[ Started: 2025-02-11 18:47:12 CET ] [ OmnipathR v3.15.7 for BioC-3.20 from https://github.com/saezlab/OmnipathR@master (b7efee8 2025-02-11 18:31:14) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * 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 ‘3.15.7’ * 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 ... WARNING Found the following significant warnings: Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param) See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... NOTE installed size is 6.7Mb 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 [2025-02-11 18:47:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-11 18:47:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:39] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-11 18:47:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-11 17:46:07 UTC; omnipath [2025-02-11 18:47:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-11 18:47:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-11 17:47:14 UTC; unix [2025-02-11 18:47:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.7 [2025-02-11 18:47:39] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-11 18:47:39] [INFO] [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); 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=2025-02-11; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-11 18:47:39] [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] [2025-02-11 18:47:39] [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 [2025-02-11 18:47:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-11 18:47:39] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-11 18:47:39] [TRACE] [OmnipathR] Contains 1 files. [2025-02-11 18:47:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-11 18:47:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-11 18:47:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-11 18:47:39] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-11 18:47:39] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-11 18:47:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:39] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-11 18:47:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:39] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-11 18:47:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:39] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-11 18:47:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:39] [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 ... WARNING ungroup: function(x, ...) ungroup.tbl_attrs: function(.data, ...) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2025-02-11 18:47:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-11 18:47:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:48] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-11 18:47:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-11 17:46:07 UTC; omnipath [2025-02-11 18:47:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-11 18:47:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-11 17:47:14 UTC; unix [2025-02-11 18:47:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.7 [2025-02-11 18:47:48] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-11 18:47:49] [INFO] [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); 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=2025-02-11; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-11 18:47:49] [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] [2025-02-11 18:47:49] [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 [2025-02-11 18:47:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-11 18:47:49] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-11 18:47:49] [TRACE] [OmnipathR] Contains 1 files. [2025-02-11 18:47:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-11 18:47:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-11 18:47:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-11 18:47:49] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-11 18:47:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-11 18:47:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-11 18:47:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-11 18:47:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-11 18:47:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:47:49] [TRACE] [OmnipathR] Cache locked: FALSE ambiguity_summarize: no visible binding for global variable ‘data’ download_base : fun: no visible binding for global variable ‘resp_status_desc’ download_base : fun: no visible global function definition for ‘headers’ download_base : fun: no visible binding for global variable ‘response’ log_welcome: no visible binding for global variable ‘pkgname’ translate_ids : : no visible binding for global variable ‘From’ xls_downloader: possible error in download_to_cache(url_key = url_key, url_key_param = url_key_param, url_param = url_param, ext = ext, http_param = http_param, post = post): unused argument (http_param = http_param) Undefined global functions or variables: From data headers pkgname resp_status_desc response Consider adding importFrom("utils", "data") to your NAMESPACE file. * 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 ... WARNING Undocumented arguments in Rd file 'ambiguity.Rd' ‘from_col’ ‘to_col’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... WARNING '::' or ':::' import not declared from: ‘httr’ * 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: go_annot_download > ### Title: Gene annotations from Gene Ontology > ### Aliases: go_annot_download > > ### ** Examples > > goa_data <- go_annot_download() [2025-02-11 18:52:14] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-02-11 18:52:14] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-02-11 18:52:14] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-02-11 18:52:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-02-11 18:52:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-11 18:52:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:52:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-11 18:52:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-11 18:52:14] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`. [2025-02-11 18:52:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-02-11 18:52:14] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-02-11 18:52:14] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-02-11 18:52:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-11 18:52:14] [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=TRUE,ssl_verifyhost=TRUE] [2025-02-11 18:52:15] [WARN] [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 1/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&' [2025-02-11 18:52:20] [TRACE] [OmnipathR] Attempt 2/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-02-11 18:52:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-11 18:52:20] [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=TRUE,ssl_verifyhost=TRUE] [2025-02-11 18:52:20] [WARN] [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 2/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&' [2025-02-11 18:52:25] [TRACE] [OmnipathR] Attempt 3/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-02-11 18:52:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-11 18:52:25] [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=TRUE,ssl_verifyhost=TRUE] [2025-02-11 18:52:25] [ERROR] [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&' [2025-02-11 18:52:25] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-11 17:46:07 UTC; omnipath [2025-02-11 18:52:25] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-11 18:52:25] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-11 17:47:14 UTC; unix [2025-02-11 18:52:25] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.7 [2025-02-11 18:52:25] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-11 18:52:25] [INFO] [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); 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=2025-02-11; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-11 18:52:25] [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] [2025-02-11 18:52:25] [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 vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&' Calls: go_annot_download ... 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, 4 WARNINGs, 3 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-02-11_1836/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2025-02-11 19:01:22 CET ]