[ Started: 2025-03-18 01:29:10 CET ] [ wppi v1.6.0 for BioC-3.21 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ] Loading required package: BiocCheck ── Installing wppi ───────────────────────────────────────────────────────────── ✔ Package installed successfully ── wppi session metadata ─────────────────────────────────────────────────────── → sourceDir: /tmp/RtmpnM4kZg/file8c4532a21724c/wppi → BiocVersion: 3.21 → Package: wppi → PackageVersion: 1.6.0 → BiocCheckDir: /mnt/disk0/build/bioc-check/wppi/bioc-3.21/2025-03-18_0127/wppi/wppi.BiocCheck → BiocCheckVersion: 1.43.12 → sourceDir: /tmp/RtmpnM4kZg/file8c4532a21724c/wppi → installDir: /tmp/RtmpnM4kZg/file8c4533f8a49ea → 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 4.5.0. * 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 for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * 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 NOTE: 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 .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * 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... * 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... [2025-03-18 01:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 01:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:29:24] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-18 01:29:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-18 00:09:00 UTC; omnipath [2025-03-18 01:29:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-18 01:29:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-18 00:09:01 UTC; unix [2025-03-18 01:29:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-18 01:29:24] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-18 01:29:24] [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=en_GB.UTF-8; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-18 01:29:24] [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] [2025-03-18 01:29:24] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); Biobase 2.67.0(2024-10-29); BiocBaseUtils 1.9.0(2024-10-29); BiocCheck 1.43.12(2025-02-21); BiocFileCache 2.15.1(2025-01-17); BiocGenerics 0.53.6(2025-01-27); BiocManager 1.30.25(2024-08-28); biocViews 1.75.0(2024-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); dbplyr 2.5.0(2024-03-19); 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); filelock 1.0.3(2023-12-11); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); graph 1.85.1(2024-12-31); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); 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 3.15.11(2025-03-18); pillar 1.10.1(2025-01-07); 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); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RBGL 1.83.0(2024-10-29); Rcpp 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); RUnit 0.4.33(2024-02-22); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringdist 0.9.15(2025-01-10); stringi 1.8.4(2024-05-06); 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(2025-03-18); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-18 01:29:24] [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 [2025-03-18 01:29:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-18 01:29:24] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-18 01:29:24] [TRACE] [OmnipathR] Contains 1 files. [2025-03-18 01:29:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-18 01:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 01:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:29:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-18 01:29:24] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-18 01:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-18 01:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-18 01:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-18 01:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-18 01:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:29:24] [TRACE] [OmnipathR] Cache locked: FALSE * 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 Package is in the Support Site Watched Tags. ── BiocCheck v1.43.12 results ────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 8 NOTES ℹ See the wppi.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2025-03-18 01:29:26 CET ]