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### Running command:
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###   /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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/methodical.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methodical/DESCRIPTION’ ... OK
* this is package ‘methodical’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 34 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:
  .BBSoptions
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 ... OK
* checking installed package size ... OK
* 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’ ‘BSgenome.Hsapiens.UCSC.hg19’
  ‘BSgenome.Hsapiens.UCSC.hg38’ ‘BiocCheck’ ‘BiocManager’ ‘BiocStyle’
  ‘MatrixGenerics’ ‘TumourMethData’ ‘annotatr’ ‘devtools’ ‘knitr’
  ‘rcmdcheck’ ‘remotes’ ‘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’
.count_covered_bases: no visible global function definition for ‘is’
.create_meth_rse_from_hdf5: no visible global function definition for
  ‘setNames’
.expand_transcript_ranges: no visible binding for global variable
  ‘transcript_name’
.find_tmrs_single: no visible global function definition for ‘is’
.split_bedgraph: no visible binding for global variable
  ‘meth_site_groups’
.split_bedgraph: no visible binding for global variable ‘total_files’
.split_bedgraph: no visible binding for global variable ‘meth_sites_df’
.split_bedgraph: no visible global function definition for ‘setNames’
.split_bedgraph: no visible binding for global variable
  ‘seqnames_column’
.split_bedgraph: no visible binding for global variable ‘start_column’
.split_bedgraph: no visible binding for global variable ‘end_column’
.split_bedgraph: no visible binding for global variable ‘value_column’
.split_bedgraph: no visible binding for global variable ‘dt_threads’
.split_bedgraph: no visible binding for global variable ‘zero_based’
.split_bedgraph: no visible binding for global variable
  ‘normalization_factor’
.split_bedgraph: no visible binding for global variable
  ‘decimal_places’
.split_bedgraph: no visible binding for global variable ‘mg’
.split_bedgraph: no visible binding for global variable
  ‘temp_chunk_dirs’
.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’
createRandomRegions: no visible global function definition for ‘is’
createRandomRegions: no visible global function definition for
  ‘seqlengths’
createRandomRegions: no visible global function definition for
  ‘overlapsAny’
expand_granges: no visible global function definition for ‘is’
expand_granges: no visible global function definition for ‘IRanges’
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’
makeMethRSEFromBedgraphs: 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 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’
plotMethylationValues: no visible global function definition for ‘is’
plotMethylationValues: no visible global function definition for
  ‘complete.cases’
plotMethylationValues: 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 colorRampPalette complete.cases cor
  decimal_places direction dt_threads end_column gene_transcripts is
  meth_cor_plot_position meth_site_groups meth_site_plot_position
  meth_site_start meth_sites_df methodical_score mg name
  normalization_factor overlapsAny p.adjust p.adjust.methods pg
  probe_groups probe_name_column probe_sites_df pt queryHits
  region_type seqlengths seqlevels seqnames_column setNames
  start_column subsetByOverlaps temp_chunk_dirs total_files
  transcript_name value_column zero_based
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "cor", "p.adjust",
             "p.adjust.methods", "pt", "setNames")
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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'calculateMethSiteTranscriptCors.Rd':
  ‘expand_upstream’ ‘expand_downstream’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: annotatePlot
> ### Title: Create a plot with genomic annotation for a plot of values at
> ###   methylation sites.
> ### Aliases: annotatePlot
> 
> ### ** Examples
> 
> # Get CpG islands from UCSC
> cpg_island_annotation <- annotatr::build_annotations(genome = "hg38", annotations = "hg38_cpgs")
Building CpG islands...
Building CpG shores...
Building CpG shelves...
Building inter-CpG-islands...
> cpg_island_annotation <- GRangesList(split(cpg_island_annotation, cpg_island_annotation$type))
> 
> # Load plot with CpG methylation correlation values for TUBB6
> data("tubb6_correlation_plot", package = "methodical")
> 
> # Add positions of CpG islands to tubb6_correlation_plot
> methodical::annotatePlot(tubb6_correlation_plot, annotation_grl = cpg_island_annotation, annotation_plot_proportion = 0.3)
Error in UseMethod("ggplot_build") : 
  no applicable method for 'ggplot_build' applied to an object of class "c('gg', 'ggplot')"
Calls: <Anonymous> ... continuous_scale -> allow_lambda -> is_formula -> ggplot_build
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
annotateGRanges 42.116  2.873  49.437
* 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, 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/library’
* installing *source* package ‘methodical’ ...
** this is package ‘methodical’ version ‘1.4.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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)