Error: unable to open database file Traceback:

[jmzhang1911]

Hello Developer,

I am encountering the following issue. Do you know how to resolve it? I look forward to your reply.

thanks

R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /share/zhangjm/software/miniconda3/envs/scverse2/lib/libopenblasp-r0.3.25.so

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=zh_CN.UTF-8        LC_COLLATE=zh_CN.UTF-8    
 [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] org.Hs.eg.db_3.16.0   AnnotationDbi_1.64.1  IRanges_2.32.0       
[4] S4Vectors_0.36.2      Biobase_2.58.0        BiocGenerics_0.44.0  
[7] clusterProfiler_4.6.2

loaded via a namespace (and not attached):
  [1] nlme_3.1-164           fs_1.6.3               bitops_1.0-7          
  [4] ggtree_3.11.1          enrichplot_1.18.4      bit64_4.0.5           
  [7] HDO.db_0.99.1          RColorBrewer_1.1-3     httr_1.4.7            
 [10] GenomeInfoDb_1.34.9    repr_1.1.6             tools_4.2.3           
 [13] utf8_1.2.4             R6_2.5.1               lazyeval_0.2.2        
 [16] DBI_1.2.2              colorspace_2.1-0       withr_3.0.0           
 [19] tidyselect_1.2.1       gridExtra_2.3          bit_4.0.5             
 [22] compiler_4.2.3         cli_3.6.2              scatterpie_0.2.1      
 [25] shadowtext_0.1.3       scales_1.3.0           yulab.utils_0.1.4     
 [28] pbdZMQ_0.3-10          stringr_1.5.1          digest_0.6.35         
 [31] gson_0.1.0             DOSE_3.24.2            XVector_0.38.0        
 [34] base64enc_0.1-3        pkgconfig_2.0.3        htmltools_0.5.8.1     
 [37] fastmap_1.1.1          rlang_1.1.3            RSQLite_2.3.6         
 [40] gridGraphics_0.5-1     generics_0.1.3         farver_2.1.1          
 [43] jsonlite_1.8.8         BiocParallel_1.32.6    GOSemSim_2.24.0       
 [46] dplyr_1.1.4            RCurl_1.98-1.14        magrittr_2.0.3        
 [49] ggplotify_0.1.2        GO.db_3.16.0           GenomeInfoDbData_1.2.9
 [52] patchwork_1.1.3        Matrix_1.6-4           Rcpp_1.0.12           
 [55] IRkernel_1.3.2         munsell_0.5.0          fansi_1.0.6           
 [58] ape_5.7-1              viridis_0.6.5          lifecycle_1.0.4       
 [61] stringi_1.8.3          ggraph_2.2.1           MASS_7.3-60           
 [64] zlibbioc_1.44.0        plyr_1.8.9             qvalue_2.30.0         
 [67] grid_4.2.3             blob_1.2.4             parallel_4.2.3        
 [70] ggrepel_0.9.4          crayon_1.5.2           lattice_0.22-5        
 [73] IRdisplay_1.1          graphlayouts_1.1.1     Biostrings_2.66.0     
 [76] cowplot_1.1.2          splines_4.2.3          KEGGREST_1.38.0       
 [79] pillar_1.9.0           fgsea_1.24.0           igraph_2.0.2          
 [82] uuid_1.1-1             reshape2_1.4.4         codetools_0.2-19      
 [85] fastmatch_1.1-4        glue_1.7.0             evaluate_0.23         
 [88] ggfun_0.1.4            downloader_0.4         data.table_1.15.4     
 [91] treeio_1.22.0          png_0.1-8              vctrs_0.6.5           
 [94] tweenr_2.0.3           gtable_0.3.4           purrr_1.0.2           
 [97] polyclip_1.10-6        tidyr_1.3.1            cachem_1.0.8          
[100] ggplot2_3.4.2          ggforce_0.4.2          tidygraph_1.3.1       
[103] tidytree_0.4.6         viridisLite_0.4.2      tibble_3.2.1          
[106] aplot_0.2.2            memoise_2.0.1         

[guidohooiveld]

Note that I am not the developer, but I have never seen this error myself or being posted here...

Obvious question: what happens if for the argument gene a simple character vector is given, and not a 'piped' object? I feel it has to do with this. So simply: gene = rownames(gene.df).