Issue using generate_homologs()

[claratejido]

Hi Daniel!

I encountered the following error when using the test data example with show_homologene() and ortholog_resource:

> ortholog_resource <- generate_homologs(op_resource = op_resource,
+                                        target_organism = 10090) # mouse
[2024-02-03 20:34:11] [WARN]    [OmnipathR] Failed to download `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data` (attempt 1/3); error: HTTP error 404.
[2024-02-03 20:34:17] [WARN]    [OmnipathR] Failed to download `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data` (attempt 2/3); error: HTTP error 404.
[2024-02-03 20:34:22] [ERROR]   [OmnipathR] Failed to download `https://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data` (attempt 3/3); error: HTTP error 404.
Error in open.connection(5L, "rb") : HTTP error 404.

I have the latest version of liana and OmnipathR, downloaded using: remotes::install_github("saezlab/OmnipathR"). For more information, find my session info below.

Thanks a lot in advance for your help,

Best wishes,

Clara

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] magrittr_2.0.3 OmnipathR_3.11.1 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[6] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0
[11] liana_0.1.13 CellChat_1.6.1 igraph_1.6.0 SCpubr_2.0.2.9000 qs_0.25.7
[16] metap_1.9 multtest_2.52.0 Biobase_2.58.0 BiocGenerics_0.44.0 openxlsx_4.2.5.2
[21] dplyr_1.1.4 ggplot2_3.4.4 Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-3

loaded via a namespace (and not attached):
[1] rsvd_1.0.5 statnet.common_4.9.0 ica_1.0-3
[4] svglite_2.1.3 foreach_1.5.2 lmtest_0.9-40
[7] crayon_1.5.2 rbibutils_2.2.16 MASS_7.3-57
[10] nlme_3.1-157 backports_1.4.1 basilisk_1.15.2004
[13] rlang_1.1.3 XVector_0.38.0 ROCR_1.0-11
[16] readxl_1.4.3 irlba_2.3.5.1 limma_3.54.2
[19] filelock_1.0.3 stringfish_0.16.0 BiocParallel_1.32.6
[22] rjson_0.2.21 bit64_4.0.5 glue_1.7.0
[25] pheatmap_1.0.12 rngtools_1.5.2 sctransform_0.4.1
[28] parallel_4.2.0 spatstat.sparse_3.0-3 AnnotationDbi_1.60.2
[31] dotCall64_1.1-1 spatstat.geom_3.2-8 tidyselect_1.2.0
[34] SummarizedExperiment_1.28.0 fitdistrplus_1.1-11 zoo_1.8-12
[37] qqconf_1.3.2 ggpubr_0.6.0 ontologyIndex_2.11
[40] xtable_1.8-4 ggnetwork_0.5.12 RcppHNSW_0.5.0
[43] evaluate_0.23 scuttle_1.8.4 Rdpack_2.6
[46] cli_3.6.2 zlibbioc_1.44.0 sn_2.1.1
[49] rstudioapi_0.15.0 miniUI_0.1.1.1 logger_0.2.2
[52] mathjaxr_1.6-0 fastDummies_1.7.3 shiny_1.8.0
[55] BiocSingular_1.14.0 xfun_0.41 clue_0.3-65
[58] cluster_2.1.3 KEGGREST_1.38.0 interactiveDisplayBase_1.34.0
[61] ggrepel_0.9.5 listenv_0.9.1 Biostrings_2.66.0
[64] png_0.1-8 future_1.33.1 withr_3.0.0
[67] bitops_1.0-7 plyr_1.8.9 cellranger_1.1.0
[70] dqrng_0.3.2 coda_0.19-4.1 pillar_1.9.0
[73] RcppParallel_5.1.7 GlobalOptions_0.1.2 cachem_1.0.8
[76] multcomp_1.4-25 GetoptLong_1.0.5 DelayedMatrixStats_1.20.0
[79] vctrs_0.6.5 ellipsis_0.3.2 generics_0.1.3
[82] RApiSerialize_0.1.2 NMF_0.26 tools_4.2.0
[85] munsell_0.5.0 DelayedArray_0.24.0 fastmap_1.1.1
[88] compiler_4.2.0 paintmap_1.0 abind_1.4-5
[91] httpuv_1.6.14 plotly_4.10.4 GenomeInfoDbData_1.2.9
[94] gridExtra_2.3 edgeR_3.40.2 lattice_0.20-45
[97] dir.expiry_1.6.0 deldir_2.0-2 mutoss_0.1-13
[100] utf8_1.2.4 later_1.3.2 BiocFileCache_2.4.0
[103] jsonlite_1.8.8 ontoProc_1.18.0 scales_1.3.0
[106] ScaledMatrix_1.6.0 graph_1.74.0 sparseMatrixStats_1.10.0
[109] pbapply_1.7-2 carData_3.0-5 lazyeval_0.2.2
[112] promises_1.2.1 car_3.1-2 doParallel_1.0.17
[115] goftest_1.2-3 spatstat.utils_3.0-4 reticulate_1.35.0
[118] sna_2.7-2 checkmate_2.3.1 rmarkdown_2.25
[121] sandwich_3.1-0 cowplot_1.1.3 statmod_1.5.0
[124] Rtsne_0.17 selectr_0.4-2 uwot_0.1.16
[127] survival_3.3-1 numDeriv_2016.8-1.1 yaml_2.3.8
[130] plotrix_3.8-4 systemfonts_1.0.5 htmltools_0.5.7
[133] memoise_2.0.1 locfit_1.5-9.8 IRanges_2.32.0
[136] viridisLite_0.4.2 digest_0.6.34 mime_0.12
[139] rappdirs_0.3.3 registry_0.5-1 spam_2.10-0
[142] RSQLite_2.3.5 future.apply_1.11.1 data.table_1.15.0
[145] blob_1.2.4 S4Vectors_0.36.2 splines_4.2.0
[148] AnnotationHub_3.4.0 RCurl_1.98-1.14 broom_1.0.5
[151] hms_1.1.3 colorspace_2.1-0 BiocManager_1.30.22
[154] mnormt_2.1.1 GenomicRanges_1.50.2 shape_1.4.6
[157] Rcpp_1.0.12 RANN_2.6.1 mvtnorm_1.2-4
[160] circlize_0.4.15 fansi_1.0.6 tzdb_0.4.0
[163] parallelly_1.36.0 R6_2.5.1 grid_4.2.0
[166] ggridges_0.5.6 lifecycle_1.0.4 bluster_1.8.0
[169] zip_2.3.1 TFisher_0.2.0 curl_5.2.0
[172] ggsignif_0.6.4 leiden_0.4.3.1 Matrix_1.6-5
[175] RcppAnnoy_0.0.22 TH.data_1.1-2 RColorBrewer_1.1-3
[178] iterators_1.0.14 spatstat.explore_3.2-6 htmlwidgets_1.6.4
[181] beachmat_2.14.2 polyclip_1.10-6 network_1.18.2
[184] timechange_0.3.0 rvest_1.0.3 ComplexHeatmap_2.14.0
[187] globals_0.16.2 patchwork_1.2.0 spatstat.random_3.2-2
[190] progressr_0.14.0 codetools_0.2-18 matrixStats_1.2.0
[193] metapod_1.6.0 FNN_1.1.4 prettyunits_1.2.0
[196] SingleCellExperiment_1.20.1 dbplyr_2.4.0 basilisk.utils_1.15.1
[199] gridBase_0.4-7 RSpectra_0.16-1 GenomeInfoDb_1.34.9
[202] gtable_0.3.4 DBI_1.2.1 ggalluvial_0.12.5
[205] stats4_4.2.0 tensor_1.5 httr_1.4.7
[208] KernSmooth_2.23-20 vroom_1.6.5 stringi_1.8.3
[211] progress_1.2.3 reshape2_1.4.4 ontologyPlot_1.6
[214] Rgraphviz_2.40.0 DT_0.31 xml2_1.3.6
[217] BiocNeighbors_1.16.0 kableExtra_1.4.0 scattermore_1.2
[220] BiocVersion_3.15.2 scran_1.26.2 bit_4.0.5
[223] MatrixGenerics_1.10.0 spatstat.data_3.0-4 pkgconfig_2.0.3
[226] rstatix_0.7.2 knitr_1.45

[dbdimitrov]

Hi @claratejido,

If you're still experiencing the issue - maybe @deeenes could help.

As this seems to be an issue with retrieving the orthology symbols for the conversion.

[deeenes]

Hi @claratejido,

Is your OmnipathR the latest from GitHub? Today it should use OMA as the default orthology resource, and I think we've fixed already the HomoloGene URL too. You can install the latest version this way:

library(remotes)
remotes::install_github('saezlab/OmnipathR')

Best,

Denes

[deeenes]

I was wrong in a couple of points here:

1. Indeed there was an issue with HomoloGene, it went offline, I think after 8 years of zombie existence NCBI finally killed it. Then last week I moved it to our own server, into the so called "rescued" repo, so our software keep working seamlessly.

2. LIANA didn't use OMA, bc it relied directly on the HomoloGene access in OmnipathR. Now I filed a PR to move LIANA from HomoloGene to OMA.

With this, I think orthology translation should be good, even better than it was before.

[Charmy0619]

Hi @deeenes,
I still have an issue getting the orthology symbols for conversion, but it's a different error. Are you able to help? Thanks.
`

show_homologene()
[2024-06-06 16:41:05] [SUCCESS] [OmnipathR] NCBI HomoloGene (rescued.omnipathdb.org): loaded 275237 records from cache
[2024-06-06 16:41:06] [WARN] [OmnipathR] HTTP 403
[2024-06-06 16:41:06] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 1/3); error: HTTP 403
[2024-06-06 16:41:11] [WARN] [OmnipathR] HTTP 403
[2024-06-06 16:41:11] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 2/3); error: HTTP 403
[2024-06-06 16:41:17] [WARN] [OmnipathR] HTTP 403
[2024-06-06 16:41:17] [ERROR] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 3/3); error: HTTP 403
Error in map_chr():
i In index: 1.
Caused by error:
! HTTP 403
Run rlang::last_trace() to see where the error occurred.
op_resource <- select_resource("Consensus")[[1]]
ortholog_resource <- generate_homologs(op_resource = op_resource, target_organism = 10090) # mouse
[2024-06-06 16:41:33] [WARN] [OmnipathR] HTTP 403
[2024-06-06 16:41:33] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 1/3); error: HTTP 403
[2024-06-06 16:41:38] [WARN] [OmnipathR] HTTP 403
[2024-06-06 16:41:38] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 2/3); error: HTTP 403
[2024-06-06 16:41:44] [WARN] [OmnipathR] HTTP 403
[2024-06-06 16:41:44] [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:
! HTTP 403
Run rlang::last_trace() to see where the error occurred.
sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
[1] Seurat_5.0.1 magrittr_2.0.3 liana_0.1.13 OmnipathR_3.13.4 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[8] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.4.4 tidyverse_2.0.0
[15] SeuratObject_5.0.1 sp_2.1-2 `

[Dalhte]

Hello there !
I also have an issue with generate_homologs (and show_homologene())
I get :

show_homologene()
[2024-10-18 13:44:27] [SUCCESS] [OmnipathR] NCBI HomoloGene (rescued.omnipathdb.org): downloaded 2 records
Erreur dans UseMethod("pull") :
pas de méthode pour 'pull' applicable pour un objet de classe "list"

and

ortholog_resource <- generate_homologs(op_resource = op_resource,

•                                    target_organism = 10116) # Rat
  

[2024-10-18 13:45:26] [SUCCESS] [OmnipathR] NCBI HomoloGene (rescued.omnipathdb.org): downloaded 2 records
Erreur dans UseMethod("filter") :
pas de méthode pour 'filter' applicable pour un objet de classe "list"

Any idea ?
Best
David