Error for guidelines_shiny

SiyiWanggou commented 4 years ago

Hi Dyno team,

I'm a user of dyno for single cell RNAseq trajectory analysis. It is really a wonderful tool. Thanks for your great work. Recently, I reinstalled my system and found the function, guidelines_shiny(), didn't work. The error information is listed below:

guidelines_shiny(dataset) Error in dots_list(...) : attempt to apply non-function
The other functions worked well. Could you help me to fix this? My sessioninfo is listed below:

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.2 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_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8
[4] LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] dyno_0.1.2 dynwrap_1.2.1 dynplot_1.0.2.9000 dynmethods_1.0.5
[5] dynguidelines_1.0.0 dynfeature_1.0.0.9000 RColorBrewer_1.1-2 forcats_0.5.0
[9] stringr_1.4.0 purrr_0.3.4 readr_1.3.1 tidyr_1.1.0
[13] tibble_3.0.1 tidyverse_1.3.0 Cairo_1.5-12 cowplot_1.0.0
[17] ggplot2_3.3.2 dplyr_1.0.0 velocyto.R_0.6 Matrix_1.2-18
[21] SeuratWrappers_0.1.0 Seurat_3.1.5

loaded via a namespace (and not attached): [1] readxl_1.3.1 backports_1.1.8 Hmisc_4.4-0 dyndimred_1.0.3.9000 [5] babelwhale_1.0.1 plyr_1.8.6 igraph_1.2.5 lazyeval_0.2.2
[9] proxyC_0.1.5 splines_3.6.3 listenv_0.8.0 digest_0.6.25
[13] foreach_1.5.0 htmltools_0.5.0 viridis_0.5.1 fansi_0.4.1
[17] magrittr_1.5 checkmate_2.0.0 carrier_0.1.0 cluster_2.1.0
[21] ROCR_1.0-11 remotes_2.1.1 graphlayouts_0.7.0 globals_0.12.5
[25] modelr_0.1.8 RcppParallel_5.0.1 dynutils_1.0.5.9000 jpeg_0.1-8.1
[29] colorspace_1.4-1 blob_1.2.1 rvest_0.3.5 rappdirs_0.3.1
[33] ggrepel_0.8.2 haven_2.3.1 xfun_0.14 crayon_1.3.4
[37] jsonlite_1.6.1 iterators_1.0.12 survival_3.2-3 zoo_1.8-8
[41] ape_5.4 glue_1.4.1 polyclip_1.10-0 gtable_0.3.0
[45] leiden_0.3.3 future.apply_1.5.0 BiocGenerics_0.32.0 dynparam_1.0.0
[49] scales_1.1.1 DBI_1.1.0 Rcpp_1.0.4.6 xtable_1.8-4
[53] viridisLite_0.3.0 htmlTable_1.13.3 reticulate_1.16 bit_1.1-15.2
[57] foreign_0.8-76 rsvd_1.0.3 Formula_1.2-3 tsne_0.1-3
[61] htmlwidgets_1.5.1 httr_1.4.1 acepack_1.4.1 ellipsis_0.3.1
[65] ica_1.0-2 farver_2.0.3 pkgconfig_2.0.3 nnet_7.3-14
[69] uwot_0.1.8 dbplyr_1.4.4 labeling_0.3 tidyselect_1.1.0
[73] rlang_0.4.6 reshape2_1.4.4 later_1.1.0.1 munsell_0.5.0
[77] cellranger_1.1.0 tools_3.6.3 cli_2.0.2 generics_0.0.2
[81] ranger_0.12.1 broom_0.5.6 ggridges_0.5.2 fastmap_1.0.1
[85] yaml_2.2.1 bit64_0.9-7 processx_3.4.2 knitr_1.28
[89] fs_1.4.1 tidygraph_1.2.0 fitdistrplus_1.1-1 lmds_0.1.0
[93] RANN_2.6.1 ggraph_2.0.3 pbapply_1.4-2 future_1.17.0
[97] nlme_3.1-148 mime_0.9 GA_3.2 xml2_1.3.2
[101] hdf5r_1.3.2 compiler_3.6.3 rstudioapi_0.11 plotly_4.9.2.1
[105] png_0.1-7 testthat_2.3.2 reprex_0.3.0 tweenr_1.0.1
[109] stringi_1.4.6 ps_1.3.3 lattice_0.20-41 vctrs_0.3.1
[113] pillar_1.4.4 lifecycle_0.2.0 BiocManager_1.30.10 lmtest_0.9-37
[117] RcppAnnoy_0.0.16 data.table_1.12.8 irlba_2.3.3 httpuv_1.5.4
[121] patchwork_1.0.0.9000 R6_2.4.1 latticeExtra_0.6-29 pcaMethods_1.78.0
[125] promises_1.1.1 KernSmooth_2.23-17 gridExtra_2.3 codetools_0.2-16
[129] MASS_7.3-51.6 assertthat_0.2.1 rje_1.10.16 withr_2.2.0
[133] sctransform_0.2.1 mgcv_1.8-31 parallel_3.6.3 hms_0.5.3
[137] grid_3.6.3 rpart_4.1-15 Rtsne_0.15 ggforce_0.3.1
[141] Biobase_2.46.0 shiny_1.4.0.2 lubridate_1.7.9 base64enc_0.1-3
[145] tinytex_0.23

rcannood commented 4 years ago

Hello @SiyiWanggou!

Thanks for posting this issue. I have fixed the underlying problem in package dynguidelines.

Please update dynguidelines by running the command: remotes::install_github("dynverse/dynguidelines").

Please reopen this issue should the problem persist.

Kind regards, Robrecht

SiyiWanggou commented 3 years ago

Hi Rcannood, Thanks for your reply. It works well for me now.

saeedfc commented 3 years ago

Hi,

I have the same issue. Tried installing dynguidlines as suggested. Restarted the r session and reloaded the libraries. Problem persists. Any help is appreciated.

> Fib
An object of class Seurat 
52011 features across 13143 samples within 3 assays 
Active assay: RNA (25697 features, 0 variable features)
 2 other assays present: SCT, integrated
 4 dimensional reductions calculated: pca, umap, harm_umap, harmony

>fib_data <- wrap_expression(
  counts = t(as.matrix(GetAssayData(Fib, assay = "RNA", slot = "counts"))),
  expression = t(as.matrix(GetAssayData(Fib, assay = "RNA", slot = "data"))),
  cell_info = Fib@meta.data
)
> guidelines <- guidelines_shiny(fib_data)
Error in dots_list(...) : attempt to apply non-function
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 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        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:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.0         stringr_1.4.0         dplyr_1.0.2           purrr_0.3.4           readr_1.4.0           tidyr_1.1.2          
 [7] tibble_3.0.4          ggplot2_3.3.2         tidyverse_1.3.0       dyno_0.1.1            dynwrap_1.2.1         dynplot_1.0.2.9000   
[13] dynmethods_1.0.5      dynguidelines_1.0.0   dynfeature_1.0.0.9000 Seurat_3.2.0         

loaded via a namespace (and not attached):
  [1] readxl_1.3.1          backports_1.1.10      dyndimred_1.0.3       babelwhale_1.0.1      plyr_1.8.6            igraph_1.2.6         
  [7] lazyeval_0.2.2        proxyC_0.1.5          splines_3.6.3         listenv_0.8.0         digest_0.6.26         foreach_1.5.0        
 [13] htmltools_0.5.0       viridis_0.5.1         fansi_0.4.1           magrittr_1.5          carrier_0.1.0         tensor_1.5           
 [19] cluster_2.1.0         ROCR_1.0-11           remotes_2.2.0         globals_0.12.5        graphlayouts_0.7.0    modelr_0.1.8         
 [25] RcppParallel_5.0.2    dynutils_1.0.5        colorspace_1.4-1      rvest_0.3.6           blob_1.2.1            rappdirs_0.3.1       
 [31] ggrepel_0.8.2         haven_2.3.1           xfun_0.18             crayon_1.3.4          jsonlite_1.7.1        spatstat_1.64-1      
 [37] spatstat.data_1.4-3   survival_3.2-7        zoo_1.8-8             iterators_1.0.12      ape_5.4-1             glue_1.4.2           
 [43] polyclip_1.10-0       gtable_0.3.0          leiden_0.3.3          future.apply_1.6.0    dynparam_1.0.1        abind_1.4-5          
 [49] scales_1.1.1          DBI_1.1.0             miniUI_0.1.1.1        Rcpp_1.0.5            viridisLite_0.3.0     xtable_1.8-4         
 [55] reticulate_1.16       rsvd_1.0.3            htmlwidgets_1.5.1     httr_1.4.2            RColorBrewer_1.1-2    ellipsis_0.3.1       
 [61] ica_1.0-2             pkgconfig_2.0.3       farver_2.0.3          uwot_0.1.8            dbplyr_1.4.4          deldir_0.1-28        
 [67] tidyselect_1.1.0      rlang_0.4.8           reshape2_1.4.4        later_1.1.0.1         cellranger_1.1.0      munsell_0.5.0        
 [73] tools_3.6.3           cli_2.1.0             generics_0.0.2        ranger_0.12.1         broom_0.7.0           ggridges_0.5.2       
 [79] fastmap_1.0.1         yaml_2.2.1            goftest_1.2-2         fs_1.5.0              processx_3.4.4        knitr_1.30           
 [85] fitdistrplus_1.1-1    tidygraph_1.2.0       lmds_0.1.0            RANN_2.6.1            ggraph_2.0.3          pbapply_1.4-3        
 [91] future_1.18.0         nlme_3.1-149          mime_0.9              GA_3.2                xml2_1.3.2            compiler_3.6.3       
 [97] rstudioapi_0.11       plotly_4.9.2.1        png_0.1-7             testthat_2.3.2        spatstat.utils_1.17-0 reprex_0.3.0         
[103] tweenr_1.0.1          stringi_1.5.3         ps_1.4.0              lattice_0.20-41       Matrix_1.2-18         vctrs_0.3.4          
[109] pillar_1.4.6          lifecycle_0.2.0       lmtest_0.9-38         RcppAnnoy_0.0.16      data.table_1.13.0     cowplot_1.1.0        
[115] irlba_2.3.3           httpuv_1.5.4          patchwork_1.0.1       R6_2.4.1              promises_1.1.1        KernSmooth_2.23-17   
[121] gridExtra_2.3         codetools_0.2-16      MASS_7.3-53           assertthat_0.2.1      rje_1.10.16           withr_2.3.0          
[127] sctransform_0.2.1     mgcv_1.8-33           parallel_3.6.3        hms_0.5.3             grid_3.6.3            rpart_4.1-15         
[133] Rtsne_0.15            ggforce_0.3.2         lubridate_1.7.9       shiny_1.5.0

Thanks and Kind regards, Saeed

dynverse / dyno

Error for guidelines_shiny #85