Multiple platform build/check report for BioC 3.20 - CHECK results for spatialDE on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4493
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4394
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 palomino8

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: 1.12.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spatialDE.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings spatialDE_1.12.0.tar.gz

StartedAt: 2025-01-21 06:10:40 -0500 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 06:16:14 -0500 (Tue, 21 Jan 2025)

EllapsedTime: 334.0 seconds

RetCode: 0

Status: OK

CheckDir: spatialDE.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:spatialDE.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings spatialDE_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/spatialDE.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'spatialDE/DESCRIPTION' ... OK
* this is package 'spatialDE' version '1.12.0'
* 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 'spatialDE' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'F:/biocbuild/bbs-3.20-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 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 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 11.64   0.74    6.18
FSV_sig           4.61   2.34   34.00
* 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-3.20-bioc/meat/spatialDE.Rcheck/00check.log'
for details.

Installation output

spatialDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL spatialDE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'spatialDE' ...
** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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(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

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, saveRDS, 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


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

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

 45%|████▌     | 45/100 [00:00<00:00, 411.44it/s][A

 95%|█████████▌| 95/100 [00:00<00:00, 438.31it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:02,  4.00it/s]

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

 33%|███▎      | 33/100 [00:00<00:00, 301.72it/s][A

 64%|██████▍   | 64/100 [00:00<00:00, 268.41it/s][A

 92%|█████████▏| 92/100 [00:00<00:00, 221.53it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:02,  2.78it/s]

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

 21%|██        | 21/100 [00:00<00:00, 192.00it/s][A

 43%|████▎     | 43/100 [00:00<00:00, 197.38it/s][A

 63%|██████▎   | 63/100 [00:00<00:00, 190.36it/s][A

 86%|████████▌ | 86/100 [00:00<00:00, 198.22it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:01<00:02,  2.36it/s]

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

 20%|██        | 20/100 [00:00<00:00, 182.86it/s][A

 43%|████▎     | 43/100 [00:00<00:00, 198.99it/s][A

 75%|███████▌  | 75/100 [00:00<00:00, 241.72it/s][A

100%|██████████| 100/100 [00:00<00:00, 236.53it/s][A

                                                  [A
Models:  40%|████      | 4/10 [00:01<00:02,  2.33it/s]

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

 18%|█▊        | 18/100 [00:00<00:00, 164.57it/s][A

 39%|███▉      | 39/100 [00:00<00:00, 180.71it/s][A

 58%|█████▊    | 58/100 [00:00<00:00, 166.34it/s][A

 75%|███████▌  | 75/100 [00:00<00:00, 162.20it/s][A

 92%|█████████▏| 92/100 [00:00<00:00, 152.18it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:02<00:02,  2.00it/s]

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

 16%|█▌        | 16/100 [00:00<00:00, 146.29it/s][A

 33%|███▎      | 33/100 [00:00<00:00, 151.66it/s][A

 51%|█████     | 51/100 [00:00<00:00, 157.56it/s][A

 67%|██████▋   | 67/100 [00:00<00:00, 153.11it/s][A

 96%|█████████▌| 96/100 [00:00<00:00, 193.51it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:02<00:02,  1.92it/s]

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

 21%|██        | 21/100 [00:00<00:00, 192.01it/s][A

 41%|████      | 41/100 [00:00<00:00, 171.75it/s][A

 59%|█████▉    | 59/100 [00:00<00:00, 168.62it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 170.57it/s][A

 96%|█████████▌| 96/100 [00:00<00:00, 168.45it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:03<00:01,  1.83it/s]

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

 22%|██▏       | 22/100 [00:00<00:00, 201.15it/s][A

 48%|████▊     | 48/100 [00:00<00:00, 222.65it/s][A

 81%|████████  | 81/100 [00:00<00:00, 258.76it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:03<00:00,  2.02it/s]

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

 20%|██        | 20/100 [00:00<00:00, 182.86it/s][A

 39%|███▉      | 39/100 [00:00<00:00, 141.46it/s][A

 56%|█████▌    | 56/100 [00:00<00:00, 147.06it/s][A

 75%|███████▌  | 75/100 [00:00<00:00, 156.77it/s][A

 94%|█████████▍| 94/100 [00:00<00:00, 162.57it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:04<00:00,  1.86it/s]

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

 19%|█▉        | 19/100 [00:00<00:00, 173.72it/s][A

 43%|████▎     | 43/100 [00:00<00:00, 200.61it/s][A

 64%|██████▍   | 64/100 [00:00<00:00, 184.63it/s][A

 83%|████████▎ | 83/100 [00:00<00:00, 180.49it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:04<00:00,  1.85it/s]
Models: 100%|██████████| 10/10 [00:04<00:00,  2.01it/s]

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

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

 30%|███       | 30/100 [00:00<00:00, 274.28it/s][A

 75%|███████▌  | 75/100 [00:00<00:00, 354.94it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:02,  3.76it/s]

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

 32%|███▏      | 32/100 [00:00<00:00, 292.59it/s][A

 65%|██████▌   | 65/100 [00:00<00:00, 297.95it/s][A

 95%|█████████▌| 95/100 [00:00<00:00, 287.14it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:02,  3.21it/s]

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

 36%|███▌      | 36/100 [00:00<00:00, 329.16it/s][A

 69%|██████▉   | 69/100 [00:00<00:00, 288.75it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 205.23it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:01<00:02,  2.61it/s]

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

 21%|██        | 21/100 [00:00<00:00, 192.00it/s][A

 41%|████      | 41/100 [00:00<00:00, 172.16it/s][A

 59%|█████▉    | 59/100 [00:00<00:00, 158.93it/s][A

 76%|███████▌  | 76/100 [00:00<00:00, 157.63it/s][A

 93%|█████████▎| 93/100 [00:00<00:00, 156.87it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:02,  2.09it/s]

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

 21%|██        | 21/100 [00:00<00:00, 192.00it/s][A

 41%|████      | 41/100 [00:00<00:00, 159.44it/s][A

 58%|█████▊    | 58/100 [00:00<00:00, 157.75it/s][A

 75%|███████▌  | 75/100 [00:00<00:00, 156.88it/s][A

 91%|█████████ | 91/100 [00:00<00:00, 153.19it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:02<00:02,  1.86it/s]

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

 29%|██▉       | 29/100 [00:00<00:00, 265.15it/s][A

 56%|█████▌    | 56/100 [00:00<00:00, 254.39it/s][A

 84%|████████▍ | 84/100 [00:00<00:00, 255.12it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:02<00:01,  2.07it/s]

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

 35%|███▌      | 35/100 [00:00<00:00, 319.99it/s][A

 67%|██████▋   | 67/100 [00:00<00:00, 303.17it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 298.30it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:03<00:01,  2.29it/s]

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

 26%|██▌       | 26/100 [00:00<00:00, 237.73it/s][A

 50%|█████     | 50/100 [00:00<00:00, 194.30it/s][A

 77%|███████▋  | 77/100 [00:00<00:00, 216.29it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:03<00:00,  2.26it/s]

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

 23%|██▎       | 23/100 [00:00<00:00, 210.27it/s][A

 45%|████▌     | 45/100 [00:00<00:00, 204.90it/s][A

 68%|██████▊   | 68/100 [00:00<00:00, 207.36it/s][A

 94%|█████████▍| 94/100 [00:00<00:00, 219.00it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:03<00:00,  2.24it/s]

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

 32%|███▏      | 32/100 [00:00<00:00, 292.58it/s][A

 67%|██████▋   | 67/100 [00:00<00:00, 308.70it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:04<00:00,  2.47it/s]
Models: 100%|██████████| 10/10 [00:04<00:00,  2.33it/s]
C:\Users\BIOCBU~1\BASILI~1\118~1.0\SPATIA~1\112~1.0\env\lib\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

 28%|██▊       | 28/100 [00:00<00:00, 254.85it/s][A

 60%|██████    | 60/100 [00:00<00:00, 276.29it/s][A

 95%|█████████▌| 95/100 [00:00<00:00, 300.69it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:02,  3.03it/s]

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

 36%|███▌      | 36/100 [00:00<00:00, 327.69it/s][A

 75%|███████▌  | 75/100 [00:00<00:00, 343.69it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:02,  3.21it/s]

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

 36%|███▌      | 36/100 [00:00<00:00, 327.74it/s][A

 71%|███████   | 71/100 [00:00<00:00, 322.33it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:02,  3.13it/s]

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

 35%|███▌      | 35/100 [00:00<00:00, 318.57it/s][A

 69%|██████▉   | 69/100 [00:00<00:00, 313.20it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:01,  3.15it/s]

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

 32%|███▏      | 32/100 [00:00<00:00, 291.33it/s][A

 66%|██████▌   | 66/100 [00:00<00:00, 302.04it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 301.31it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.11it/s]

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

 32%|███▏      | 32/100 [00:00<00:00, 291.33it/s][A

 64%|██████▍   | 64/100 [00:00<00:00, 291.31it/s][A

 96%|█████████▌| 96/100 [00:00<00:00, 291.32it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  3.03it/s]

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

 35%|███▌      | 35/100 [00:00<00:00, 318.58it/s][A

 68%|██████▊   | 68/100 [00:00<00:00, 307.88it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 296.15it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:02<00:00,  3.03it/s]

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

 29%|██▉       | 29/100 [00:00<00:00, 265.14it/s][A

 56%|█████▌    | 56/100 [00:00<00:00, 234.67it/s][A

 80%|████████  | 80/100 [00:00<00:00, 192.07it/s][A

100%|██████████| 100/100 [00:00<00:00, 188.89it/s][A

                                                  [A
Models:  80%|████████  | 8/10 [00:02<00:00,  2.57it/s]

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

 24%|██▍       | 24/100 [00:00<00:00, 219.44it/s][A

 53%|█████▎    | 53/100 [00:00<00:00, 246.31it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 223.63it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:03<00:00,  2.50it/s]

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

 37%|███▋      | 37/100 [00:00<00:00, 338.18it/s][A

 75%|███████▌  | 75/100 [00:00<00:00, 343.61it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:03<00:00,  2.76it/s]
Models: 100%|██████████| 10/10 [00:03<00:00,  2.86it/s]

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

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

 48%|████▊     | 48/100 [00:00<00:00, 438.88it/s][A

 95%|█████████▌| 95/100 [00:00<00:00, 433.47it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:02,  4.27it/s]

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

 33%|███▎      | 33/100 [00:00<00:00, 301.71it/s][A

 64%|██████▍   | 64/100 [00:00<00:00, 268.40it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 290.39it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:02,  3.34it/s]

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

 24%|██▍       | 24/100 [00:00<00:00, 219.43it/s][A

 57%|█████▋    | 57/100 [00:00<00:00, 267.83it/s][A

 91%|█████████ | 91/100 [00:00<00:00, 287.48it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:00<00:02,  3.13it/s]

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

 34%|███▍      | 34/100 [00:00<00:00, 310.85it/s][A

 69%|██████▉   | 69/100 [00:00<00:00, 316.23it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:01,  3.16it/s]

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

 31%|███       | 31/100 [00:00<00:00, 283.44it/s][A

 64%|██████▍   | 64/100 [00:00<00:00, 294.18it/s][A

 98%|█████████▊| 98/100 [00:00<00:00, 301.17it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  3.12it/s]

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

 32%|███▏      | 32/100 [00:00<00:00, 292.58it/s][A

 63%|██████▎   | 63/100 [00:00<00:00, 287.19it/s][A

 92%|█████████▏| 92/100 [00:00<00:00, 277.13it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:01<00:01,  2.99it/s]

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

 32%|███▏      | 32/100 [00:00<00:00, 292.60it/s][A

 64%|██████▍   | 64/100 [00:00<00:00, 292.58it/s][A

 94%|█████████▍| 94/100 [00:00<00:00, 284.22it/s][A

                                                 [A
Models:  70%|███████   | 7/10 [00:02<00:01,  2.97it/s]

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

 29%|██▉       | 29/100 [00:00<00:00, 265.14it/s][A

 56%|█████▌    | 56/100 [00:00<00:00, 254.39it/s][A

 83%|████████▎ | 83/100 [00:00<00:00, 250.44it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:02<00:00,  2.82it/s]

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

 34%|███▍      | 34/100 [00:00<00:00, 310.85it/s][A

 66%|██████▌   | 66/100 [00:00<00:00, 256.92it/s][A

 97%|█████████▋| 97/100 [00:00<00:00, 268.01it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:03<00:00,  2.81it/s]

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

 22%|██▏       | 22/100 [00:00<00:00, 201.15it/s][A

 43%|████▎     | 43/100 [00:00<00:00, 195.77it/s][A

 67%|██████▋   | 67/100 [00:00<00:00, 206.57it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:03<00:00,  2.66it/s]
Models: 100%|██████████| 10/10 [00:03<00:00,  2.91it/s]

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

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

 36%|███▌      | 36/100 [00:00<00:00, 329.15it/s][A

 69%|██████▉   | 69/100 [00:00<00:00, 313.01it/s][A

                                                 [A
Models:  10%|█         | 1/10 [00:00<00:02,  3.20it/s]

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

 37%|███▋      | 37/100 [00:00<00:00, 338.28it/s][A

 71%|███████   | 71/100 [00:00<00:00, 297.18it/s][A

                                                 [A
Models:  20%|██        | 2/10 [00:00<00:02,  3.11it/s]

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

 34%|███▍      | 34/100 [00:00<00:00, 310.84it/s][A

 67%|██████▋   | 67/100 [00:00<00:00, 305.48it/s][A

 98%|█████████▊| 98/100 [00:00<00:00, 294.84it/s][A

                                                 [A
Models:  30%|███       | 3/10 [00:01<00:02,  2.95it/s]

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

 34%|███▍      | 34/100 [00:00<00:00, 310.86it/s][A

 66%|██████▌   | 66/100 [00:00<00:00, 300.10it/s][A

 98%|█████████▊| 98/100 [00:00<00:00, 296.66it/s][A

                                                 [A
Models:  40%|████      | 4/10 [00:01<00:02,  2.99it/s]

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

 30%|███       | 30/100 [00:00<00:00, 274.28it/s][A

 60%|██████    | 60/100 [00:00<00:00, 274.28it/s][A

 88%|████████▊ | 88/100 [00:00<00:00, 249.65it/s][A

                                                 [A
Models:  50%|█████     | 5/10 [00:01<00:01,  2.77it/s]

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

 19%|█▉        | 19/100 [00:00<00:00, 173.71it/s][A

 37%|███▋      | 37/100 [00:00<00:00, 167.90it/s][A

 58%|█████▊    | 58/100 [00:00<00:00, 178.89it/s][A

 79%|███████▉  | 79/100 [00:00<00:00, 184.06it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 183.63it/s][A

                                                 [A
Models:  60%|██████    | 6/10 [00:02<00:01,  2.36it/s]

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

 24%|██▍       | 24/100 [00:00<00:00, 219.43it/s][A

 48%|████▊     | 48/100 [00:00<00:00, 219.42it/s][A

 70%|███████   | 70/100 [00:00<00:00, 211.08it/s][A

100%|██████████| 100/100 [00:00<00:00, 236.03it/s][A

                                                  [A
Models:  70%|███████   | 7/10 [00:02<00:01,  2.33it/s]

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

 34%|███▍      | 34/100 [00:00<00:00, 310.87it/s][A

 66%|██████▌   | 66/100 [00:00<00:00, 239.20it/s][A

 91%|█████████ | 91/100 [00:00<00:00, 200.47it/s][A

                                                 [A
Models:  80%|████████  | 8/10 [00:03<00:00,  2.29it/s]

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

 29%|██▉       | 29/100 [00:00<00:00, 265.15it/s][A

 56%|█████▌    | 56/100 [00:00<00:00, 203.17it/s][A

 78%|███████▊  | 78/100 [00:00<00:00, 202.35it/s][A

 99%|█████████▉| 99/100 [00:00<00:00, 188.49it/s][A

                                                 [A
Models:  90%|█████████ | 9/10 [00:03<00:00,  2.17it/s]

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

 22%|██▏       | 22/100 [00:00<00:00, 200.27it/s][A

 57%|█████▋    | 57/100 [00:00<00:00, 269.88it/s][A

 94%|█████████▍| 94/100 [00:00<00:00, 300.43it/s][A

                                                 [A
Models: 100%|██████████| 10/10 [00:04<00:00,  2.32it/s]
Models: 100%|██████████| 10/10 [00:04<00:00,  2.47it/s]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
  61.26    2.71   72.01

Example timings

spatialDE.Rcheck/spatialDE-Ex.timings

name	user	system	elapsed
FSV_sig	4.61	2.34	34.00
mockSVG	0.18	0.02	0.17
modelSearch	2.58	0.18	1.49
model_search	1.94	0.22	1.07
multiGenePlots	2.59	0.19	1.88
regress_out	0.25	0.02	0.19
run	1.19	0.14	0.67
spatialDE	1.33	0.18	0.78
spatialPatterns	1.47	0.14	0.91
spatial_patterns	11.64	0.74	6.18
stabilize	0.34	0.01	0.21