ReactomeGSA analysis fails with HTTP 505 error

[crazyxiaoj]

Hello ReactomeGSA maintainers,

Thank you for developing and maintaining ReactomeGSA. Today, I encountered an error when submitting an analysis request to the ReactomeGSA server:

Error in start_reactome_analysis(request = request, compress = compress,  : 
  Request failed (505 - HTTP Version Not Supported): An unexpected error occurred. The development team was informed. Please try again later.

Could you please check whether there is an issue with the ReactomeGSA server?

Thank you for your help and for maintaining this package.

[jgriss]

Hi @crazyxiaoj ,

Thanks a lot for reporting this issue! Unfortunately, we currently cannot reproduce it. It may be caused by the package used to perform the HTTP requests. Could you therefore send us an output of your sessionInfo() to check which version might be causing it?

[crazyxiaoj]

Thank you for your quick response. Below is my sessionInfo() output:

r$> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 24.04.2 LTS

Matrix products: default
BLAS/LAPACK: /data/nas2/software/miniconda3/envs/R4.3.3/lib/libopenblasp-r0.3.29.so;  LAPACK version 3.12.0

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

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] ReactomeGSA.data_1.16.1 edgeR_3.42.4            limma_3.56.2           
[4] ReactomeGSA_1.14.0      Seurat_5.3.0            SeuratObject_5.1.0     
[7] sp_2.2-0               

loaded via a namespace (and not attached):
  [1] bitops_1.0-9           deldir_2.0-4           pbapply_1.7-2         
  [4] gridExtra_2.3          rlang_1.3.0            magrittr_2.0.3        
  [7] RcppAnnoy_0.0.22       matrixStats_1.5.0      ggridges_0.5.6        
 [10] compiler_4.3.3         spatstat.geom_3.4-1    png_0.1-8             
 [13] vctrs_0.6.5            reshape2_1.4.4         stringr_1.5.1         
 [16] pkgconfig_2.0.3        fastmap_1.2.0          caTools_1.18.3        
 [19] promises_1.3.2         purrr_1.0.4            jsonlite_2.0.0        
 [22] goftest_1.2-3          later_1.4.2            spatstat.utils_3.1-4  
 [25] irlba_2.3.5.1          parallel_4.3.3         cluster_2.1.8.1       
 [28] R6_2.6.1               ica_1.0-3              stringi_1.8.7         
 [31] RColorBrewer_1.1-3     spatstat.data_3.1-6    reticulate_1.42.0     
 [34] parallelly_1.44.0      spatstat.univar_3.1-3  lmtest_0.9-40         
 [37] scattermore_1.2        Rcpp_1.1.2             tensor_1.5            
 [40] future.apply_1.11.3    zoo_1.8-14             sctransform_0.4.2     
 [43] httpuv_1.6.15          Matrix_1.6-5           splines_4.3.3         
 [46] igraph_2.0.3           tidyselect_1.2.1       dichromat_2.0-0.1     
 [49] abind_1.4-5            gplots_3.2.0           codetools_0.2-20      
 [52] spatstat.random_3.4-1  miniUI_0.1.2           spatstat.explore_3.4-3
 [55] curl_6.2.2             listenv_0.9.1          lattice_0.22-7        
 [58] tibble_3.2.1           plyr_1.8.9             shiny_1.10.0          
 [61] ROCR_1.0-11            Rtsne_0.17             future_1.49.0         
 [64] fastDummies_1.7.5      survival_3.8-3         polyclip_1.10-7       
 [67] fitdistrplus_1.2-2     pillar_1.10.2          KernSmooth_2.23-26    
 [70] plotly_4.10.4          generics_0.1.4         RcppHNSW_0.6.0        
 [73] ggplot2_3.5.2          scales_1.4.0           gtools_3.9.5          
 [76] globals_0.18.0         xtable_1.8-4           glue_1.8.0            
 [79] lazyeval_0.2.2         tools_4.3.3            data.table_1.17.4     
 [82] RSpectra_0.16-2        locfit_1.5-9.12        RANN_2.6.2            
 [85] dotCall64_1.2          cowplot_1.1.3          grid_4.3.3            
 [88] tidyr_1.3.1            colorspace_2.1-1       nlme_3.1-168          
 [91] patchwork_1.3.0        cli_3.6.6              spatstat.sparse_3.1-0 
 [94] spam_2.11-1            viridisLite_0.4.2      dplyr_1.1.4           
 [97] uwot_0.2.3             gtable_0.3.6           digest_0.6.37         
[100] progressr_0.15.1       ggrepel_0.9.6          htmlwidgets_1.6.4     
[103] farver_2.1.2           htmltools_0.5.8.1      lifecycle_1.0.5       
[106] httr_1.4.7             mime_0.13              MASS_7.3-60.0.1

Thank you again for your help.