##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:TumourMethData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings TumourMethData_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-data-experiment/meat/TumourMethData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-21 17:33:23 UTC
* checking for file ‘TumourMethData/DESCRIPTION’ ... OK
* this is package ‘TumourMethData’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
There is circular dependency in the installation order:
  One or more packages in
  'SummarizedExperiment', 'base', 'BSgenome.Hsapiens.UCSC.hg19',
  'dplyr', 'ExperimentHub', 'ExperimentHubData', 'GenomicRanges',
  'HDF5Array', 'knitr', 'methodical', 'methrix', 'openxlsx', 'R.utils',
  'readr', 'rhdf5', 'rmarkdown', 'stringr', 'TCGAutils', 'tibble',
  'usethis', 'xlsx', 'methods', 'MatrixGenerics', 'Biobase', 'utils',
  'stats', 'tools', 'Matrix', 'BiocGenerics', 'S4Vectors', 'IRanges',
  'Seqinfo', 'S4Arrays', 'DelayedArray', 'BSgenome', 'cli', 'generics',
  'glue', 'lifecycle', 'magrittr', 'pillar', 'R6', 'rlang',
  'tidyselect', 'vctrs', 'AnnotationHub', 'BiocFileCache',
  'BiocManager', 'rappdirs', 'AnnotationHubData', 'DBI', 'httr',
  'curl', 'stats4', 'SparseArray', 'h5mread', 'evaluate', 'highr',
  'xfun', 'yaml', 'ggplot2', 'annotatr', 'BiocCheck', 'BiocParallel',
  'BiocStyle', 'Biostrings', 'BSgenome.Hsapiens.UCSC.hg38', 'cowplot',
  'data.table', 'devtools', 'foreach', 'GenomeInfoDb', 'rcmdcheck',
  'RcppRoll', 'remotes', 'rtracklayer', 'scales', 'tidyr',
  'DelayedMatrixStats', 'parallel', 'matrixStats', 'graphics',
  'grDevices', 'Rcpp', 'stringi', 'zip', 'R.oo', 'R.methodsS3',
  'clipr', 'crayon', 'hms', 'vroom', 'withr', 'cpp11', 'tzdb',
  'rhdf5filters', 'Rhdf5lib', 'bslib', 'fontawesome', 'htmltools',
  'jquerylib', 'jsonlite', 'tinytex', 'AnnotationDbi', 'BiocBaseUtils',
  'GenomicFeatures', 'GenomicDataCommons', 'MultiAssayExperiment',
  'RaggedExperiment', 'rvest', 'xml2', 'pkgconfig', 'desc', 'fs',
  'gert', 'gh', 'purrr', 'rprojroot', 'rstudioapi', 'whisker', 'rJava',
  'xlsxjars', 'grid', 'lattice', 'abind', 'BiocIO', 'XVector',
  'Rsamtools', 'utf8', 'RSQLite', 'BiocVersion', 'httr2', 'dbplyr',
  'filelock', 'biocViews', 'graph', 'OrganismDbi', 'AnnotationForge',
  'futile.logger', 'XML', 'RCurl', 'mime', 'openssl', 'gtable',
  'isoband', 'S7', 'regioneR', 'reshape2', 'callr', 'codetools',
  'commonmark', 'stringdist', 'snow', 'BH', 'bookdown', 'ellipsis',
  'memoise', 'miniUI', 'pak', 'pkgbuild', 'pkgdown', 'pkgload',
  'profvis', 'roxygen2', 'rversions', 'sessioninfo', 'testthat',
  'urlchecker', 'iterators', 'UCSC.utils', 'digest', 'prettyunits',
  'xopen', 'GenomicAlignments', 'restfulr', 'farver', 'labeling',
  'RColorBrewer', 'viridisLite', 'sparseMatrixStats', 'bit64',
  'progress', 'biocmake', 'base64enc', 'cachem', 'fastmap', 'sass',
  'KEGGREST', 'selectr', 'askpass', 'credentials', 'sys', 'gitcreds',
  'ini', 'bitops', 'Rhtslib', 'blob', 'RBGL', 'RUnit', 'lambda.r',
  'futile.options', 'plyr', 'processx', 'shiny', 'downlit', 'ragg',
  'htmlwidgets', 'brew', 'brio', 'praise', 'ps', 'waldo', 'cigarillo',
  'rjson', 'bit', 'dir.expiry', 'png', 'formatR', 'httpuv', 'later',
  'otel', 'promises', 'sourcetools', 'xtable', 'fansi', 'systemfonts',
  'textshaping', 'diffobj'
  depend on this package (for the versions on the repositories).

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.24-data-experiment/meat/TumourMethData.Rcheck/00check.log’
for details.