[ Started: 2026-10-19 18:53:06 CEST ]
[ wppi v1.6.0 for BioC-3.24 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ]
[ R version 4.6.1 Patched (2026-10-12 r90666) -- "Happy Hop" at /opt/R-4.6-patched/bin ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘wppi’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-10-19 18:53:18] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-10-19 18:53:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-10-19 16:33:42 UTC; omnipath
[2026-10-19 18:53:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-10-19 18:53:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.1; ; 2026-10-19 16:33:44 UTC; unix
[2026-10-19 18:53:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-10-19 18:53:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-10-19 18:53:18] [INFO]    [OmnipathR] Session info: [version=R version 4.6.1 Patched (2026-10-12 r90666); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-10-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-10-19 18:53:18] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-4.6-patched/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-10-19 18:53:18] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.6(2026-09-01); blob 1.3.0(2026-01-14); bslib 0.12.0(2026-08-04); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 8.1.0(2026-10-14); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.9(2026-09-01); httr2 1.3.0(2026-07-13); igraph 2.3.4(2026-09-30); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.52(2026-09-06); later 1.4.8(2026-03-05); lattice 0.23-1(2026-08-12); lifecycle 1.0.5(2026-01-08); logger 0.4.3(2026-08-24); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); Matrix 1.7-6(2026-07-25); memoise 2.0.1(2021-11-26); OmnipathR 4.1.0(2026-10-19); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.2(2026-07-05); readr 2.2.0(2026-02-19); readxl 1.6.0(2026-10-17); rlang 1.3.0(2026-07-05); rmarkdown 2.32(2026-09-01); RSQLite 3.53.3(2026-06-30); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.4(2026-06-04); stringi 1.8.9(2026-08-04); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.3(2026-06-19); wppi 1.6.0(2026-10-19); xfun 0.62(2026-10-16); XML 3.99-0.25(2026-09-27); xml2 1.6.0(2026-06-22); yaml 2.3.12(2025-12-10); zip 3.0.2(2026-08-04)
[2026-10-19 18:53:18] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Contains 1 files.
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-10-19 18:53:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-10-19 18:53:18] [INFO]    [wppi] Executing WPPI workflow.
[2026-10-19 18:53:18] [INFO]    [wppi] Collecting database knowledge.
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] Bypassing call: `OmnipathR::hpo_download()`.
[2026-10-19 18:53:18] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.

Quitting from wppi_workflow.Rmd:79-102 [workflow]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `UseMethod()`:
! no applicable method for 'select' applied to an object of class "NULL"
---
Backtrace:
    ▆
 1. ├─wppi::score_candidate_genes_from_PPI(genes_interest)
 2. │ ├─databases %||% ...
 3. │ └─wppi::wppi_data(...)
 4. │   └─wppi::wppi_hpo_data()
 5. │     └─... %>% distinct()
 6. ├─dplyr::distinct(.)
 7. └─dplyr::select(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
no applicable method for 'select' applied to an object of class "NULL"
--- failed re-building ‘wppi_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘wppi_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2026-10-19 18:53:18 CEST ]