Hi,
In our today's run, our pipeline entered an endless loop when calling perform_reactome_analysis(compress = FALSE). This is the relevant log:
INFO [2026-06-19 16:59:22] [Pathways] Submitting request to Reactome API...
INFO [2026-06-19 16:59:27] [Pathways] Reactome Analysis submitted succesfully
INFO [2026-06-19 16:59:28] [Pathways]
INFO [2026-06-19 16:59:28] [Pathways]
INFO [2026-06-19 16:59:28] [Pathways] Updating to new REACTOME version...
INFO [2026-06-19 16:59:28] [Pathways]
INFO [2026-06-19 16:59:28] [Pathways]
INFO [2026-06-19 16:59:28] [Pathways] Running analysis [>---------------------------------------------------------:]
INFO [2026-06-19 16:59:30] [Pathways]
INFO [2026-06-19 16:59:30] [Pathways]
INFO [2026-06-19 16:59:30] [Pathways] Converting dataset RNA-seq...
INFO [2026-06-19 16:59:30] [Pathways] Running analysis [>---------------------------------------------------------:]
INFO [2026-06-19 16:59:30] [Pathways]
INFO [2026-06-19 16:59:30] [Pathways] Running analysis [==>-------------------------------------------------------:]
INFO [2026-06-19 16:59:31] [Pathways]
INFO [2026-06-19 16:59:31] [Pathways]
INFO [2026-06-19 16:59:31] [Pathways] Mapping identifiers...
INFO [2026-06-19 16:59:31] [Pathways] Running analysis [==>-------------------------------------------------------:]
INFO [2026-06-19 16:59:31] [Pathways]
INFO [2026-06-19 16:59:31] [Pathways] Running analysis [=====>----------------------------------------------------:]
INFO [2026-06-19 16:59:33] [Pathways]
INFO [2026-06-19 16:59:33] [Pathways]
INFO [2026-06-19 16:59:33] [Pathways] Performing gene set analysis using Camera
INFO [2026-06-19 16:59:33] [Pathways] Running analysis [=====>----------------------------------------------------:]
INFO [2026-06-19 16:59:33] [Pathways]
INFO [2026-06-19 16:59:33] [Pathways] Running analysis [===========>----------------------------------------------:]
INFO [2026-06-19 16:59:35] [Pathways]
INFO [2026-06-19 16:59:35] [Pathways]
INFO [2026-06-19 16:59:35] [Pathways] Analysing dataset 'RNA-seq' using Camera
INFO [2026-06-19 16:59:35] [Pathways] Running analysis [===========>----------------------------------------------:]
INFO [2026-06-19 16:59:35] [Pathways]
INFO [2026-06-19 16:59:35] [Pathways] Running analysis [==================================>-----------------------:]
INFO [2026-06-19 16:59:36] [Pathways]
INFO [2026-06-19 16:59:36] [Pathways] Running analysis [========================================>-----------------:]
INFO [2026-06-19 16:59:38] [Pathways]
INFO [2026-06-19 16:59:38] [Pathways] Running analysis [=============================================>------------:]
INFO [2026-06-19 16:59:42] [Pathways]
INFO [2026-06-19 16:59:42] [Pathways]
INFO [2026-06-19 16:59:42] [Pathways] Creating REACTOME visualization
INFO [2026-06-19 16:59:42] [Pathways] Running analysis [=============================================>------------:]
INFO [2026-06-19 16:59:42] [Pathways]
INFO [2026-06-19 16:59:42] [Pathways] Running analysis [===================================================>------:]
WARN [2026-06-19 17:00:06] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '503 Service Unavailable'
INFO [2026-06-19 17:00:06] [Pathways]
INFO [2026-06-19 17:00:06] [Pathways]
INFO [2026-06-19 17:00:06] [Pathways] Unknown
INFO [2026-06-19 17:00:06] [Pathways] Running analysis [===================================================>------:]
INFO [2026-06-19 17:00:06] [Pathways]
INFO [2026-06-19 17:00:06] [Pathways] Running analysis [----------------------------------------------------------:]
WARN [2026-06-19 17:00:23] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '503 Service Unavailable'
WARN [2026-06-19 17:00:41] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '503 Service Unavailable'
WARN [2026-06-19 17:01:00] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '503 Service Unavailable'
WARN [2026-06-19 17:01:19] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '503 Service Unavailable'
WARN [2026-06-19 17:01:27] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '404 Not Found'
WARN [2026-06-19 17:01:28] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '404 Not Found'
WARN [2026-06-19 17:01:30] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '404 Not Found'
WARN [2026-06-19 17:01:31] [Pathways] cannot open URL 'https://gsa.reactome.org/0.1/status/3920b942-6c00-11f1-b7f1-e2738a25604a': HTTP status was '404 Not Found'
And it continued the last lines for > 2h, until the run was manually stopped. Maybe the initial call to start_reactome_analysis returned an ID although there was some internal problem. It might also be related to some get_reactome_analysis_status response returning error = function(e) list(completed = 0, description = "Unknown", status = "running"). The subsequent calls to get_reactome_analysis_status seem to not have errored although the response was 404, leading to the error counter not building up.
Hi,
In our today's run, our pipeline entered an endless loop when calling
perform_reactome_analysis(compress = FALSE). This is the relevant log:And it continued the last lines for > 2h, until the run was manually stopped. Maybe the initial call to
start_reactome_analysisreturned an ID although there was some internal problem. It might also be related to someget_reactome_analysis_statusresponse returningerror = function(e) list(completed = 0, description = "Unknown", status = "running"). The subsequent calls toget_reactome_analysis_statusseem to not have errored although the response was 404, leading to the error counter not building up.