Sparse_Marginsum Error Running IterativeLSI

[S-Rajhans]

Hello, I'm trying to subset a cell population in mouse samples from my existing ArchR project and re-run clustering/dimensional analysis. I'm able to subset and create a new project but am consistently getting this error at the IterativeLSI step. I'm not too sure how to interpret the R_sparse_marginsum readout, so would really appreciate any insight.

I’ve checked the version of the Matrix package as well (1.6.1-1) so I can’t figure out what’s causing this.

ArchR-addIterativeLSI-3334516593484e-Date-2023-11-21_Time-13-14-39.699038.log

+   ArchRProj = duct2,
+   useMatrix = "TileMatrix", 
+   name = "IterativeLSI", 
+   iterations = 2, 
+   clusterParams = list( #See Seurat::FindClusters
+     resolution = c(0.4), 
+     sampleCells = 10000, 
+     n.start = 10
+   ), 
+   varFeatures = 25000, 
+   dimsToUse = 1:5,
+   force = TRUE
+ )
Checking Inputs...
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-3334516593484e-Date-2023-11-21_Time-13-14-39.699038.log
If there is an issue, please report to github with logFile!
2023-11-21 13:14:40.754279 : Computing Total Across All Features, 0.008 mins elapsed.
2023-11-21 13:14:42.515783 : Computing Top Features, 0.038 mins elapsed.
###########
2023-11-21 13:14:46.103587 : Running LSI (1 of 2) on Top Features, 0.097 mins elapsed.
###########
2023-11-21 13:14:46.138874 : Creating Partial Matrix, 0.098 mins elapsed.
2023-11-21 13:14:54.908973 : Computing LSI, 0.244 mins elapsed.
 
************************************************************
2023-11-21 13:14:55.197164 : ERROR Found in .computeLSI for  
LogFile = ArchRLogs/ArchR-addIterativeLSI-3334516593484e-Date-2023-11-21_Time-13-14-39.699038.log
 
<simpleError in .local(x, na.rm, dims, ...): object 'R_sparse_marginsum' not found>
 
************************************************************
 
 
************************************************************
2023-11-21 13:14:55.33462 : ERROR Found in .LSIPartialMatrix for  
LogFile = ArchRLogs/ArchR-addIterativeLSI-3334516593484e-Date-2023-11-21_Time-13-14-39.699038.log
 
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
 
************************************************************
 
Error in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList,  : 
  Exiting See Error Above```

[rcorces]

Hi @S-Rajhans! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.

__In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[lichtenj]

I have the same issue when running peakAnnoEnrichment(). It seems to have an underlying issue since my pipeline worked until a couple of weeks ago but now dies.

This is my sessionInfo()

R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.7 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /usr/local/intel/2022.1.2.146/mkl/2022.0.2/lib/intel64/libmkl_rt.so.2; LAPACK version 3.9.0

Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection

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: America/New_York
tzcode source: system (glibc)

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

other attached packages:
[1] rhdf5_2.46.0 SummarizedExperiment_1.32.0
[3] Biobase_2.62.0 MatrixGenerics_1.14.0
[5] Rcpp_1.0.11 Matrix_1.6-1
[7] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1
[9] IRanges_2.36.0 S4Vectors_0.40.1
[11] BiocGenerics_0.48.1 matrixStats_1.1.0
[13] data.table_1.14.8 stringr_1.5.1
[15] plyr_1.8.9 magrittr_2.0.3
[17] ggplot2_3.4.4 gtable_0.3.4
[19] gtools_3.9.4 gridExtra_2.3
[21] ArchR_1.0.2

loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 SparseArray_1.2.2
[4] bitops_1.0-7 stringi_1.8.1 lattice_0.22-5
[7] fansi_1.0.5 scales_1.2.1 abind_1.4-5
[10] cli_3.6.1 rlang_1.1.2 crayon_1.5.2
[13] XVector_0.42.0 munsell_0.5.0 withr_2.5.2
[16] DelayedArray_0.28.0 S4Arrays_1.2.0 parallel_4.3.0
[19] tools_4.3.0 dplyr_1.1.3 colorspace_2.1-0
[22] Rhdf5lib_1.24.0 GenomeInfoDbData_1.2.11 vctrs_0.6.4
[25] R6_2.5.1 lifecycle_1.0.4 zlibbioc_1.48.0
[28] pkgconfig_2.0.3 pillar_1.9.0 glue_1.6.2
[31] tibble_3.2.1 tidyselect_1.2.0 rhdf5filters_1.14.1
[34] Cairo_1.6-1 compiler_4.3.0 RCurl_1.98-1.13

[S-Rajhans]

@lichtenj I know that recent updates to Matrix have been causing problems across its dependencies (Seurat, Monocle, irlba) but it seems even the old 1.6.1 versions we're using are causing similar errors.

[yimingsun12138]

@lichtenj I know that recent updates to Matrix have been causing problems across its dependencies (Seurat, Monocle, irlba) but it seems even the old 1.6.1 versions we're using are causing similar errors.

Matrix 1.6-1 works for me, but I found that Seurat 5 is depend on Matrix 1.6-3. Maybe your problem is caused by Seurat update? I used callr to call a seperated R session with old version Seurat Matrix installed libpath, it worked well.

[lichtenj]

@lichtenj I know that recent updates to Matrix have been causing problems across its dependencies (Seurat, Monocle, irlba) but it seems even the old 1.6.1 versions we're using are causing similar errors.

Matrix 1.6-1 works for me, but I found that Seurat 5 is depend on Matrix 1.6-3. Maybe your problem is caused by Seurat update? I used callr to call a seperated R session with old version Seurat Matrix installed libpath, it worked well.

Thanks, I tried to force the versions of Seurat (4.4.0), SeuratObject (4.1.4) and Matrix (1.6.1.1) to previous states but I am still running into the same error. Any chance you could post the latest sessionInfo() that worked for you?

[yimingsun12138]

@lichtenj I know that recent updates to Matrix have been causing problems across its dependencies (Seurat, Monocle, irlba) but it seems even the old 1.6.1 versions we're using are causing similar errors.

Matrix 1.6-1 works for me, but I found that Seurat 5 is depend on Matrix 1.6-3. Maybe your problem is caused by Seurat update? I used callr to call a seperated R session with old version Seurat Matrix installed libpath, it worked well.

Thanks, I tried to force the versions of Seurat (4.4.0), SeuratObject (4.1.4) and Matrix (1.6.1.1) to previous states but I am still running into the same error. Any chance you could post the latest sessionInfo() that worked for you?

Here is my sessionInfo(), hope it helps:

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] uwot_0.1.16                 nabor_0.5.0                 rhdf5_2.46.0                SummarizedExperiment_1.32.0
 [5] Biobase_2.62.0              MatrixGenerics_1.14.0       Rcpp_1.0.11                 GenomicRanges_1.54.1       
 [9] GenomeInfoDb_1.38.1         IRanges_2.36.0              S4Vectors_0.40.1            BiocGenerics_0.48.1        
[13] matrixStats_1.1.0           data.table_1.14.8           stringr_1.5.1               plyr_1.8.9                 
[17] magrittr_2.0.3              gtable_0.3.4                gtools_3.9.5                gridExtra_2.3              
[21] ArchR_1.0.2                 Matrix_1.6-1                ggplot2_3.4.4               SeuratObject_4.1.4         
[25] Seurat_4.4.0               

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3       rstudioapi_0.15.0        jsonlite_1.8.7           spatstat.utils_3.0-4     farver_2.1.1            
  [6] BiocIO_1.12.0            zlibbioc_1.48.0          vctrs_0.6.4              ROCR_1.0-11              Rsamtools_2.18.0        
 [11] Cairo_1.6-1              spatstat.explore_3.2-5   RCurl_1.98-1.13          S4Arrays_1.2.0           htmltools_0.5.7         
 [16] Rhdf5lib_1.24.0          SparseArray_1.2.2        sctransform_0.4.1        parallelly_1.36.0        KernSmooth_2.23-22      
 [21] htmlwidgets_1.6.3        ica_1.0-3                plotly_4.10.3            zoo_1.8-12               GenomicAlignments_1.38.0
 [26] igraph_1.5.1             mime_0.12                lifecycle_1.0.4          pkgconfig_2.0.3          R6_2.5.1                
 [31] fastmap_1.1.1            GenomeInfoDbData_1.2.11  fitdistrplus_1.1-11      future_1.33.0            shiny_1.8.0             
 [36] digest_0.6.33            colorspace_2.1-0         patchwork_1.1.3          ps_1.7.5                 tensor_1.5              
 [41] irlba_2.3.5.1            labeling_0.4.3           progressr_0.14.0         fansi_1.0.5              spatstat.sparse_3.0-3   
 [46] httr_1.4.7               polyclip_1.10-6          abind_1.4-5              compiler_4.3.2           withr_2.5.2             
 [51] BiocParallel_1.36.0      MASS_7.3-60              DelayedArray_0.28.0      rjson_0.2.21             tools_4.3.2             
 [56] lmtest_0.9-40            httpuv_1.6.12            future.apply_1.11.0      goftest_1.2-3            glue_1.6.2              
 [61] restfulr_0.0.15          callr_3.7.3              rhdf5filters_1.14.1      nlme_3.1-163             promises_1.2.1          
 [66] Rtsne_0.16               cluster_2.1.4            reshape2_1.4.4           generics_0.1.3           spatstat.data_3.0-3     
 [71] tidyr_1.3.0              sp_2.1-1                 utf8_1.2.4               XVector_0.42.0           spatstat.geom_3.2-7     
 [76] RcppAnnoy_0.0.21         ggrepel_0.9.4            RANN_2.6.1               pillar_1.9.0             later_1.3.1             
 [81] splines_4.3.2            dplyr_1.1.4              lattice_0.22-5           rtracklayer_1.62.0       survival_3.5-7          
 [86] deldir_1.0-9             tidyselect_1.2.0         Biostrings_2.70.1        miniUI_0.1.1.1           pbapply_1.7-2           
 [91] scattermore_1.2          stringi_1.8.1            yaml_2.3.7               lazyeval_0.2.2           codetools_0.2-19        
 [96] tibble_3.2.1             cli_3.6.1                xtable_1.8-4             reticulate_1.34.0        munsell_0.5.0           
[101] processx_3.8.2           globals_0.16.2           spatstat.random_3.2-1    png_0.1-8                XML_3.99-0.15           
[106] ellipsis_0.3.2           bitops_1.0-7             listenv_0.9.0            viridisLite_0.4.2        scales_1.2.1            
[111] ggridges_0.5.4           crayon_1.5.2             leiden_0.4.3.1           purrr_1.0.2              rlang_1.1.2             
[116] cowplot_1.1.1

[YesseniaCQ]

我知道最近对 Matrix 的更新在其依赖项（Seurat、Monocle、irlba）中引起了问题，但似乎即使是我们使用的旧 1.6.1 版本也会导致类似的错误。

矩阵 1.6-1 对我有用，但我发现修拉 5 依赖于矩阵 1.6-3。也许您的问题是由修拉更新引起的？我使用 callr 调用一个单独的 R 会话，旧版本的 Seurat Matrix 安装了 libpath，效果很好。

谢谢，我试图将 Seurat （4.4.0）、SeuratObject （4.1.4） 和 Matrix （1.6.1.1） 的版本强制到以前的状态，但我仍然遇到同样的错误。你有没有机会发布对你有用的最新sessionInfo（）？

我知道最近对 Matrix 的更新在其依赖项（Seurat、Monocle、irlba）中引起了问题，但似乎即使是我们使用的旧 1.6.1 版本也会导致类似的错误。

矩阵 1.6-1 对我有用，但我发现修拉 5 依赖于矩阵 1.6-3。也许您的问题是由修拉更新引起的？我使用 callr 调用一个单独的 R 会话，旧版本的 Seurat Matrix 安装了 libpath，效果很好。

谢谢，我试图将 Seurat （4.4.0）、SeuratObject （4.1.4） 和 Matrix （1.6.1.1） 的版本强制到以前的状态，但我仍然遇到同样的错误。你有没有机会发布对你有用的最新sessionInfo（）？

@lichtenj I know that recent updates to Matrix have been causing problems across its dependencies (Seurat, Monocle, irlba) but it seems even the old 1.6.1 versions we're using are causing similar errors.

Matrix 1.6-1 works for me, but I found that Seurat 5 is depend on Matrix 1.6-3. Maybe your problem is caused by Seurat update? I used callr to call a seperated R session with old version Seurat Matrix installed libpath, it worked well.

Thanks, I tried to force the versions of Seurat (4.4.0), SeuratObject (4.1.4) and Matrix (1.6.1.1) to previous states but I am still running into the same error. Any chance you could post the latest sessionInfo() that worked for you?

I have the same issue when I running IterativeLSI (seurat_4.4.0、seuratobject_4.1.4、archr_1.0.2、matrix_1.6.1.1). Have you resolved it now?Waiting for your message hopefully...

[yimingsun12138]

我知道最近对 Matrix 的更新在其依赖项（Seurat、Monocle、irlba）中引起了问题，但似乎即使是我们使用的旧 1.6.1 版本也会导致类似的错误。

矩阵 1.6-1 对我有用，但我发现修拉 5 依赖于矩阵 1.6-3。也许您的问题是由修拉更新引起的？我使用 callr 调用一个单独的 R 会话，旧版本的 Seurat Matrix 安装了 libpath，效果很好。

谢谢，我试图将 Seurat （4.4.0）、SeuratObject （4.1.4） 和 Matrix （1.6.1.1） 的版本强制到以前的状态，但我仍然遇到同样的错误。你有没有机会发布对你有用的最新sessionInfo（）？

我知道最近对 Matrix 的更新在其依赖项（Seurat、Monocle、irlba）中引起了问题，但似乎即使是我们使用的旧 1.6.1 版本也会导致类似的错误。

矩阵 1.6-1 对我有用，但我发现修拉 5 依赖于矩阵 1.6-3。也许您的问题是由修拉更新引起的？我使用 callr 调用一个单独的 R 会话，旧版本的 Seurat Matrix 安装了 libpath，效果很好。

谢谢，我试图将 Seurat （4.4.0）、SeuratObject （4.1.4） 和 Matrix （1.6.1.1） 的版本强制到以前的状态，但我仍然遇到同样的错误。你有没有机会发布对你有用的最新sessionInfo（）？

@lichtenj I know that recent updates to Matrix have been causing problems across its dependencies (Seurat, Monocle, irlba) but it seems even the old 1.6.1 versions we're using are causing similar errors.

Matrix 1.6-1 works for me, but I found that Seurat 5 is depend on Matrix 1.6-3. Maybe your problem is caused by Seurat update? I used callr to call a seperated R session with old version Seurat Matrix installed libpath, it worked well.

Thanks, I tried to force the versions of Seurat (4.4.0), SeuratObject (4.1.4) and Matrix (1.6.1.1) to previous states but I am still running into the same error. Any chance you could post the latest sessionInfo() that worked for you?

I have the same issue when I running IterativeLSI (seurat_4.4.0、seuratobject_4.1.4、archr_1.0.2、matrix_1.6.1.1). Have you resolved it now?Waiting for your message hopefully...

My R session works well all the time, can you show me your error message and your operation system?

[emidalla]

Hello, having exactly the same error (Error in .local(x, na.rm, dims, ...): object 'R_sparse_marginsum' not found) while running the 'peakAnnoEnrichment' function.
Here is my sessionInfo:

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3;  LAPACK version 3.9.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
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: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] tensor_1.5                        abind_1.4-5                      
 [3] motifmatchr_1.24.0                JASPAR2020_0.99.10               
 [5] chromVARmotifs_0.2.0              presto_1.0.0                     
 [7] magick_2.8.2                      ggrepel_0.9.5                    
 [9] circlize_0.4.15                   ComplexHeatmap_2.18.0            
[11] pheatmap_1.0.12                   harmony_1.2.0                    
[13] uwot_0.1.16                       nabor_0.5.0                      
[15] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.70.1                  
[17] rtracklayer_1.62.0                BiocIO_1.12.0                    
[19] Biostrings_2.70.2                 XVector_0.42.0                   
[21] RSpectra_0.16-1                   irlba_2.3.5.1                    
[23] repr_1.1.6                        anndata_0.7.5.6                  
[25] SeuratObject_4.1.4                Seurat_4.4.0                     
[27] hexbin_1.28.3                     devtools_2.4.5                   
[29] usethis_2.2.2                     rhdf5_2.46.1                     
[31] SummarizedExperiment_1.32.0       Biobase_2.62.0                   
[33] MatrixGenerics_1.14.0             Rcpp_1.0.12                      
[35] Matrix_1.6-1.1                    GenomicRanges_1.54.1             
[37] GenomeInfoDb_1.38.5               IRanges_2.36.0                   
[39] S4Vectors_0.40.2                  BiocGenerics_0.48.1              
[41] matrixStats_1.2.0                 data.table_1.15.0                
[43] stringr_1.5.1                     plyr_1.8.9                       
[45] magrittr_2.0.3                    ggplot2_3.4.4                    
[47] gtable_0.3.4                      gtools_3.9.5                     
[49] gridExtra_2.3                     ArchR_1.0.2                      

loaded via a namespace (and not attached):
  [1] fs_1.6.3                    spatstat.sparse_3.0-3      
  [3] bitops_1.0-7                DirichletMultinomial_1.44.0
  [5] TFBSTools_1.40.0            httr_1.4.7                 
  [7] RColorBrewer_1.1-3          doParallel_1.0.17          
  [9] profvis_0.3.8               tools_4.3.2                
 [11] sctransform_0.4.1           utf8_1.2.4                 
 [13] R6_2.5.1                    lazyeval_0.2.2             
 [15] rhdf5filters_1.14.1         GetoptLong_1.0.5           
 [17] urlchecker_1.0.1            withr_3.0.0                
 [19] sp_2.1-3                    progressr_0.14.0           
 [21] cli_3.6.2                   Cairo_1.6-2                
 [23] spatstat.explore_3.2-6      labeling_0.4.3             
 [25] spatstat.data_3.0-4         readr_2.1.5                
 [27] ggridges_0.5.6              pbapply_1.7-2              
 [29] Rsamtools_2.18.0            pbdZMQ_0.3-11              
 [31] R.utils_2.12.3              parallelly_1.36.0          
 [33] sessioninfo_1.2.2           RSQLite_2.3.5              
 [35] generics_0.1.3              shape_1.4.6                
 [37] ica_1.0-3                   spatstat.random_3.2-2      
 [39] dplyr_1.1.4                 GO.db_3.18.0               
 [41] fansi_1.0.6                 R.methodsS3_1.8.2          
 [43] lifecycle_1.0.4             yaml_2.3.8                 
 [45] SparseArray_1.2.3           Rtsne_0.17                 
 [47] blob_1.2.4                  promises_1.2.1             
 [49] crayon_1.5.2                dir.expiry_1.10.0          
 [51] miniUI_0.1.1.1              lattice_0.22-5             
 [53] cowplot_1.1.3               annotate_1.80.0            
 [55] KEGGREST_1.42.0             pillar_1.9.0               
 [57] rjson_0.2.21                future.apply_1.11.1        
 [59] codetools_0.2-19            leiden_0.4.3.1             
 [61] glue_1.7.0                  remotes_2.4.2.1            
 [63] vctrs_0.6.5                 png_0.1-8                  
 [65] poweRlaw_0.80.0             assertthat_0.2.1           
 [67] cachem_1.0.8                S4Arrays_1.2.0             
 [69] mime_0.12                   pracma_2.4.4               
 [71] survival_3.5-7              SingleCellExperiment_1.24.0
 [73] iterators_1.0.14            shinythemes_1.2.0          
 [75] ellipsis_0.3.2              fitdistrplus_1.1-11        
 [77] ROCR_1.0-11                 nlme_3.1-164               
 [79] bit64_4.0.5                 filelock_1.0.3             
 [81] RcppAnnoy_0.0.22            KernSmooth_2.23-22         
 [83] DBI_1.2.1                   colorspace_2.1-0           
 [85] seqLogo_1.68.0              tidyselect_1.2.0           
 [87] bit_4.0.5                   compiler_4.3.2             
 [89] curl_5.2.0                  hdf5r_1.3.9                
 [91] basilisk.utils_1.14.1       rhandsontable_0.3.8        
 [93] DelayedArray_0.28.0         plotly_4.10.4              
 [95] caTools_1.18.2              scales_1.3.0               
 [97] lmtest_0.9-40               rappdirs_0.3.3             
 [99] digest_0.6.34               goftest_1.2-3              
[101] spatstat.utils_3.0-4        basilisk_1.14.3            
[103] RhpcBLASctl_0.23-42         htmltools_0.5.7            
[105] pkgconfig_2.0.3             base64enc_0.1-3            
[107] fastmap_1.1.1               rlang_1.1.3                
[109] GlobalOptions_0.1.2         htmlwidgets_1.6.4          
[111] shiny_1.8.0                 farver_2.1.1               
[113] zoo_1.8-12                  jsonlite_1.8.8             
[115] BiocParallel_1.36.0         R.oo_1.26.0                
[117] RCurl_1.98-1.14             GenomeInfoDbData_1.2.11    
[119] dotCall64_1.1-1             patchwork_1.2.0            
[121] Rhdf5lib_1.24.2             IRkernel_1.3.2             
[123] munsell_0.5.0               reticulate_1.35.0          
[125] stringi_1.8.3               zlibbioc_1.48.0            
[127] MASS_7.3-60.0.1             pkgbuild_1.4.3             
[129] listenv_0.9.1               CNEr_1.38.0                
[131] deldir_2.0-2                IRdisplay_1.1              
[133] splines_4.3.2               hms_1.1.3                  
[135] igraph_1.4.1                uuid_1.2-0                 
[137] spatstat.geom_3.2-8         reshape2_1.4.4             
[139] pkgload_1.3.4               TFMPvalue_0.0.9            
[141] XML_3.99-0.16.1             evaluate_0.23              
[143] BiocManager_1.30.22         tzdb_0.4.0                 
[145] foreach_1.5.2               httpuv_1.6.14              
[147] RANN_2.6.1                  tidyr_1.3.1                
[149] purrr_1.0.2                 polyclip_1.10-6            
[151] future_1.33.1               clue_0.3-65                
[153] scattermore_1.2             xtable_1.8-4               
[155] restfulr_0.0.15             later_1.3.2                
[157] viridisLite_0.4.2           tibble_3.2.1               
[159] AnnotationDbi_1.64.1        memoise_2.0.1              
[161] GenomicAlignments_1.38.2    cluster_2.1.6              
[163] globals_0.16.2      

[nigiord]

The problem occurs when executing this line in my case:

ArchR/R/AnnotationPeaks.R

Line 844 in d9e741c

nO <- Matrix::colSums(assay(regionMat))

Basically it looks like yet another problem with the Matrix package since version 1.6-2 (see #2050 for instance), but apparently it also occurs with 1.6-1.1.

The error is raised if you try to apply Matrix::colSums on any sparse Matrix, so it is not directly caused by ArchR. For instance:

Matrix::rsparsematrix(10, 5, 0.2) |> Matrix::colSums()

Error in .local(x, na.rm, dims, ...) :
object 'R_sparse_marginsum' not found

Solution

The real culprit is apparently the package TFBSTools.

Run the following:

BiocManager::install("TFBSTools", type = "source", force = TRUE)

then restart your R session. More details and explanation here: satijalab/seurat#8202 (comment) but I’m not sure why the problem occurs with Matrix 1.6.1-1 though.

[nansne]

The problem occurs when executing this line in my case:

ArchR/R/AnnotationPeaks.R

Line 844 in d9e741c

nO <- Matrix::colSums(assay(regionMat))

Basically it looks like yet another problem with the Matrix package since version 1.6-2 (see #2050 for instance), but apparently it also occurs with 1.6-1.1.

The error is raised if you try to apply on any sparse Matrix, so it is not directly caused by ArchR. For instance:Matrix::colSums

Matrix::rsparsematrix(10, 5, 0.2) |> Matrix::colSums()

Error in .local(x, na.rm, dims, ...) :
object 'R_sparse_marginsum' not found

Solution

The real culprit is apparently the package TFBSTools.

Run the following:

BiocManager::install("TFBSTools", type = "source", force = TRUE)

then restart your R session. More details and explanation here: satijalab/seurat#8202 (comment) but I’m not sure why the problem occurs with Matrix 1.6.1-1 though.

Yeah! It works to my enviroment.
Thank you!