Single-cell data integration error

jnmark commented 4 years ago

Hello,

I am trying to re-execute the spatial vignette here: https://satijalab.org/seurat/v3.2/spatial_vignette.html

(I specified re-execute because I ran through it successfully a month ago without errors)

But now, while performing the integration with sc-RNA step, I get the following error for the Allen reference atlas processing step:

allen_reference <- SCTransform(allen_reference, ncells = 3000, verbose = FALSE) %>% RunPCA(verbose = FALSE) %>% RunUMAP(dims = 1:30) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': missing value where TRUE/FALSE needed DimPlot(allen_reference, reduction = "umap", group.by = "subclass", label = TRUE) Error: Cannot find 'umap' in this Seurat object

I haven't made any changes to the code or the data since a month ago. I also re-downloaded the data, Seurat today in order to make sure everything was up to date (just FYI, I tried the newest Seurat v4.0 as well as v3.2.2), but the error still persists.

Any clue what might have happened? Thanks!

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

ChristophH commented 4 years ago

This looks like it's related to a bug in the sctransform package. Could you install sctransform from the develop branch and re-try? remotes::install_github("ChristophH/sctransform@develop")

BatLaB-cell commented 4 years ago

Hello, I have the exact same error with SCTransform function.

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': missing value where TRUE/FALSE needed

I am using Seurat v4 and I 've installed SCTransform from the develop branch but it does not work. Any other idea?

davidyanglee commented 4 years ago

Same error using SCTransform (during future_lapply). Running Seurat v4 as well.

lixin4306ren commented 4 years ago

I'm using Seurat V3.2.2 and got the same error.

mariaimaz commented 4 years ago

Same error here, Seurat V3.2.2 also. Worked fine on previous workflow run through.

shokohirosue commented 4 years ago

I got the same error, tried V3.2.1 and V3.2.2

ccruizm commented 4 years ago

I also got the same error. Any solution? Thanks in advance

zjzace commented 4 years ago

This bug can be fixed by downgrading the sctranform package to the old version, v0.3.0. This works well for me.

install.packages("v0.3.0.tar.gz", repos = NULL, type="source")

ChristophH commented 4 years ago

I cannot reproduce the error with Seurat 3.9.9.9008 (from the seurat release/4.0.0 branch) and sctransform 0.3.1.9002 (from the sctransform develop branch).

If you are on sctransform v0.3.1 (the current CRAN release) you could also change the SCTransform call to SCTransform(allen_reference, ncells = 3000, verbose = FALSE, method = 'glmGamPoi') This will use a different method for parameter estimation during normalization. Note that for this to work the glmGamPoi package needs to be installed.

bassanio commented 4 years ago

Hi,

I am getting error the same error.

As a test I used the same data set in Seurat 4 and Seurat 3. Down below is the Commands,sessionInfo and error I got

Seurat 4

MyData[["percent.mt"]] <- PercentageFeatureSet(MyData, pattern = "^MT-")
MyData <- subset(MyData, subset = nFeature_RNA > 200 & nFeature_RNA < 5200 & percent.mt < 10)

MyData <- SCTransform(MyData, verbose = FALSE)

Error & Session info

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': missing value where TRUE/FALSE needed
Calls: SCTransform ... resolve.list -> signalConditionsASAP -> signalConditions
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: Software/Seurat4/lib/libopenblasp-r0.3.12.so

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       

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

other attached packages:
[1] patchwork_1.0.1       ggplot2_3.3.2         SeuratDisk_0.0.0.9013
[4] Seurat_3.9.9.9008    

loaded via a namespace (and not attached):
 [1] nlme_3.1-150          matrixStats_0.57.0    bit64_4.0.5          
 [4] RcppAnnoy_0.0.16      RColorBrewer_1.1-2    httr_1.4.2           
 [7] sctransform_0.3.1     tools_4.0.3           R6_2.5.0             
[10] irlba_2.3.3           rpart_4.1-15          KernSmooth_2.23-18   
[13] uwot_0.1.8.9001       lazyeval_0.2.2        mgcv_1.8-33          
[16] colorspace_1.4-1      withr_2.3.0           tidyselect_1.1.0     
[19] gridExtra_2.3         bit_4.0.4             compiler_4.0.3       
[22] cli_2.1.0             hdf5r_1.3.3           plotly_4.9.2.1       
[25] scales_1.1.1          lmtest_0.9-38         spatstat.data_1.4-3  
[28] ggridges_0.5.2        pbapply_1.4-3         spatstat_1.64-1      
[31] goftest_1.2-2         stringr_1.4.0         digest_0.6.27        
[34] spatstat.utils_1.17-0 pkgconfig_2.0.3       htmltools_0.5.0      
[37] fastmap_1.0.1         htmlwidgets_1.5.2     rlang_0.4.8          
[40] shiny_1.5.0           generics_0.1.0        zoo_1.8-8            
[43] jsonlite_1.7.1        ica_1.0-2             dplyr_1.0.2          
[46] magrittr_1.5          Matrix_1.2-18         fansi_0.4.1          
[49] Rcpp_1.0.5            munsell_0.5.0         abind_1.4-5          
[52] reticulate_1.18       lifecycle_0.2.0       stringi_1.5.3        
[55] MASS_7.3-53           Rtsne_0.15            plyr_1.8.6           
[58] grid_4.0.3            parallel_4.0.3        listenv_0.8.0        
[61] promises_1.1.1        ggrepel_0.8.2         crayon_1.3.4         
[64] miniUI_0.1.1.1        deldir_0.1-29         lattice_0.20-41      
[67] cowplot_1.1.0         splines_4.0.3         tensor_1.5           
[70] pillar_1.4.6          igraph_1.2.6          future.apply_1.6.0   
[73] reshape2_1.4.4        codetools_0.2-16      leiden_0.3.4         
[76] glue_1.4.2            data.table_1.13.2     png_0.1-7            
[79] vctrs_0.3.4           httpuv_1.5.4          gtable_0.3.0         
[82] RANN_2.6.1            purrr_0.3.4           polyclip_1.10-0      
[85] tidyr_1.1.2           assertthat_0.2.1      future_1.19.1        
[88] rsvd_1.0.3            mime_0.9              xtable_1.8-4         
[91] later_1.1.0.1         survival_3.2-7        viridisLite_0.3.0    
[94] tibble_3.0.4          cluster_2.1.0         globals_0.13.1       
[97] fitdistrplus_1.1-1    ellipsis_0.3.1        ROCR_1.0-11

Seurat 3

MyData[["percent.mt"]] <- PercentageFeatureSet(MyData, pattern = "^MT-")
MyData <- subset(MyData, subset = nFeature_RNA > 200 & nFeature_RNA < 5200 & percent.mt < 10)
MyData <- SCTransform(MyData, vars.to.regress = "percent.mt", verbose = FALSE)

Session info no error

R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: Seurat/lib/R/lib/libRblas.so
LAPACK: Seurat/lib/R/lib/libRlapack.so

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       

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

other attached packages:
[1] ggplot2_3.2.1      cowplot_1.0.0      RColorBrewer_1.1-2 dplyr_0.8.3       
[5] sctransform_0.2.0  Seurat_3.1.1      

loaded via a namespace (and not attached):
 [1] nlme_3.1-137        tsne_0.1-3          bitops_1.0-6       
 [4] RcppAnnoy_0.0.14    httr_1.4.1          tools_3.5.0        
 [7] backports_1.1.5     R6_2.2.2            irlba_2.3.3        
[10] KernSmooth_2.23-15  uwot_0.1.4          lazyeval_0.2.2     
[13] colorspace_1.4-1    withr_2.1.2         npsurv_0.4-0       
[16] tidyselect_0.2.5    gridExtra_2.3       compiler_3.5.0     
[19] plotly_4.9.1        caTools_1.17.1.2    scales_1.0.0       
[22] lmtest_0.9-37       ggridges_0.5.1      pbapply_1.4-2      
[25] stringr_1.4.0       digest_0.6.22       R.utils_2.9.0      
[28] pkgconfig_2.0.3     htmltools_0.4.0     bibtex_0.4.2       
[31] htmlwidgets_1.5.1   rlang_0.4.1         zoo_1.8-6          
[34] jsonlite_1.6        ica_1.0-2           gtools_3.8.1       
[37] R.oo_1.23.0         magrittr_1.5        Matrix_1.2-14      
[40] Rcpp_1.0.3          munsell_0.5.0       ape_5.3            
[43] reticulate_1.13     lifecycle_0.1.0     R.methodsS3_1.7.1  
[46] stringi_1.4.3       gbRd_0.4-11         MASS_7.3-49        
[49] gplots_3.0.1.1      Rtsne_0.15          plyr_1.8.4         
[52] grid_3.5.0          parallel_3.5.0      gdata_2.18.0       
[55] listenv_0.7.0       ggrepel_0.8.1       crayon_1.3.4       
[58] lattice_0.20-35     splines_3.5.0       SDMTools_1.1-221.1 
[61] zeallot_0.1.0       pillar_1.4.2        igraph_1.2.4.1     
[64] future.apply_1.3.0  reshape2_1.4.3      codetools_0.2-15   
[67] leiden_0.3.1        glue_1.3.1          lsei_1.2-0         
[70] metap_1.1           data.table_1.12.6   RcppParallel_4.4.4 
[73] vctrs_0.2.0         png_0.1-7           Rdpack_0.11-0      
[76] gtable_0.3.0        RANN_2.6.1          purrr_0.3.3        
[79] tidyr_1.0.0         future_1.15.0       assertthat_0.2.1   
[82] rsvd_1.0.2          survival_2.41-3     viridisLite_0.3.0  
[85] tibble_2.1.3        cluster_2.0.7-1     globals_0.12.4     
[88] fitdistrplus_1.0-14 ROCR_1.0-7

Updating: When I used the result of SCT transform from the Seurat 3 version and input it to the Seurat 4 the analysis finished without errors

MyData <- readRDS("Batch1_2Samples_SCTransform.Rds")
reference <- LoadH5Seurat("Seurat4/PBMC_REF/pbmc_multimodal.h5seurat")

anchors <- FindTransferAnchors(
  reference = reference,
  query = MyData,
  normalization.method = "SCT",
  reference.reduction = "spca",
  dims = 1:50
)

MyData <- MapQuery(
  anchorset = anchors,
  query = MyData,
  reference = reference,
  refdata = list(
    celltype.l1 = "celltype.l1",
    celltype.l2 = "celltype.l2",
    predicted_ADT = "ADT"
  ),
  reference.reduction = "spca", 
  reduction.model = "wnn.umap"
)

saveRDS (MyData, file="MyData.Rds")

yuhanH commented 3 years ago

Hi, this SCTransform error should be fixed in sctransform version v0.3.2 If you still have the error when you use the version v0.3.2 of sctransform, i will reopen this issue.

denvercal1234GitHub commented 3 years ago

Hi @yuhanH - When I run SCTransform() on my Seurat object. It still shows the error. Would you mind helping me address it? Thank you so much!

yuhanH commented 3 years ago

Hi, what is your sctransform package version?

denvercal1234GitHub commented 3 years ago

Hi @yuhanH - It is Seurat_3.2.2 and sctransform_0.3.1.

I tried to install the 3.2. but it does not work. Are the codes below the right ones to use? Thank you so much!

remotes::install_github("ChristophH/sctransform@develop")

or? 

devtools::install_github(repo = 'ChristophH/sctransform')

sessionInfo("Seurat") R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS 10.16

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

attached base packages: character(0)

other attached packages: [1] Seurat_3.2.2

loaded via [1] utils_4.0.2 [5] RColorBrewer_1.1-2 [9] R6_2.4.1 [13] uwot_0.1.8 [17] withr_2.3.0 [21] pastecs_1.3.21 [25] scales_1.1.1 [29] pbapply_1.4-3 [33] digest_0.6.27 [37] fastmap_1.0.1 [41] rstudioapi_0.11 [45] jsonlite_1.7.1 [49] magrittr_1.5 [53] munsell_0.5.0 [57] stringi_1.5.3 [61] grid_4.0.2 [65] promises_1.1.1 [69] methods_4.0.2 [73] splines_4.0.2 [77] boot_1.3-25 [81] leiden_0.3.3 [85] vctrs_0.3.4 [89] RANN_2.6.1 [93] future_1.19.1 [97] xtable_1.8-4 [101] tibble_3.0.4 [105] fitdistrplus_1.1-1 a namespace (and not attached): nlme_3.1-150 matrixStats_0.57.0 RcppAnnoy_0.0.16
httr_1.4.2 sctransform_0.3.1 tools_4.0.2
irlba_2.3.3 rpart_4.1-15 KernSmooth_2.23-17
lazyeval_0.2.2 mgcv_1.8-33 colorspace_1.4-1
tidyselect_1.1.0 gridExtra_2.3 compiler_4.0.2
datasets_4.0.2 plotly_4.9.2.1 base_4.0.2
lmtest_0.9-38 spatstat.data_1.4-3 ggridges_0.5.2
spatstat_1.64-1 goftest_1.2-2 stringr_1.4.0
spatstat.utils_1.17-0 pkgconfig_2.0.3 htmltools_0.5.0
grDevices_4.0.2 htmlwidgets_1.5.2 rlang_0.4.8
shiny_1.5.0 generics_0.0.2 zoo_1.8-8
gtools_3.8.2 ica_1.0-2 dplyr_1.0.2
patchwork_1.0.1 Matrix_1.2-18 Rcpp_1.0.5
abind_1.4-5 reticulate_1.18 lifecycle_0.2.0
MASS_7.3-53 Rtsne_0.15 plyr_1.8.6
gdata_2.18.0 parallel_4.0.2 listenv_0.8.0
ggrepel_0.8.2 crayon_1.3.4 miniUI_0.1.1.1
deldir_0.1-29 lattice_0.20-41 cowplot_1.1.0
tensor_1.5 pillar_1.4.6 igraph_1.2.6
future.apply_1.6.0 reshape2_1.4.4 codetools_0.2-16
glue_1.4.2 data.table_1.13.2 png_0.1-7
httpuv_1.5.4 graphics_4.0.2 gtable_0.3.0
purrr_0.3.4 polyclip_1.10-0 tidyr_1.1.2
ggplot2_3.3.2 rsvd_1.0.3 mime_0.9
later_1.1.0.1 survival_3.2-7 viridisLite_0.3.0
stats_4.0.2 cluster_2.1.0 globals_0.13.1
ellipsis_0.3.1 ROCR_1.0-11

yuhanH commented 3 years ago

The version 0.3.2 of sctransform is on CRAN now. You can install it by install.packages. install.packages("sctransform")

denvercal1234GitHub commented 3 years ago

Thank you, Yuhan!

bobermayer commented 3 years ago

Hi, I'm getting the error with Seurat 4.0.0 and sctransform 0.3.2 when trying to use the Multimodel Reference Mapping vignette with the most recent pbmc_multimodal.h5seurat object

reference <- LoadH5Seurat("pbmc_multimodal.h5seurat")
InstallData('pbmc3k')
pbmc3k <- SCTransform(pbmc3k, verbose = FALSE)
anchors <- FindTransferAnchors(
  reference = reference,
  query = pbmc3k,
  normalization.method = "SCT",
  reference.reduction = "spca",
  dims = 1:50
)
Normalizing query using reference SCT model
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': undefined columns selected

here's my sessionInfo:

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
[1] sctransform_0.3.2       pbmc3k.SeuratData_3.1.4 SeuratData_0.2.1        ggplot2_3.3.3          
[5] SeuratDisk_0.0.0.9015   SeuratObject_4.0.0      Seurat_4.0.0

downgrading to sctransform v3.0 is somehow not compatible with Seurat v4. any ideas? it used to work with Seurat 3.9xxx

I tried this also using a slightly different setup (rstudio server vs. singularity image), now I get the error

Error in slot(object = reference[[reference.assay]], name = "SCTModel.list") : 
  no slot of name "SCTModel.list" for this object of class "Assay"

here the sessionInfo. possibly the slightly different versions of SeuratDisk make it so the SCTModel.list is not properly read

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /opt/R/4.0.3/lib/R/lib/libRblas.so
LAPACK: /opt/R/4.0.3/lib/R/lib/libRlapack.so

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       

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

other attached packages:
[1] sctransform_0.3.2       pbmc3k.SeuratData_3.1.4 SeuratData_0.2.1        ggplot2_3.3.3          
[5] SeuratDisk_0.0.0.9014   SeuratObject_4.0.0      Seurat_4.0.0

yuhanH commented 3 years ago

HI, @bobermayer I would suggest you update your SeuratDisk version to the latest one 0.0.0.9018. The old version of SeuratDisk cannot load the H5Seurat with SCTAssay.

bobermayer commented 3 years ago

thanks, great, that works indeed, on both systems.

Lopo358 commented 3 years ago

I am getting the same error, but when running immune.combined <- IntegrateData(anchorset = immune.anchors)

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': invalid character indexing

sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
 [1] sctransform_0.3.2.9006      biomaRt_2.46.3              forcats_0.5.1              
 [4] stringr_1.4.0               dplyr_1.0.6                 purrr_0.3.4                
 [7] readr_1.4.0                 tidyr_1.1.3                 tibble_3.1.2               
[10] tidyverse_1.3.1             cowplot_1.1.1               scater_1.18.6              
[13] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 GenomicRanges_1.42.0       
[16] GenomeInfoDb_1.26.7         IRanges_2.24.1              S4Vectors_0.28.1           
[19] MatrixGenerics_1.2.1        matrixStats_0.59.0          metap_1.4                  
[22] multtest_2.46.0             Biobase_2.50.0              BiocGenerics_0.36.1        
[25] MetaDE_2.2.3                patchwork_1.1.1             ggplot2_3.3.3              
[28] SeuratDisk_0.0.0.9019       SeuratObject_4.0.1          Seurat_4.0.2

yuhanH commented 3 years ago

hi @Lopo358 Would you mind to open a new issue and show the scripts you used? Thanks

Lopo358 commented 3 years ago

hi @Lopo358 Would you mind to open a new issue and show the scripts you used? Thanks

Sorry, after starting from scratch with a new virtual environment and updating all the packages and modules, the error was resolved, thanks to the comments above

yuhanH commented 3 years ago

hi @Lopo358 Would you mind to open a new issue and show the scripts you used? Thanks

Sorry, after starting from scratch with a new virtual environment and updating all the packages and modules, the error was resolved, thanks to the comments above

Good to know. Thanks

zqsha commented 2 years ago

I updated SeuratDisk and sctransform, but it reported the same error.

> sessionInfo('SeuratDisk')
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.0

Matrix products: default
BLAS:   /usr/shared/apps/R/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/shared/apps/R/R-4.0.3/lib64/R/lib/libRlapack.so

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

attached base packages:
character(0)

other attached packages:
[1] SeuratDisk_0.0.0.9019

loaded via a namespace (and not attached):
 [1] processx_3.5.2    compiler_4.0.3    R6_2.5.1          rprojroot_2.0.2
 [5] cli_3.1.0         graphics_4.0.3    prettyunits_1.1.1 tools_4.0.3
 [9] withr_2.4.3       utils_4.0.3       curl_4.3.2        grDevices_4.0.3
[13] crayon_1.4.2      remotes_2.4.2     stats_4.0.3       datasets_4.0.3
[17] callr_3.7.0       methods_4.0.3     pkgbuild_1.3.1    ps_1.6.0
[21] base_4.0.3

> sessionInfo('Seurat')
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.0

Matrix products: default
BLAS:   /usr/shared/apps/R/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/shared/apps/R/R-4.0.3/lib64/R/lib/libRlapack.so

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

attached base packages:
character(0)

other attached packages:
[1] Seurat_4.0.6

loaded via a namespace (and not attached):
 [1] processx_3.5.2    compiler_4.0.3    R6_2.5.1          rprojroot_2.0.2
 [5] cli_3.1.0         graphics_4.0.3    prettyunits_1.1.1 tools_4.0.3
 [9] withr_2.4.3       utils_4.0.3       curl_4.3.2        grDevices_4.0.3
[13] crayon_1.4.2      remotes_2.4.2     stats_4.0.3       datasets_4.0.3
[17] callr_3.7.0       methods_4.0.3     pkgbuild_1.3.1    ps_1.6.0
[21] base_4.0.3


> sessionInfo('sctransform')
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.0

Matrix products: default
BLAS:   /usr/shared/apps/R/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/shared/apps/R/R-4.0.3/lib64/R/lib/libRlapack.so

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

attached base packages:
character(0)

other attached packages:
[1] sctransform_0.3.2

loaded via a namespace (and not attached):
  [1] rsvd_1.0.5                    ica_1.0-2                     class_7.3-17                  ps_1.6.0                     
  [5] Rsamtools_2.6.0               foreach_1.5.1                 lmtest_0.9-39                 rprojroot_2.0.2              
  [9] crayon_1.4.2                  spatstat.core_2.3-2           MASS_7.3-53                   nlme_3.1-149                 
 [13] backports_1.4.1               reprex_2.0.1                  BayesLogit_2.1                rlang_0.4.12                 
 [17] caret_6.0-90                  XVector_0.30.0                ROCR_1.0-11                   readxl_1.3.1                 
 [21] SparseM_1.81                  irlba_2.3.5                   callr_3.7.0                   limma_3.46.0                 
 [25] scater_1.18.6                 base_4.0.3                    BiocParallel_1.24.1           rjson_0.2.20                 
 [29] bit64_4.0.5                   harmony_0.1.0                 glue_1.6.0                    pheatmap_1.0.12              
 [33] parallel_4.0.3                processx_3.5.2                vipor_0.4.5                   SeuratDisk_0.0.0.9019        
 [37] spatstat.sparse_2.1-0         AnnotationDbi_1.52.0          BiocGenerics_0.36.1           dotCall64_1.0-1              
 [41] stxBrain.SeuratData_0.1.1     spatstat.geom_2.3-1           mcmc_0.9-7                    haven_2.4.3                  
 [45] tidyselect_1.1.1              SummarizedExperiment_1.20.0   usethis_2.1.5                 SeuratObject_4.0.4           
 [49] fitdistrplus_1.1-6            attempt_0.3.1                 XML_3.99-0.5                  tidyr_1.1.4                  
 [53] zoo_1.8-9                     GenomicAlignments_1.26.0      MatrixModels_0.5-0            xtable_1.8-4                 
 [57] magrittr_2.0.1                ggplot2_3.3.5                 scuttle_1.0.4                 cli_3.1.0                    
 [61] zlibbioc_1.36.0               rstudioapi_0.13               miniUI_0.1.1.1                bslib_0.3.1                  
 [65] bmp_0.3                       rpart_4.1-15                  rafalib_1.0.0                 spruce_0.99.0                
 [69] maps_3.4.0                    fields_13.3                   shiny_1.7.1                   BiocSingular_1.6.0           
 [73] xfun_0.29                     pkgbuild_1.3.1                cluster_2.1.0                 tibble_3.0.4                 
 [77] interactiveDisplayBase_1.28.0 quantreg_5.86                 ggrepel_0.9.1                 listenv_0.8.0                
 [81] shinyWidgets_0.6.2            Biostrings_2.58.0             png_0.1-7                     future_1.23.0                
 [85] ipred_0.9-12                  withr_2.4.3                   bitops_1.0-7                  ggforce_0.3.3                
 [89] plyr_1.8.6                    cellranger_1.1.0              dockerfiler_0.1.4             pROC_1.18.0                  
 [93] dqrng_0.3.0                   SeuratData_0.2.1              coda_0.19-4                   pillar_1.6.4                 
 [97] cachem_1.0.6                  utils_4.0.3                   fs_1.5.2                      scatterplot3d_0.3-41         
[101] hdf5r_1.3.3                   tidyverse_1.3.1               graphics_4.0.3                DelayedMatrixStats_1.12.3    
[105] vctrs_0.3.8                   ellipsis_0.3.2                generics_0.1.1                lava_1.6.10                  
[109] tools_4.0.3                   beeswarm_0.4.0                munsell_0.5.0                 tweenr_1.0.2                 
[113] DelayedArray_0.16.3           fastmap_1.1.0                 compiler_4.0.3                pkgload_1.2.4                
[117] abind_1.4-5                   httpuv_1.6.4                  rtracklayer_1.50.0            segmented_1.3-4              
[121] ExperimentHub_1.16.1          sessioninfo_1.2.2             plotly_4.10.0                 prodlim_2019.11.13           
[125] GenomeInfoDbData_1.2.4        gridExtra_2.3                 MCMCpack_1.6-0                roxygen2_7.1.2               
[129] edgeR_3.32.1                  lattice_0.20-41               deldir_1.0-6                  utf8_1.2.2                   
[133] later_1.3.0                   dplyr_1.0.7                   recipes_0.1.17                BiocFileCache_1.14.0         
[137] jsonlite_1.7.2                scales_1.1.1                  datasets_4.0.3                pbapply_1.5-0                
[141] sparseMatrixStats_1.2.1       lazyeval_0.2.2                promises_1.2.0.1              doParallel_1.0.16            
[145] goftest_1.2-3                 spatstat.utils_2.3-0          reticulate_1.22               cowplot_1.1.1                
[149] statmod_1.4.36                Rtsne_0.15                    forcats_0.5.1                 Biobase_2.50.0               
[153] uwot_0.1.11                   igraph_1.2.6                  survival_3.2-7                yaml_2.2.1                   
[157] stats_4.0.3                   htmltools_0.5.2               memoise_2.0.1                 Seurat_4.0.6                 
[161] locfit_1.5-9.4                IRanges_2.24.1                PCAtools_2.2.0                viridisLite_0.4.0            
[165] digest_0.6.29                 assertthat_0.2.1              mime_0.12                     rappdirs_0.3.3               
[169] tiff_0.1-10                   spam_2.7-0                    RSQLite_2.2.9                 future.apply_1.8.1           
[173] Rmisc_1.5                     jaffelab_0.99.30              remotes_2.4.2                 data.table_1.14.2            
[177] blob_1.2.2                    S4Vectors_0.28.1              splines_4.0.3                 googledrive_2.0.0            
[181] AnnotationHub_2.22.1          benchmarkme_1.0.7             RCurl_1.98-1.2                broom_0.7.10                 
[185] hms_1.1.1                     modelr_0.1.8                  colorspace_2.0-2              BiocManager_1.30.16          
[189] ggbeeswarm_0.6.0              GenomicRanges_1.42.0          nnet_7.3-14                   sass_0.4.0                   
[193] Rcpp_1.0.7                    RANN_2.6.1                    mvtnorm_1.1-3                 fansi_0.5.0                  
[197] conquer_1.2.1                 tzdb_0.2.0                    truncnorm_1.0-8               ModelMetrics_1.2.2.2         
[201] parallelly_1.30.0             R6_2.5.1                      grid_4.0.3                    ggridges_0.5.3               
[205] lifecycle_1.0.1               bluster_1.0.0                 curl_4.3.2                    leiden_0.3.9                 
[209] testthat_3.1.1                jquerylib_0.1.4               SpatialExperiment_1.0.0       benchmarkmeData_1.0.4        
[213] Matrix_1.4-0                  spatialLIBD_1.2.1             desc_1.4.0                    config_0.3.1                 
[217] RcppAnnoy_0.0.19              RColorBrewer_1.1-2            iterators_1.0.13              gower_0.2.2                  
[221] stringr_1.4.0                 htmlwidgets_1.5.4             beachmat_2.6.4                polyclip_1.10-0              
[225] purrr_0.3.4                   rvest_1.0.2                   mgcv_1.8-33                   dbarts_0.9-20                
[229] globals_0.14.0                readbitmap_0.1.5              methods_4.0.3                 patchwork_1.1.1              
[233] codetools_0.2-16              grDevices_4.0.3               matrixStats_0.61.0            lubridate_1.8.0              
[237] prettyunits_1.1.1             SingleCellExperiment_1.12.0   dbplyr_2.1.1                  GenomeInfoDb_1.26.7          
[241] gtable_0.3.0                  DBI_1.1.2                     ggalluvial_0.12.3             stats4_4.0.3                 
[245] Polychrome_1.3.1              tensor_1.5                    httr_1.4.2                    KernSmooth_2.23-17           
[249] stringi_1.7.6                 reshape2_1.4.4                farver_2.1.0                  viridis_0.6.2                
[253] timeDate_3043.102             maple_0.99.1                  DT_0.20                       xml2_1.3.2                   
[257] BiocNeighbors_1.8.2           readr_2.1.1                   golem_0.3.1                   scattermore_0.7              
[261] BiocVersion_3.12.0            scran_1.18.7                  bit_4.0.4                     jpeg_0.1-9                   
[265] MatrixGenerics_1.2.1          spatstat.data_2.1-2           pkgconfig_2.0.3               gargle_1.2.0                 
[269] knitr_1.37   ```

yuhanH commented 2 years ago

hi @zqsha Could you open a new issue with more detailed descriptions and post your scripts?

zqsha commented 2 years ago

Yes, sure. I have opened and edited a new issue and added more details.

AleksZakirov commented 1 year ago

Encountered the same error message. Setting the method = 'glmGamPoi', as recommended by @ChristophH resolved the issue for me.

satijalab / seurat

Single-cell data integration error #3618