Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 2032/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPIAT 1.8.0  (landing page)
Yuzhou Feng
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/SPIAT
git_branch: RELEASE_3_20
git_last_commit: 2b7ebac
git_last_commit_date: 2024-10-29 11:14:38 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SPIAT on kjohnson1

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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-12-21 10:30:30 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 10:36:49 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 379.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SPIAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SPIAT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* 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 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                  24.430  1.261  26.337
calculate_percentage_of_grids                   7.848  0.103   8.032
calculate_pairwise_distances_between_celltypes  5.902  0.665   6.611
* 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.


Installation output

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-arm64/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)

Tests output

SPIAT.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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, 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
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 
 71.007   3.701  75.247 

Example timings

SPIAT.Rcheck/SPIAT-Ex.timings

nameusersystemelapsed
AUC_of_cross_function0.2060.0100.217
R_BC2.0930.0482.153
average_marker_intensity_within_radius0.0620.0030.065
average_minimum_distance0.0210.0020.023
average_nearest_neighbor_index0.2490.0050.257
average_percentage_of_cells_within_radius1.4040.0241.440
calculate_cell_proportions0.0150.0010.016
calculate_cross_functions0.1770.0070.185
calculate_distance_to_margin1.1880.0241.222
calculate_entropy0.0100.0000.011
calculate_minimum_distances_between_celltypes0.0180.0010.020
calculate_pairwise_distances_between_celltypes5.9020.6656.611
calculate_percentage_of_grids7.8480.1038.032
calculate_proportions_of_cells_in_structure1.2940.0241.341
calculate_spatial_autocorrelation3.0390.0413.091
calculate_summary_distances_between_celltypes3.4020.2453.721
calculate_summary_distances_of_cells_to_borders1.1990.0941.336
composition_of_neighborhoods1.2360.2571.505
compute_gradient0.0610.0020.063
crossing_of_crossK0.1570.0160.174
define_celltypes0.5970.0050.604
define_structure1.4490.0511.508
dimensionality_reduction_plot24.430 1.26126.337
entropy_gradient_aggregated0.6130.0250.641
format_cellprofiler_to_spe0.1050.0030.108
format_codex_to_spe0.0870.0020.090
format_colData_to_spe0.0970.0020.099
format_halo_to_spe0.4790.0440.528
format_image_to_spe0.1120.0020.115
format_inform_to_spe0.2240.0230.249
format_spe_to_ppp0.0190.0010.020
grid_metrics2.6650.0372.710
identify_bordering_cells0.6260.0110.640
identify_neighborhoods2.2850.2302.529
image_splitter0.8560.0090.868
marker_intensity_boxplot0.3290.0060.336
marker_prediction_plot0.6570.0310.696
marker_surface_plot0.2320.0280.264
marker_surface_plot_stack0.2100.0300.239
measure_association_to_cell_properties0.5500.0070.559
mixing_score_summary0.0210.0010.022
number_of_cells_within_radius0.0140.0010.014
plot_average_intensity0.3520.0150.370
plot_cell_categories0.2250.0070.233
plot_cell_distances_violin1.2750.1051.389
plot_cell_marker_levels0.1890.0060.195
plot_cell_percentages0.4130.0070.423
plot_composition_heatmap4.4210.2914.746
plot_distance_heatmap2.6240.2282.889
plot_marker_level_heatmap0.3770.0340.413
predict_phenotypes1.1370.0241.166
select_celltypes0.0480.0020.050