Multiple platform build/check report for BioC 3.22 - CHECK results for spatialDE on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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*

CHECK results for spatialDE on nebbiolo2

To the developers/maintainers of the spatialDE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialDE.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: spatialDE

Version: 1.15.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialDE_1.15.1.tar.gz

StartedAt: 2025-10-29 04:14:13 -0400 (Wed, 29 Oct 2025)

EndedAt: 2025-10-29 04:19:44 -0400 (Wed, 29 Oct 2025)

EllapsedTime: 331.2 seconds

RetCode: 0

Status: OK

CheckDir: spatialDE.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialDE_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘spatialDE/DESCRIPTION’ ... OK
* this is package ‘spatialDE’ version ‘1.15.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘spatialDE’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck/00install.out’ for details.
* 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 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mockSVG.Rd: SpatialExperiment-class
  modelSearch.Rd: SpatialExperiment-class
  multiGenePlots.Rd: SpatialExperiment-class
  spatialDE.Rd: SpatialExperiment-class
  spatialPatterns.Rd: SpatialExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
spatial_patterns 11.372  6.188   8.781
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck/00check.log’
for details.

Installation output

spatialDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL spatialDE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘spatialDE’ ...
** this is package ‘spatialDE’ version ‘1.15.1’
** using non-staged installation via StagedInstall field
** R
** data
** 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
* DONE (spatialDE)

Tests output

spatialDE.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(spatialDE)
> 
> test_check("spatialDE")
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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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


Models:   0%|          | 0/10 [00:00<?, ?it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 50%|█████     | 50/100 [00:00<00:00, 491.38it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.01it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 359.74it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 351.73it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:02,  3.99it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 353.19it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 340.95it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  3.68it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 33%|███▎      | 33/100 [00:00<00:00, 320.68it/s][A

 66%|██████▌   | 66/100 [00:00<00:00, 319.52it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:01,  3.49it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 33%|███▎      | 33/100 [00:00<00:00, 324.30it/s][A

 66%|██████▌   | 66/100 [00:00<00:00, 324.61it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 321.89it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.38it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 33%|███▎      | 33/100 [00:00<00:00, 329.70it/s][A

 66%|██████▌   | 66/100 [00:00<00:00, 319.52it/s][A

 98%|█████████▊| 98/100 [00:00<00:00, 314.14it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.30it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 34%|███▍      | 34/100 [00:00<00:00, 329.88it/s][A

 68%|██████▊   | 68/100 [00:00<00:00, 330.56it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:02<00:00,  3.29it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 32%|███▏      | 32/100 [00:00<00:00, 316.92it/s][A

 66%|██████▌   | 66/100 [00:00<00:00, 325.61it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 325.30it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.27it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 344.26it/s][A

 70%|███████   | 70/100 [00:00<00:00, 260.08it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.12it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 343.79it/s][A

 71%|███████   | 71/100 [00:00<00:00, 349.55it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.24it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.36it/s]
Warning! ELBO dit not converge after 100 iters!

Models:   0%|          | 0/10 [00:00<?, ?it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 50%|█████     | 50/100 [00:00<00:00, 494.50it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  4.93it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 40%|████      | 40/100 [00:00<00:00, 394.60it/s][A

 80%|████████  | 80/100 [00:00<00:00, 361.53it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:01,  4.03it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 38%|███▊      | 38/100 [00:00<00:00, 371.00it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 351.52it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  3.74it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 357.80it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 340.07it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:01,  3.58it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 346.00it/s][A

 70%|███████   | 70/100 [00:00<00:00, 329.73it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.46it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 369.44it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 350.75it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.44it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 367.07it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 345.42it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:01<00:00,  3.44it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 358.60it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 342.06it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.43it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 354.02it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 341.54it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.44it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 39%|███▉      | 39/100 [00:00<00:00, 379.84it/s][A

 77%|███████▋  | 77/100 [00:00<00:00, 375.27it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.52it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.55it/s]
/var/cache/basilisk/1.21.5/spatialDE/1.15.1/env/lib/python3.11/site-packages/pandas/core/internals/blocks.py:351: RuntimeWarning: invalid value encountered in log
  result = func(self.values, **kwargs)

Models:   0%|          | 0/10 [00:00<?, ?it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 50%|█████     | 50/100 [00:00<00:00, 492.30it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.10it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 42%|████▏     | 42/100 [00:00<00:00, 418.91it/s][A

 84%|████████▍ | 84/100 [00:00<00:00, 386.99it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:01,  4.28it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 363.28it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 349.06it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  3.86it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 358.38it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 342.51it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:01,  3.66it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 341.85it/s][A

 70%|███████   | 70/100 [00:00<00:00, 324.34it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.51it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 343.25it/s][A

 70%|███████   | 70/100 [00:00<00:00, 330.10it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.43it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 360.17it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 352.23it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:01<00:00,  3.45it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 362.01it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 350.55it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.46it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 38%|███▊      | 38/100 [00:00<00:00, 373.28it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 361.59it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.50it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 39%|███▉      | 39/100 [00:00<00:00, 386.17it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 377.84it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.57it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.61it/s]

Models:   0%|          | 0/10 [00:00<?, ?it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 49%|████▉     | 49/100 [00:00<00:00, 479.83it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.02it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 40%|████      | 40/100 [00:00<00:00, 399.09it/s][A

 80%|████████  | 80/100 [00:00<00:00, 382.25it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:02,  3.94it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 359.93it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 348.01it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  3.69it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 342.92it/s][A

 70%|███████   | 70/100 [00:00<00:00, 329.29it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:01,  3.51it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 34%|███▍      | 34/100 [00:00<00:00, 339.49it/s][A

 68%|██████▊   | 68/100 [00:00<00:00, 323.83it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.41it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 346.41it/s][A

 70%|███████   | 70/100 [00:00<00:00, 330.24it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.37it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 347.43it/s][A

 70%|███████   | 70/100 [00:00<00:00, 337.95it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:02<00:00,  3.36it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 353.76it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 342.47it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.38it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 367.95it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 355.77it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.42it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 39%|███▉      | 39/100 [00:00<00:00, 384.42it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 375.95it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.51it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.51it/s]

Models:   0%|          | 0/10 [00:00<?, ?it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 49%|████▉     | 49/100 [00:00<00:00, 489.70it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.10it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 42%|████▏     | 42/100 [00:00<00:00, 419.98it/s][A

 84%|████████▍ | 84/100 [00:00<00:00, 385.45it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:01,  4.30it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 368.02it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 362.30it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  3.92it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 361.12it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 351.92it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:01,  3.71it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 342.27it/s][A

 70%|███████   | 70/100 [00:00<00:00, 324.13it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.54it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 338.46it/s][A

 69%|██████▉   | 69/100 [00:00<00:00, 327.74it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.44it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 35%|███▌      | 35/100 [00:00<00:00, 346.41it/s][A

 70%|███████   | 70/100 [00:00<00:00, 337.81it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:01<00:00,  3.40it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 36%|███▌      | 36/100 [00:00<00:00, 359.08it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 343.34it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.41it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 38%|███▊      | 38/100 [00:00<00:00, 376.38it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 362.32it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.45it/s]

  0%|          | 0/100 [00:00<?, ?it/s][A

 40%|████      | 40/100 [00:00<00:00, 396.58it/s][A

 80%|████████  | 80/100 [00:00<00:00, 385.72it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.57it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.61it/s]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 43.081   7.828  42.694

Example timings

spatialDE.Rcheck/spatialDE-Ex.timings

name	user	system	elapsed
FSV_sig	2.870	1.400	3.241
mockSVG	0.139	0.006	0.145
modelSearch	1.222	0.632	1.038
model_search	1.047	0.627	0.847
multiGenePlots	2.190	0.552	2.226
regress_out	0.086	0.007	0.094
run	0.562	0.266	0.495
spatialDE	0.663	0.365	0.582
spatialPatterns	0.747	0.533	0.654
spatial_patterns	11.372	6.188	8.781
stabilize	0.056	0.038	0.047