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Description
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 Metadata
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