Mac-related issue - empty data.frame

[toobiwankenobi]

Sorry, I can't reproduce the error on my end (I don't have access to a Mac).
I've tested the code on both Windows and Ubuntu. It seems to an issue with
the library on Mac which I can't help you debug.
Perhaps the maintainer of httr can provide some help if you have a minimally reproducible example, e.g.:

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")

So this means a dependency of UniProt.ws is not working properly?

Essentially, yes. Please file an issue with httr and they may help you further.

Update: I've asked a colleague to run the code for me and they are also seeing an empty data.frame on Mac.
The issue is present with both httr and httr2.

Best regards,
Marcel

Originally posted by @LiNk-NY in #28 (comment)

[toobiwankenobi]

I contacted the dev's of httr2. The problem is unrelated to httr2 as the following command successfully returns data.

result <- request("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") |>
+     req_perform()

The problem persists and I can't neither use mapUniProt() nor queryUniProt() as originally described in this issue.

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] httr2_1.0.7            data.table_1.16.4      queryup_1.0.5          lubridate_1.9.4        stringr_1.5.1          purrr_1.0.2            readr_2.1.5            tibble_3.2.1          
 [9] tidyverse_2.0.0        EnhancedVolcano_1.24.0 RColorBrewer_1.1-3     forcats_1.0.0          dplyr_1.1.4            MetBrewer_0.2.0        ggrepel_0.9.6          ggbeeswarm_0.7.2      
[17] ggplot2_3.5.1          tidyr_1.3.1            UniProt.ws_2.46.1      RSQLite_2.3.9          BiocGenerics_0.52.0   

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1        vipor_0.4.7             farver_2.1.2            blob_1.2.4              filelock_1.0.3          Biostrings_2.74.1       fastmap_1.2.0          
 [8] BiocFileCache_2.14.0    digest_0.6.37           timechange_0.3.0        lifecycle_1.0.4         KEGGREST_1.46.0         httpcache_1.2.0         magrittr_2.0.3         
[15] compiler_4.4.2          rlang_1.1.4             progress_1.2.3          tools_4.4.2             yaml_2.3.10             knitr_1.49              prettyunits_1.2.0      
[22] labeling_0.4.3          bit_4.5.0.1             curl_6.1.0              withr_3.0.2             grid_4.4.2              stats4_4.4.2            colorspace_2.1-1       
[29] scales_1.3.0            cli_3.6.3               rmarkdown_2.29          crayon_1.5.3            generics_0.1.3          rstudioapi_0.17.1       httr_1.4.7             
[36] tzdb_0.4.0              BiocBaseUtils_1.8.0     DBI_1.2.3               cachem_1.1.0            zlibbioc_1.52.0         AnnotationDbi_1.68.0    BiocManager_1.30.25    
[43] XVector_0.46.0          vctrs_0.6.5             jsonlite_1.8.9          IRanges_2.40.1          hms_1.1.3               S4Vectors_0.44.0        bit64_4.5.2            
[50] beeswarm_0.4.0          glue_1.8.0              stringi_1.8.4           gtable_0.3.6            GenomeInfoDb_1.42.1     UCSC.utils_1.2.0        munsell_0.5.1          
[57] pillar_1.10.0           rappdirs_0.3.3          htmltools_0.5.8.1       GenomeInfoDbData_1.2.13 R6_2.5.1                dbplyr_2.5.0            evaluate_1.0.1         
[64] Biobase_2.66.0          png_0.1-8               memoise_2.0.1           rjsoncons_1.3.1         Rcpp_1.0.13-1           xfun_0.49               pkgconfig_2.0.3 

[LiNk-NY]

Please link the issue you opened next time.
r-lib/httr2#624
It looks like the gzip content is not automatically decompressed and I am not sure why that is.
It is a Mac-only issue because both Linux and Windows run the code without a problem.
I will wait for the httr2 maintainer's response.

[toobiwankenobi]

Hi @LiNk-NY
Ok, thank you for your support!