed 
 62.234   2.076  64.298 

Example timings

SPIAT.Rcheck/SPIAT-Ex.timings

nameusersystemelapsed
AUC_of_cross_function0.1580.0090.169
R_BC1.7730.0331.807
average_marker_intensity_within_radius0.0500.0020.052
average_minimum_distance0.0200.0010.021
average_nearest_neighbor_index0.2220.0300.253
average_percentage_of_cells_within_radius0.9040.0120.917
calculate_cell_proportions0.0110.0000.011
calculate_cross_functions0.1530.0000.153
calculate_distance_to_margin1.0620.0001.063
calculate_entropy0.0080.0010.008
calculate_minimum_distances_between_celltypes0.0140.0000.014
calculate_pairwise_distances_between_celltypes4.6420.2754.917
calculate_percentage_of_grids7.2460.0487.293
calculate_proportions_of_cells_in_structure1.1880.0331.222
calculate_spatial_autocorrelation2.9880.0503.038
calculate_summary_distances_between_celltypes2.7940.1912.985
calculate_summary_distances_of_cells_to_borders1.0900.0451.134
composition_of_neighborhoods1.0740.1521.226
compute_gradient0.0530.0000.053
crossing_of_crossK0.1070.0000.108
define_celltypes0.6080.0010.609
define_structure1.3370.0171.353
dimensionality_reduction_plot20.725 0.10020.826
entropy_gradient_aggregated0.4840.0620.546
format_cellprofiler_to_spe0.1060.0140.121
format_codex_to_spe0.0930.0050.098
format_colData_to_spe0.0930.0070.100
format_halo_to_spe0.4010.1110.508
format_image_to_spe0.0950.0050.100
format_inform_to_spe0.1630.0470.209
format_spe_to_ppp0.0150.0000.016
grid_metrics2.6850.0452.730
identify_bordering_cells0.5810.0090.589
identify_neighborhoods1.8670.1872.054
image_splitter0.8150.0020.816
marker_intensity_boxplot0.2750.0010.276
marker_prediction_plot1.2910.0021.294
marker_surface_plot0.1900.0030.193
marker_surface_plot_stack0.2170.0030.221
measure_association_to_cell_properties0.3810.0010.382
mixing_score_summary0.0150.0000.015
number_of_cells_within_radius0.0110.0000.010
plot_average_intensity0.2550.0000.255
plot_cell_categories0.2130.0010.214
plot_cell_distances_violin0.9540.0120.966
plot_cell_marker_levels0.1770.0000.177
plot_cell_percentages0.3710.0010.372
plot_composition_heatmap3.2320.0573.289
plot_distance_heatmap2.9480.0012.950
plot_marker_level_heatmap0.3570.0010.358
predict_phenotypes1.5890.0051.594
select_celltypes0.0440.0000.045