Couldn't connect to server while using "pathways"
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@fduguchunhui-22926
Last seen 19 days ago
United States

Cannot retrieve pathways from any database, such as "Reactome" and "Kegg". I have confirmed that I have internet access.

humanReactome <- pathways("hsapiens", "reactome")

Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to connect to graphiteweb.bio.unipd.it port 443 after 7173 ms: Couldn't connect to server
Error in fetchRemote(name, path) : 
  cannot download pathway data: are you offline?
 version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.6.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
 [1] lubridate_1.9.3 forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4     purrr_1.0.2    
 [6] readr_2.1.5     tidyr_1.3.1     tibble_3.2.1    ggplot2_3.5.1   tidyverse_2.0.0
[11] graphite_1.50.0

loaded via a namespace (and not attached):
 [1] KEGGREST_1.44.0         gtable_0.3.5            xfun_0.43              
 [4] Biobase_2.64.0          tzdb_0.4.0              vctrs_0.6.5            
 [7] tools_4.4.0             generics_0.1.3          stats4_4.4.0           
[10] curl_5.2.1              fansi_1.0.6             AnnotationDbi_1.66.0   
[13] RSQLite_2.3.6           highr_0.10              blob_1.2.4             
[16] pkgconfig_2.0.3         S4Vectors_0.42.0        graph_1.82.0           
[19] lifecycle_1.0.4         GenomeInfoDbData_1.2.12 compiler_4.4.0         
[22] Biostrings_2.72.0       munsell_0.5.1           GenomeInfoDb_1.40.0    
[25] pillar_1.9.0            crayon_1.5.2            cachem_1.0.8           
[28] tidyselect_1.2.1        stringi_1.8.3           fastmap_1.1.1          
[31] grid_4.4.0              colorspace_2.1-0        cli_3.6.2              
[34] magrittr_2.0.3          utf8_1.2.4              withr_3.0.0            
[37] scales_1.3.0            UCSC.utils_1.0.0        rappdirs_0.3.3         
[40] bit64_4.0.5             timechange_0.3.0        XVector_0.44.0         
[43] httr_1.4.7              bit_4.0.5               png_0.1-8              
[46] hms_1.1.3               memoise_2.0.1           evaluate_0.23          
[49] knitr_1.46              IRanges_2.38.0          rlang_1.1.3            
[52] glue_1.7.0              DBI_1.2.2               BiocManager_1.30.23    
[55] BiocGenerics_0.50.0     rstudioapi_0.16.0       jsonlite_1.8.8         
[58] R6_2.5.1                zlibbioc_1.50.0
graphite • 248 views
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Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the package that causes this.

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You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site.

Can you put a tag for the relevant software instead? DESeq2 doesn't have a function pathways().

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@james-w-macdonald-5106
Last seen 2 days ago
United States

As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide enough description of the problem so that people can reproduce.

I cannot reproduce the issue, and it is likely that this is just a transient problem at the graphite server that has since been resolved.

> library(graphite)
> z <- pathways("hsapiens","reactome")
> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] graphite_1.50.0    
[2] BiocManager_1.30.23

loaded via a namespace (and not attached):
 [1] crayon_1.5.2           
 [2] vctrs_0.6.5            
 [3] httr_1.4.7             
 [4] cli_3.6.2              
 [5] rlang_1.1.3            
 [6] DBI_1.2.2              
 [7] UCSC.utils_1.0.0       
 [8] png_0.1-8              
 [9] jsonlite_1.8.8         
[10] bit_4.0.5              
[11] S4Vectors_0.42.0       
[12] Biostrings_2.72.0      
[13] graph_1.82.0           
[14] stats4_4.4.0           
[15] KEGGREST_1.44.0        
[16] rappdirs_0.3.3         
[17] Biobase_2.64.0         
[18] fastmap_1.1.1          
[19] GenomeInfoDb_1.40.0    
[20] IRanges_2.38.0         
[21] memoise_2.0.1          
[22] compiler_4.4.0         
[23] RSQLite_2.3.6          
[24] blob_1.2.4             
[25] XVector_0.44.0         
[26] R6_2.5.1               
[27] curl_5.2.1             
[28] GenomeInfoDbData_1.2.12
[29] AnnotationDbi_1.66.0   
[30] tools_4.4.0            
[31] bit64_4.0.5            
[32] zlibbioc_1.50.0        
[33] BiocGenerics_0.50.0    
[34] cachem_1.0.8           
>

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