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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maser_1.27.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/maser.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maser’ version ‘1.27.1’
* 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 ‘maser’ 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 ... 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 whether startup messages can be suppressed ... 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
availableFeaturesUniprotKB: no visible global function definition for
  'read.csv'
availableFeaturesUniprotKB: no visible binding for global variable
  'Category'
availableFeaturesUniprotKB: no visible binding for global variable
  'Name'
filterByIds: no visible binding for global variable 'ID'
mapTranscriptsA3SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsA5SSevent: no visible global function definition for
  'subjectHits'
mapTranscriptsMXEevent: no visible global function definition for
  'subjectHits'
mapTranscriptsRIevent: no visible global function definition for
  'subjectHits'
mapTranscriptsSEevent: no visible global function definition for
  'subjectHits'
overlappingFeatures: no visible global function definition for
  'subjectHits'
urlTracksUniprotKB: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  Category ID Name read.csv subjectHits
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘maser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mapProteinFeaturesToEvents
> ### Title: Mapping of splice events to UniprotKB protein features.
> ### Aliases: mapProteinFeaturesToEvents
> 
> ### ** Examples
> 
> ## Create the maser object
> path <- system.file("extdata", file.path("MATS_output"), package = "maser")
> hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
> hypoxia_filt <- filterByCoverage(hypoxia, avg_reads = 5)
> 
> ## Ensembl GTF annotation for SRSF6
> gtf_path <- system.file("extdata", file.path("GTF", "SRSF6_Ensembl85.gtf"),
+  package = "maser")
> ens_gtf <- rtracklayer::import.gff(gtf_path)
> 
> ## Retrieve gene specific splice events
> srsf6_events <- geneEvents(hypoxia_filt, geneS = "SRSF6")
> 
> ## Map splicing events to transcripts
> srsf6_mapped <- mapTranscriptsToEvents(srsf6_events, ens_gtf)
> 
> ## Annotate splice events with protein domains
> srsf6_annot <- mapProteinFeaturesToEvents(srsf6_mapped, tracks = "domain")
Warning in download.file(file, tmpFile, method = method, mode = "wb", quiet = !showProgress) :
  downloaded length 0 != reported length 196
Warning in download.file(file, tmpFile, method = method, mode = "wb", quiet = !showProgress) :
  cannot open URL 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_beds/UP000005640_9606_domain.bed': HTTP status was '404 Not Found'
Error in download.file(file, tmpFile, method = method, mode = "wb", quiet = !showProgress) : 
  cannot open URL 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_beds/UP000005640_9606_domain.bed'
Calls: mapProteinFeaturesToEvents ... mclapply -> lapply -> FUN -> <Anonymous> -> download.file
Execution halted
* 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/maser.Rcheck/00check.log’
for details.