##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/methodical.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methodical/DESCRIPTION’ ... OK
* this is package ‘methodical’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
extractMethSitesFromGenome               240.851 20.078 265.575
liftoverMethRSE                          183.433 14.804 206.522
annotateGRanges                           60.599  4.592  74.432
makeMethRSEFromBedgraphs                  12.016 10.966  10.896
makeMethRSEFromArrayFiles                 15.830  7.096  18.974
calculateMethSiteTranscriptCors           10.793  1.122  12.075
summarizeRegionMethylation                 8.348  3.288  12.674
calculateRegionMethylationTranscriptCors   8.220  2.983  11.130
annotatePlot                               5.645  0.177   6.299
* 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 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/methodical.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methodical
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘methodical’ ...
** 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)