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.