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saezlab / liana

LIANA: a LIgand-receptor ANalysis frAmework
https://saezlab.github.io/liana/
GNU General Public License v3.0
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Issue using generate_homologs() #137

Open claratejido opened 8 months ago

claratejido commented 8 months ago

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 commented 8 months ago

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 commented 8 months ago

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 commented 7 months ago

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 commented 4 months ago

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 `