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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:methodical.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings methodical_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/methodical.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: 2026-04-29 06:23:47 UTC
* checking for file ‘methodical/DESCRIPTION’ ... OK
* this is package ‘methodical’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Vignette dependency required without any vignettes: ‘knitr’

Imports includes 32 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 ... OK
* 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 ... INFO
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data      4.6Mb
    extdata   1.3Mb
* checking package 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘AnnotationHub’ ‘BiocCheck’ ‘BiocManager’ ‘BiocStyle’
  ‘MatrixGenerics’ ‘TumourMethData’ ‘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
.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’
.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’
.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’
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’
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’
liftoverMethRSE: no visible global function definition for ‘is’
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’
summarizeRegionMethylation: no visible global function definition for
  ‘is’
summarizeRegionMethylation: no visible global function definition for
  ‘seqlevels’
Undefined global functions or variables:
  chunk col2rgb colorRampPalette complete.cases cor direction is
  meth_cor_plot_position meth_fraction meth_reads
  meth_site_plot_position meth_site_start methodical_score modifyList
  p.adjust p.adjust.methods pt queryHits region_type seqlevels setNames
  subsetByOverlaps test 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 ... OK
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'data(package=)' call not declared from: ‘methrix’
* 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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
makeMethRSEFromInputFiles  8.202  0.034   8.240
summarizeRegionMethylation 6.600  0.003   6.603
extractMethSitesFromGenome 4.992  0.179   5.172
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/methodical.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL methodical
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘methodical’ ...
** this is package ‘methodical’ version ‘1.9.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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)