[ Started: 2025-05-29 03:56:03 CEST ] [ wppi v1.6.0 for BioC-3.21 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ] * using log directory ‘/mnt/disk0/build/bioc-check/wppi/bioc-3.21/2025-05-29_0352/wppi/wppi.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 ‘wppi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wppi’ version ‘1.6.0’ * 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 ‘wppi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Licence stub is invalid DCF. * 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 [2025-05-29 03:56:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:56:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:33] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:56:33] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild [2025-05-29 03:56:33] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16 [2025-05-29 03:56:33] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 01:31:37 UTC; unix [2025-05-29 03:56:33] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-05-29 03:56:33] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-05-29 03:56:33] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-29 03:56:33] [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] [2025-05-29 03:56:33] [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 6.2.3(2025-05-24); 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); lattice 0.22-6(2024-03-20); 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); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); 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 2.3.11(2025-05-04); 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 3.2.1(2023-03-20); 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); wppi 1.6.0(2025-05-29); 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) [2025-05-29 03:56:33] [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 [2025-05-29 03:56:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-29 03:56:33] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:56:33] [TRACE] [OmnipathR] Contains 1 files. [2025-05-29 03:56:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-29 03:56:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:56:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:56:33] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-29 03:56:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-29 03:56:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-29 03:56:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-29 03:56:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-29 03:56:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:33] [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 [2025-05-29 03:56:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:56:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:56:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild [2025-05-29 03:56:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16 [2025-05-29 03:56:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 01:31:37 UTC; unix [2025-05-29 03:56:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-05-29 03:56:44] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-05-29 03:56:45] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-29 03:56:45] [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] [2025-05-29 03:56:45] [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 6.2.3(2025-05-24); 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); lattice 0.22-6(2024-03-20); 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); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); 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 2.3.11(2025-05-04); 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 3.2.1(2023-03-20); 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); wppi 1.6.0(2025-05-29); 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) [2025-05-29 03:56:45] [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 [2025-05-29 03:56:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-29 03:56:45] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:56:45] [TRACE] [OmnipathR] Contains 1 files. [2025-05-29 03:56:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-29 03:56:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:56:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:56:45] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-29 03:56:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-29 03:56:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-29 03:56:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-29 03:56:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-29 03:56:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:56:45] [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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘wppi-Ex.R’ failed The error most likely occurred in: > ### Name: common_neighbors > ### Title: Shared neighbors of connected vertices > ### Aliases: common_neighbors > > ### ** Examples > > graph_op <- graph_from_op(wppi_omnipath_data()) Warning in (function (...) : 'function (...) { .Deprecated("post_translational") post_translational(...) }' is deprecated. Use 'post_translational' instead. See help("Deprecated") [2025-05-29 03:57:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-29 03:57:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions] [2025-05-29 03:57:03] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-05-29 03:57:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:03] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-05-29 03:57:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:03] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-05-29 03:57:03] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-05-29 03:57:03] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-05-29 03:57:03] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-05-29 03:57:03] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-05-29 03:57:03] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-05-29 03:57:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-05-29 03:57:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-29 03:57:03] [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] [2025-05-29 03:57:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-05-29 03:57:03] [TRACE] [OmnipathR] Sending HTTP request. [2025-05-29 03:57:03] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-05-29 03:57:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-29 03:57:03] [TRACE] [OmnipathR] Downloaded 1014 bytes in 0.106337s from www.ensembl.org (9.3 Kb/s); Redirect: 0s, DNS look up: 0.008734s, Connection: 0.027247s, Pretransfer: 0.084535s, First byte at: 0.106151s [2025-05-29 03:57:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: 3220:F86B0:68CF89:693AD6:68342168; Server: GitHub.com; X-Cache-Hits: 144; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: b38606e54e1a5f22fd750fdd1febb73bd169c715; Content-Encoding: gzip; Date: Thu, 29 May 2025 01:57:03 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600023-LCY; Pragma: no-cache; X-Timer: S1748483824.881426,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"681dc811-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 304; Content-Length: 1014 [2025-05-29 03:57:03] [TRACE] [OmnipathR] Response headers: [X-GitHub-Request-Id=3220:F86B0:68CF89:693AD6:68342168,Server=GitHub.com,X-Cache-Hits=144,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=b38606e54e1a5f22fd750fdd1febb73bd169c715,Content-Encoding=gzip,Date=Thu, 29 May 2025 01:57:03 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600023-LCY,Pragma=no-cache,X-Timer=S1748483824.881426,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"681dc811-8aa",Via=1.1 varnish,Connection=keep-alive,Age=304,Content-Length=1014] [2025-05-29 03:57:04] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-05-29 03:57:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:04] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" Backtrace: ▆ 1. ├─wppi::graph_from_op(wppi_omnipath_data()) 2. │ └─op_data %>% ... 3. ├─dplyr::select(., -c(source_genesymbol, target_genesymbol)) 4. ├─wppi::wppi_omnipath_data() 5. │ └─... %>% select(seq(10)) 6. ├─dplyr::select(., seq(10)) 7. ├─rlang::exec(., !!!omnipath_param) 8. ├─OmnipathR (local) ``(entity_type = "protein") 9. │ └─OmnipathR::post_translational(...) 10. │ ├─rlang::exec(omnipath_query, !!!args) 11. │ └─OmnipathR (local) ``(...) 12. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 13. ├─OmnipathR:::omnipath_check_param(.) 14. │ └─param$organisms %<>% map_int(ncbi_taxid) 15. ├─purrr::map_int(., ncbi_taxid) 16. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 17. │ ├─purrr:::with_indexed_errors(...) 18. │ │ └─base::withCallingHandlers(...) 19. │ ├─purrr:::call_with_cleanup(...) 20. │ └─OmnipathR (local) .f(.x[[i]], ...) 21. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 22. ├─purrr::map_int(., taxon_name, "ncbi") 23. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 24. │ ├─purrr:::with_indexed_errors(...) 25. │ │ └─base::withCallingHandlers(...) 26. │ ├─purrr:::call_with_cleanup(...) 27. │ └─OmnipathR (local) .f(.x[[i]], ...) 28. │ ├─... %>% if_null_len0(NA) 29. │ └─OmnipathR::get_db("organisms") 30. │ └─OmnipathR::load_db(key, param = param) 31. │ ├─rlang::exec(loader, !!!param) 32. │ └─OmnipathR (local) ``() 33. │ ├─... %>% ... 34. │ └─OmnipathR::ensembl_organisms() 35. │ ├─... %>% ... 36. │ └─OmnipathR::ensembl_organisms_raw() 37. │ └─... %>% html_table() 38. ├─OmnipathR:::if_null_len0(., NA) 39. │ └─value1 %>% is_empty_2 %>% if (value2) value1 40. ├─OmnipathR:::is_empty_2(.) 41. │ └─value %>% ... 42. ├─dplyr::first(.) 43. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm) 44. │ └─vctrs::vec_size(x) 45. ├─dplyr::pull(., name_type) 46. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name)) 47. ├─dplyr::select(., -latin_name.x, -latin_name.y) 48. ├─dplyr::mutate(...) 49. ├─dplyr::full_join(...) 50. ├─dplyr::mutate(...) 51. ├─dplyr::select(...) 52. ├─rvest::html_table(.) 53. └─base::.handleSimpleError(...) 54. └─purrr (local) h(simpleError(msg, call)) 55. └─cli::cli_abort(...) 56. └─rlang::abort(...) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘wppi_workflow.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-05-29 03:57:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:57:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild [2025-05-29 03:57:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16 [2025-05-29 03:57:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 01:31:37 UTC; unix [2025-05-29 03:57:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-05-29 03:57:07] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-05-29 03:57:07] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-29 03:57:07] [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] [2025-05-29 03:57:07] [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); bslib 0.9.0(2025-01-30); 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 6.2.3(2025-05-24); 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); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); 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); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); 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 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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); wppi 1.6.0(2025-05-29); 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) [2025-05-29 03:57:07] [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 [2025-05-29 03:57:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-29 03:57:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:57:07] [TRACE] [OmnipathR] Contains 2 files. [2025-05-29 03:57:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-29 03:57:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-29 03:57:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-29 03:57:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-29 03:57:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-29 03:57:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-29 03:57:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-29 03:57:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:07] [TRACE] [OmnipathR] Cache locked: FALSE [2025-05-29 03:57:07] [INFO] [wppi] Executing WPPI workflow. [2025-05-29 03:57:08] [INFO] [wppi] Collecting database knowledge. [2025-05-29 03:57:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-05-29 03:57:08] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-05-29 03:57:08] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-05-29 03:57:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-05-29 03:57:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:08] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`. [2025-05-29 03:57:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-05-29 03:57:08] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-05-29 03:57:08] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-05-29 03:57:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-29 03:57:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-29 03:57:08] [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] [2025-05-29 03:57:09] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-05-29 03:57:09] [TRACE] [OmnipathR] Downloaded 13.4 Kb in 1.059355s from purl.obolibrary.org (12.7 Kb/s); Redirect: 0.60733s, DNS look up: 0.005028s, Connection: 0.022961s, Pretransfer: 0.124538s, First byte at: 1.058386s [2025-05-29 03:57:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Thu, 29 May 2025 01:57:08 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; cf-cache-status: DYNAMIC; Set-Cookie: __cf_bm=yNRQH8y1I7aschEFGPjNBr0iX1_.OHjABbRMmUsmshQ-1748483828-1.0.1.1-4uZDepycqW223rNjuqcizR7uvuIfinK6FJVQojToMtVNDShP8liLbtJ6Zq5yc7mvGCsxks5szcX1s2nqMpwlKrZiQi_C7bvlD9uRgj8DWJU; path=/; expires=Thu, 29-May-25 02:27:08 GMT; domain=.obolibrary.org; HttpOnly; Server: cloudflare; CF-RAY: 947261157be12c0e-STR; HTTP/2 302 ; date: Thu, 29 May 2025 01:57:08 GMT; content-type: text/html; charset=utf-8; content-length: 0; 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x-cache-hits: 327, 0; x-timer: S1748483829.742955,VS0,VE1; content-length: 19774160 [2025-05-29 03:57:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-05-29 03:57:10] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1] [2025-05-29 03:57:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:10] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`. [2025-05-29 03:57:10] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316793 records [2025-05-29 03:57:10] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-05-29 03:57:10] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-05-29 03:57:10] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-05-29 03:57:10] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-05-29 03:57:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:10] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`. [2025-05-29 03:57:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-05-29 03:57:10] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-05-29 03:57:10] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-05-29 03:57:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-29 03:57:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-29 03:57:10] [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] [2025-05-29 03:57:10] [TRACE] [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/Rtmpje5c0l/goa_human.gaf.gz` [2025-05-29 03:57:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-29 03:57:11] [TRACE] [OmnipathR] Downloaded 14.4 Mb in 0.21536s from current.geneontology.org (66.7 Mb/s); Redirect: 0s, DNS look up: 0.017138s, Connection: 0.026305s, Pretransfer: 0.026342s, First byte at: 0.036448s [2025-05-29 03:57:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Content-Type: application/gzip; Content-Length: 15072128; Connection: keep-alive; x-amz-meta-build-pipeline: release; x-amz-meta-build-number: 374; Last-Modified: Fri, 21 Mar 2025 23:00:01 GMT; Server: AmazonS3; Date: Thu, 29 May 2025 01:54:53 GMT; ETag: "00dbc6cee947ef028b88882c153d42e4-2"; X-Cache: Hit from cloudfront; Via: 1.1 b7c8b552077b93dc0acaa0b82d11fa62.cloudfront.net (CloudFront); X-Amz-Cf-Pop: FRA56-P8; X-Amz-Cf-Id: XqraqEVvgHjBU6iLx475y6XqdAz2I3sXEjVfLf_PskS53XTfQ6e6XA==; Age: 138 [2025-05-29 03:57:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-05-29 03:57:18] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1] [2025-05-29 03:57:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:18] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`. [2025-05-29 03:57:19] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 969176 records [2025-05-29 03:57:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-29 03:57:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions] [2025-05-29 03:57:19] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-05-29 03:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:19] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-05-29 03:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:19] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-05-29 03:57:19] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-05-29 03:57:19] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-05-29 03:57:19] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-05-29 03:57:19] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-05-29 03:57:19] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-05-29 03:57:19] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-05-29 03:57:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-29 03:57:19] [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] [2025-05-29 03:57:19] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-05-29 03:57:19] [TRACE] [OmnipathR] Sending HTTP request. [2025-05-29 03:57:19] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-05-29 03:57:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-29 03:57:19] [TRACE] [OmnipathR] Downloaded 1014 bytes in 0.107847s from www.ensembl.org (9.2 Kb/s); Redirect: 0s, DNS look up: 0.001138s, Connection: 0.019535s, Pretransfer: 0.086172s, First byte at: 0.107784s [2025-05-29 03:57:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: 3220:F86B0:68CF89:693AD6:68342168; Server: GitHub.com; X-Cache-Hits: 3; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: 78134cced5aece73c16203fa07ba37755a8cda7f; Content-Encoding: gzip; Date: Thu, 29 May 2025 01:57:19 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600079-LCY; Pragma: no-cache; X-Timer: S1748483839.415858,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"681dc811-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 321; Content-Length: 1014 [2025-05-29 03:57:19] [TRACE] [OmnipathR] Response headers: [X-GitHub-Request-Id=3220:F86B0:68CF89:693AD6:68342168,Server=GitHub.com,X-Cache-Hits=3,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=78134cced5aece73c16203fa07ba37755a8cda7f,Content-Encoding=gzip,Date=Thu, 29 May 2025 01:57:19 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600079-LCY,Pragma=no-cache,X-Timer=S1748483839.415858,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"681dc811-8aa",Via=1.1 varnish,Connection=keep-alive,Age=321,Content-Length=1014] [2025-05-29 03:57:19] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-05-29 03:57:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-29 03:57:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-29 03:57:19] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. Quitting from wppi_workflow.Rmd:79-102 [workflow] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `UseMethod()`: ! no applicable method for 'html_table' applied to an object of class "xml_missing" --- failed re-building ‘wppi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘wppi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs See ‘/mnt/disk0/build/bioc-check/wppi/bioc-3.21/2025-05-29_0352/wppi/wppi.Rcheck/00check.log’ for details. [ Finished: 2025-05-29 03:57:22 CEST ]