Error in `dplyr::select()`: ! <text>:1:5: unexpected symbol about clustree

[zhangdudu0]

R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /sdc1/R/R-4.0.4/lib64/R/lib/libRblas.so
LAPACK: /sdc1/R/R-4.0.4/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    
 [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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] harmony_1.0                 Rcpp_1.0.9                  clustree_0.5.0              dplyr_1.0.10               
 [5] ggraph_2.1.0                scHCL_0.1.1                 SingleR_1.4.1               SummarizedExperiment_1.20.0
 [9] Biobase_2.50.0              GenomicRanges_1.42.0        GenomeInfoDb_1.26.7         IRanges_2.24.1             
[13] S4Vectors_0.28.1            BiocGenerics_0.36.1         MatrixGenerics_1.2.1        matrixStats_0.62.0         
[17] getopt_1.20.3               stringr_1.4.1               ggplot2_3.3.6               sp_1.5-0                   
[21] SeuratObject_4.1.2          Seurat_4.0.5.9000          

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  reticulate_1.18             tidyselect_1.2.0            htmlwidgets_1.5.4          
  [5] grid_4.0.4                  BiocParallel_1.24.1         Rtsne_0.16                  munsell_0.5.0              
  [9] codetools_0.2-18            ica_1.0-3                   DT_0.17                     future_1.28.0              
 [13] miniUI_0.1.1.1              withr_2.5.0                 spatstat.random_2.2-0       colorspace_2.0-3           
 [17] progressr_0.11.0            ggalluvial_0.12.3           rstudioapi_0.13             SingleCellExperiment_1.12.0
 [21] ROCR_1.0-11                 tensor_1.5                  listenv_0.8.0               GenomeInfoDbData_1.2.4     
 [25] polyclip_1.10-0             farver_2.1.1                pheatmap_1.0.12             parallelly_1.32.1          
 [29] vctrs_0.4.2                 generics_0.1.3              R6_2.5.1                    doParallel_1.0.17          
 [33] graphlayouts_0.8.3          rsvd_1.0.3                  VGAM_1.1-7                  bitops_1.0-7               
 [37] spatstat.utils_3.0-1        DelayedArray_0.16.3         assertthat_0.2.1            promises_1.2.0.1           
 [41] scales_1.2.1                rgeos_0.5-9                 gtable_0.3.1                beachmat_2.6.4             
 [45] globals_0.16.1              goftest_1.2-3               tidygraph_1.2.2             rlang_1.0.4                
 [49] splines_4.0.4               lazyeval_0.2.2              spatstat.geom_3.0-3         checkmate_2.0.0            
 [53] reshape2_1.4.4              abind_1.4-5                 backports_1.2.1             httpuv_1.6.6               
 [57] tools_4.0.4                 cubature_2.0.4.5            ellipsis_0.3.2              spatstat.core_2.4-4        
 [61] RColorBrewer_1.1-3          ggridges_0.5.3              plyr_1.8.7                  sparseMatrixStats_1.2.1    
 [65] zlibbioc_1.36.0             purrr_0.3.5                 RCurl_1.98-1.9              rpart_4.1-15               
 [69] deldir_1.0-6                pbapply_1.5-0               viridis_0.6.2               cowplot_1.1.1              
 [73] zoo_1.8-11                  ggrepel_0.9.1               cluster_2.1.1               fs_1.5.2                   
 [77] magrittr_2.0.3              data.table_1.14.4           scattermore_0.8             SparseM_1.81               
 [81] lmtest_0.9-40               RANN_2.6.1                  truncdist_1.0-2             fitdistrplus_1.1-8         
 [85] gsl_2.1-7.1                 patchwork_1.1.1             mime_0.12                   xtable_1.8-4               
 [89] gridExtra_2.3               compiler_4.0.4              tibble_3.1.8                KernSmooth_2.23-18         
 [93] crayon_1.5.2                htmltools_0.5.3             mgcv_1.8-34                 later_1.3.0                
 [97] tidyr_1.2.1                 powerTCR_1.10.3             DBI_1.1.1                   tweenr_2.0.2               
[101] MASS_7.3-53.1               Matrix_1.5-1                permute_0.9-7               cli_3.4.0                  
[105] evd_2.3-6.1                 igraph_1.3.5                pkgconfig_2.0.3             plotly_4.10.0              
[109] spatstat.sparse_3.0-0       foreach_1.5.2               stringdist_0.9.8            XVector_0.30.0             
[113] digest_0.6.30               sctransform_0.3.5           RcppAnnoy_0.0.20            vegan_2.6-4                
[117] spatstat.data_3.0-0         leiden_0.4.3                uwot_0.1.10                 DelayedMatrixStats_1.12.3  
[121] evmix_2.12                  shiny_1.7.3                 lifecycle_1.0.1             nlme_3.1-152               
[125] jsonlite_1.8.3              BiocNeighbors_1.8.2         viridisLite_0.4.1           limma_3.46.0               
[129] fansi_1.0.3                 pillar_1.8.1                lattice_0.20-41             fastmap_1.1.0              
[133] httr_1.4.4                  survival_3.2-7              glue_1.6.2                  png_0.1-7                  
[137] shinythemes_1.2.0           iterators_1.0.14            scRepertoire_1.3.5          ggforce_0.4.1              
[141] stringi_1.7.8               BiocSingular_1.6.0          irlba_2.3.5.1               future.apply_1.9.1 ```

[zhangdudu0]

When I run under windows, it is successful

> pbmc <- readRDS("D:/APP/zctmp/pbmc_harmony_filter.rds")
> clustree([email protected], prefix = "RNA_snn_res.")

> sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

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

other attached packages:
[1] clustree_0.5.0     ggraph_2.1.0       ggplot2_3.3.6      sp_1.5-0          
[5] SeuratObject_4.1.2

loaded via a namespace (and not attached):
  [1] Seurat_4.2.0          Rtsne_0.16            colorspace_2.0-3     
  [4] deldir_1.0-6          ellipsis_0.3.2        ggridges_0.5.4       
  [7] spatstat.data_3.0-0   leiden_0.4.3          listenv_0.8.0        
 [10] farver_2.1.1          graphlayouts_0.8.3    ggrepel_0.9.1        
 [13] fansi_1.0.3           codetools_0.2-18      splines_4.2.2        
 [16] polyclip_1.10-4       jsonlite_1.8.3        ica_1.0-3            
 [19] cluster_2.1.4         png_0.1-7             rgeos_0.5-9          
 [22] uwot_0.1.14           ggforce_0.4.1         shiny_1.7.3          
 [25] sctransform_0.3.5     spatstat.sparse_3.0-0 compiler_4.2.2       
 [28] httr_1.4.4            backports_1.4.1       Matrix_1.5-1         
 [31] fastmap_1.1.0         lazyeval_0.2.2        cli_3.4.1            
 [34] later_1.3.0           tweenr_2.0.2          htmltools_0.5.3      
 [37] tools_4.2.2           igraph_1.3.5          gtable_0.3.1         
 [40] glue_1.6.2            RANN_2.6.1            reshape2_1.4.4       
 [43] dplyr_1.0.10          Rcpp_1.0.9            scattermore_0.8      
 [46] vctrs_0.5.0           nlme_3.1-160          progressr_0.11.0     
 [49] lmtest_0.9-40         spatstat.random_2.2-0 stringr_1.4.1        
 [52] globals_0.16.1        mime_0.12             miniUI_0.1.1.1       
 [55] lifecycle_1.0.3       irlba_2.3.5.1         goftest_1.2-3        
 [58] future_1.28.0         MASS_7.3-58.1         zoo_1.8-11           
 [61] scales_1.2.1          tidygraph_1.2.2       spatstat.core_2.4-4  
 [64] promises_1.2.0.1      spatstat.utils_3.0-1  parallel_4.2.2       
 [67] RColorBrewer_1.1-3    reticulate_1.26       pbapply_1.5-0        
 [70] gridExtra_2.3         rpart_4.1.19          stringi_1.7.8        
 [73] checkmate_2.1.0       rlang_1.0.6           pkgconfig_2.0.3      
 [76] matrixStats_0.62.0    lattice_0.20-45       ROCR_1.0-11          
 [79] purrr_0.3.5           tensor_1.5            patchwork_1.1.2      
 [82] htmlwidgets_1.5.4     labeling_0.4.2        cowplot_1.1.1        
 [85] tidyselect_1.2.0      parallelly_1.32.1     RcppAnnoy_0.0.20     
 [88] plyr_1.8.7            magrittr_2.0.3        R6_2.5.1             
 [91] generics_0.1.3        mgcv_1.8-41           pillar_1.8.1         
 [94] withr_2.5.0           fitdistrplus_1.1-8    survival_3.4-0       
 [97] abind_1.4-5           tibble_3.1.8          future.apply_1.9.1   
[100] KernSmooth_2.23-20    utf8_1.2.2            spatstat.geom_3.0-3  
[103] plotly_4.10.0         viridis_0.6.2         grid_4.2.2           
[106] data.table_1.14.4     digest_0.6.30         xtable_1.8-4         
[109] tidyr_1.2.1           httpuv_1.6.6          munsell_0.5.0        
[112] viridisLite_0.4.1 

[lazappi]

Hi @zhangdudu0

Thanks for giving {clustree} a go! I'm not quite sure from your message what code you ran or what the error is. Can you please post a small reproducible example? Please use the Markdown formatting for code instead of pasting an image, something like this:

```r
# <Code for your example goes here>
```

[JoyOtten]

HI, I have the exact same error:
Error in dplyr::select():
! :1:5: unexpected symbol
1: Use of
^

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

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] dplyr_1.0.10 clustree_0.5.0 ggraph_2.1.0 ggplot2_3.3.6 SeuratObject_4.1.3
[6] sp_1.5-1

loaded via a namespace (and not attached):
[1] Seurat_4.2.0 Rtsne_0.16 colorspace_2.0-3 deldir_1.0-6
[5] ellipsis_0.3.2 ggridges_0.5.3 rstudioapi_0.13 spatstat.data_3.0-0
[9] leiden_0.4.3 listenv_0.8.0 farver_2.1.1 graphlayouts_0.8.4
[13] ggrepel_0.9.1 fansi_1.0.3 codetools_0.2-18 splines_4.1.2
[17] polyclip_1.10-0 jsonlite_1.8.4 ica_1.0-2 cluster_2.1.3
[21] rgeos_0.5-9 png_0.1-8 uwot_0.1.14 ggforce_0.4.1
[25] shiny_1.7.4 sctransform_0.3.5 spatstat.sparse_3.0-0 compiler_4.1.2
[29] httr_1.4.4 backports_1.4.1 assertthat_0.2.1 Matrix_1.5-3
[33] fastmap_1.1.0 lazyeval_0.2.2 cli_3.4.1 later_1.3.0
[37] tweenr_2.0.2 htmltools_0.5.4 tools_4.1.2 igraph_1.3.4
[41] gtable_0.3.1 glue_1.6.2 RANN_2.6.1 reshape2_1.4.4
[45] Rcpp_1.0.9 scattermore_0.8 cellranger_1.1.0 vctrs_0.4.2
[49] nlme_3.1-157 progressr_0.13.0 lmtest_0.9-40 spatstat.random_3.0-1
[53] stringr_1.4.1 globals_0.16.2 mime_0.12 miniUI_0.1.1.1
[57] lifecycle_1.0.1 irlba_2.3.5 goftest_1.2-3 future_1.30.0
[61] MASS_7.3-56 zoo_1.8-11 scales_1.2.1 tidygraph_1.2.1
[65] spatstat.core_2.4-4 promises_1.2.0.1 spatstat.utils_3.0-1 parallel_4.1.2
[69] RColorBrewer_1.1-3 reticulate_1.26 pbapply_1.5-0 gridExtra_2.3
[73] rpart_4.1.16 stringi_1.7.12 checkmate_2.0.0 rlang_1.0.4
[77] pkgconfig_2.0.3 matrixStats_0.63.0 lattice_0.20-45 ROCR_1.0-11
[81] purrr_0.3.4 tensor_1.5 patchwork_1.1.1 htmlwidgets_1.6.1
[85] cowplot_1.1.1 tidyselect_1.2.0 parallelly_1.33.0 RcppAnnoy_0.0.20
[89] plyr_1.8.8 magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[93] DBI_1.1.3 mgcv_1.8-40 pillar_1.8.1 withr_2.5.0
[97] fitdistrplus_1.1-8 survival_3.3-1 abind_1.4-5 tibble_3.1.8
[101] future.apply_1.10.0 crayon_1.5.2 KernSmooth_2.23-20 utf8_1.2.2
[105] spatstat.geom_3.0-3 plotly_4.10.1 viridis_0.6.2 readxl_1.4.0
[109] grid_4.1.2 data.table_1.14.6 digest_0.6.31 xtable_1.8-4
[113] tidyr_1.2.1 httpuv_1.6.8 munsell_0.5.0 viridisLite_0.4.1

[lazappi]

Hi @JoyOtten. As I mentioned in my last comment it would be really helpful if you can post the code you ran and the whole error message. An example dataset would also be useful if you can share one.

[JoyOtten]

Hi @lazappi. Hereby the code I used:
seurat_clust <- FindClusters(seurat, algorithm = 4, method = "igraph", graph.name = NULL, resolution = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1))
p1 <- clustree(seurat_clust, prefix = "SCT_snn_res.")
plot(p1)
Error in dplyr::select():
! :1:5: unexpected symbol
1: Use of
^

I also found out that this is a specific error code in R4.1.2 for me when I'm running the clustree code with R4.0.2 I have no error code.

R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.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
[7] base

other attached packages:
[1] Matrix_1.5-1 leiden_0.4.2 reticulate_1.25
[4] clustree_0.5.0 ggraph_2.0.5 stringr_1.4.0
[7] ggplot2_3.3.6 dplyr_1.0.9 SeuratObject_4.0.4
[10] Seurat_4.0.2

loaded via a namespace (and not attached):
[1] fgsea_1.16.0 Rtsne_0.16
[3] colorspace_2.0-3 deldir_1.0-6
[5] ellipsis_0.3.2 ggridges_0.5.3
[7] rprojroot_2.0.3 qvalue_2.22.0
[9] rstudioapi_0.13 spatstat.data_2.2-0
[11] listenv_0.8.0 farver_2.1.0
[13] graphlayouts_0.8.0 bit64_4.0.5
[15] ggrepel_0.9.1 AnnotationDbi_1.52.0
[17] fansi_1.0.3 codetools_0.2-18
[19] splines_4.0.2 GOSemSim_2.16.1
[21] cachem_1.0.6 polyclip_1.10-0
[23] jsonlite_1.8.0 ica_1.0-2
[25] GO.db_3.12.1 cluster_2.1.3
[27] png_0.1-7 uwot_0.1.11
[29] ggforce_0.3.3 shiny_1.7.1
[31] sctransform_0.3.3 spatstat.sparse_2.1-1
[33] compiler_4.0.2 httr_1.4.3
[35] backports_1.4.1 assertthat_0.2.1
[37] fastmap_1.1.0 lazyeval_0.2.2
[39] cli_3.3.0 later_1.3.0
[41] tweenr_1.0.2 htmltools_0.5.2
[43] tools_4.0.2 igraph_1.3.1
[45] gtable_0.3.0 glue_1.6.2
[47] DO.db_2.9 RANN_2.6.1
[49] reshape2_1.4.4 rappdirs_0.3.3
[51] fastmatch_1.1-3 Rcpp_1.0.8.3
[53] Biobase_2.50.0 scattermore_0.8
[55] vctrs_0.4.1 nlme_3.1-157
[57] lmtest_0.9-40 spatstat.random_2.2-0
[59] globals_0.15.0 mime_0.12
[61] miniUI_0.1.1.1 lifecycle_1.0.1
[63] irlba_2.3.5 goftest_1.2-3
[65] future_1.25.0 DOSE_3.16.0
[67] MASS_7.3-56 zoo_1.8-10
[69] scales_1.2.0 tidygraph_1.2.1
[71] spatstat.core_2.4-4 promises_1.2.0.1
[73] spatstat.utils_2.3-1 parallel_4.0.2
[75] RColorBrewer_1.1-3 memoise_2.0.1
[77] pbapply_1.5-0 gridExtra_2.3
[79] rpart_4.1.16 RSQLite_2.2.12
[81] stringi_1.7.6 S4Vectors_0.28.1
[83] checkmate_2.0.0 BiocGenerics_0.36.1
[85] BiocParallel_1.24.1 rlang_1.0.2
[87] pkgconfig_2.0.3 matrixStats_0.62.0
[89] lattice_0.20-45 ROCR_1.0-11
[91] purrr_0.3.4 tensor_1.5
[93] patchwork_1.1.1 htmlwidgets_1.5.4
[95] bit_4.0.4 cowplot_1.1.1
[97] tidyselect_1.1.2 here_1.0.1
[99] parallelly_1.31.1 RcppAnnoy_0.0.19
[101] plyr_1.8.7 magrittr_2.0.3
[103] R6_2.5.1 IRanges_2.24.1
[105] generics_0.1.2 DBI_1.1.2
[107] pillar_1.7.0 withr_2.5.0
[109] mgcv_1.8-40 fitdistrplus_1.1-8
[111] survival_3.3-1 abind_1.4-5
[113] tibble_3.1.7 future.apply_1.9.0
[115] crayon_1.5.1 KernSmooth_2.23-20
[117] utf8_1.2.2 spatstat.geom_2.4-0
[119] plotly_4.10.0 viridis_0.6.2
[121] grid_4.0.2 data.table_1.14.2
[123] blob_1.2.2 digest_0.6.29
[125] xtable_1.8-4 tidyr_1.2.0
[127] httpuv_1.6.5 stats4_4.0.2
[129] munsell_0.5.0 viridisLite_0.4.0

[lazappi]

Are you able to share the object that is failing (just before running the clustree() function)? I tried using an example dataset and didn't have any issues. If you could replicate the same error with an example dataset that would also be helpful.

pancreas <- scRNAseq::SegerstolpePancreasData()
seurat <- as.Seurat(pancreas, counts = "counts", data = NULL)
Seurat::DefaultAssay(seurat) <- "endogenous"
seurat <- NormalizeData(seurat)
seurat <- FindVariableFeatures(seurat)
seurat <- ScaleData(seurat)
seurat <- RunPCA(seurat)
seurat <- FindNeighbors(seurat)
seurat <- FindClusters(seurat, algorithm = 4, method = "igraph", graph.name = NULL, resolution = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1))
clustree(seurat, prefix = "endogenous_snn_res.")

It would also be useful if you could run traceback() to help find exactly where the error is coming from.

I also noticed you have different versions of {dply} in the different R environments so maybe that could have something to do with it?

[lazappi]

If there's no follow up to this I will close the issue