##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('gINTomics_1.9.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing gINTomics ────────────────────────────────────────────────────────
✔ Package installed successfully
── gINTomics session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2HpSg7/filea6f6a6e533bfb/gINTomics
→ BiocVersion: 3.24
→ Package: gINTomics
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/gINTomics.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp2HpSg7/filea6f6a6e533bfb/gINTomics
→ installDir: /tmp/Rtmp2HpSg7/filea6f6a3f55d964
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gINTomics ──────────────────────────────────────────────
* 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 4.4.0 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 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 (39%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • gINTomics.Rmd
* Checking package installation calls in R code...
* Checking for library/require of gINTomics...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/helper_functions.R (line 563, column 50)
    • R/helper_functions.R (line 579, column 31)
    • R/helper_functions.R (line 593, column 31)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/observers_shiny.R (line 846, column 5)
    • ...
    • print() in R/observers_shiny.R (line 909, column 7)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/modules_shiny.R (line 290, column 18)
  • <<- in R/observers_shiny.R (line 1191, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 55
functions greater than 50 lines.
  The longest 5 functions are:
    • .gint_subItem_coefDistribGenomic() (R/interface_shiny.R): 225 lines
    • ...
    • server() (R/outputs_shiny.R): 140 lines
* Checking man page documentation...
[2026-05-09 06:56:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-09 06:56:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 06:56:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-09 06:56:01] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-09 06:56:01] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-05-08
[2026-05-09 06:56:01] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-08 19:08:51 UTC; unix
[2026-05-09 06:56:01] [INFO]    [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-09 06:56:01] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-09 06:56:01] [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 06:56:01] [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 06:56:02] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.75.0(2026-05-08); 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); BiocIO 1.23.3(2026-05-08); BiocManager 1.30.27(2025-11-14); BiocParallel 1.47.0(2026-05-08); biocViews 1.81.0(2026-05-08); Biostrings 2.81.1(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); cigarillo 1.3.0(2026-05-08); circlize 0.4.18(2026-04-04); cli 3.6.6(2026-04-09); clisymbols 1.2.0(2017-05-21); clue 0.3-68(2026-03-26); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.29.0(2026-05-08); 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); DelayedArray 0.39.1(2026-05-08); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.1(2026-04-03); DT 0.34.0(2025-09-02); 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); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); GenomicAlignments 1.49.0(2026-05-08); GenomicFeatures 1.65.0(2026-05-08); GenomicRanges 1.65.0(2026-05-08); GetoptLong 1.1.1(2026-04-08); ggplot2 4.0.3(2026-04-22); gINTomics 1.9.0(2026-05-08); GlobalOptions 0.1.4(2026-04-08); 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); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.17(2026-03-18); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); InteractiveComplexHeatmap 1.21.0(2026-05-08); IRanges 2.47.0(2026-05-08); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.53.0(2026-05-08); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); 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); MASS 7.3-65(2025-02-28); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.25.0(2026-05-08); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.43.0(2026-05-08); mime 0.13(2025-03-17); MultiAssayExperiment 1.39.0(2026-05-08); OmnipathR 4.1.0(2026-05-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-9(2026-03-15); 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); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); Rsamtools 2.29.0(2026-05-08); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.73.0(2026-05-08); RUnit 0.4.33.1(2025-06-17); rvest 1.0.5(2025-08-29); S4Arrays 1.13.0(2026-05-08); S4Vectors 0.51.1(2026-05-08); S7 0.2.2(2026-04-22); scales 1.4.0(2025-04-24); Seqinfo 1.3.0(2026-05-08); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.13.2(2026-05-08); stringdist 0.9.17(2026-01-16); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.43.0(2026-05-08); svglite 2.2.2(2025-10-21); systemfonts 1.3.2(2026-03-05); textshaping 1.0.5(2026-03-06); 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); viridisLite 0.4.3(2026-02-04); 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); xtable 1.8-8(2026-02-22); XVector 0.53.0(2026-05-08); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-09 06:56:02] [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 06:56:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] Contains 1 files.
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 06:56:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-05-09 06:56:02] [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 06:56:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 06:56:02] [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 06:56:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 06:56:02] [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 06:56:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-09 06:56:02] [TRACE]   [OmnipathR] Cache locked: FALSE



* 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; 55 lines (1%) are > 80 characters long.
  First few lines:
    • R/downloads.R#L183 #' @importFrom TxDb.Hsapiens.UCSC.hg38.k ...
    • ...
    • vignettes/gINTomics.Rmd#L261 Here is the output of sessionInfo() on t ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1119 lines (12%) are
not.
  First few lines:
    • R/downloads.R#L5 speci ...
    • ...
    • vignettes/gINTomics.Rmd#L164 ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 10 NOTES
ℹ See the gINTomics.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.