error loading collectTRI regulon
0
0
Entering edit mode
@22d77658
Last seen 24 days ago
United States

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
decoupleR OmnipathR • 320 views
ADD COMMENT
0
Entering edit mode

Hello, Please follow this ticket: https://github.com/saezlab/CollecTRI/issues/19 I'll fix this very soon, hopefully tomorrow!

ADD REPLY
0
Entering edit mode

Thank you!

I don't know if you have looked into this already, but today I am getting a different error:

net<-get_collectri(organism='human', split_complexes=False)

[2024-06-12 10:32:36] [SUCCESS] [OmnipathR] Downloaded 64495 interactions.

Error: object 'False' not found

ADD REPLY
1
Entering edit mode

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 False instead of FALSE.

ADD REPLY
0
Entering edit mode

Fantastic. Thank you very much. Everything has been sorted out

ADD REPLY

Login before adding your answer.

Traffic: 665 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6