Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 2046/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPIAT 1.6.1  (landing page)
Yuzhou Feng
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/SPIAT
git_branch: RELEASE_3_19
git_last_commit: 7d43d42
git_last_commit_date: 2024-06-26 12:00:39 -0400 (Wed, 26 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped


CHECK results for SPIAT on palomino3

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: 1.6.1
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPIAT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SPIAT_1.6.1.tar.gz
StartedAt: 2024-06-27 06:30:14 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 06:37:07 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 412.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SPIAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPIAT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SPIAT_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SPIAT.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.6.1'
* 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                  23.56   0.07   23.66
calculate_percentage_of_grids                  12.01   0.21   12.24
calculate_spatial_autocorrelation               5.86   0.07    5.93
grid_metrics                                    5.84   0.08    5.92
calculate_pairwise_distances_between_celltypes  5.10   0.58    5.70
* 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-3.19-bioc/meat/SPIAT.Rcheck/00check.log'
for details.


Installation output

SPIAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SPIAT
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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)

Tests output

SPIAT.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
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, 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 
  76.46    4.20   79.40 

Example timings

SPIAT.Rcheck/SPIAT-Ex.timings

nameusersystemelapsed
AUC_of_cross_function0.220.040.27
R_BC1.520.051.60
average_marker_intensity_within_radius0.080.020.10
average_minimum_distance0.030.000.03
average_nearest_neighbor_index0.440.010.45
average_percentage_of_cells_within_radius2.750.052.80
calculate_cell_proportions0.010.000.01
calculate_cross_functions0.140.030.18
calculate_distance_to_margin1.790.031.81
calculate_entropy0.010.000.01
calculate_minimum_distances_between_celltypes0.030.000.04
calculate_pairwise_distances_between_celltypes5.100.585.70
calculate_percentage_of_grids12.01 0.2112.24
calculate_proportions_of_cells_in_structure1.770.041.80
calculate_spatial_autocorrelation5.860.075.93
calculate_summary_distances_between_celltypes2.260.332.59
calculate_summary_distances_of_cells_to_borders1.490.101.58
composition_of_neighborhoods2.140.562.70
compute_gradient0.070.000.06
crossing_of_crossK0.150.010.17
define_celltypes0.780.030.82
define_structure2.770.042.79
dimensionality_reduction_plot23.56 0.0723.66
entropy_gradient_aggregated0.560.100.65
format_cellprofiler_to_spe0.310.040.36
format_codex_to_spe0.250.020.27
format_colData_to_spe0.250.000.25
format_halo_to_spe0.880.160.98
format_image_to_spe0.250.000.25
format_inform_to_spe0.430.070.49
format_spe_to_ppp0.050.000.04
grid_metrics5.840.085.92
identify_bordering_cells0.750.000.75
identify_neighborhoods1.220.381.60
image_splitter1.880.031.89
marker_intensity_boxplot0.330.000.33
marker_prediction_plot0.810.030.84
marker_surface_plot0.260.080.36
marker_surface_plot_stack0.290.090.37
measure_association_to_cell_properties0.360.030.40
mixing_score_summary0.010.000.01
number_of_cells_within_radius0.020.000.02
plot_average_intensity0.290.000.29
plot_cell_categories0.350.000.35
plot_cell_distances_violin1.330.161.48
plot_cell_marker_levels0.210.030.25
plot_cell_percentages0.500.060.56
plot_composition_heatmap4.190.724.91
plot_distance_heatmap2.470.212.67
plot_marker_level_heatmap1.580.071.66
predict_phenotypes1.430.071.49
select_celltypes0.060.000.06