Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-12 12:06 -0400 (Tue, 12 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (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 2057/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SPIAT 1.11.0 (landing page) Yuzhou Feng
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
SPIAT.Rcheck/SPIAT-Ex.timings
name | user | system | elapsed | |
AUC_of_cross_function | 0.158 | 0.009 | 0.169 | |
R_BC | 1.773 | 0.033 | 1.807 | |
average_marker_intensity_within_radius | 0.050 | 0.002 | 0.052 | |
average_minimum_distance | 0.020 | 0.001 | 0.021 | |
average_nearest_neighbor_index | 0.222 | 0.030 | 0.253 | |
average_percentage_of_cells_within_radius | 0.904 | 0.012 | 0.917 | |
calculate_cell_proportions | 0.011 | 0.000 | 0.011 | |
calculate_cross_functions | 0.153 | 0.000 | 0.153 | |
calculate_distance_to_margin | 1.062 | 0.000 | 1.063 | |
calculate_entropy | 0.008 | 0.001 | 0.008 | |
calculate_minimum_distances_between_celltypes | 0.014 | 0.000 | 0.014 | |
calculate_pairwise_distances_between_celltypes | 4.642 | 0.275 | 4.917 | |
calculate_percentage_of_grids | 7.246 | 0.048 | 7.293 | |
calculate_proportions_of_cells_in_structure | 1.188 | 0.033 | 1.222 | |
calculate_spatial_autocorrelation | 2.988 | 0.050 | 3.038 | |
calculate_summary_distances_between_celltypes | 2.794 | 0.191 | 2.985 | |
calculate_summary_distances_of_cells_to_borders | 1.090 | 0.045 | 1.134 | |
composition_of_neighborhoods | 1.074 | 0.152 | 1.226 | |
compute_gradient | 0.053 | 0.000 | 0.053 | |
crossing_of_crossK | 0.107 | 0.000 | 0.108 | |
define_celltypes | 0.608 | 0.001 | 0.609 | |
define_structure | 1.337 | 0.017 | 1.353 | |
dimensionality_reduction_plot | 20.725 | 0.100 | 20.826 | |
entropy_gradient_aggregated | 0.484 | 0.062 | 0.546 | |
format_cellprofiler_to_spe | 0.106 | 0.014 | 0.121 | |
format_codex_to_spe | 0.093 | 0.005 | 0.098 | |
format_colData_to_spe | 0.093 | 0.007 | 0.100 | |
format_halo_to_spe | 0.401 | 0.111 | 0.508 | |
format_image_to_spe | 0.095 | 0.005 | 0.100 | |
format_inform_to_spe | 0.163 | 0.047 | 0.209 | |
format_spe_to_ppp | 0.015 | 0.000 | 0.016 | |
grid_metrics | 2.685 | 0.045 | 2.730 | |
identify_bordering_cells | 0.581 | 0.009 | 0.589 | |
identify_neighborhoods | 1.867 | 0.187 | 2.054 | |
image_splitter | 0.815 | 0.002 | 0.816 | |
marker_intensity_boxplot | 0.275 | 0.001 | 0.276 | |
marker_prediction_plot | 1.291 | 0.002 | 1.294 | |
marker_surface_plot | 0.190 | 0.003 | 0.193 | |
marker_surface_plot_stack | 0.217 | 0.003 | 0.221 | |
measure_association_to_cell_properties | 0.381 | 0.001 | 0.382 | |
mixing_score_summary | 0.015 | 0.000 | 0.015 | |
number_of_cells_within_radius | 0.011 | 0.000 | 0.010 | |
plot_average_intensity | 0.255 | 0.000 | 0.255 | |
plot_cell_categories | 0.213 | 0.001 | 0.214 | |
plot_cell_distances_violin | 0.954 | 0.012 | 0.966 | |
plot_cell_marker_levels | 0.177 | 0.000 | 0.177 | |
plot_cell_percentages | 0.371 | 0.001 | 0.372 | |
plot_composition_heatmap | 3.232 | 0.057 | 3.289 | |
plot_distance_heatmap | 2.948 | 0.001 | 2.950 | |
plot_marker_level_heatmap | 0.357 | 0.001 | 0.358 | |
predict_phenotypes | 1.589 | 0.005 | 1.594 | |
select_celltypes | 0.044 | 0.000 | 0.045 | |