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.
This is my session info:
> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DEGreport_1.42.0 ReactomeContentService4R_1.9.0 curl_6.2.2 ReactomeGSA_1.20.0
[5] data.table_1.17.2 enrichplot_1.26.6 gprofiler2_0.2.3 clusterProfiler_4.14.6
[9] AnnotationHub_3.14.0 BiocFileCache_2.14.0 dbplyr_2.5.0 VennDiagram_1.7.3
[13] edgeR_4.4.2 limma_3.62.2 rhdf5_2.50.2 readxl_1.4.5
[17] itertools_0.1-3 apeglm_1.28.0 doParallel_1.0.17 iterators_1.0.14
[21] foreach_1.5.2 EnhancedVolcano_1.24.0 ggrepel_0.9.6 geneplotter_1.84.0
[25] annotate_1.84.0 XML_3.99-0.18 AnnotationDbi_1.68.0 lattice_0.22-7
[29] DESeq2_1.46.0 SummarizedExperiment_1.36.0 Biobase_2.66.0 MatrixGenerics_1.18.1
[33] matrixStats_1.5.0 GenomicRanges_1.58.0 GenomeInfoDb_1.42.3 IRanges_2.40.1
[37] S4Vectors_0.44.0 BiocGenerics_0.52.0 plotly_4.10.4 ggplot2_3.5.2
[41] tibble_3.2.1 BiocParallel_1.40.2 tximport_1.34.0 gtools_3.9.5
[45] yaml_2.3.10 magrittr_2.0.3 viridisLite_0.4.2 futile.logger_1.4.3
[49] gridExtra_2.3 DT_0.33 kableExtra_1.4.0 knitr_1.50
[53] here_1.0.1 readr_2.1.5 tidyr_1.3.1 stringr_1.5.1
[57] purrr_1.0.4 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] fs_1.6.6 bitops_1.0-9 httr_1.4.7 RColorBrewer_1.1-3 numDeriv_2016.8-1.1
[6] backports_1.5.0 tools_4.4.2 utf8_1.2.5 R6_2.6.1 mgcv_1.9-3
[11] lazyeval_0.2.2 rhdf5filters_1.18.1 GetoptLong_1.0.5 withr_3.0.2 prettyunits_1.2.0
[16] cli_3.6.5 textshaping_1.0.1 formatR_1.14 logging_0.10-108 labeling_0.4.3
[21] sass_0.4.10 mvtnorm_1.3-3 systemfonts_1.2.3 yulab.utils_0.2.0 gson_0.1.0
[26] DOSE_4.0.1 svglite_2.2.1 R.utils_2.13.0 bbmle_1.0.25.1 rstudioapi_0.17.1
[31] RSQLite_2.3.11 generics_0.1.4 gridGraphics_0.5-1 shape_1.4.6.1 crosstalk_1.2.1
[36] vroom_1.6.5 GO.db_3.20.0 Matrix_1.7-3 abind_1.4-8 R.methodsS3_1.8.2
[41] lifecycle_1.0.4 gplots_3.2.0 qvalue_2.38.0 SparseArray_1.6.2 blob_1.2.4
[46] promises_1.3.2 crayon_1.5.3 bdsmatrix_1.3-7 ggtangle_0.0.6 cowplot_1.1.3
[51] KEGGREST_1.46.0 magick_2.8.6 pillar_1.10.2 ComplexHeatmap_2.22.0 fgsea_1.32.4
[56] rjson_0.2.23 codetools_0.2-20 fastmatch_1.1-6 glue_1.8.0 ggfun_0.1.8
[61] vctrs_0.6.5 png_0.1-8 treeio_1.30.0 cellranger_1.1.0 gtable_0.3.6
[66] emdbook_1.3.13 cachem_1.1.0 xfun_0.52 S4Arrays_1.6.0 mime_0.13
[71] ConsensusClusterPlus_1.70.0 coda_0.19-4.1 statmod_1.5.0 nlme_3.1-168 ggtree_3.14.0
[76] bit64_4.6.0-1 progress_1.2.3 filelock_1.0.3 rprojroot_2.0.4 bslib_0.9.0
[81] KernSmooth_2.23-26 colorspace_2.1-1 DBI_1.2.3 mnormt_2.1.1 tidyselect_1.2.1
[86] bit_4.6.0 compiler_4.4.2 xml2_1.3.8 ggdendro_0.2.0 DelayedArray_0.32.0
[91] scales_1.4.0 caTools_1.18.3 psych_2.5.3 rappdirs_0.3.3 digest_0.6.37
[96] rmarkdown_2.29 XVector_0.46.0 htmltools_0.5.8.1 pkgconfig_2.0.3 fastmap_1.2.0
[101] rlang_1.1.6 GlobalOptions_0.1.2 htmlwidgets_1.6.4 UCSC.utils_1.2.0 shiny_1.10.0
[106] farver_2.1.2 jquerylib_0.1.4 jsonlite_2.0.0 GOSemSim_2.32.0 R.oo_1.27.1
[111] GenomeInfoDbData_1.2.13 ggplotify_0.1.2 patchwork_1.3.0 Rhdf5lib_1.28.0 Rcpp_1.0.14
[116] ape_5.8-1 stringi_1.8.7 zlibbioc_1.52.0 MASS_7.3-65 plyr_1.8.9
[121] forcats_1.0.1 Biostrings_2.74.1 splines_4.4.2 hms_1.1.3 circlize_0.4.16
[126] locfit_1.5-9.12 igraph_2.1.4 reshape2_1.4.4 futile.options_1.0.1 BiocVersion_3.20.0
[131] evaluate_1.0.3 lambda.r_1.2.4 BiocManager_1.30.25 tzdb_0.5.0 httpuv_1.6.16
[136] reshape_0.8.9 clue_0.3-66 broom_1.0.8 xtable_1.8-4 tidytree_0.4.6
[141] later_1.4.2 ragg_1.3.3 aplot_0.2.5 memoise_2.0.1 cluster_2.1.8.1
Update: had the same problem today again.
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.This is my session info:
Update: had the same problem today again.