`hpaDownload()` is failing unless `version="example/build-in"`
Opened this issue · 3 comments
Hey! I have tried a lot of things for downloadList, but any call of hpaDownload is failing, except when using example/build-in datasets. Any ideas? Thanks a lot!
example:
> library(HPAanalyze)
>
> dat <- hpaDownload("Normal tissue", "example")
Only the followings are example/built-in datasets:
- Normal tissue
- Pathology
- Subcellular location
Other datasets will not be loaded
> summary(dat)
Length Class Mode
normal_tissue 6 tbl_df list
>
> dat <- hpaDownload("Normal tissue")
trying URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
Error in download.file(url = downloadDatasets$urls[[i]], destfile = temp) :
cannot open URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip'
In addition: Warning message:
In download.file(url = downloadDatasets$urls[[i]], destfile = temp) :
cannot open URL 'https://www.proteinatlas.org/download/normal_tissue.tsv.zip': HTTP status was '404 Not Found'
session info:
> sessionInfo()
R version 4.4.1 Patched (2024-07-08 r86893)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.2.1
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/Madrid
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] HPAanalyze_1.24.0 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 zip_2.3.1 cli_3.6.3 rlang_1.1.4 stringi_1.8.4 generics_0.1.3
[7] glue_1.8.0 colorspace_2.1-1 scales_1.3.0 fansi_1.0.6 grid_4.4.1 munsell_0.5.1
[13] tibble_3.2.1 openxlsx_4.2.7.1 lifecycle_1.0.4 compiler_4.4.1 Rcpp_1.0.13-1 pkgconfig_2.0.3
[19] rstudioapi_0.17.1 R6_2.5.1 tidyselect_1.2.1 utf8_1.2.4 pillar_1.9.0 magrittr_2.0.3
[25] tools_4.4.1 gtable_0.3.6 xml2_1.3.6 ggplot2_3.5.1
I have found the same issue. It looks like the previous link: "https://www.proteinatlas.org/download/subcellular_location.tsv.zip" doesn't host the data anymore. In the website i found this other link "https://www.proteinatlas.org/download/tsv/subcellular_locations.tsv.zip" which seems to be working, if it could be loaded into hpaDownload function maybe would work.
If you find another solution i would appreciate to know it
If you'd like, you can download the latest version of any data you want manually from the website "https://www.proteinatlas.org/about/download", and unzip it and load into R. It worked for me.
Sure, though I was hoping for a programmatic way of doing this. I now have a solution where I read the data directly into R fro the web, without downloading any files locally. I assume this is what the package was designed to do. Maybe it'll be solved eventually...