Hi,

If I try to run the example of the function run from the spatialDE package I get an error apparently related to the basilisk interface to Python:

library(spatialDE)

example(run)

run> ## Mock up a SpatialExperiment object wit 400 cells and 3 genes
run> set.seed(42)

run> mock <- mockSVG(size = 20, tot_genes = 3, de_genes = 1)

run> stabilized <- stabilize(mock$counts)
Error in py_module_import(module, convert = convert) : 
  ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/rcastelo/.cache/R/basilisk/1.14.3/spatialDE/1.8.1/env/lib/python3.9/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-39-x86_64-linux-gnu.so)
Run `reticulate::py_last_error()` for details.
WARNING: ignoring environment value of R_HOME
Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
  one node produced an error: could not find function "use_condaenv"
> traceback()
12: stop("one node produced an error: ", firstmsg, domain = NA)
11: checkForRemoteErrors(lapply(cl, recvResult))
10: clusterCall(proc, envstripper(useBasiliskEnv), envpath = envpath)
9: basiliskStart(env, full.activation = full.activation)
8: .activate_fallback(proc, testload, env = env, envpath = envpath, 
       full.activation = full.activation)
7: basiliskStart(spatialDE_env, testload = "scipy.optimize")
6: stabilize(mock$counts) at Rex287b897b2b79b#11
5: eval(ei, envir)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix, 
       getOption("prompt")), continue.echo = paste0(prompt.prefix, 
       getOption("continue")), verbose = verbose, max.deparse.length = Inf, 
       encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
1: example(run)

This is an attempt on a Ubuntu 20.04, any hint on how to make it run will be highly appreciated. Please find below my session information.

Thanks!

> sessionInfo( )
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /home/rcastelo/Soft/R/R-4.3.2/lib/R/lib/libRblas.so 
LAPACK: /home/rcastelo/Soft/R/R-4.3.2/lib/R/lib/libRlapack.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Madrid
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] spatialDE_1.8.1 colorout_1.3-0 

loaded via a namespace (and not attached):
 [1] utf8_1.2.4                  generics_0.1.3             
 [3] SparseArray_1.2.3           bitops_1.0-7               
 [5] lattice_0.22-5              magrittr_2.0.3             
 [7] grid_4.3.2                  jsonlite_1.8.8             
 [9] Matrix_1.6-5                backports_1.4.1            
[11] GenomeInfoDb_1.38.6         gridExtra_2.3              
[13] fansi_1.0.6                 SingleCellExperiment_1.24.0
[15] scales_1.3.0                abind_1.4-5                
[17] cli_3.6.2                   rlang_1.1.3                
[19] crayon_1.5.2                XVector_0.42.0             
[21] basilisk.utils_1.14.1       Biobase_2.62.0             
[23] munsell_0.5.0               withr_3.0.0                
[25] DelayedArray_0.28.0         S4Arrays_1.2.0             
[27] parallel_4.3.2              tools_4.3.2                
[29] dir.expiry_1.10.0           checkmate_2.3.1            
[31] dplyr_1.1.4                 colorspace_2.1-0           
[33] ggplot2_3.4.4               SpatialExperiment_1.12.0   
[35] filelock_1.0.3              GenomeInfoDbData_1.2.11    
[37] basilisk_1.14.3             SummarizedExperiment_1.32.0
[39] BiocGenerics_0.48.1         reticulate_1.35.0          
[41] png_0.1-8                   vctrs_0.6.5                
[43] R6_2.5.1                    matrixStats_1.2.0          
[45] stats4_4.3.2                lifecycle_1.0.4            
[47] magick_2.8.2                zlibbioc_1.48.0            
[49] S4Vectors_0.40.2            IRanges_2.36.0             
[51] pkgconfig_2.0.3             pillar_1.9.0               
[53] gtable_0.3.4                glue_1.7.0                 
[55] Rcpp_1.0.12                 tibble_3.2.1               
[57] GenomicRanges_1.54.1        tidyselect_1.2.0           
[59] MatrixGenerics_1.14.0       rjson_0.2.21               
[61] compiler_4.3.2              RCurl_1.98-1.14

There are some possible solutions here.