| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:52 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the SPIAT package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1919/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPIAT 1.1.4 (landing page) Yuzhou Feng
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: SPIAT |
| Version: 1.1.4 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPIAT.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SPIAT_1.1.4.tar.gz |
| StartedAt: 2022-12-29 03:50:17 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 03:55:14 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 296.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SPIAT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPIAT.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SPIAT_1.1.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/SPIAT.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.1.4'
* 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 ... OK
* checking top-level files ... OK
* 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 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 15.91 0.13 16.03
calculate_percentage_of_grids 7.13 0.08 7.20
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
SPIAT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SPIAT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 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 1 | SKIP 0 | PASS 80 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 80 ]
>
> proc.time()
user system elapsed
52.93 2.28 55.21
SPIAT.Rcheck/SPIAT-Ex.timings
| name | user | system | elapsed | |
| AUC_of_cross_function | 0.22 | 0.01 | 0.24 | |
| R_BC | 1.3 | 0.1 | 1.4 | |
| average_marker_intensity_within_radius | 0.05 | 0.00 | 0.05 | |
| average_minimum_distance | 0.01 | 0.00 | 0.01 | |
| average_nearest_neighbor_index | 0.22 | 0.01 | 0.24 | |
| average_percentage_of_cells_within_radius | 1.24 | 0.00 | 1.23 | |
| calculate_cell_proportions | 0.01 | 0.00 | 0.02 | |
| calculate_cross_functions | 0.11 | 0.00 | 0.11 | |
| calculate_distance_to_margin | 1.05 | 0.00 | 1.05 | |
| calculate_entropy | 0.01 | 0.00 | 0.01 | |
| calculate_minimum_distances_between_celltypes | 0 | 0 | 0 | |
| calculate_pairwise_distances_between_celltypes | 3.83 | 0.40 | 4.25 | |
| calculate_percentage_of_grids | 7.13 | 0.08 | 7.20 | |
| calculate_proportions_of_cells_in_structure | 1.01 | 0.07 | 1.08 | |
| calculate_spatial_autocorrelation | 3.88 | 0.03 | 3.90 | |
| calculate_summary_distances_between_celltypes | 2.00 | 0.09 | 2.10 | |
| calculate_summary_distances_of_cells_to_borders | 0.97 | 0.13 | 1.09 | |
| composition_of_neighborhoods | 1.39 | 0.09 | 1.48 | |
| compute_gradient | 0.05 | 0.00 | 0.05 | |
| crossing_of_crossK | 0.09 | 0.03 | 0.12 | |
| define_celltypes | 0.64 | 0.02 | 0.66 | |
| define_structure | 1.27 | 0.01 | 1.28 | |
| dimensionality_reduction_plot | 15.91 | 0.13 | 16.03 | |
| entropy_gradient_aggregated | 0.39 | 0.01 | 0.41 | |
| format_cellprofiler_to_spe | 0.13 | 0.00 | 0.13 | |
| format_codex_to_spe | 0.13 | 0.00 | 0.13 | |
| format_colData_to_spe | 0.12 | 0.00 | 0.12 | |
| format_halo_to_spe | 0.55 | 0.19 | 0.72 | |
| format_image_to_spe | 0.12 | 0.00 | 0.13 | |
| format_inform_to_spe | 0.33 | 0.09 | 0.34 | |
| format_spe_to_ppp | 0.02 | 0.00 | 0.02 | |
| grid_metrics | 3.90 | 0.03 | 3.94 | |
| identify_bordering_cells | 0.49 | 0.00 | 0.48 | |
| identify_neighborhoods | 0.61 | 0.11 | 0.72 | |
| image_splitter | 1.12 | 0.08 | 1.21 | |
| marker_intensity_boxplot | 0.22 | 0.01 | 0.23 | |
| marker_prediction_plot | 1.06 | 0.00 | 1.06 | |
| marker_surface_plot | 0.19 | 0.02 | 0.22 | |
| marker_surface_plot_stack | 0.25 | 0.05 | 0.30 | |
| measure_association_to_cell_properties | 0.42 | 0.00 | 0.42 | |
| mixing_score_summary | 0.02 | 0.00 | 0.02 | |
| number_of_cells_within_radius | 0 | 0 | 0 | |
| plot_average_intensity | 0.23 | 0.01 | 0.25 | |
| plot_cell_categories | 0.25 | 0.00 | 0.25 | |
| plot_cell_distances_violin | 0.83 | 0.06 | 0.89 | |
| plot_cell_marker_levels | 0.14 | 0.00 | 0.14 | |
| plot_cell_percentages | 0.5 | 0.0 | 0.5 | |
| plot_composition_heatmap | 3.08 | 0.14 | 3.22 | |
| plot_distance_heatmap | 2.28 | 0.16 | 2.43 | |
| plot_marker_level_heatmap | 0.31 | 0.08 | 0.40 | |
| predict_phenotypes | 1.21 | 0.11 | 1.31 | |
| select_celltypes | 0.03 | 0.00 | 0.03 | |