[ Started: 2026-06-02 21:12:44 CEST ] [ OmnipathR v3.18.4 for BioC-3.22 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_22 (efaae39 2026-01-20 15:40:26) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.18.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: doc 5.4Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2026-06-02 21:13:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-02 21:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:16] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-06-02 21:13:16] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-06-02 19:11:18 UTC; omnipath [2026-06-02 21:13:16] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-06-02 21:13:16] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-06-02 19:12:47 UTC; unix [2026-06-02 21:13:16] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-06-02 21:13:16] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-06-02 21:13:16] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-06-02; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-06-02 21:13:16] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-06-02 21:13:16] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-06-02); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.58(2026-06-01); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-06-02 21:13:16] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-06-02 21:13:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-06-02 21:13:16] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-06-02 21:13:16] [TRACE] [OmnipathR] Contains 1 files. [2026-06-02 21:13:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-06-02 21:13:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-02 21:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-06-02 21:13:16] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-06-02 21:13:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-06-02 21:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-06-02 21:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-06-02 21:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-06-02 21:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:16] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2026-06-02 21:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-02 21:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:27] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-06-02 21:13:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-06-02 19:11:18 UTC; omnipath [2026-06-02 21:13:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-06-02 21:13:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-06-02 19:12:47 UTC; unix [2026-06-02 21:13:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-06-02 21:13:27] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-06-02 21:13:27] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-06-02; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-06-02 21:13:27] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-06-02 21:13:27] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-06-02); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.58(2026-06-01); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-06-02 21:13:27] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-06-02 21:13:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-06-02 21:13:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-06-02 21:13:27] [TRACE] [OmnipathR] Contains 1 files. [2026-06-02 21:13:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-06-02 21:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-02 21:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-06-02 21:13:27] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-06-02 21:13:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-06-02 21:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-06-02 21:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-06-02 21:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-06-02 21:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:13:27] [TRACE] [OmnipathR] Cache locked: FALSE cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’ patch_httr2_keep_handle: no visible binding for global variable ‘handle’ patch_httr2_keep_handle: no visible global function definition for ‘ORIGINAL’ Undefined global functions or variables: ORIGINAL enzyme_genesymbol handle * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: hpo_download > ### Title: Downloads protein annotations from Human Phenotype Ontology > ### Aliases: hpo_download > > ### ** Examples > > hpo_data <- hpo_download() [2026-06-02 21:21:55] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-06-02 21:21:55] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2026-06-02 21:21:55] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2026-06-02 21:21:55] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2026-06-02 21:21:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-02 21:21:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:21:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-06-02 21:21:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-06-02 21:21:55] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`. [2026-06-02 21:21:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2026-06-02 21:21:55] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2026-06-02 21:21:55] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2026-06-02 21:21:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-06-02 21:21:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-06-02 21:21:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-06-02 21:21:55] [TRACE] [OmnipathR] HTTP v2 GET: status 502. [2026-06-02 21:21:55] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.383168s from purl.obolibrary.org (0 bytes/s); Redirect: 0.232506s, DNS look up: 0.023458s, Connection: 0.036177s, Pretransfer: 0.072602s, First byte at: 0.382871s [2026-06-02 21:21:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Tue, 02 Jun 2026 19:21:55 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; Server: cloudflare; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; set-cookie: __cf_bm=rSAHW_tzr3J07ZIoOuee.IdlEWAfNX5LaOT1tA6BLc8-1780428115.4885693-1.0.1.1-lUjMIokgwqDWyriLX5YbxJ0yk39Awj3OnAUxpt4cbAZ5he3IwydPkiErX2BrkEQSQHIAqL5.Yym0vT9nWmZNVnWr6rHd_Z0O_PX_aNj16IMXI9eF1p37AeFd_gDyyXMa; HttpOnly; Path=/; Domain=obolibrary.org; Expires=Tue, 02 Jun 2026 19:51:55 GMT; cf-cache-status: DYNAMIC; CF-RAY: a058d2e9cac7e859-STR; HTTP/2 502 ; date: Tue, 02 Jun 2026 19:21:55 GMT; content-type: text/html; content-length: 55118; etag: "6a1ece24-d74e"; server: github.com; x-frame-options: DENY; strict-transport-security: max-age=31536000; includeSubDomains; preload; set-cookie: _gh_sess=Kfivqdpyws8ur7xSfE4dmBpmGd8GKrkmcey4GWDcGynyQ7tF7LaZueBlELuw%2BbNyZeLnNeNqZNqOm6oQK3tGzw9LbESn7sM5%2B%2Fs5u5eqO%2BDJCVgkmUdOEr5%2B4m0QUpORnurYUaO2u5LexjZliOp0oPce%2FvvKPSj%2Fev7b6V%2FB0qkXwvwh3NwVey50vmFu23DBoW8oZeSWIblH84ss%2Bwns%2FJT3CAAYueNeWfrZIj010Joa1cBTQyBs7Rt14JCO4Y0uhuZRpM270tfsU1QUcXmC9A%3D%3D--r5zGk1ai9M2ZuVmz--IRLcbmWg57LFfD2A8rlH%2BQ%3D%3D; path=/; HttpOnly; secure; SameSite=Lax; set-cookie: _octo=GH1.1.1602621442.1780428115; expires=Wed, 02 Jun 2027 19:21:55 GMT; domain=.github.com; path=/; secure; SameSite=Lax; set-cookie: logged_in=no; expires=Wed, 02 Jun 2027 19:21:55 GMT; domain=.github.com; path=/; HttpOnly; secure; SameSite=Lax; x-github-request-id: C5A6:23C56B:12B6CDC0:1006EF30:6A1F2D53 [2026-06-02 21:21:55] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 502 [2026-06-02 21:21:55] [WARN] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 1/3); error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 502 [2026-06-02 21:22:00] [TRACE] [OmnipathR] Attempt 2/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2026-06-02 21:22:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-06-02 21:22:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-06-02 21:22:00] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-06-02 21:22:01] [TRACE] [OmnipathR] HTTP v2 GET: status 502. [2026-06-02 21:22:01] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.272677s from purl.obolibrary.org (0 bytes/s); Redirect: 0.192112s, DNS look up: 0.003002s, Connection: 0.014423s, Pretransfer: 0.079983s, First byte at: 0.272428s [2026-06-02 21:22:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Tue, 02 Jun 2026 19:22:01 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; Server: cloudflare; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; set-cookie: __cf_bm=LNm2_It5bjbw1oqIDNwAOaxkXP4atM010l7vzutnzXw-1780428120.9594183-1.0.1.1-FZLx.lE3C0Wbf1sV71YrDLsiXcQb8ccLQp.mte_oRvSEwRXC6ABc1y3as3.KkoItv9Xm7EsLLOCz8czHZChFni7r2dV3w31g8NHY13ZMrf3Fo8WoQspZx5bUe6EbKo9I; HttpOnly; Path=/; Domain=obolibrary.org; Expires=Tue, 02 Jun 2026 19:52:01 GMT; cf-cache-status: DYNAMIC; CF-RAY: a058d30bf998e859-STR; HTTP/2 502 ; date: Tue, 02 Jun 2026 19:21:55 GMT; content-type: text/html; content-length: 55118; etag: "6a1ece24-d74e"; server: github.com; x-frame-options: DENY; strict-transport-security: max-age=31536000; includeSubDomains; preload; set-cookie: _gh_sess=eutOaV0fnMJq8%2BUqFBSubLRjZjrgyjrSYvplCLjjx8Ebw5Gcv7zvh5I0lDwvpy0uXiWSVMp%2FcEp%2BUwOQksr%2FScVhiYIiqQ8LVpOIK2KUwOSVO5UdWgtm%2Bd5NJzUoHgn9ewIJ9Q2v54dcv6Rdsp0l0Fz%2Bc2UcB3G24OATlD1n7OvUAEKQhWYkich70DOzqAk1Gf5CTcJ%2BumGAghPhUZBDatosYkFNLTYBzxLj2eSRXSxdMhetnFJJY9mYQvTyJrR4teZ5CeKo%2BpqwlhE42b8g%2Fw%3D%3D--88uwixkY1%2BIZ9jIk--5%2FGBl1LWuX8VzoGGdeyD4A%3D%3D; path=/; HttpOnly; secure; SameSite=Lax; set-cookie: _octo=GH1.1.2075632674.1780428121; expires=Wed, 02 Jun 2027 19:22:01 GMT; domain=.github.com; path=/; secure; SameSite=Lax; set-cookie: logged_in=no; expires=Wed, 02 Jun 2027 19:22:01 GMT; domain=.github.com; path=/; HttpOnly; secure; SameSite=Lax; x-github-request-id: C5B2:207FB1:124885A3:FAED7FD:6A1F2D59 [2026-06-02 21:22:01] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 502 [2026-06-02 21:22:01] [WARN] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 2/3); error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 502 [2026-06-02 21:22:06] [TRACE] [OmnipathR] Attempt 3/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2026-06-02 21:22:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-06-02 21:22:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-06-02 21:22:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-06-02 21:22:06] [TRACE] [OmnipathR] HTTP v2 GET: status 502. [2026-06-02 21:22:06] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.261551s from purl.obolibrary.org (0 bytes/s); Redirect: 0.208568s, DNS look up: 0.004086s, Connection: 0.014474s, Pretransfer: 0.04995s, First byte at: 0.261298s [2026-06-02 21:22:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Tue, 02 Jun 2026 19:22:06 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; Server: cloudflare; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; set-cookie: __cf_bm=.OZsJyVuy1T11gMhqUIdfOuX_tk0ONKFNhgKWTdUagM-1780428126.314272-1.0.1.1-PLqMo8IXKz35C5_3.e05MriVK5qG5E.mJJfoVAOldevdvth.BKAq3YAVfuiLDochRupR9n9JvZJMgXqm2BN5gJfPDOBABdi5OowikHlHemobUSfwQiN_zXOolLK9GcUV; HttpOnly; Path=/; Domain=obolibrary.org; Expires=Tue, 02 Jun 2026 19:52:06 GMT; cf-cache-status: DYNAMIC; CF-RAY: a058d32d7b876e96-STR; HTTP/2 502 ; date: Tue, 02 Jun 2026 19:21:55 GMT; content-type: text/html; content-length: 55118; etag: "6a1ece24-d74e"; server: github.com; x-frame-options: DENY; strict-transport-security: max-age=31536000; includeSubDomains; preload; set-cookie: _gh_sess=O5neaGM7bqlBHOqR9JcdPNxMkcH6OsZe67%2F1YUA2XKUDSpTI6vahQgfm2ouw40ceySHq20xTYcmRQjfXfsBxS6D%2FQSZzfd4LK1qF%2BZtCCGxbF3CADwaawvMthddkA%2FTLKESB0OkUKA%2BJYLfOL0vk4DYR7MLgdvTGF7AEF%2BVB5Sdczk3nOvfIdMFAibwsaw6qAVZyoKKpBeyQyx0TOsxwR1agK5cIaDFdV0GwsIB7LwBrAJkXl5%2Fkc4%2BjSLy%2BRqZujadN1ZMW40NmNGZKjim%2Fzw%3D%3D--YEYKEfHMBUnKV07M--cBvKPRwqK32psuZNmHWQiw%3D%3D; path=/; HttpOnly; secure; SameSite=Lax; set-cookie: _octo=GH1.1.605474118.1780428126; expires=Wed, 02 Jun 2027 19:22:06 GMT; domain=.github.com; path=/; secure; SameSite=Lax; set-cookie: logged_in=no; expires=Wed, 02 Jun 2027 19:22:06 GMT; domain=.github.com; path=/; HttpOnly; secure; SameSite=Lax; x-github-request-id: B6AE:C32FE:12B6428C:100861D6:6A1F2D5E [2026-06-02 21:22:06] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 502 [2026-06-02 21:22:06] [ERROR] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 3/3); error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 502 [2026-06-02 21:22:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-06-02 19:11:18 UTC; omnipath [2026-06-02 21:22:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-06-02 21:22:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-06-02 19:12:47 UTC; unix [2026-06-02 21:22:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-06-02 21:22:06] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-06-02 21:22:06] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-06-02; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-06-02 21:22:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-06-02 21:22:06] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-06-02); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.3(2026-04-11); vroom 1.7.1(2026-03-31); withr 3.0.2(2024-10-28); xfun 0.58(2026-06-01); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-06-02 21:22:06] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE Error in (function (url, curlopt = list(), callback = NULL, compr = NULL, : Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 502 Calls: hpo_download ... omnipath_cache_save -> saveRDS -> exec -> Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 68.956 0.041 69.132 curated_ligrec_stats 28.641 1.418 38.883 filter_extra_attrs 19.099 3.047 22.570 all_uniprots 17.739 0.848 31.600 extra_attr_values 9.593 1.118 11.052 extra_attrs_to_cols 9.666 0.828 10.863 go_annot_download 8.449 0.573 8.542 giant_component 7.025 0.406 7.722 filter_by_resource 6.081 0.275 6.719 has_extra_attrs 5.308 0.696 6.036 extra_attrs 4.925 0.807 5.794 filter_intercell 4.953 0.419 5.291 curated_ligand_receptor_interactions 4.613 0.307 5.954 ensembl_id_mapping_table 1.536 0.168 217.853 biomart_query 0.798 0.064 18.885 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-06-02_2100/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-06-02 21:35:29 CEST ]