Skip to content

httr does not retrieve data proberly #758

Description

@toobiwankenobi

httr is a dependency of the Bioconductor package UniProt.ws. It is used to query data in the UniProt database.
This dependency is causing issues when using UniProt.ws. Essentially, it does not retrieve the data properly. I described the problem in this issue. It seems to be mac specific problem, as the code works on windows and ubuntu. It fails with both httr and httr2.

Example (returns NA)

httr::GET("https://rest.uniprot.org/uniprotkb/search?query=organism_id%3A9606%20OR%20gene_exact%3AA2M&fields=id%2Caccession%2Cgene_primary%2Corganism_name%2Cprotein_name%2Creviewed&format=tsv&size=25")
> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.0.1

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: Europe/Zurich
tzcode source: internal

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

other attached packages:
[1] UniProt.ws_2.46.1   RSQLite_2.3.9       BiocGenerics_0.52.0

loaded via a namespace (and not attached):
 [1] generics_0.1.3          hms_1.1.3               digest_0.6.37           magrittr_2.0.3          evaluate_1.0.1          fastmap_1.2.0          
 [7] blob_1.2.4              jsonlite_1.8.9          progress_1.2.3          AnnotationDbi_1.68.0    GenomeInfoDb_1.42.1     DBI_1.2.3              
[13] httr_1.4.7              UCSC.utils_1.2.0        Biostrings_2.74.1       cli_3.6.3               rlang_1.1.4             crayon_1.5.3           
[19] dbplyr_2.5.0            XVector_0.46.0          Biobase_2.66.0          bit64_4.5.2             cachem_1.1.0            yaml_2.3.10            
[25] BiocBaseUtils_1.8.0     tools_4.4.2             memoise_2.0.1           dplyr_1.1.4             GenomeInfoDbData_1.2.13 filelock_1.0.3         
[31] curl_6.0.1              vctrs_0.6.5             rjsoncons_1.3.1         R6_2.5.1                png_0.1-8               stats4_4.4.2           
[37] lifecycle_1.0.4         BiocFileCache_2.14.0    zlibbioc_1.52.0         KEGGREST_1.46.0         S4Vectors_0.44.0        IRanges_2.40.1         
[43] bit_4.5.0.1             pkgconfig_2.0.3         pillar_1.10.0           glue_1.8.0              xfun_0.49               tibble_3.2.1           
[49] tidyselect_1.2.1        rstudioapi_0.17.1       knitr_1.49              htmltools_0.5.8.1       rmarkdown_2.29          compiler_4.4.2         
[55] prettyunits_1.2.0    

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions