Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-01 11:40:32 -0400 (Wed, 01 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4627 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4376 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 1983/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SPIAT 1.5.3 (landing page) Yuzhou Feng
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.5.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPIAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPIAT_1.5.3.tar.gz |
StartedAt: 2024-04-30 11:39:56 -0400 (Tue, 30 Apr 2024) |
EndedAt: 2024-04-30 12:00:18 -0400 (Tue, 30 Apr 2024) |
EllapsedTime: 1221.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SPIAT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPIAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPIAT_1.5.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SPIAT.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SPIAT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SPIAT’ version ‘1.5.3’ * 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 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 36.699 2.521 60.440 calculate_percentage_of_grids 24.782 0.497 45.574 calculate_spatial_autocorrelation 11.657 0.129 20.073 grid_metrics 10.587 0.091 16.645 plot_composition_heatmap 8.698 0.343 14.594 calculate_pairwise_distances_between_celltypes 5.869 2.231 15.224 plot_distance_heatmap 3.999 0.433 6.484 R_BC 3.851 0.222 7.825 define_structure 3.927 0.122 6.459 calculate_summary_distances_between_celltypes 2.877 0.978 6.260 calculate_summary_distances_of_cells_to_borders 3.447 0.262 5.981 calculate_proportions_of_cells_in_structure 3.545 0.074 6.255 calculate_distance_to_margin 3.428 0.138 6.508 image_splitter 3.500 0.041 6.143 composition_of_neighborhoods 2.843 0.343 5.134 average_percentage_of_cells_within_radius 2.730 0.074 5.849 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/SPIAT.Rcheck/00check.log’ for details.
SPIAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SPIAT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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(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, 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 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 125.877 6.962 212.254
SPIAT.Rcheck/SPIAT-Ex.timings
name | user | system | elapsed | |
AUC_of_cross_function | 0.336 | 0.021 | 0.634 | |
R_BC | 3.851 | 0.222 | 7.825 | |
average_marker_intensity_within_radius | 0.108 | 0.007 | 0.203 | |
average_minimum_distance | 0.035 | 0.005 | 0.089 | |
average_nearest_neighbor_index | 0.753 | 0.012 | 1.388 | |
average_percentage_of_cells_within_radius | 2.730 | 0.074 | 5.849 | |
calculate_cell_proportions | 0.028 | 0.003 | 0.062 | |
calculate_cross_functions | 0.423 | 0.016 | 0.814 | |
calculate_distance_to_margin | 3.428 | 0.138 | 6.508 | |
calculate_entropy | 0.021 | 0.002 | 0.063 | |
calculate_minimum_distances_between_celltypes | 0.036 | 0.001 | 0.042 | |
calculate_pairwise_distances_between_celltypes | 5.869 | 2.231 | 15.224 | |
calculate_percentage_of_grids | 24.782 | 0.497 | 45.574 | |
calculate_proportions_of_cells_in_structure | 3.545 | 0.074 | 6.255 | |
calculate_spatial_autocorrelation | 11.657 | 0.129 | 20.073 | |
calculate_summary_distances_between_celltypes | 2.877 | 0.978 | 6.260 | |
calculate_summary_distances_of_cells_to_borders | 3.447 | 0.262 | 5.981 | |
composition_of_neighborhoods | 2.843 | 0.343 | 5.134 | |
compute_gradient | 0.135 | 0.003 | 0.220 | |
crossing_of_crossK | 0.252 | 0.007 | 0.410 | |
define_celltypes | 3.005 | 0.087 | 4.882 | |
define_structure | 3.927 | 0.122 | 6.459 | |
dimensionality_reduction_plot | 36.699 | 2.521 | 60.440 | |
entropy_gradient_aggregated | 0.982 | 0.069 | 1.743 | |
format_cellprofiler_to_spe | 0.440 | 0.006 | 0.666 | |
format_codex_to_spe | 0.407 | 0.006 | 0.626 | |
format_colData_to_spe | 0.441 | 0.004 | 0.669 | |
format_halo_to_spe | 1.149 | 0.110 | 1.790 | |
format_image_to_spe | 0.439 | 0.005 | 0.637 | |
format_inform_to_spe | 0.697 | 0.059 | 1.208 | |
format_spe_to_ppp | 0.034 | 0.001 | 0.056 | |
grid_metrics | 10.587 | 0.091 | 16.645 | |
identify_bordering_cells | 1.655 | 0.018 | 3.350 | |
identify_neighborhoods | 1.588 | 0.248 | 3.710 | |
image_splitter | 3.500 | 0.041 | 6.143 | |
marker_intensity_boxplot | 0.665 | 0.009 | 0.970 | |
marker_prediction_plot | 1.298 | 0.043 | 1.957 | |
marker_surface_plot | 0.476 | 0.084 | 0.809 | |
marker_surface_plot_stack | 0.576 | 0.083 | 0.974 | |
measure_association_to_cell_properties | 0.815 | 0.012 | 1.185 | |
mixing_score_summary | 0.037 | 0.001 | 0.053 | |
number_of_cells_within_radius | 0.026 | 0.001 | 0.043 | |
plot_average_intensity | 0.656 | 0.007 | 0.956 | |
plot_cell_categories | 0.460 | 0.020 | 0.885 | |
plot_cell_distances_violin | 2.037 | 0.269 | 4.673 | |
plot_cell_marker_levels | 0.392 | 0.009 | 0.843 | |
plot_cell_percentages | 0.930 | 0.017 | 1.967 | |
plot_composition_heatmap | 8.698 | 0.343 | 14.594 | |
plot_distance_heatmap | 3.999 | 0.433 | 6.484 | |
plot_marker_level_heatmap | 0.832 | 0.071 | 1.855 | |
predict_phenotypes | 2.620 | 0.053 | 4.632 | |
select_celltypes | 0.112 | 0.002 | 0.182 | |