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This page was generated on 2025-08-14 12:05 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1170/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maser 1.27.1  (landing page)
Diogo F.T. Veiga
Snapshot Date: 2025-08-13 13:45 -0400 (Wed, 13 Aug 2025)
git_url: https://git.bioconductor.org/packages/maser
git_branch: devel
git_last_commit: 684a35f
git_last_commit_date: 2025-07-23 12:30:32 -0400 (Wed, 23 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for maser on nebbiolo2

To the developers/maintainers of the maser package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maser.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: maser
Version: 1.27.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maser.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maser_1.27.1.tar.gz
StartedAt: 2025-08-14 00:07:42 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 00:14:40 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 417.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: maser.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maser.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maser_1.27.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maser.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 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) :
  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 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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/meat/maser.Rcheck/00check.log’
for details.


Installation output

maser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘maser’ ...
** this is package ‘maser’ version ‘1.27.1’
** 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)

Tests output


Example timings

maser.Rcheck/maser-Ex.timings

nameusersystemelapsed
PSI-Maser-character-method0.6070.0040.613
PSI0.6290.0450.674
annotation-Maser-method0.5010.0010.501
availableFeaturesUniprotKB0.0740.0020.224
boxplot_PSI_levels2.6750.1122.787
counts-Maser-method0.5170.0400.557
display1.4020.0231.426
dotplot1.2360.0111.247
filterByCoverage0.8730.0010.874
filterByEventId0.7900.0020.792
geneEvents0.7640.0190.782
granges-Maser-method0.5490.0010.551