getURL() failed

[saezlab]

getURL() failed

[deeenes]

Hi Sigve,

Thanks for your report. We know about this issue, it is a server side error, it happens if for some resource the license is unknown. We will fix it still today, I will close this issue once fixed.

Best wishes,

Denes

[asumann]

Hi @deeenes,

I am getting a similar error with this code in the vignette. Hope you can help me figure that out.

HPA_small <- import_omnipath_annotations(
  proteins = c('TP53', 'LMNA'),
  resources = c('HPA_tissue'),
  wide = TRUE
)

Error in (function (URL, FUN, ..., N.TRIES = 1L)  : 
  omnipath_download() failed:
  URL: https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=TP53,LMNA&license=academic
  error: cannot open the connection to 'https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=TP53,LMNA&license=academic'
In addition: Warning message:
In file(file, "rt") :
  cannot open URL 'https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=TP53,LMNA&license=academic': HTTP status was '500 Internal Server Error'

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] OmnipathR_2.0.0 jsonlite_1.7.2  tidyr_1.1.2     qgraph_1.6.9    igraph_1.2.6    openxlsx_4.2.3 
[7] purrr_0.3.4     tibble_3.0.6    dplyr_1.0.4    

loaded via a namespace (and not attached):
 [1] splines_4.0.2       tmvnsim_1.0-2       gtools_3.8.2        Formula_1.2-4      
 [5] assertthat_0.2.1    BiocManager_1.30.10 stats4_4.0.2        latticeExtra_0.6-29
 [9] yaml_2.2.1          remotes_2.2.0       pbivnorm_0.6.0      pillar_1.4.7       
[13] backports_1.2.1     lattice_0.20-41     glue_1.4.2          digest_0.6.27      
[17] RColorBrewer_1.1-2  checkmate_2.0.0     colorspace_2.0-0    htmltools_0.5.1.1  
[21] Matrix_1.3-2        plyr_1.8.6          psych_2.0.12        pkgconfig_2.0.3    
[25] corpcor_1.6.9       scales_1.1.1        glasso_1.11         jpeg_0.1-8.1       
[29] fdrtool_1.2.16      htmlTable_2.1.0     generics_0.1.0      ggplot2_3.3.3      
[33] ellipsis_0.3.1      pbapply_1.4-3       nnet_7.3-15         cli_2.3.0          
[37] mnormt_2.0.2        survival_3.2-7      magrittr_2.0.1      crayon_1.4.0       
[41] fansi_0.4.2         nlme_3.1-152        foreign_0.8-81      tools_4.0.2        
[45] data.table_1.13.6   lifecycle_0.2.0     stringr_1.4.0       munsell_0.5.0      
[49] cluster_2.1.0       zip_2.1.1           packrat_0.5.0       compiler_4.0.2     
[53] rlang_0.4.10        grid_4.0.2          rstudioapi_0.13     htmlwidgets_1.5.3  
[57] lavaan_0.6-7        base64enc_0.1-3     gtable_0.3.0        curl_4.3           
[61] abind_1.4-5         DBI_1.1.1           reshape2_1.4.4      R6_2.5.0           
[65] gridExtra_2.3       knitr_1.31          utf8_1.1.4          Hmisc_4.4-2        
[69] stringi_1.5.3       parallel_4.0.2      Rcpp_1.0.6          vctrs_0.3.6        
[73] rpart_4.1-15        png_0.1-7           tidyselect_1.1.0    xfun_0.20  

All the best,
Asuman

[deeenes]

Hi Asuman,

Looks like it was a temporary disruption, probably the server was overloaded.
The same query was successful for me. Let me know if you are still experiencing this issue.

Best,

Denes

[asumann]

Works perfectly now, many thanks!