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Hi, I am trying to load the CollecTRI network using decoupleR and am getting the follwing error:
Does anybody have any suggestions? Thanks!
net = get_collectri(organism='human', split_complexes=False)
2024-06-11 15:13:22] [WARN] [OmnipathR] HTTP 403
[2024-06-11 15:13:22] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-11 15:13:27] [WARN] [OmnipathR] HTTP 403
[2024-06-11 15:13:27] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-11 15:13:32] [WARN] [OmnipathR] HTTP 403
[2024-06-11 15:13:32] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
Error in `map_int()`:
i In index: 1.
Caused by error in `map_int()`:
i In index: 1.
Caused by error:
! HTTP 403
Run `rlang::last_trace()` to see where the error occurred.
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
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: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] OmnipathR_3.10.1 decoupleR_2.8.0 MetaIntegrator_2.1.3 RcisTarget_1.23.1 GOSemSim_2.28.1 qgraph_1.9.8 heatmaply_1.5.0
[8] viridis_0.6.5 viridisLite_0.4.2 plotly_4.10.4 GSEAmining_1.12.0 msigdbr_7.5.1 DOSE_3.28.2 enrichplot_1.22.0
[15] clusterProfiler_4.10.1 VennDiagram_1.7.3 futile.logger_1.4.3 DEGreport_1.39.6 data.table_1.15.4 ggridges_0.5.6 variancePartition_1.32.5
[22] BiocParallel_1.36.0 org.Mm.eg.db_3.18.0 biomaRt_2.58.2 org.Hs.eg.db_3.18.0 AnnotationDbi_1.64.1 IRanges_2.36.0 S4Vectors_0.40.2
[29] Biobase_2.62.0 BiocGenerics_0.48.1 edgeR_4.0.16 limma_3.58.1 corrplot_0.92 lubridate_1.9.3 forcats_1.0.0
[36] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0
[43] gridExtra_2.3 reshape2_1.4.4 treemapify_2.5.6 ggparliament_2.1.5 ggpubr_0.6.0 pheatmap_1.0.12 factoextra_1.0.7
[50] ggplot2_3.5.1 cinaR_0.2.3 arrow_16.1.0
loaded via a namespace (and not attached):
[1] R.methodsS3_1.8.2 GSEABase_1.64.0 progress_1.2.3 nnet_7.3-19 ggfittext_0.10.2 Biostrings_2.70.3
[7] vctrs_0.6.5 digest_0.6.35 png_0.1-8 corpcor_1.6.10 shape_1.4.6.1 registry_0.5-1
[13] ggrepel_0.9.5 MASS_7.3-60.0.1 reshape_0.8.9 httpuv_1.6.15 foreach_1.5.2 qvalue_2.34.0
[19] withr_3.0.0 psych_2.4.3 xfun_0.44 ggfun_0.1.5 memoise_2.0.1 gson_0.1.0
[25] tidytree_0.4.6 GlobalOptions_0.1.2 gtools_3.9.5 pbapply_1.7-2 R.oo_1.26.0 logging_0.10-108
[31] Formula_1.2-5 prettyunits_1.2.0 promises_1.3.0 KEGGREST_1.42.0 httr_1.4.7 rstatix_0.7.2
[37] rstudioapi_0.16.0 generics_0.1.3 base64enc_0.1-3 babelgene_22.9 curl_5.2.1 zlibbioc_1.48.2
[43] ggraph_2.2.1 polyclip_1.10-6 ca_0.71.1 GenomeInfoDbData_1.2.11 quadprog_1.5-8 SparseArray_1.2.4
[49] xtable_1.8-4 doParallel_1.0.17 evaluate_0.24.0 S4Arrays_1.2.1 BiocFileCache_2.10.2 hms_1.1.3
[55] GenomicRanges_1.54.1 ggwordcloud_0.6.2 colorspace_2.1-0 filelock_1.0.3 ROCR_1.0-11 readxl_1.4.3
[61] magrittr_2.0.3 later_1.3.2 ggtree_3.10.1 lattice_0.22-6 XML_3.99-0.16.1 shadowtext_0.1.3
[67] cowplot_1.1.3 matrixStats_1.3.0 Hmisc_5.1-3 pillar_1.9.0 nlme_3.1-165 iterators_1.0.14
[73] caTools_1.18.2 compiler_4.3.1 stringi_1.8.4 TSP_1.2-4 tokenizers_0.3.0 minqa_1.2.7
[79] SummarizedExperiment_1.32.0 dendextend_1.17.1 plyr_1.8.9 crayon_1.5.2 abind_1.4-5 ggdendro_0.2.0
[85] gridGraphics_0.5-1 locfit_1.5-9.9 graphlayouts_1.1.1 bit_4.0.5 fastmatch_1.1-4 codetools_0.2-20
[91] GetoptLong_1.0.5 mime_0.12 tidytext_0.4.2 remaCor_0.0.18 splines_4.3.1 circlize_0.4.16
[97] Rcpp_1.0.12 sparseMatrixStats_1.14.0 dbplyr_2.5.0 HDO.db_0.99.1 cellranger_1.1.0 gridtext_0.1.5
[103] knitr_1.47 blob_1.2.4 utf8_1.2.4 clue_0.3-65 lme4_1.1-35.3 pbivnorm_0.6.0
[109] fs_1.6.4 checkmate_2.3.1 DelayedMatrixStats_1.24.0 logger_0.3.0 Rdpack_2.6 ggsignif_0.6.4
[115] ggplotify_0.1.2 lavaan_0.6-18 Matrix_1.6-5 statmod_1.5.0 tzdb_0.4.0 fANCOVA_0.6-1
[121] tweenr_2.0.3 pkgconfig_2.0.3 tools_4.3.1 cachem_1.1.0 RhpcBLASctl_0.23-42 rbibutils_2.2.16
[127] RSQLite_2.3.7 rvest_1.0.4 DBI_1.2.3 numDeriv_2016.8-1.1 fastmap_1.2.0 rmarkdown_2.27
[133] scales_1.3.0 broom_1.0.6 patchwork_1.2.0 BiocManager_1.30.23 graph_1.80.0 carData_3.0-5
[139] rpart_4.1.23 farver_2.1.2 aod_1.3.3 tidygraph_1.3.1 scatterpie_0.2.3 yaml_2.3.8
[145] MatrixGenerics_1.14.0 foreign_0.8-86 cli_3.6.2 webshot_0.5.5 lifecycle_1.0.4 mvtnorm_1.2-5
[151] lambda.r_1.2.4 backports_1.5.0 annotate_1.80.0 timechange_0.3.0 gtable_0.3.5 rjson_0.2.21
[157] parallel_4.3.1 ape_5.8 SnowballC_0.7.1 jsonlite_1.8.8 seriation_1.5.5 bitops_1.0-7
[163] bit64_4.0.5 assertthat_0.2.1 glasso_1.11 yulab.utils_0.1.4 janeaustenr_1.0.0 futile.options_1.0.1
[169] R.utils_2.12.3 pbkrtest_0.5.2 lazyeval_0.2.2 shiny_1.8.1.1 ConsensusClusterPlus_1.66.0 htmltools_0.5.8.1
[175] GO.db_3.18.0 rappdirs_0.3.3 formatR_1.14 glue_1.7.0 XVector_0.42.0 RCurl_1.98-1.14
[181] treeio_1.26.0 mnormt_2.1.1 jpeg_0.1-10 AUCell_1.24.0 EnvStats_2.8.1 boot_1.3-30
[187] igraph_2.0.3 R6_2.5.1 DESeq2_1.42.1 gplots_3.1.3.1 fdrtool_1.2.17 labeling_0.4.3
[193] cluster_2.1.6 aplot_0.2.2 GenomeInfoDb_1.38.8 nloptr_2.0.3 DelayedArray_0.28.0 tidyselect_1.2.1
[199] htmlTable_2.4.2 ggforce_0.4.2 xml2_1.3.6 car_3.1-2 munsell_0.5.1 KernSmooth_2.23-24
[205] htmlwidgets_1.6.4 fgsea_1.28.0 ComplexHeatmap_2.18.0 RColorBrewer_1.1-3 rlang_1.1.4 lmerTest_3.1-3
[211] ggnewscale_0.4.10 fansi_1.0.6
Hello, Please follow this ticket: https://github.com/saezlab/CollecTRI/issues/19 I'll fix this very soon, hopefully tomorrow!
Thank you!
I don't know if you have looked into this already, but today I am getting a different error:
I fixed the original, Ensembl HTTP 403 error only now, see here. If you've seen it gone earlier today, only shows that this error appears randomly, it depends on many factors.
The second error, the one here above, is directly from the line executed in the console: by accident you typed
Falseinstead ofFALSE.Fantastic. Thank you very much. Everything has been sorted out