bzhanglab / WebGestaltR

R package for WebGestalt
https://bzhanglab.github.io/WebGestaltR/
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Error using WebGestaltR() in Loading ID list step #18

Closed isha-ashi closed 1 year ago

isha-ashi commented 1 year ago

While using WebGestaltR() function; I encounter following error:

Loading the functional categories...
Error in `select()`:                                                                                                                                                                            
! <text>:1:5: unexpected symbol
1: Use of
        ^
Run `rlang::last_error()` to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)
> rlang::last_error()
<simpleError in select(geneSet, -.data$database): <text>:1:5: unexpected symbol
1: Use of
        ^>

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS:   /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2

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] harmony_0.1.0     Rcpp_1.0.9        WebGestaltR_0.4.4

loaded via a namespace (and not attached):
  [1] Seurat_4.3.0           Rtsne_0.16             colorspace_2.0-3       deldir_1.0-6           ellipsis_0.3.2         ggridges_0.5.4        
  [7] spatstat.data_3.0-0    rstudioapi_0.13        leiden_0.4.3           listenv_0.8.0          ggrepel_0.9.2          bit64_4.0.5           
 [13] fansi_1.0.3            codetools_0.2-18       splines_4.2.0          doParallel_1.0.17      knitr_1.39             polyclip_1.10-4       
 [19] jsonlite_1.8.3         apcluster_1.4.9        ica_1.0-3              cluster_2.1.3          png_0.1-7              uwot_0.1.14           
 [25] spatstat.sparse_3.0-0  shiny_1.7.3            sctransform_0.3.5      readr_2.1.2            compiler_4.2.0         httr_1.4.4            
 [31] assertthat_0.2.1       SeuratObject_4.1.3     Matrix_1.5-3           fastmap_1.1.0          lazyeval_0.2.2         cli_3.4.1             
 [37] later_1.3.0            htmltools_0.5.3        tools_4.2.0            igraph_1.3.5           gtable_0.3.1           glue_1.6.2            
 [43] RANN_2.6.1             reshape2_1.4.4         dplyr_1.0.10           doRNG_1.8.2            scattermore_0.8        vctrs_0.4.1           
 [49] nlme_3.1-157           spatstat.explore_3.0-5 svglite_2.1.0.9000     progressr_0.11.0       iterators_1.0.14       lmtest_0.9-40         
 [55] spatstat.random_3.0-1  xfun_0.31              stringr_1.4.1          globals_0.16.2         mime_0.12              miniUI_0.1.1.1        
 [61] lifecycle_1.0.1        irlba_2.3.5.1          rngtools_1.5.2         goftest_1.2-3          future_1.29.0          MASS_7.3-57           
 [67] zoo_1.8-11             scales_1.2.1           vroom_1.5.7            spatstat.utils_3.0-1   hms_1.1.1              promises_1.2.0.1      
 [73] parallel_4.2.0         RColorBrewer_1.1-3     curl_4.3.3             gridExtra_2.3          reticulate_1.26        pbapply_1.6-0         
 [79] ggplot2_3.3.6          stringi_1.7.8          foreach_1.5.2          rlang_1.0.4            pkgconfig_2.0.3        systemfonts_1.0.4     
 [85] matrixStats_0.63.0     lattice_0.20-45        tensor_1.5             ROCR_1.0-11            purrr_0.3.5            patchwork_1.1.2       
 [91] htmlwidgets_1.5.4      cowplot_1.1.1          bit_4.0.4              tidyselect_1.2.0       parallelly_1.32.1      RcppAnnoy_0.0.20      
 [97] plyr_1.8.8             magrittr_2.0.3         R6_2.5.1               generics_0.1.3         DBI_1.1.3              pillar_1.8.1          
[103] whisker_0.4            withr_2.5.0            fitdistrplus_1.1-8     abind_1.4-5            survival_3.3-1         sp_1.5-1              
[109] tibble_3.1.8           future.apply_1.10.0    crayon_1.5.2           KernSmooth_2.23-20     utf8_1.2.2             spatstat.geom_3.0-3   
[115] plotly_4.10.1          tzdb_0.3.0             grid_4.2.0             data.table_1.14.6      digest_0.6.30          xtable_1.8-4          
[121] tidyr_1.2.1            httpuv_1.6.6           munsell_0.5.0          viridisLite_0.4.1     

My assumption is error is occuring at line 160 geneSet <- select(geneSet, -.data$database) in loadGeneSet() function. Can this be fixed?

yxngl commented 1 year ago

Thanks. This should only affect when you input database as a single database wrapped in list e.g. c("A").