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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MetaProViz_4.1.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MetaProViz ───────────────────────────────────────────────────────
✔ Package installed successfully
── MetaProViz session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZjkI6p/filed4bdc7d09b453/MetaProViz
→ BiocVersion: 3.24
→ Package: MetaProViz
→ PackageVersion: 4.1.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MetaProViz.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZjkI6p/filed4bdc7d09b453/MetaProViz
→ installDir: /tmp/RtmpZjkI6p/filed4bdc3d49225c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MetaProViz ─────────────────────────────────────────────
* 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...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.4 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Reactome
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (15%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of MetaProViz...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/RefactorPriorKnoweldge.R (line 2386, column 9)
    • ...
    • print() in R/RefactorPriorKnoweldge.R (line 3126, column 13)
* 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 71
functions greater than 50 lines.
  The longest 5 functions are:
    • mca_core() (R/MetaboliteClusteringAnalysis.R): 1686 lines
    • ...
    • mapping_ambiguity() (R/RefactorPriorKnoweldge.R): 574 lines
* Checking man page documentation...
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 07:10:09] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-09 07:10:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-09 07:10:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-05-08
[2026-05-09 07:10:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-08 19:08:51 UTC; unix
[2026-05-09 07:10:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-09 07:10:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-09 07:10:09] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=en_US.UTF-8; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-09; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-09 07:10:09] [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; 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=/home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-09 07:10:09] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); Biobase 2.73.1(2026-05-08); BiocBaseUtils 1.15.0(2026-05-08); BiocCheck 1.49.4(2026-05-08); BiocFileCache 3.3.0(2026-05-08); BiocGenerics 0.59.0(2026-05-08); BiocManager 1.30.27(2025-11-14); biocViews 1.81.0(2026-05-08); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); dbplyr 2.5.2(2026-02-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); EnhancedVolcano 1.31.0(2026-05-08); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); 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); ggplot2 4.0.3(2026-04-22); ggrepel 0.9.8(2026-03-17); glue 1.8.1(2026-04-17); graph 1.91.0(2026-05-08); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 4.1.0(2026-05-08); OmnipathR 4.1.0(2026-05-08); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); 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); promises 1.5.0(2025-11-01); 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(2026-05-08); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1-1.1(2026-04-24); RCurl 1.98-1.18(2026-03-21); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); RUnit 0.4.33.1(2025-06-17); rvest 1.0.5(2025-08-29); S7 0.2.2(2026-04-22); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringdist 0.9.17(2026-01-16); stringi 1.8.7(2025-03-27); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-09 07:10:09] [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
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Contains 1 files.
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 07:10:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 07:10:09] [TRACE]   [OmnipathR] Cache locked: FALSE
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • checkmatch_pk_to_data.Rd
    • ...
    • translate_id.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • checkmatch_pk_to_data.Rd
    • ...
    • translate_id.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • checkmatch_pk_to_data.Rd
    • ...
    • translate_id.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 1434 lines (6%) are > 80 characters long.
  First few lines:
    • R/DifferentialMetaboliteAnalysis.R#L38 #' @param metadata_info Named
    character ...
    • ...
    • vignettes/quick-start.Rmd#L473 For a detailed example of the visualisat
    ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 8 NOTES
ℹ See the MetaProViz.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.