[ Started: 2025-06-14 02:32:47 CEST ] [ OmnipathR v3.15.99 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (02b2582 2025-05-22 13:00:44) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck’ * using R Under development (unstable) (2025-02-12 r87715) * 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 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.15.99’ * 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 [2025-06-14 02:33:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:16] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-06-14 02:33:16] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-06-14 00:31:39 UTC; omnipath [2025-06-14 02:33:16] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-06-14 02:33:16] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-14 00:32:50 UTC; unix [2025-06-14 02:33:16] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-06-14 02:33:16] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-06-14 02:33:16] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-06-14; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-06-14 02:33:16] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-06-14 02:33:16] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.3.0(2025-06-06); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-06-14); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); 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 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.1(2025-06-08); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-06-14 02:33:16] [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 [2025-06-14 02:33:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-14 02:33:16] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-06-14 02:33:16] [TRACE] [OmnipathR] Contains 1 files. [2025-06-14 02:33:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-14 02:33:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-06-14 02:33:16] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-06-14 02:33:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-06-14 02:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-06-14 02:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-06-14 02:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-06-14 02:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:16] [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 [2025-06-14 02:33:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:27] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-06-14 02:33:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-06-14 00:31:39 UTC; omnipath [2025-06-14 02:33:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-06-14 02:33:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-14 00:32:50 UTC; unix [2025-06-14 02:33:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-06-14 02:33:27] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-06-14 02:33:27] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-06-14; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-06-14 02:33:27] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-06-14 02:33:27] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.3.0(2025-06-06); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-06-14); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); 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 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.1(2025-06-08); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-06-14 02:33:27] [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 [2025-06-14 02:33:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-14 02:33:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-06-14 02:33:27] [TRACE] [OmnipathR] Contains 1 files. [2025-06-14 02:33:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-14 02:33:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-06-14 02:33:27] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-06-14 02:33:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-06-14 02:33:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-06-14 02:33:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-06-14 02:33:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-06-14 02:33:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:27] [TRACE] [OmnipathR] Cache locked: FALSE * 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: > ### Name: all_uniprots > ### Title: A table with all UniProt records > ### Aliases: all_uniprots > > ### ** Examples > > human_swissprot_entries <- all_uniprots(fields = 'id') [2025-06-14 02:33:52] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-06-14 02:33:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:52] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-06-14 02:33:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:52] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-06-14 02:33:52] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-06-14 02:33:52] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-06-14 02:33:52] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-06-14 02:33:52] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-06-14 02:33:52] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-06-14 02:33:52] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-06-14 02:33:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-06-14 02:33:52] [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] [2025-06-14 02:33:52] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-06-14 02:33:52] [TRACE] [OmnipathR] Sending HTTP request. [2025-06-14 02:33:52] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-06-14 02:33:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-06-14 02:33:52] [TRACE] [OmnipathR] Downloaded 31.1 Kb in 0.239842s from www.ensembl.org (129.6 Kb/s); Redirect: 0s, DNS look up: 0.012433s, Connection: 0.030908s, Pretransfer: 0.094409s, First byte at: 0.216008s [2025-06-14 02:33:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Sat, 14 Jun 2025 00:33:52 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31840; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Sun, 15 Jun 2025 00:33:52 GMT; Set-cookie: ENSEMBL_HINX_SESSION=80d8a7e1a4cc60d10b0367d5689bdd70093c697f7d2c2e50313e3d6c; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Sun, 15 Jun 2025 00:33:52 GMT; Set-cookie: ENSEMBL_HINX_SESSION=80d8a7e1a4cc60d10b0367d5689bdd70093c697f7d2c2e50313e3d6c; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-31.ebi.ac.uk [2025-06-14 02:33:52] [TRACE] [OmnipathR] Response headers: [Date=Sat, 14 Jun 2025 00:33:52 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31840,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Sun, 15 Jun 2025 00:33:52 GMT,Set-cookie=ENSEMBL_HINX_SESSION=80d8a7e1a4cc60d10b0367d5689bdd70093c697f7d2c2e50313e3d6c; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Sun, 15 Jun 2025 00:33:52 GMT,Set-cookie=ENSEMBL_HINX_SESSION=80d8a7e1a4cc60d10b0367d5689bdd70093c697f7d2c2e50313e3d6c; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-31.ebi.ac.uk] [2025-06-14 02:33:52] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-06-14 02:33:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:52] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-06-14 02:33:52] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-06-14 02:33:52] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-06-14 02:33:52] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-06-14 02:33:52] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-06-14 02:33:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:53] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-06-14 02:33:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-06-14 02:33:53] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-06-14 02:33:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-06-14 02:33:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-06-14 02:33:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-06-14 02:33:53] [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] [2025-06-14 02:33:53] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-06-14 02:33:53] [TRACE] [OmnipathR] Downloaded 7.9 Kb in 0.070179s from omabrowser.org (113.1 Kb/s); Redirect: 0s, DNS look up: 0.00096s, Connection: 0.01244s, Pretransfer: 0.054599s, First byte at: 0.070045s [2025-06-14 02:33:53] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 14 Jun 2025 00:33:53 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-06-14 02:33:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-06-14 02:33:53] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-06-14 02:33:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:53] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-06-14 02:33:53] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-06-14 02:33:53] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id [2025-06-14 02:33:53] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-06-14 02:33:53] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`. [2025-06-14 02:33:53] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` [2025-06-14 02:33:53] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`. [2025-06-14 02:33:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-14 02:33:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-14 02:33:53] [INFO] [OmnipathR] Cache item `80e22dce504c916061293773267b3f34dea718f3` version 1: status changed from `unknown` to `started`. [2025-06-14 02:33:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/80e22dce504c916061293773267b3f34dea718f3-1.rds`. [2025-06-14 02:33:53] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` [2025-06-14 02:33:53] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` [2025-06-14 02:33:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-06-14 02:33:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-06-14 02:33:53] [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] [2025-06-14 02:33:55] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-06-14 02:33:55] [TRACE] [OmnipathR] Downloaded 27 bytes in 2.22842s from rest.uniprot.org (12 bytes/s); Redirect: 0s, DNS look up: 0.00077s, Connection: 0.019213s, Pretransfer: 0.072408s, First byte at: 2.228338s [2025-06-14 02:33:55] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 14 Jun 2025 00:33:55 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025 [2025-06-14 02:34:55] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-06-14 02:35:00] [TRACE] [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` [2025-06-14 02:35:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-06-14 02:35:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-06-14 02:35:00] [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] [2025-06-14 02:35:02] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-06-14 02:35:02] [TRACE] [OmnipathR] Downloaded 27 bytes in 1.893537s from rest.uniprot.org (14 bytes/s); Redirect: 0s, DNS look up: 0.001404s, Connection: 0.020736s, Pretransfer: 0.093956s, First byte at: 1.893509s [2025-06-14 02:35:02] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 14 Jun 2025 00:35:02 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025 [2025-06-14 02:36:02] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-06-14 02:36:07] [TRACE] [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` [2025-06-14 02:36:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-06-14 02:36:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-06-14 02:36:07] [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] [2025-06-14 02:36:09] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-06-14 02:36:09] [TRACE] [OmnipathR] Downloaded 27 bytes in 2.052174s from rest.uniprot.org (13 bytes/s); Redirect: 0s, DNS look up: 0.001271s, Connection: 0.019922s, Pretransfer: 0.078812s, First byte at: 2.052132s [2025-06-14 02:36:09] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 14 Jun 2025 00:36:09 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025 [2025-06-14 02:38:08] [ERROR] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) [2025-06-14 02:38:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-06-14 00:31:39 UTC; omnipath [2025-06-14 02:38:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-06-14 02:38:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-14 00:32:50 UTC; unix [2025-06-14 02:38:08] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-06-14 02:38:08] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-06-14 02:38:08] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-06-14; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-06-14 02:38:08] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-06-14 02:38:08] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.3.0(2025-06-06); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-06-14); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); 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 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.1(2025-06-08); rvest 1.0.4(2024-02-12); selectr 0.4-2(2019-11-20); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-06-14 02:38:08] [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 (con, what, n = 1L, size = NA_integer_, signed = TRUE, : Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2) Calls: all_uniprots ... omnipath_cache_save -> saveRDS -> exec -> Execution halted * 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-3.21/2025-06-14_0218/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2025-06-14 02:58:03 CEST ]