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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methodical.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methodical_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/methodical.Rcheck’
* using R Under development (unstable) (2026-03-26 r89717)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-09 23:09:39 UTC
* using option ‘--no-vignettes’
* checking for file ‘methodical/DESCRIPTION’ ... OK
* this is package ‘methodical’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  ..pdf
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘methodical’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in '.split_meth_array_files_into_chunks(array_files = array_files, ': unused argument (normalization_factor = normalization_factor) 
  Note: possible error in '.write_chunks_to_hdf5(hdf5_sink = setup$hdf5_sink, ': unused argument (hdf5_sink = setup$hdf5_sink) 
  Note: possible error in '.create_meth_rse_from_hdf5(hdf5_filepath = setup$hdf5_filepath, ': unused argument (meth_sites_df = probe_sites_df) 
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/methodical.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... INFO
  installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data      8.6Mb
    extdata   1.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘AnnotationHub’ ‘BiocCheck’ ‘BiocManager’ ‘BiocStyle’
  ‘MatrixGenerics’ ‘TumourMethData’ ‘annotatr’ ‘devtools’ ‘knitr’
  ‘rcmdcheck’ ‘remotes’ ‘rhdf5’ ‘usethis’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘HDF5Array:::.serialize_HDF5SummarizedExperiment’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.chunk_regions’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calculate_regions_intersections: no visible global function definition
  for ‘is’
.chunk_regions: no visible global function definition for ‘is’
.chunk_regions: no visible global function definition for
  ‘subsetByOverlaps’
.collapse_strands: no visible binding for global variable ‘total_reads’
.collapse_strands: no visible binding for global variable
  ‘meth_fraction’
.count_covered_bases: no visible global function definition for ‘is’
.create_meth_rse_from_hdf5: no visible global function definition for
  ‘setNames’
.find_tmrs_single: no visible global function definition for ‘is’
.set_meth_df_columns: no visible binding for global variable
  ‘total_reads’
.set_meth_df_columns: no visible binding for global variable
  ‘meth_fraction’
.set_meth_df_columns: no visible binding for global variable
  ‘meth_reads’
.set_meth_df_columns: no visible binding for global variable
  ‘unmeth_reads’
.split_meth_array_file: no visible binding for global variable
  ‘probe_groups’
.split_meth_array_file: no visible binding for global variable
  ‘total_files’
.split_meth_array_file: no visible binding for global variable
  ‘probe_sites_df’
.split_meth_array_file: no visible global function definition for
  ‘setNames’
.split_meth_array_file: no visible binding for global variable
  ‘probe_name_column’
.split_meth_array_file: no visible binding for global variable
  ‘beta_value_column’
.split_meth_array_file: no visible binding for global variable
  ‘normalization_factor’
.split_meth_array_file: no visible binding for global variable
  ‘decimal_places’
.split_meth_array_file: no visible binding for global variable ‘name’
.split_meth_array_file: no visible binding for global variable ‘pg’
.split_meth_array_file: no visible binding for global variable
  ‘temp_chunk_dirs’
.split_meth_array_file: no visible binding for global variable
  ‘dt_threads’
.split_meth_array_files_into_chunks: no visible binding for global
  variable ‘name’
.summarize_chunk_methylation: no visible global function definition for
  ‘subsetByOverlaps’
.tss_correlations: no visible global function definition for ‘setNames’
.write_chunks_to_hdf5: no visible binding for global variable ‘chunk’
annotateGRanges: no visible global function definition for ‘is’
annotatePlot: no visible global function definition for ‘is’
annotatePlot: no visible global function definition for
  ‘colorRampPalette’
annotatePlot: no visible global function definition for
  ‘subsetByOverlaps’
annotatePlot: no visible binding for global variable ‘region_type’
calculateMethSiteTranscriptCors: no visible global function definition
  for ‘is’
calculateMethSiteTranscriptCors: no visible binding for global variable
  ‘chunk’
calculateMethSiteTranscriptCors: no visible global function definition
  for ‘subsetByOverlaps’
calculateMethSiteTranscriptCors: no visible global function definition
  for ‘setNames’
calculateRegionMethylationTranscriptCors: no visible global function
  definition for ‘is’
calculateRegionMethylationTranscriptCors: no visible binding for global
  variable ‘p.adjust.methods’
calculateRegionMethylationTranscriptCors : <anonymous>: no visible
  global function definition for ‘setNames’
calculateRegionMethylationTranscriptCors: no visible global function
  definition for ‘p.adjust’
calculateSmoothedMethodicalScores: no visible global function
  definition for ‘is’
correct_correlation_pvalues: no visible binding for global variable
  ‘p.adjust.methods’
correct_correlation_pvalues: no visible global function definition for
  ‘p.adjust’
expand_granges: no visible global function definition for ‘is’
expand_granges: no visible global function definition for ‘IRanges’
export_bedGraph_from_rse: no visible global function definition for
  ‘is’
export_bedGraph_from_rse: no visible binding for global variable ‘test’
extractGRangesMethSiteValues: no visible global function definition for
  ‘is’
extractMethSitesFromGenome: no visible global function definition for
  ‘is’
kallistoIndex: no visible global function definition for ‘is’
kallistoQuantify: no visible global function definition for ‘is’
kallistoQuantify: no visible global function definition for ‘setNames’
liftoverMethRSE: no visible global function definition for ‘is’
makeMethRSEFromArrayFiles: no visible global function definition for
  ‘is’
makeMethRSEFromArrayFiles: possible error in
  .split_meth_array_files_into_chunks(array_files = array_files,
  probe_name_column = probe_name_column, beta_value_column =
  beta_value_column, file_grid_columns = setup$file_grid_columns,
  probe_ranges = probe_ranges, probe_groups = setup$meth_site_groups,
  temp_chunk_dirs = setup$temp_chunk_dirs, normalization_factor =
  normalization_factor, decimal_places = decimal_places, BPPARAM =
  BPPARAM): unused argument (normalization_factor =
  normalization_factor)
makeMethRSEFromArrayFiles: possible error in
  .write_chunks_to_hdf5(hdf5_sink = setup$hdf5_sink, hdf5_grid =
  setup$hdf5_grid, temp_chunk_dirs = setup$temp_chunk_dirs,
  files_in_chunks = setup$files_in_chunks): unused argument (hdf5_sink
  = setup$hdf5_sink)
makeMethRSEFromArrayFiles: possible error in
  .create_meth_rse_from_hdf5(hdf5_filepath = setup$hdf5_filepath,
  hdf5_dir = hdf5_dir, meth_sites_df = probe_sites_df, sample_metadata
  = sample_metadata): unused argument (meth_sites_df = probe_sites_df)
makeMethRSEFromInputFiles: no visible global function definition for
  ‘is’
maskRangesInRSE: no visible global function definition for ‘is’
maskRangesInRSE: no visible global function definition for ‘queryHits’
methrixToRSE: no visible global function definition for ‘is’
plotMethSiteCorCoefs: no visible global function definition for ‘is’
plotMethSiteCorCoefs: no visible global function definition for
  ‘col2rgb’
plotMethSiteCorCoefs: no visible binding for global variable ‘cor’
plotMethSiteCorCoefs: no visible global function definition for
  ‘complete.cases’
plotMethSiteCorCoefs: no visible binding for global variable
  ‘meth_cor_plot_position’
plotMethodicalScores: no visible global function definition for ‘is’
plotMethodicalScores: no visible global function definition for
  ‘seqlevels’
plotMethodicalScores: no visible binding for global variable
  ‘meth_site_start’
plotMethodicalScores: no visible binding for global variable
  ‘meth_site_plot_position’
plotMethodicalScores: no visible binding for global variable
  ‘methodical_score’
plotMethodicalScores: no visible binding for global variable ‘cor’
plotRegionValues: no visible global function definition for ‘is’
plotRegionValues: no visible global function definition for ‘col2rgb’
plotRegionValues: no visible global function definition for
  ‘complete.cases’
plotRegionValues: no visible global function definition for
  ‘modifyList’
plotRegionValues: no visible binding for global variable
  ‘meth_site_plot_position’
plotTMRs: no visible global function definition for ‘is’
plotTMRs: no visible binding for global variable ‘direction’
plotTMRs: no visible global function definition for ‘setNames’
rangesRelativeToTSS: no visible global function definition for ‘is’
rapidCorTest: no visible global function definition for ‘is’
rapidCorTest: no visible binding for global variable ‘p.adjust.methods’
rapidCorTest: no visible global function definition for ‘cor’
rapidCorTest: no visible global function definition for ‘pt’
rapidCorTest: no visible global function definition for ‘p.adjust’
sampleMethSites: no visible global function definition for ‘is’
strandedDistance: no visible global function definition for ‘is’
sumTranscriptValuesForGenes: no visible global function definition for
  ‘is’
sumTranscriptValuesForGenes : <anonymous>: no visible global function
  definition for ‘is’
sumTranscriptValuesForGenes: no visible binding for global variable
  ‘gene_transcripts’
summarizeRegionMethylation: no visible global function definition for
  ‘is’
summarizeRegionMethylation: no visible global function definition for
  ‘seqlevels’
Undefined global functions or variables:
  IRanges beta_value_column chunk col2rgb colorRampPalette
  complete.cases cor decimal_places direction dt_threads
  gene_transcripts is meth_cor_plot_position meth_fraction meth_reads
  meth_site_plot_position meth_site_start methodical_score modifyList
  name normalization_factor p.adjust p.adjust.methods pg probe_groups
  probe_name_column probe_sites_df pt queryHits region_type seqlevels
  setNames subsetByOverlaps temp_chunk_dirs test total_files
  total_reads unmeth_reads
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "cor", "p.adjust",
             "p.adjust.methods", "pt", "setNames")
  importFrom("utils", "modifyList")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) kallistoQuantify.Rd:34: Lost braces; missing escapes or markup?
    34 | {merged_output_prefix}_counts_merged.tsv.gz and {merged_output_prefix}_tpm_merged.tsv.gz. Default prefix is "kallisto_transcript" i.e. default output merged output files are
       | ^
checkRd: (-1) kallistoQuantify.Rd:34: Lost braces; missing escapes or markup?
    34 | {merged_output_prefix}_counts_merged.tsv.gz and {merged_output_prefix}_tpm_merged.tsv.gz. Default prefix is "kallisto_transcript" i.e. default output merged output files are
       |                                                 ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘TumourMethDatasets’ ‘hg38_cpg_islands’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘methodical-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeMethRSEFromArrayFiles
> ### Title: Create a HDF5-backed RangedSummarizedExperiment for methylation
> ###   values in array files
> ### Aliases: makeMethRSEFromArrayFiles
> 
> ### ** Examples
> 
> # Get human CpG sites for hg38 genome build
> data("infinium_450k_probe_granges_hg19", package = "methodical")
> 
> # Get paths to array files
> array_files <- list.files(path = system.file('extdata', package = 'methodical'), 
+   pattern = ".txt.gz", full.names = TRUE)
> 
> # Create sample metadata
> sample_metadata <- data.frame(
+   tcga_project = "LUAD",
+   sample_type = "Tumour", submitter = gsub("_01.tsv.gz", "", basename(array_files)),
+   row.names = gsub(".tsv.gz", "", basename(array_files))
+ )
> 
> # Create a HDF5-backed RangedSummarizedExperiment from array files using default chumk dimensions
> meth_rse <- makeMethRSEFromArrayFiles(array_files = array_files, 
+  probe_ranges = infinium_450k_probe_granges_hg19, 
+  sample_metadata = sample_metadata, hdf5_dir =  paste0(tempdir(), "/array_file_hdf5_1"))
Error in HDF5Array::HDF5RealizationSink(dim = as.integer(c(length(meth_sites),  : 
  unused argument (dataset_name = "beta")
Calls: makeMethRSEFromArrayFiles -> .make_meth_rse_setup
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
annotateGRanges 10.809  0.476  13.277
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/methodical.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methodical
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘methodical’ ...
** this is package ‘methodical’ version ‘1.7.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in '.split_meth_array_files_into_chunks(array_files = array_files, ': unused argument (normalization_factor = normalization_factor) 
Note: possible error in '.write_chunks_to_hdf5(hdf5_sink = setup$hdf5_sink, ': unused argument (hdf5_sink = setup$hdf5_sink) 
Note: possible error in '.create_meth_rse_from_hdf5(hdf5_filepath = setup$hdf5_filepath, ': unused argument (meth_sites_df = probe_sites_df) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methodical)