Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2032/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SPIAT 1.8.0 (landing page) Yuzhou Feng
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.8.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPIAT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SPIAT_1.8.0.tar.gz |
StartedAt: 2024-12-20 06:18:52 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:25:34 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 402.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SPIAT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPIAT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SPIAT_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SPIAT.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SPIAT/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SPIAT' version '1.8.0' * 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 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 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 22.49 0.05 22.61 calculate_percentage_of_grids 9.25 0.17 9.44 calculate_pairwise_distances_between_celltypes 6.01 0.56 6.58 plot_composition_heatmap 5.27 0.48 6.14 * 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: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/SPIAT.Rcheck/00check.log' for details.
SPIAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SPIAT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'SPIAT' ... ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb 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 72.42 4.35 75.54
SPIAT.Rcheck/SPIAT-Ex.timings
name | user | system | elapsed | |
AUC_of_cross_function | 0.34 | 0.03 | 0.31 | |
R_BC | 1.89 | 0.14 | 2.08 | |
average_marker_intensity_within_radius | 0.03 | 0.02 | 0.04 | |
average_minimum_distance | 0.01 | 0.00 | 0.02 | |
average_nearest_neighbor_index | 0.22 | 0.00 | 0.21 | |
average_percentage_of_cells_within_radius | 2.02 | 0.01 | 2.04 | |
calculate_cell_proportions | 0.03 | 0.00 | 0.03 | |
calculate_cross_functions | 0.25 | 0.00 | 0.25 | |
calculate_distance_to_margin | 1.44 | 0.02 | 1.45 | |
calculate_entropy | 0.01 | 0.00 | 0.02 | |
calculate_minimum_distances_between_celltypes | 0.02 | 0.00 | 0.01 | |
calculate_pairwise_distances_between_celltypes | 6.01 | 0.56 | 6.58 | |
calculate_percentage_of_grids | 9.25 | 0.17 | 9.44 | |
calculate_proportions_of_cells_in_structure | 1.64 | 0.02 | 1.65 | |
calculate_spatial_autocorrelation | 3.68 | 0.03 | 3.71 | |
calculate_summary_distances_between_celltypes | 3.40 | 0.33 | 3.73 | |
calculate_summary_distances_of_cells_to_borders | 1.56 | 0.03 | 1.59 | |
composition_of_neighborhoods | 2.47 | 0.31 | 2.79 | |
compute_gradient | 0.05 | 0.00 | 0.04 | |
crossing_of_crossK | 0.11 | 0.02 | 0.13 | |
define_celltypes | 0.78 | 0.04 | 0.83 | |
define_structure | 1.73 | 0.03 | 1.76 | |
dimensionality_reduction_plot | 22.49 | 0.05 | 22.61 | |
entropy_gradient_aggregated | 0.66 | 0.06 | 0.72 | |
format_cellprofiler_to_spe | 0.12 | 0.00 | 0.12 | |
format_codex_to_spe | 0.14 | 0.00 | 0.15 | |
format_colData_to_spe | 0.11 | 0.00 | 0.10 | |
format_halo_to_spe | 0.66 | 0.14 | 0.91 | |
format_image_to_spe | 0.12 | 0.00 | 0.13 | |
format_inform_to_spe | 0.28 | 0.16 | 0.36 | |
format_spe_to_ppp | 0.02 | 0.00 | 0.01 | |
grid_metrics | 3.45 | 0.02 | 3.49 | |
identify_bordering_cells | 0.5 | 0.0 | 0.5 | |
identify_neighborhoods | 1.39 | 0.42 | 1.81 | |
image_splitter | 1.30 | 0.02 | 1.32 | |
marker_intensity_boxplot | 0.42 | 0.00 | 0.42 | |
marker_prediction_plot | 0.91 | 0.05 | 0.95 | |
marker_surface_plot | 0.22 | 0.07 | 2.55 | |
marker_surface_plot_stack | 0.21 | 0.04 | 0.26 | |
measure_association_to_cell_properties | 0.55 | 0.01 | 0.57 | |
mixing_score_summary | 0.02 | 0.00 | 0.01 | |
number_of_cells_within_radius | 0.01 | 0.00 | 0.02 | |
plot_average_intensity | 0.33 | 0.00 | 0.33 | |
plot_cell_categories | 0.38 | 0.00 | 0.37 | |
plot_cell_distances_violin | 1.12 | 0.16 | 1.28 | |
plot_cell_marker_levels | 0.19 | 0.00 | 0.19 | |
plot_cell_percentages | 0.56 | 0.06 | 0.62 | |
plot_composition_heatmap | 5.27 | 0.48 | 6.14 | |
plot_distance_heatmap | 3.59 | 0.30 | 3.90 | |
plot_marker_level_heatmap | 0.52 | 0.11 | 0.62 | |
predict_phenotypes | 1.62 | 0.13 | 1.75 | |
select_celltypes | 0.03 | 0.01 | 0.05 | |