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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Moonlight2R_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Moonlight2R.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 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 ‘Moonlight2R’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TFinfluence: no visible binding for global variable ‘HGVSp_Short’
TFinfluence : <anonymous>: no visible binding for global variable
  ‘mutation’
TFinfluence : <anonymous>: no visible binding for global variable
  ‘stab_class’
TFinfluence: no visible binding for global variable ‘GENE’
TFinfluence: no visible binding for global variable ‘Target’
TFinfluence: no visible binding for global variable ‘TF’
TFinfluence: no visible binding for global variable ‘mutation’
TFinfluence: no visible binding for global variable ‘protein’
TFinfluence: no visible binding for global variable ‘tf_mutation’
TFinfluence: no visible binding for global variable ‘InteractionType’
TFinfluence: no visible binding for global variable ‘stab_class’
TFinfluence: no visible binding for global variable ‘logFC_target’
loadMAVISp: no visible binding for global variable ‘filepath’
plotHeatmap: no visible global function definition for ‘add_tile’
plotHeatmap: no visible global function definition for ‘add_bar’
Undefined global functions or variables:
  GENE HGVSp_Short InteractionType TF Target add_bar add_tile filepath
  logFC_target mutation protein stab_class tf_mutation
* 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Moonlight2R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GMA
> ### Title: GMA This function carries out Gene Methylation Analysis
> ### Aliases: GMA
> 
> ### ** Examples
> 
> data("dataMethyl")
> data("dataFilt")
> data("dataPRA")
> data("DEGsmatrix")
> data("LUAD_sample_anno")
> data("NCG")
> data("EncodePromoters")
> data("MetEvidenceDriver")
> pattern <- "^(.{4}-.{2}-.{4}-.{2}).*"
> dataFilt_subset <- dataFilt[,1:10]
> colnames(dataFilt_subset) <- sub(pattern, "\\1", colnames(dataFilt_subset))
> dataGMA <- GMA(dataMET = dataMethyl, dataEXP = dataFilt_subset,
+ dataPRA = dataPRA, dataDEGs = DEGsmatrix,
+ sample_info = LUAD_sample_anno, met_platform = "HM450",
+ prevalence_filter = NULL,
+ output_dir = "./GMAresults", cores = 1, roadmap.epigenome.ids = "E096",
+ roadmap.epigenome.groups = NULL)
Running Regular mode...
Fetching probe annotation...
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
require(“GenomicRanges”)
Found 8 samples with both methylation and gene expression data.
Modeling gene expression...

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Found 23 transcriptionally predictive probes.
Found 17 samples in group.1 and 6 samples in group.2

Starting Beta mixture modeling.
Running Beta mixture model on 23 probes and on 17 samples.

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  |                                                                      |   0%Warning: executing %dopar% sequentially: no parallel backend registered

Found 23 differentially methylated CpGs
Identifying functional CpG-gene pairs...

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Found 1 functional probe-gene pairs.
Saving the EpiMix results to the output directory...
Running Enhancer mode...
Fetching probe annotation...
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Found 17 samples in group.1 and 6 samples in group.2
Fetching enhancer CpGs from Roadmap Epigenomics...
Downloading chromatin states from the Roadmap Epigenomics...
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

	Identifed 65057 enhancer CpGs from the epigenome E096 
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Error: reached elapsed time limit
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
GLS 2.839  1.141   9.175
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/Moonlight2R.Rcheck/00check.log’
for details.