scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
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0
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inzirio ▴ 10
@inzirio-13571
Last seen 5 months ago
Italy

I just updated a few packages, and Matrix is one of them (now version 1.6-2).

After that, runUMAP stopped to work producing this error:

Error: processing vignette 'cell_type_annotation.Rmd' failed with diagnostics: function 'as_cholmod_sparse' not provided by package 'Matrix'

library(MouseGastrulationData)
library(scater)
sce <- WTChimeraData(samples = 5, type = "processed")
sce <- logNormCounts(sce)
sce <- runPCA(sce)
sce <- runUMAP(sce, dimred = "PCA")

My sessionInfo( )

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Rome
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] scater_1.30.0                ggplot2_3.4.4                scuttle_1.12.0              
 [4] MouseGastrulationData_1.16.0 SpatialExperiment_1.12.0     SingleCellExperiment_1.24.0 
 [7] SummarizedExperiment_1.32.0  Biobase_2.62.0               GenomicRanges_1.54.1        
[10] GenomeInfoDb_1.38.1          IRanges_2.36.0               S4Vectors_0.40.1            
[13] BiocGenerics_0.48.1          MatrixGenerics_1.14.0        matrixStats_1.1.0           

loaded via a namespace (and not attached):
 [1] DBI_1.1.3                     bitops_1.0-7                 
 [3] gridExtra_2.3                 rlang_1.1.2                  
 [5] magrittr_2.0.3                compiler_4.3.0               
 [7] RSQLite_2.3.3                 DelayedMatrixStats_1.24.0    
 [9] png_0.1-8                     vctrs_0.6.4                  
[11] pkgconfig_2.0.3               crayon_1.5.2                 
[13] fastmap_1.1.1                 dbplyr_2.4.0                 
[15] magick_2.8.1                  XVector_0.42.0               
[17] ellipsis_0.3.2                utf8_1.2.4                   
[19] promises_1.2.1                ggbeeswarm_0.7.2             
[21] purrr_1.0.2                   bit_4.0.5                    
[23] xfun_0.41                     zlibbioc_1.48.0              
[25] cachem_1.0.8                  beachmat_2.18.0              
[27] blob_1.2.4                    later_1.3.1                  
[29] DelayedArray_0.28.0           BiocParallel_1.36.0          
[31] interactiveDisplayBase_1.40.0 irlba_2.3.5.1                
[33] parallel_4.3.0                R6_2.5.1                     
[35] Rcpp_1.0.11                   knitr_1.45                   
[37] FNN_1.1.3.2                   httpuv_1.6.12                
[39] Matrix_1.6-2                  tidyselect_1.2.0             
[41] viridis_0.6.4                 rstudioapi_0.15.0            
[43] abind_1.4-5                   yaml_2.3.7                   
[45] codetools_0.2-19              curl_5.1.0                   
[47] lattice_0.22-5                tibble_3.2.1                 
[49] shiny_1.7.5.1                 withr_2.5.2                  
[51] KEGGREST_1.42.0               BumpyMatrix_1.10.0           
[53] BiocFileCache_2.10.1          ExperimentHub_2.10.0         
[55] Biostrings_2.70.1             pillar_1.9.0                 
[57] BiocManager_1.30.22           filelock_1.0.2               
[59] generics_0.1.3                RCurl_1.98-1.13              
[61] BiocVersion_3.18.0            sparseMatrixStats_1.14.0     
[63] munsell_0.5.0                 scales_1.2.1                 
[65] xtable_1.8-4                  glue_1.6.2                   
[67] tools_4.3.0                   AnnotationHub_3.10.0         
[69] BiocNeighbors_1.20.0          ScaledMatrix_1.10.0          
[71] grid_4.3.0                    AnnotationDbi_1.64.1         
[73] colorspace_2.1-0              GenomeInfoDbData_1.2.11      
[75] beeswarm_0.4.0                BiocSingular_1.18.0          
[77] vipor_0.4.5                   rsvd_1.0.5                   
[79] cli_3.6.1                     rappdirs_0.3.3               
[81] fansi_1.0.5                   viridisLite_0.4.2            
[83] S4Arrays_1.2.0                dplyr_1.1.3                  
[85] uwot_0.1.16                   gtable_0.3.4                 
[87] digest_0.6.33                 ggrepel_0.9.4                
[89] SparseArray_1.2.2             rjson_0.2.21                 
[91] memoise_2.0.1                 htmltools_0.5.7              
[93] lifecycle_1.0.4               httr_1.4.7                   
[95] mime_0.12                     bit64_4.0.5   

Thanks

runUMAP scater Matrix • 6.4k views
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1
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mhem ▴ 10
@mhem-19823
Last seen 5 months ago
Germany

No, need to downgrade Matrix. Reinstalling irlba is sufficient, as I also wrote in StackOverflow https://stackoverflow.com/questions/77442906/runumap-code-error-after-merged-spatial-transcriptomic-objects, and stole from here: https://github.com/bwlewis/irlba/issues/70.

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0
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Yes, that's the right way to do it. But it's important to reinstall irlba from source: install.packages("irlba", type="source", force=TRUE).

See https://github.com/bwlewis/irlba/issues/70

If you are on a Mac, you'll need to have Xcode for this to work.

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@james-w-macdonald-5106
Last seen 1 minute ago
United States

Downgrading to Matrix_1.6-1 may help.

0
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Thanks, I saw the slack-overflow thread, but I don't think it solves the problem in the long run.

Also, I tried to do that in my GHA and the problem didn't solve.

I was hoping for an update of the scater package.

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0
Entering edit mode

As far as I can tell there's no problem with scater; the issue is with Matrix and irlba. There's not much I can do to fix two upstream dependencies.

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thanks for the clarification!

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