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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:methodical.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings methodical_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/methodical.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘methodical/DESCRIPTION’ ... OK
* this is package ‘methodical’ version ‘1.1.0’
* 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 ... 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 ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
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’ ‘.tss_iterator’
* 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’
.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’
createRandomRegions: no visible global function definition for ‘is’
createRandomRegions: no visible global function definition for
  ‘seqlengths’
createRandomRegions: no visible global function definition for
  ‘overlapsAny’
extractGRangesMethSiteValues: no visible global function definition for
  ‘is’
extractMethSitesFromGenome: no visible global function definition for
  ‘is’
findTMRs: 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:
  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
  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 ... 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"))
Processing file 1 out of 2: /home/biocbuild/bbs-3.20-bioc/R/site-library/methodical/extdata/TCGA_05_4384_01.txt.gz


Processing file 2 out of 2: /home/biocbuild/bbs-3.20-bioc/R/site-library/methodical/extdata/TCGA_05_4390_01.txt.gz


Writing chunk 1 out of 1

Serialize RangedSummarizedExperiment object to RDS file:
  /tmp/Rtmpqjn9IQ/array_file_hdf5_1/se.rds
Error in saveRDS(x, file = rds_path) : 
  RangedSummarizedExperiment object contains out-of-memory data so cannot
  be serialized reliably. Please use saveHDF5SummarizedExperiment() from
  the HDF5Array package instead. Also see '?containsOutOfMemoryData' in
  the BiocGenerics package for some context.
Calls: makeMethRSEFromArrayFiles ... .create_meth_rse_from_hdf5 -> <Anonymous> -> saveRDS -> saveRDS
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/methodical.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL methodical
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)