Multiple platform build/check report for BioC 3.21 - CHECK results for spatialDE on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
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 nebbiolo1

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: 1.14.1

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings spatialDE_1.14.1.tar.gz

StartedAt: 2025-04-24 03:01:17 -0400 (Thu, 24 Apr 2025)

EndedAt: 2025-04-24 03:08:00 -0400 (Thu, 24 Apr 2025)

EllapsedTime: 403.4 seconds

RetCode: 0

Status: OK

CheckDir: spatialDE.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings spatialDE_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/spatialDE.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘spatialDE/DESCRIPTION’ ... OK
* this is package ‘spatialDE’ version ‘1.14.1’
* 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-3.21-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 54.276  1.502  54.083
FSV_sig           6.655  1.338   7.405
* 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-3.21-bioc/meat/spatialDE.Rcheck/00check.log’
for details.

Installation output

spatialDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL spatialDE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘spatialDE’ ...
** this is package ‘spatialDE’ version ‘1.14.1’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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: 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


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

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

 55%|█████▌    | 55/100 [00:00<00:00, 549.92it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.56it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 384.92it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 385.40it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:01,  4.38it/s]

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

 38%|███▊      | 38/100 [00:00<00:00, 374.18it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 372.18it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  4.02it/s]

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

 36%|███▌      | 36/100 [00:00<00:00, 355.61it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 354.13it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:00<00:01,  3.82it/s]

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

 36%|███▌      | 36/100 [00:00<00:00, 350.92it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 348.78it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.68it/s]

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

 36%|███▌      | 36/100 [00:00<00:00, 355.14it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 354.48it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.63it/s]

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

 36%|███▌      | 36/100 [00:00<00:00, 354.75it/s][A

 73%|███████▎  | 73/100 [00:00<00:00, 359.69it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:01<00:00,  3.60it/s]

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

 36%|███▌      | 36/100 [00:00<00:00, 359.07it/s][A

 72%|███████▏  | 72/100 [00:00<00:00, 352.75it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.58it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 381.95it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 299.44it/s][A

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

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

 42%|████▏     | 42/100 [00:00<00:00, 418.01it/s][A

 84%|████████▍ | 84/100 [00:00<00:00, 401.85it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.59it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.70it/s]

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

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

 54%|█████▍    | 54/100 [00:00<00:00, 535.50it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.17it/s]

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

 41%|████      | 41/100 [00:00<00:00, 405.91it/s][A

 82%|████████▏ | 82/100 [00:00<00:00, 386.71it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:01,  4.26it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 385.49it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 364.39it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  3.94it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 382.56it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 365.20it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:01,  3.80it/s]

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

 38%|███▊      | 38/100 [00:00<00:00, 376.25it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 359.86it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.71it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 386.57it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 366.23it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.68it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 386.56it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 372.05it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:01<00:00,  3.68it/s]

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

 38%|███▊      | 38/100 [00:00<00:00, 372.65it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 366.06it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.67it/s]

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

 40%|████      | 40/100 [00:00<00:00, 393.56it/s][A

 80%|████████  | 80/100 [00:00<00:00, 384.19it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.72it/s]

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

 42%|████▏     | 42/100 [00:00<00:00, 410.05it/s][A

 84%|████████▍ | 84/100 [00:00<00:00, 401.79it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.79it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.81it/s]
/home/biocbuild/.cache/R/basilisk/1.20.0/spatialDE/1.14.1/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

 55%|█████▌    | 55/100 [00:00<00:00, 545.35it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.47it/s]

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

 45%|████▌     | 45/100 [00:00<00:00, 445.59it/s][A

 90%|█████████ | 90/100 [00:00<00:00, 420.65it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:01,  4.62it/s]

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

 41%|████      | 41/100 [00:00<00:00, 408.73it/s][A

 82%|████████▏ | 82/100 [00:00<00:00, 387.43it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  4.26it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 388.86it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 364.22it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:00<00:01,  3.99it/s]

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

 38%|███▊      | 38/100 [00:00<00:00, 378.93it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 367.11it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.87it/s]

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

 38%|███▊      | 38/100 [00:00<00:00, 376.08it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 364.94it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.79it/s]

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

 40%|████      | 40/100 [00:00<00:00, 393.83it/s][A

 80%|████████  | 80/100 [00:00<00:00, 375.92it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:01<00:00,  3.77it/s]

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

 40%|████      | 40/100 [00:00<00:00, 393.03it/s][A

 80%|████████  | 80/100 [00:00<00:00, 379.59it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.78it/s]

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

 42%|████▏     | 42/100 [00:00<00:00, 414.04it/s][A

 84%|████████▍ | 84/100 [00:00<00:00, 391.33it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.82it/s]

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

 44%|████▍     | 44/100 [00:00<00:00, 433.14it/s][A

 88%|████████▊ | 88/100 [00:00<00:00, 416.44it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.91it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.95it/s]

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

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

 56%|█████▌    | 56/100 [00:00<00:00, 554.98it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.55it/s]

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

 45%|████▌     | 45/100 [00:00<00:00, 449.72it/s][A

 90%|█████████ | 90/100 [00:00<00:00, 425.38it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:01,  4.69it/s]

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

 41%|████      | 41/100 [00:00<00:00, 407.75it/s][A

 82%|████████▏ | 82/100 [00:00<00:00, 391.92it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  4.30it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 384.62it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 375.12it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:00<00:01,  4.06it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 382.19it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 368.45it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.92it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 381.22it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 368.16it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.84it/s]

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

 40%|████      | 40/100 [00:00<00:00, 397.55it/s][A

 80%|████████  | 80/100 [00:00<00:00, 377.65it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:01<00:00,  3.82it/s]

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

 40%|████      | 40/100 [00:00<00:00, 398.10it/s][A

 80%|████████  | 80/100 [00:00<00:00, 381.00it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.82it/s]

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

 42%|████▏     | 42/100 [00:00<00:00, 413.75it/s][A

 84%|████████▍ | 84/100 [00:00<00:00, 393.50it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.84it/s]

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

 43%|████▎     | 43/100 [00:00<00:00, 422.25it/s][A

 86%|████████▌ | 86/100 [00:00<00:00, 410.68it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.92it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.98it/s]

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

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

 54%|█████▍    | 54/100 [00:00<00:00, 539.50it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:01,  5.47it/s]

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

 46%|████▌     | 46/100 [00:00<00:00, 449.73it/s][A

 91%|█████████ | 91/100 [00:00<00:00, 425.81it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:01,  4.66it/s]

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

 41%|████      | 41/100 [00:00<00:00, 407.25it/s][A

 82%|████████▏ | 82/100 [00:00<00:00, 389.00it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:01,  4.28it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 389.30it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 376.42it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:00<00:01,  4.05it/s]

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

 39%|███▉      | 39/100 [00:00<00:00, 380.52it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 370.00it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.92it/s]

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

 37%|███▋      | 37/100 [00:00<00:00, 366.46it/s][A

 74%|███████▍  | 74/100 [00:00<00:00, 359.93it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.81it/s]

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

 40%|████      | 40/100 [00:00<00:00, 395.00it/s][A

 80%|████████  | 80/100 [00:00<00:00, 378.32it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:01<00:00,  3.79it/s]

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

 40%|████      | 40/100 [00:00<00:00, 397.07it/s][A

 80%|████████  | 80/100 [00:00<00:00, 382.04it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  3.80it/s]

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

 42%|████▏     | 42/100 [00:00<00:00, 413.21it/s][A

 84%|████████▍ | 84/100 [00:00<00:00, 394.74it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:02<00:00,  3.84it/s]

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

 44%|████▍     | 44/100 [00:00<00:00, 430.46it/s][A

 88%|████████▊ | 88/100 [00:00<00:00, 415.63it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:02<00:00,  3.93it/s]
Models: 100%|██████████| 10/10 [00:02<00:00,  3.98it/s]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 42.076   7.209  42.524

Example timings

spatialDE.Rcheck/spatialDE-Ex.timings

name	user	system	elapsed
FSV_sig	6.655	1.338	7.405
mockSVG	0.145	0.021	0.166
modelSearch	3.221	0.366	3.220
model_search	2.976	0.377	2.929
multiGenePlots	2.199	0.291	2.179
regress_out	0.088	0.009	0.097
run	1.488	0.124	1.501
spatialDE	1.588	0.191	1.558
spatialPatterns	1.248	0.800	1.105
spatial_patterns	54.276	1.502	54.083
stabilize	0.044	0.006	0.050