decoupleR::get_collectri [WARN]

[Xinlei672]

Hi, I have an issue about get_collectri function.
net<-decoupleR::get_collectri(organism='mouse',split_complexes=FALSE)
[2024-12-05 16:11:18] [WARN] [OmnipathR] Accessing collectri as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
Error in if (.keep) . else select(., -!!evs_col) :
argument is of length zero

[deeenes]

HI, A download error happens which is silenced by error handling but should be visible in the log (especially if you set it trace: OmnipathR::omnipath_set_console_loglevel("trace")). However, an easier way to find out is to call the download itself directly:

library(readr)
ci <- read_tsv('https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic')

[Xinlei672]

Hi. When I run the OmnipathR::omnipath_set_console_loglevel("trace"), the log as below:

OmnipathR::omnipath_set_console_loglevel("trace")
net<-get_collectri(organism='mouse',split_complexes=FALSE)
[2024-12-06 08:51:25] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names.
[2024-12-06 08:51:25] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-12-06 08:51:25] [TRACE] [OmnipathR] Cache file path: /Users/sxl/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-12-06 08:51:25] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt.
[2024-12-06 08:51:25] [INFO] [OmnipathR] No version is available for key 30e690cbb55dfc63b5903ab337f34ffc2f4be397 (https://omabrowser.org/All/oma-species.txt).
[2024-12-06 08:51:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=10090,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2024-12-06 08:51:25] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names.
[2024-12-06 08:51:25] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-12-06 08:51:25] [TRACE] [OmnipathR] Cache file path: /Users/sxl/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-12-06 08:51:25] [TRACE] [OmnipathR] Looking up in cache: https://omabrowser.org/All/oma-species.txt.
[2024-12-06 08:51:25] [INFO] [OmnipathR] No version is available for key 30e690cbb55dfc63b5903ab337f34ffc2f4be397 (https://omabrowser.org/All/oma-species.txt).
[2024-12-06 08:51:25] [WARN] [OmnipathR] Accessing collectri as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2024-12-06 08:51:25] [TRACE] [OmnipathR] Looking up in cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_10090.tsv.gz
[2024-12-06 08:51:25] [TRACE] [OmnipathR] Loaded data from RDS /Users/sxl/Library/Caches/OmnipathR/7baa50ccf837dbf0b346d11598cae7736f26599a-1.rds.
[2024-12-06 08:51:25] [INFO] [OmnipathR] Loaded from cache: http://no-tls.static.omnipathdb.org/resources/interactions_collectri_10090.tsv.gz
[2024-12-06 08:51:25] [TRACE] [OmnipathR] Converting JSON column evidences to list.
[2024-12-06 08:51:27] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
Error in if (.keep) . else select(., -!!evs_col) :
argument is of length zero

Thanks

[PauBadiaM]

Any updates on this @deeenes ?