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httr does not retrieve data proberly #758

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toobiwankenobi opened this issue Jan 6, 2025 · 0 comments
Open

httr does not retrieve data proberly #758

toobiwankenobi opened this issue Jan 6, 2025 · 0 comments

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@toobiwankenobi
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toobiwankenobi commented Jan 6, 2025

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    
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