Error when running "net <- get_collectri(organism='human', split_complexes=FALSE)"

[kasayadior]

Hi,

I am trying to run the decoupleR pipeline for TF enrichment analysis.
Please help.

Trying the code using OmnipathR:

net <- get_collectri(organism='human', split_complexes=FALSE)
Error: 'static_table' is not an exported object from 'namespace:OmnipathR'
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.4 (Ootpa)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el8-x86_64/lib/libopenblas_skylakexp-r0.3.13.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base

other attached packages:
[1] decoupleR_2.9.7

loaded via a namespace (and not attached):
[1] Rcpp_1.0.13 cellranger_1.1.0 later_1.3.2
[4] pillar_1.9.0 compiler_4.1.0 OmnipathR_3.13.27
[7] remotes_2.4.2.1 prettyunits_1.2.0 progress_1.2.3
[10] tools_4.1.0 pkgbuild_1.2.0 digest_0.6.37
[13] jsonlite_1.8.9 lifecycle_1.0.4 tibble_3.2.1
[16] checkmate_2.3.2 lattice_0.22-5 pkgconfig_2.0.3
[19] rlang_1.1.4 Matrix_1.6-3 igraph_2.0.3
[22] cli_3.6.3 rstudioapi_0.15.0 yaml_2.3.10
[25] curl_5.2.1 parallel_4.1.0 xfun_0.45
[28] xml2_1.3.6 withr_3.0.1 dplyr_1.1.4
[31] stringr_1.5.1 httr_1.4.7 rappdirs_0.3.3
[34] hms_1.1.3 generics_0.1.3 vctrs_0.6.5
[37] rprojroot_2.0.4 grid_4.1.0 tidyselect_1.2.1
[40] glue_1.8.0 R6_2.5.1 processx_3.8.4
[43] fansi_1.0.6 parallelly_1.38.0 readxl_1.4.3
[46] BiocParallel_1.28.3 callr_3.7.6 tzdb_0.4.0
[49] readr_2.1.5 tidyr_1.3.1 purrr_1.0.2
[52] logger_0.3.0 magrittr_2.0.3 ps_1.7.5
[55] backports_1.5.0 utf8_1.2.4 tinytex_0.32
[58] stringi_1.8.4 crayon_1.5.3

[deeenes]

Hi, I think since the server is back it will work fine as I suggested at the other issue. Let me know if you still experience any issue.