[ Started: 2026-10-26 19:53:22 CET ] [ 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 ] Loading required package: BiocCheck ── Installing wppi ───────────────────────────────────────────────────────────── ✔ Package installed successfully ── wppi session metadata ─────────────────────────────────────────────────────── → sourceDir: /tmp/Rtmp4Oa2N3/filed552e2df8cf6a/wppi → BiocVersion: 3.24 → Package: wppi → PackageVersion: 1.6.0 → BiocCheckDir: /mnt/disk0/build/bioc-check/wppi/bioc-3.24/2026-10-26_1951/wppi/wppi.BiocCheck → BiocCheckVersion: 1.49.33 → sourceDir: /tmp/Rtmp4Oa2N3/filed552e2df8cf6a/wppi → installDir: /tmp/Rtmp4Oa2N3/filed552e4d72d457/lib → isTarBall: TRUE → platform: unix ── Running BiocCheck on wppi ─────────────────────────────────────────────────── * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking version number validity... ! WARNING: y of x.y.z version should be odd in devel * Checking R version dependency... ℹ NOTE: Update R version dependency from 4.1 to 4.6.0 * Checking package size... * Checking individual file sizes... * Checking biocViews... * Checking that biocViews are present... * Checking package type based on biocViews... → Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * Checking build system compatibility... * Checking if 'Package:' field matches directory / tarball... * Checking for Version: field... * Checking DESCRIPTION readability... * Checking validity of DESCRIPTION fields... * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * Checking for whitespace in DESCRIPTION field names... * Checking for proper Description: field... * Checking for Bioconductor software dependencies... ! WARNING: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission. * Checking for pinned package versions in DESCRIPTION... * Checking for 'fnd' role in Authors@R... ℹ No 'fnd' role found in 'Authors@R'. If the work is supported by a grant, consider adding the 'fnd' role to the list of authors. * Checking CITATION... ℹ (Optional) CITATION file not found. Only include a CITATION file if there is a preprint or publication for this Bioconductor package. Note that Bioconductor packages are not required to have a CITATION file but it is useful both for users and for tracking Bioconductor project-wide metrics. When including a CITATION file, add the publication using the 'doi' argument of 'bibentry()'. * Checking NAMESPACE... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... ℹ NOTE: Vignette(s) found with missing chunk labels Found in files: • wppi_workflow.Rmd * Checking package installation calls in R code... * Checking for library/require of wppi... * Checking coding practice... ℹ NOTE: Avoid 1:...; use seq_len() or seq_along() Found in files: • WPPI_functions.R (line 296, column 15) * Checking parsed R code in R directory, examples, vignettes... [2026-10-26 19:53:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-26 19:53:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-26 19:53:42] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-10-26 19:53:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-10-26 18:23:05 UTC; omnipath [2026-10-26 19:53:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-10-26 19:53:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.1; ; 2026-10-26 18:23:07 UTC; unix [2026-10-26 19:53:42] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.2 [2026-10-26 19:53:42] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-10-26 19:53:42] [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=en_GB.UTF-8; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-10-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-10-26 19:53:42] [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] [2026-10-26 19:53:42] [INFO] [OmnipathR] Loaded packages: askpass 1.2.1(2024-10-04); backports 1.5.1(2026-04-03); Biobase 2.73.2(2026-07-29); BiocBaseUtils 1.15.1(2026-05-10); BiocCheck 1.49.33(2026-10-19); BiocFileCache 3.3.0(2026-04-28); BiocGenerics 0.59.12(2026-08-11); BiocManager 1.30.27(2025-11-14); biocViews 1.81.1(2026-07-08); bit 4.6.0(2025-03-06); bit64 4.8.6(2026-09-01); bitops 1.1-0(2026-07-30); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); callr 3.8.0(2026-06-05); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); credentials 2.0.3(2025-09-12); curl 8.1.0(2026-10-14); DBI 1.3.0(2026-02-25); dbplyr 2.6.0(2026-06-17); 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); filelock 1.0.3(2023-12-11); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); gert 2.5.0(2026-10-14); glue 1.8.1(2026-04-17); graph 1.91.0(2026-04-28); 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); 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 4.1.2(2026-10-26); openssl 2.4.2(2026-06-09); 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 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); ps 1.9.3(2026-04-20); 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); RBGL 1.89.0(2026-04-28); Rcpp 1.1.2(2026-07-05); RCurl 1.98-1.20(2026-08-21); 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); RUnit 0.4.33.1(2025-06-17); rvest 1.0.5(2025-08-29); sessioninfo 1.2.4(2026-06-04); stringdist 0.9.17(2026-01-16); stringi 1.8.9(2026-08-04); stringr 1.6.0(2025-11-04); sys 3.4.3(2024-10-04); 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(2026-10-26); 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) [2026-10-26 19:53:42] [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 [2026-10-26 19:53:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-10-26 19:53:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-10-26 19:53:42] [TRACE] [OmnipathR] Contains 1 files. [2026-10-26 19:53:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-10-26 19:53:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-26 19:53:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-26 19:53:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-10-26 19:53:42] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-10-26 19:53:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-10-26 19:53:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-26 19:53:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-10-26 19:53:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-26 19:53:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-10-26 19:53:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-26 19:53:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-10-26 19:53:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-26 19:53:42] [TRACE] [OmnipathR] Cache locked: FALSE * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 2 functions greater than 50 lines. The longest 5 functions are: • score_candidate_genes_from_PPI() (R/WPPI_app.R): 111 lines • weighted_adj() (R/WPPI_functions.R): 94 lines * Checking man page documentation... * Checking package NEWS... * Checking unit tests... ℹ NOTE: Consider adding unit tests. We strongly encourage them. See https://contributions.bioconductor.org/tests.html * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... ℹ NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters long. First few lines: • vignettes/wppi_workflow.Rmd#L41 it's possible to use custom databases. ... • vignettes/wppi_workflow.Rmd#L222 plot(graph_op_1,vertex.label = ifelse(sc ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 15 lines (1%) are not. First few lines: • R/WPPI_functions.R#L297 i <- adj_i[w] ... • ... • R/WPPI_functions.R#L314 functional_annot(HPO_data, gen ... ℹ See https://contributions.bioconductor.org/r-code.html ℹ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking if package already exists in CRAN... * Checking for bioc-devel mailing list subscription... ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel * Checking for support site registration... ℹ Maintainer is registered at support site. ℹ 'wppi' is already in your 'Watched Tags' on the Support Site. ── BiocCheck v1.49.33 results ────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 8 NOTES ℹ See the wppi.BiocCheck folder and run `browseVignettes(package = 'BiocCheck')` for details. [ Finished: 2026-10-26 19:53:44 CET ]