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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:maser.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings maser_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/maser.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: 2026-05-06 05:20:16 UTC
* checking for file ‘maser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maser’ version ‘1.31.0’
* 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 ‘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 loading without being on the library search path ... 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) :
  URL 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_beds/UP000005640_9606_domain.bed': status was 'SSL connect error'
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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-9-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-10-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-11-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/maser.Rcheck/vign_test/maser/vignettes/Introduction_files/figure-html/unnamed-chunk-16-1.png" but not available.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Protein_mapping.Rmd’ using rmarkdown

Quitting from Protein_mapping.Rmd:118-122 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_beds/UP000005640_9606_dna_bind.bed'
---
Backtrace:
    ▆
 1. └─maser::mapProteinFeaturesToEvents(...)
 2.   └─parallel::mclapply(features, createGRangesUniprotKBtrack, mc.cores = ncores)
 3.     └─base::lapply(X = X, FUN = FUN, ...)
 4.       └─maser (local) FUN(X[[i]], ...)
 5.         └─data.table::fread(...)
 6.           └─utils::download.file(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Protein_mapping.Rmd' failed with diagnostics:
cannot open URL 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_beds/UP000005640_9606_dna_bind.bed'
--- failed re-building ‘Protein_mapping.Rmd’

SUMMARY: processing the following file failed:
  ‘Protein_mapping.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/maser.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL maser
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘maser’ ...
** this is package ‘maser’ version ‘1.31.0’
** using staged installation
** R
** 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 (maser)