Error in generate_homologs

[PpGrApee]

Hello! WThank you for the nice package. I have problems when I use the following code.
ortholog_resource <- generate_homologs(op_resource = op_resource, target_organism =10090, columns = c("source_genesymbol", "target_genesymbol"), max_homologs = 5)
And there is the error:
One-to-many homolog matches:
Error in mutate():
ℹ In argument: across(all_of(columns), ~recode.character2(.x, .missing_fun = .missing_fun)).
Caused by error in across():
! Can't compute column source_genesymbol.
Caused by error in recode.character2():
! No replacements provided.
Run rlang::last_trace() to see where the error occurred.

I have tried install from this PR #174, but not work.

[pushpinder-bu]

Hi, I am facing the same issue, you found any solution for it?

[deeenes]

Hi @PpGrApee & @pushpinder-bu, To make this work, indeed the changes in PR #174 are required. The rest of the thing is a transient download failure, which is surprising bc no risky downloads are involved here. It could happen due to a temporary, maybe partial, downtime of ensembl.org, or a condition related to the local network where you run the script. First I recommend to try the download again with an empty cache, with the latest version of OmnipathR. If you still experience an error, please share the OmnipathR log:

library(remotes)
remotes::install_github(repo = "saezlab/liana", ref = remotes::github_pull(174L))
remotes::install_github("saezlab/OmnipathR@devel")

library(OmnipathR)
library(liana)

omnipath_set_cachedir(tempdir())
options(omnipathr.curl_verbose = TRUE)

h <- homologene_download(10090L, 9606L, "genesymbol")

# try your liana code here, it should do the same call to `homologene_download` as above

# if fails, please share the contents of the OmnipathR log:
omnipath_logfile()

[pushpinder-bu]

Below is the log file

[2025-02-25 10:14:57] [TRACE] [OmnipathR] Reading JSON from /usr2/postdoc/bpushpin/.cache/OmnipathR/cache.json (encoding: UTF-8).
[2025-02-25 10:14:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-25 10:14:57] [INFO] [OmnipathR] Initialized cache: /usr2/postdoc/bpushpin/.cache/OmnipathR.
[2025-02-25 10:14:57] [INFO] [OmnipathR] Package OmnipathR packaged: 2025-02-24 21:44:09 UTC; bpushpin
[2025-02-25 10:14:57] [INFO] [OmnipathR] Package OmnipathR date/publication: NA
[2025-02-25 10:14:57] [INFO] [OmnipathR] Package OmnipathR built: R 4.4.0; ; 2025-02-24 21:44:10 UTC; unix
[2025-02-25 10:14:57] [INFO] [OmnipathR] Package OmnipathR version: 3.15.9
[2025-02-25 10:14:57] [INFO] [OmnipathR] Package OmnipathR repository: NA
[2025-02-25 10:14:58] [INFO] [OmnipathR] Session info: [version=R version 4.4.0 (2024-04-24); os=AlmaLinux 8.10 (Cerulean Leopard); system=x86_64, linux-gnu; ui=RStudio; language=(EN); collate=en_US.UTF-8; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-25; rstudio=2024.04.2+764 Chocolate Cosmos (server); pandoc=3.1.11 @ /usr/local/ood/rstudio-server-2024.04.2-764/bin/quarto/bin/tools/x86_64/ (via rmarkdown)]
[2025-02-25 10:14:58] [INFO] [OmnipathR] External libraries: [cairo=1.15.12; cairoFT=; pango=1.42.3; png=1.6.34; jpeg=6.2; tiff=LIBTIFF, Version 4.0.9; tcl=8.6.8; curl=7.61.1; zlib=1.2.11; bzlib=1.0.6, 6-Sept-2010; xz=5.2.4; deflate=; PCRE=10.32 2018-09-10; ICU=60.3; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.28; readline=7.0; BLAS=FlexiBLAS NETLIB; lapack=FlexiBLAS NETLIB; lapack_version=3.11.0]
[2025-02-25 10:14:58] [INFO] [OmnipathR] CURL: version: 7.61.1; headers: 7.61.1; ssl_version: OpenSSL/1.1.1k; libz_version: 1.2.11; libssh_version: libssh/0.9.6/openssl/zlib; libidn_version: 2.2.0; host: x86_64-redhat-linux-gnu; protocols: dict, file, ftp, ftps, gopher, http, https, imap, imaps, ldap, ldaps, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: FALSE
[2025-02-25 10:14:58] [TRACE] [OmnipathR] Reading JSON from /usr2/postdoc/bpushpin/R/x86_64-pc-linux-gnu-library/4.4/OmnipathR/db/db_def.json (encoding: UTF-8).
[2025-02-25 10:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-25 10:14:58] [TRACE] [OmnipathR] Reading JSON from /usr2/postdoc/bpushpin/R/x86_64-pc-linux-gnu-library/4.4/OmnipathR/internal/magic_bytes.json (encoding: UTF-8).
[2025-02-25 10:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-25 10:14:58] [TRACE] [OmnipathR] Reading JSON from /usr2/postdoc/bpushpin/R/x86_64-pc-linux-gnu-library/4.4/OmnipathR/internal/urls.json (encoding: UTF-8).
[2025-02-25 10:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-25 10:14:58] [TRACE] [OmnipathR] Reading JSON from /usr2/postdoc/bpushpin/R/x86_64-pc-linux-gnu-library/4.4/OmnipathR/internal/id_types.json (encoding: UTF-8).
[2025-02-25 10:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-25 10:32:04] [INFO] [OmnipathR] Setting up new cache directory /scratch/319949.1.ood/RtmpzHZ0PT.
[2025-02-25 10:32:04] [TRACE] [OmnipathR] Reading JSON from /scratch/319949.1.ood/RtmpzHZ0PT/cache.json (encoding: UTF-8).
[2025-02-25 10:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-25 10:32:14] [INFO] [OmnipathR] Loading database Ensembl and OMA organism names.
[2025-02-25 10:32:14] [TRACE] [OmnipathR] Reading JSON from /scratch/319949.1.ood/RtmpzHZ0PT/cache.json (encoding: UTF-8).
[2025-02-25 10:32:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-25 10:32:14] [INFO] [OmnipathR] Looking up in cache https://www.ensembl.org/info/about/species.html: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-25 10:32:14] [TRACE] [OmnipathR] Reading JSON from /scratch/319949.1.ood/RtmpzHZ0PT/cache.json (encoding: UTF-8).
[2025-02-25 10:32:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-25 10:32:14] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-25 10:32:14] [TRACE] [OmnipathR] Cache file path: /scratch/319949.1.ood/RtmpzHZ0PT/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-25 10:32:14] [INFO] [OmnipathR] Retrieving URL: https://www.ensembl.org/info/about/species.html
[2025-02-25 10:32:14] [TRACE] [OmnipathR] Downloading by httr2 in download_base.
[2025-02-25 10:32:14] [TRACE] [OmnipathR] Attempt 1/3: https://www.ensembl.org/info/about/species.html
[2025-02-25 10:32:14] [TRACE] [OmnipathR] Preparing httr2 request.
[2025-02-25 10:32:14] [TRACE] [OmnipathR] The following curl options are not available: [tcp_keepcnt,upkeep_interval_ms]
[2025-02-25 10:32:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=TRUE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-25 10:32:14] [TRACE] [OmnipathR] Sending HTTP request.
[2025-02-25 10:32:14] [TRACE] [OmnipathR] CURL DEBUG[* ]: CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
[2025-02-25 10:32:14] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 1/3); error: Invalid or unsupported value when setting curl option 'ssl_verifyhost'
[2025-02-25 10:32:19] [TRACE] [OmnipathR] Attempt 2/3: https://www.ensembl.org/info/about/species.html
[2025-02-25 10:32:19] [TRACE] [OmnipathR] Preparing httr2 request.
[2025-02-25 10:32:19] [TRACE] [OmnipathR] The following curl options are not available: [tcp_keepcnt,upkeep_interval_ms]
[2025-02-25 10:32:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=TRUE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-25 10:32:19] [TRACE] [OmnipathR] Sending HTTP request.
[2025-02-25 10:32:19] [TRACE] [OmnipathR] CURL DEBUG[* ]: CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
[2025-02-25 10:32:19] [WARN] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 2/3); error: Invalid or unsupported value when setting curl option 'ssl_verifyhost'
[2025-02-25 10:32:24] [TRACE] [OmnipathR] Attempt 3/3: https://www.ensembl.org/info/about/species.html
[2025-02-25 10:32:24] [TRACE] [OmnipathR] Preparing httr2 request.
[2025-02-25 10:32:24] [TRACE] [OmnipathR] The following curl options are not available: [tcp_keepcnt,upkeep_interval_ms]
[2025-02-25 10:32:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=TRUE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-25 10:32:24] [TRACE] [OmnipathR] Sending HTTP request.
[2025-02-25 10:32:24] [TRACE] [OmnipathR] CURL DEBUG[* ]: CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
[2025-02-25 10:32:24] [ERROR] [OmnipathR] Failed to download https://www.ensembl.org/info/about/species.html (attempt 3/3); error: Invalid or unsupported value when setting curl option 'ssl_verifyhost'
[2025-02-25 10:32:24] [INFO] [OmnipathR] Package OmnipathR packaged: 2025-02-25 15:31:27 UTC; bpushpin
[2025-02-25 10:32:24] [INFO] [OmnipathR] Package OmnipathR date/publication: NA
[2025-02-25 10:32:24] [INFO] [OmnipathR] Package OmnipathR built: R 4.4.0; ; 2025-02-25 15:31:28 UTC; unix
[2025-02-25 10:32:24] [INFO] [OmnipathR] Package OmnipathR version: 3.15.9
[2025-02-25 10:32:24] [INFO] [OmnipathR] Package OmnipathR repository: NA
[2025-02-25 10:32:25] [INFO] [OmnipathR] Session info: [version=R version 4.4.0 (2024-04-24); os=AlmaLinux 8.10 (Cerulean Leopard); system=x86_64, linux-gnu; ui=RStudio; language=(EN); collate=en_US.UTF-8; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-25; rstudio=2024.04.2+764 Chocolate Cosmos (server); pandoc=3.1.11 @ /usr/local/ood/rstudio-server-2024.04.2-764/bin/quarto/bin/tools/x86_64/ (via rmarkdown)]
[2025-02-25 10:32:25] [INFO] [OmnipathR] External libraries: [cairo=1.15.12; cairoFT=; pango=1.42.3; png=1.6.34; jpeg=6.2; tiff=LIBTIFF, Version 4.0.9; tcl=8.6.8; curl=7.61.1; zlib=1.2.11; bzlib=1.0.6, 6-Sept-2010; xz=5.2.4; deflate=; PCRE=10.32 2018-09-10; ICU=60.3; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.28; readline=7.0; BLAS=FlexiBLAS NETLIB; lapack=FlexiBLAS NETLIB; lapack_version=3.11.0]
[2025-02-25 10:32:25] [INFO] [OmnipathR] CURL: version: 7.61.1; headers: 7.61.1; ssl_version: OpenSSL/1.1.1k; libz_version: 1.2.11; libssh_version: libssh/0.9.6/openssl/zlib; libidn_version: 2.2.0; host: x86_64-redhat-linux-gnu; protocols: dict, file, ftp, ftps, gopher, http, https, imap, imaps, ldap, ldaps, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: FALSE

[deeenes]

Thanks @pushpinder-bu, so this makes clear the error happens when curl rejects value 1 for the ssl_verifyhost option. Why you get this error while others don't, the reason is the very old libcurl in your system, it's 7 years old (version 7.61.1). Still, this error can be addressed by passing a correct value (and then maybe you see another error downstream of this one):

library(OmnipathR)

omnipath_set_cachedir(tempdir())
options(omnipathr.curl_verbose = TRUE)
options(omnipathr.ssl_verifyhost = 2L)

h <- homologene_download(10090L, 9606L, "genesymbol")

omnipath_logfile()

To prevent this error in the future, I'll also update the default of this option in OmnipathR to 2L.