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This page was generated on 2023-10-16 11:35:48 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1986/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPIAT 1.2.3  (landing page)
Yuzhou Feng
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SPIAT
git_branch: RELEASE_3_17
git_last_commit: 7ed4529
git_last_commit_date: 2023-09-07 01:31:59 -0400 (Thu, 07 Sep 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for SPIAT on nebbiolo1


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: 1.2.3
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SPIAT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SPIAT_1.2.3.tar.gz
StartedAt: 2023-10-16 01:21:57 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 01:31:25 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 568.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SPIAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SPIAT.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SPIAT_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SPIAT.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SPIAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPIAT’ version ‘1.2.3’
* 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 ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 19.881  0.036  19.918
calculate_percentage_of_grids  8.370  0.028   8.399
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SPIAT.Rmd’ using ‘UTF-8’... OK
  ‘basic_analysis.Rmd’ using ‘UTF-8’... OK
  ‘cell-colocalisation.Rmd’ using ‘UTF-8’... OK
  ‘data_reading-formatting.Rmd’ using ‘UTF-8’... OK
  ‘neighborhood.Rmd’ using ‘UTF-8’... OK
  ‘quality-control_visualisation.Rmd’ using ‘UTF-8’... OK
  ‘spatial-heterogeneity.Rmd’ using ‘UTF-8’... OK
  ‘tissue-structure.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SPIAT.Rcheck/00check.log’
for details.



Installation output

SPIAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SPIAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, sort, 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 
 65.250   3.009  68.189 

Example timings

SPIAT.Rcheck/SPIAT-Ex.timings

nameusersystemelapsed
AUC_of_cross_function0.2070.0240.232
R_BC1.8100.0641.875
average_marker_intensity_within_radius0.0430.0040.047
average_minimum_distance0.0180.0000.019
average_nearest_neighbor_index0.2720.0120.284
average_percentage_of_cells_within_radius1.2610.0201.280
calculate_cell_proportions0.0120.0000.012
calculate_cross_functions0.1570.0000.156
calculate_distance_to_margin1.150.001.15
calculate_entropy0.0100.0000.009
calculate_minimum_distances_between_celltypes0.0110.0040.015
calculate_pairwise_distances_between_celltypes4.2820.7004.982
calculate_percentage_of_grids8.3700.0288.399
calculate_proportions_of_cells_in_structure1.3290.0041.334
calculate_spatial_autocorrelation4.3110.0284.338
calculate_summary_distances_between_celltypes2.6250.1522.777
calculate_summary_distances_of_cells_to_borders1.1790.0201.199
composition_of_neighborhoods1.7010.1361.838
compute_gradient0.0490.0000.049
crossing_of_crossK0.1120.0000.113
define_celltypes0.7590.0000.760
define_structure1.5260.0321.558
dimensionality_reduction_plot19.881 0.03619.918
entropy_gradient_aggregated0.4670.0320.499
format_cellprofiler_to_spe0.1750.0120.186
format_codex_to_spe0.1890.0080.197
format_colData_to_spe0.1890.0080.197
format_halo_to_spe0.5420.0970.616
format_image_to_spe0.1680.0040.172
format_inform_to_spe0.2770.0440.301
format_spe_to_ppp0.0180.0000.018
grid_metrics4.0260.0164.043
identify_bordering_cells0.5820.0000.583
identify_neighborhoods0.7650.1200.885
image_splitter1.3240.0081.332
marker_intensity_boxplot0.2790.0000.279
marker_prediction_plot0.6170.0040.621
marker_surface_plot0.2030.0160.220
marker_surface_plot_stack0.1940.0080.202
measure_association_to_cell_properties0.4440.0040.448
mixing_score_summary0.0160.0000.016
number_of_cells_within_radius0.0070.0040.010
plot_average_intensity0.2580.0000.258
plot_cell_categories0.2890.0000.289
plot_cell_distances_violin1.0070.0121.018
plot_cell_marker_levels0.1640.0000.164
plot_cell_percentages0.6210.0040.625
plot_composition_heatmap3.7340.0803.815
plot_distance_heatmap0.9890.0161.005
plot_marker_level_heatmap0.3980.0000.397
predict_phenotypes0.9050.0000.905
select_celltypes0.0440.0000.045