Multiple platform build/check report for BioC 3.22 - CHECK results for spatialDE on kjohnson3

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
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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 kjohnson3

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialDE_1.15.1.tar.gz

StartedAt: 2025-10-24 22:14:44 -0400 (Fri, 24 Oct 2025)

EndedAt: 2025-10-24 22:16:21 -0400 (Fri, 24 Oct 2025)

EllapsedTime: 97.1 seconds

RetCode: 0

Status: OK

CheckDir: spatialDE.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialDE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialDE_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ‘/Users/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 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 7.843  0.131   4.078
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialDE.Rcheck/00check.log’
for details.

Installation output

spatialDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialDE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

                                       [A

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

                                       [A
Models:  20%|██        | 2/10 [00:00<00:00, 12.75it/s]

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

                                       [A

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

                                       [A
Models:  40%|████      | 4/10 [00:00<00:00, 11.34it/s]

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

                                       [A

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

                                       [A
Models:  60%|██████    | 6/10 [00:00<00:00, 11.50it/s]

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

                                       [A

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

                                       [A
Models:  80%|████████  | 8/10 [00:00<00:00, 11.73it/s]

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

                                       [A

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

                                       [A
Models: 100%|██████████| 10/10 [00:00<00:00, 11.71it/s]
Models: 100%|██████████| 10/10 [00:00<00:00, 11.70it/s]

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

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

                                       [A

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

                                       [A
Models:  20%|██        | 2/10 [00:00<00:00, 15.10it/s]

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

                                       [A

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

                                       [A
Models:  40%|████      | 4/10 [00:00<00:00, 12.55it/s]

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

100%|██████████| 100/100 [00:00<00:00, 995.60it/s][A

                                                  [A

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

                                       [A
Models:  60%|██████    | 6/10 [00:00<00:00, 11.20it/s]

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

                                       [A

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

                                       [A
Models:  80%|████████  | 8/10 [00:00<00:00, 11.44it/s]

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

                                       [A

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

                                       [A
Models: 100%|██████████| 10/10 [00:00<00:00, 11.49it/s]
Models: 100%|██████████| 10/10 [00:00<00:00, 11.71it/s]
/Users/biocbuild/Library/Caches/org.R-project.R/R/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

                                       [A

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

                                       [A
Models:  20%|██        | 2/10 [00:00<00:00, 15.90it/s]

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

                                       [A

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

                                       [A
Models:  40%|████      | 4/10 [00:00<00:00, 13.46it/s]

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

                                       [A

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

                                       [A
Models:  60%|██████    | 6/10 [00:00<00:00,  8.94it/s]

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

 96%|█████████▌| 96/100 [00:00<00:00, 956.36it/s][A

                                                 [A

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

                                       [A
Models:  80%|████████  | 8/10 [00:00<00:00,  9.19it/s]

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

                                       [A

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

                                       [A
Models: 100%|██████████| 10/10 [00:00<00:00, 10.22it/s]
Models: 100%|██████████| 10/10 [00:00<00:00, 10.32it/s]

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

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

                                       [A

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

                                       [A
Models:  20%|██        | 2/10 [00:00<00:00, 15.33it/s]

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

                                       [A

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

                                       [A
Models:  40%|████      | 4/10 [00:00<00:00, 13.70it/s]

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

                                       [A

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

                                       [A
Models:  60%|██████    | 6/10 [00:00<00:00, 12.74it/s]

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

                                       [A

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

                                       [A
Models:  80%|████████  | 8/10 [00:00<00:00, 12.75it/s]

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

                                       [A

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

                                       [A
Models: 100%|██████████| 10/10 [00:00<00:00, 12.38it/s]
Models: 100%|██████████| 10/10 [00:00<00:00, 12.76it/s]

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

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

                                       [A

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

                                       [A
Models:  20%|██        | 2/10 [00:00<00:00, 15.80it/s]

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

                                       [A

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

                                       [A
Models:  40%|████      | 4/10 [00:00<00:00, 13.24it/s]

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

                                       [A

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

                                       [A
Models:  60%|██████    | 6/10 [00:00<00:00, 12.79it/s]

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

                                       [A

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

                                       [A
Models:  80%|████████  | 8/10 [00:00<00:00, 12.09it/s]

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

                                       [A

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

                                       [A
Models: 100%|██████████| 10/10 [00:00<00:00, 11.68it/s]
Models: 100%|██████████| 10/10 [00:00<00:00, 12.22it/s]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 16.579   0.511  14.691 
/Users/biocbuild/.pyenv/versions/3.11.13/lib/python3.11/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '

Example timings

spatialDE.Rcheck/spatialDE-Ex.timings

name	user	system	elapsed
FSV_sig	3.008	0.360	3.858
mockSVG	0.530	0.073	0.406
modelSearch	0.821	0.027	0.454
model_search	0.776	0.030	0.405
multiGenePlots	1.017	0.022	0.547
regress_out	0.027	0.001	0.028
run	0.311	0.008	0.188
spatialDE	0.421	0.013	0.221
spatialPatterns	0.537	0.009	0.275
spatial_patterns	7.843	0.131	4.078
stabilize	0.035	0.001	0.020