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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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get_progeny and organism = 'mouse' reports an error #129

Closed fedenichetti closed 1 month ago

fedenichetti commented 1 month ago

Hi there, I get an error with get_progeny and setting organism = 'mouse':

net <- get_progeny(organism = 'mouse', top = 100) [2024-06-12 12:00:03] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. Error in UseMethod("mutate") : no applicable method for 'mutate' applied to an object of class "list" In addition: Warning message: In .ensure_safe_path(.) : OmnipathR: Falling back to path /var/folders/d7/7k20s5nx4l58y2qh9395cn0m0000gn/T//RtmpRi99Zn/omnipathr-20240612-1200.log instead of //omnipathr-log/omnipathr-20240612-1200.log. R version 4.4.0 (2024-04-24) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.5

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/Rome tzcode source: internal

attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] DESeq2_1.44.0 circlize_0.4.16 ComplexHeatmap_2.20.0 rstatix_0.7.2 dlookr_0.6.3 limma_3.60.2 [7] ggfortify_0.4.17 ggpubr_0.6.0 ggridges_0.5.6 readxl_1.4.3 org.Mm.eg.db_3.19.1 AnnotationDbi_1.66.0 [13] clusterProfiler_4.12.0 decoupleR_2.10.0 SummarizedExperiment_1.34.0 GenomicRanges_1.56.0 GenomeInfoDb_1.40.1 IRanges_2.38.0 [19] S4Vectors_0.42.0 MatrixGenerics_1.16.0 matrixStats_1.3.0 janitor_2.2.0 lubridate_1.9.3 forcats_1.0.0 [25] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 [31] ggplot2_3.5.1 tidyverse_2.0.0 viper_1.38.0 Biobase_2.64.0 BiocGenerics_0.50.0 dorothea_1.16.0

loaded via a namespace (and not attached): [1] segmented_2.1-0 fs_1.6.4 reactable_0.4.4 enrichplot_1.24.0 HDO.db_0.99.1 httr_1.4.7 RColorBrewer_1.1-3 doParallel_1.0.17 [9] tools_4.4.0 backports_1.5.0 utf8_1.2.4 R6_2.5.1 mgcv_1.9-1 lazyeval_0.2.2 GetoptLong_1.0.5 withr_3.0.0 [17] prettyunits_1.2.0 gridExtra_2.3 cli_3.6.2 gt_0.10.1 pacman_0.5.1 scatterpie_0.2.3 labeling_0.4.3 proxy_0.4-27 [25] systemfonts_1.1.0 yulab.utils_0.1.4 gson_0.1.0 svglite_2.1.3 gfonts_0.2.0 DOSE_3.30.1 showtext_0.9-7 parallelly_1.37.1 [33] bcellViper_1.40.0 sysfonts_0.8.9 rstudioapi_0.16.0 RSQLite_2.3.7 httpcode_0.3.0 generics_0.1.3 gridGraphics_0.5-1 shape_1.4.6.1 [41] vroom_1.6.5 car_3.1-2 GO.db_3.19.1 Matrix_1.7-0 fansi_1.0.6 logger_0.3.0 abind_1.4-5 lifecycle_1.0.4 [49] yaml_2.3.8 snakecase_0.11.1 carData_3.0-5 gtsummary_1.7.2 qvalue_2.36.0 SparseArray_1.4.8 Rtsne_0.17 blob_1.2.4 [57] promises_1.3.0 crayon_1.5.2 lattice_0.22-6 cowplot_1.1.3 KEGGREST_1.44.0 pillar_1.9.0 knitr_1.47 fgsea_1.30.0 [65] rjson_0.2.21 codetools_0.2-20 fastmatch_1.1-4 glue_1.7.0 beepr_1.3 pagedown_0.20 ggfun_0.1.5 fontLiberation_0.1.0 [73] data.table_1.15.4 broom.helpers_1.15.0 vctrs_0.6.5 png_0.1-8 treeio_1.28.0 EnhancedVolcano_1.22.0 cellranger_1.1.0 gtable_0.3.5 [81] kernlab_0.9-32 cachem_1.1.0 OmnipathR_3.11.10 xfun_0.44 S4Arrays_1.4.1 mime_0.12 tidygraph_1.3.1 survival_3.7-0 [89] audio_0.1-11 iterators_1.0.14 showtextdb_3.0 statmod_1.5.0 nlme_3.1-165 ggtree_3.12.0 bit64_4.0.5 fontquiver_0.2.1 [97] progress_1.2.3 KernSmooth_2.23-24 colorspace_2.1-0 DBI_1.2.3 tidyselect_1.2.1 bit_4.0.5 compiler_4.4.0 extrafontdb_1.0 [105] curl_5.2.1 rvest_1.0.4 xml2_1.3.6 fontBitstreamVera_0.1.1 DelayedArray_0.30.1 plotly_4.10.4 shadowtext_0.1.3 checkmate_2.3.1 [113] scales_1.3.0 rappdirs_0.3.3 digest_0.6.35 mixtools_2.0.0 rmarkdown_2.27 XVector_0.44.0 htmltools_0.5.8.1 pkgconfig_2.0.3 [121] extrafont_0.19 fastmap_1.2.0 rlang_1.1.4 GlobalOptions_0.1.2 htmlwidgets_1.6.4 UCSC.utils_1.0.0 shiny_1.8.1.1 farver_2.1.2 [129] jsonlite_1.8.8 BiocParallel_1.38.0 GOSemSim_2.30.0 magrittr_2.0.3 kableExtra_1.4.0 GenomeInfoDbData_1.2.12 ggplotify_0.1.2 patchwork_1.2.0 [137] munsell_0.5.1 Rcpp_1.0.12 ape_5.8 viridis_0.6.5 gdtools_0.3.7 stringi_1.8.4 ggraph_2.2.1 zlibbioc_1.50.0 [145] MASS_7.3-60.2 plyr_1.8.9 hrbrthemes_0.8.7 parallel_4.4.0 ggrepel_0.9.5 Biostrings_2.72.1 graphlayouts_1.1.1 splines_4.4.0 [153] hms_1.1.3 locfit_1.5-9.9 igraph_2.0.3 ggsignif_0.6.4 reshape2_1.4.4 crul_1.4.2 evaluate_0.24.0 selectr_0.4-2 [161] tzdb_0.4.0 foreach_1.5.2 tweenr_2.0.3 httpuv_1.6.15 Rttf2pt1_1.3.12 polyclip_1.10-6 clue_0.3-65 ggforce_0.4.2 [169] broom_1.0.6 xtable_1.8-4 e1071_1.7-14 tidytree_0.4.6 later_1.3.2 viridisLite_0.4.2 class_7.3-22 aplot_0.2.2 [177] memoise_2.0.1 cluster_2.1.6 timechange_0.3.0

deeenes commented 1 month ago

Hello, I think we fixed this in 3.11.16, about 3 weeks ago. I recommend updating OmnipathR from git:

remotes::install_github('saezlab/OmnipathR')
fedenichetti commented 1 month ago

Worked after installing the developer version, as you suggested, thanks!