graphite package SSL certificate
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@d1ec5898
Last seen 3 months ago
United States

Could not use the pathways function in graphite starting 2021.12.04 on my mac, but it runs just fine on windows:(

d <- pathways("dmelanogaster","reactome")

Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  SSL certificate problem: certificate has expired
Error in fetchRemote(name, path) : 
  cannot download pathway data: are you offline?


sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] clusterProfiler_4.2.0 Matrix_1.3-4          pracma_2.3.3          cosinor_1.1           rlist_0.4.6.2        
 [6] igraph_1.2.9          plotly_4.10.0         ggplot2_3.3.5         stringr_1.4.0         org.Dm.eg.db_3.14.0  
[11] org.Hs.eg.db_3.14.0   AnnotationDbi_1.56.2  IRanges_2.28.0        S4Vectors_0.32.3      Biobase_2.54.0       
[16] BiocGenerics_0.40.0   graphite_1.40.0      

loaded via a namespace (and not attached):
  [1] ggtree_3.2.1           fgsea_1.20.0           colorspace_2.0-2       ellipsis_0.3.2         qvalue_2.26.0         
  [6] XVector_0.34.0         aplot_0.1.1            rstudioapi_0.13        farver_2.1.0           graphlayouts_0.7.2    
 [11] ggrepel_0.9.1          bit64_4.0.5            scatterpie_0.1.7       fansi_0.5.0            splines_4.1.2         
 [16] cachem_1.0.6           GOSemSim_2.20.0        knitr_1.36             polyclip_1.10-0        jsonlite_1.7.2        
 [21] GO.db_3.14.0           png_0.1-7              graph_1.72.0           ggforce_0.3.3          shiny_1.7.1           
 [26] compiler_4.1.2         httr_1.4.2             backports_1.4.0        assertthat_0.2.1       fastmap_1.1.0         
 [31] lazyeval_0.2.2         later_1.3.0            tweenr_1.0.2           htmltools_0.5.2        tools_4.1.2           
 [36] gtable_0.3.0           glue_1.5.1             GenomeInfoDbData_1.2.7 reshape2_1.4.4         DO.db_2.9             
 [41] dplyr_1.0.7            rappdirs_0.3.3         fastmatch_1.1-3        Rcpp_1.0.7             enrichplot_1.14.1     
 [46] jquerylib_0.1.4        vctrs_0.3.8            Biostrings_2.62.0      nlme_3.1-153           ape_5.5               
 [51] ggraph_2.0.5           xfun_0.28              mime_0.12              lifecycle_1.0.1        DOSE_3.20.1           
 [56] zlibbioc_1.40.0        MASS_7.3-54            scales_1.1.1           tidygraph_1.2.0        promises_1.2.0.1      
 [61] parallel_4.1.2         RColorBrewer_1.1-2     curl_4.3.2             yaml_2.2.1             memoise_2.0.1         
 [66] gridExtra_2.3          ggfun_0.0.4            downloader_0.4         sass_0.4.0             yulab.utils_0.0.4     
 [71] stringi_1.7.6          RSQLite_2.2.8          tidytree_0.3.6         checkmate_2.0.0        BiocParallel_1.28.2   
 [76] GenomeInfoDb_1.30.0    rlang_0.4.12           pkgconfig_2.0.3        bitops_1.0-7           evaluate_0.14         
 [81] lattice_0.20-45        purrr_0.3.4            treeio_1.18.1          patchwork_1.1.1        htmlwidgets_1.5.4     
 [86] shadowtext_0.0.9       bit_4.0.4              tidyselect_1.1.1       plyr_1.8.6             magrittr_2.0.1        
 [91] R6_2.5.1               generics_0.1.1         DBI_1.1.1              pillar_1.6.4           withr_2.4.3           
 [96] KEGGREST_1.34.0        RCurl_1.98-1.5         tibble_3.1.6           crayon_1.4.2           utf8_1.2.2            
[101] rmarkdown_2.11         viridis_0.6.2          grid_4.1.2             data.table_1.14.2      blob_1.2.2            
[106] digest_0.6.29          xtable_1.8-4           tidyr_1.1.4            httpuv_1.6.3           gridGraphics_0.5-1    
[111] munsell_0.5.0          ggplotify_0.1.0        viridisLite_0.4.0      bslib_0.3.1
graphite • 366 views
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@gabrielesales-6826
Last seen 4 months ago
European Union

Hi, the problem you describe occurs when graphite tries to download pathway data from the web. You're using High Sierra, a macOS version released in 2017 which no longer receives security updates. For this reason, the software does not recognize security (SSL) certificates that have been released recently.

There are two ways to solve this problem. First, you could follow the procedure described below to update manually the list of accepted certificates.

Certificate Expired Error

I would strongly suggest, though, to update the entire OS. This would fix the specific issue, but would also provide other critical security updates.

Best, Gabriele

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Thank you so much!

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