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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.18.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.18.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 ... OK
* 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
[2025-11-18 06:46:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 06:46:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:32] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 06:46:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 06:46:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 06:46:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:20 UTC; unix
[2025-11-18 06:46:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 06:46:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 06:46:32] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-18 06:46:33] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-18 06:46:33] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 06:46:33] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-18 06:46:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:33] [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
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:50] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 06:46:50] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 06:46:50] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 06:46:50] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:20 UTC; unix
[2025-11-18 06:46:50] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 06:46:50] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 06:46:50] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-18 06:46:50] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-18 06:46:50] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 06:46:50] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:46:50] [TRACE]   [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
Undefined global functions or variables:
  enzyme_genesymbol
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: go_annot_download
> ### Title: Gene annotations from Gene Ontology
> ### Aliases: go_annot_download
> 
> ### ** Examples
> 
> goa_data <- go_annot_download()
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-11-18 06:56:07] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:56:07] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-11-18 06:56:07] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/RtmpsaLm3v/goa_human.gaf.gz`
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Downloaded 6.3 Kb in 0.05641s from current.geneontology.org (112.4 Kb/s); Redirect: 0s, DNS look up: 0.02307s, Connection: 0.035373s, Pretransfer: 0.035445s, First byte at: 0.056288s
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Date: Tue, 18 Nov 2025 11:56:07 GMT; Content-Type: text/html; charset=UTF-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; Expires: Thu, 01 Jan 1970 00:00:01 GMT; Referrer-Policy: same-origin; X-Frame-Options: SAMEORIGIN; Vary: accept-encoding; Server: cloudflare; CF-RAY: 9a07486349d5d694-IAD
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-11-18 06:56:07] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 06:56:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-18 06:56:07] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
Error in `filter()`:
ℹ In argument: `aspect %in% aspects`.
Caused by error:
! `..1` must be of size 100 or 1, not size 0.
Backtrace:
     ▆
  1. ├─OmnipathR::go_annot_download()
  2. │ └─... %T>% load_success()
  3. ├─OmnipathR:::load_success(.)
  4. │ └─from_cache %<>% if_null(data %>% is_from_cache)
  5. ├─OmnipathR:::if_null(., data %>% is_from_cache)
  6. │ └─value1 %>% is.null %>% if (value2) value1
  7. ├─data %>% is_from_cache
  8. ├─OmnipathR:::is_from_cache(.)
  9. │ └─obj %>% attr("origin") %>% ...
 10. ├─dplyr::filter(., aspect %in% aspects)
 11. ├─dplyr:::filter.data.frame(., aspect %in% aspects)
 12. │ └─dplyr:::filter_rows(.data, dots, by)
 13. │   └─dplyr:::filter_eval(...)
 14. │     ├─base::withCallingHandlers(...)
 15. │     └─mask$eval_all_filter(dots, env_filter)
 16. │       └─dplyr (local) eval()
 17. ├─dplyr:::dplyr_internal_error(...)
 18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
 19. │   └─rlang:::signal_abort(cnd, .file)
 20. │     └─base::signalCondition(cnd)
 21. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 22.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                91.031  0.080  92.714
filter_extra_attrs                   48.688  7.648  65.744
curated_ligrec_stats                 44.266  3.441 128.390
all_uniprots                         24.085  1.331  39.923
extra_attrs_to_cols                  13.349  1.384  14.738
extra_attr_values                    12.455  1.567  16.742
find_all_paths                       13.220  0.473  18.055
giant_component                      12.476  0.909  17.083
filter_by_resource                   11.902  0.419  18.133
filter_intercell                     11.380  0.877  21.158
extra_attrs                           7.323  1.166   8.522
curated_ligand_receptor_interactions  6.680  0.874  20.311
ensembl_id_mapping_table              2.372  0.165  21.972
annotated_network                     1.630  0.185   5.461
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.