Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-14 12:05 -0400 (Thu, 14 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (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 1170/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maser 1.27.1 (landing page) Diogo F.T. Veiga
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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.
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)
maser.Rcheck/maser-Ex.timings
name | user | system | elapsed | |
PSI-Maser-character-method | 0.607 | 0.004 | 0.613 | |
PSI | 0.629 | 0.045 | 0.674 | |
annotation-Maser-method | 0.501 | 0.001 | 0.501 | |
availableFeaturesUniprotKB | 0.074 | 0.002 | 0.224 | |
boxplot_PSI_levels | 2.675 | 0.112 | 2.787 | |
counts-Maser-method | 0.517 | 0.040 | 0.557 | |
display | 1.402 | 0.023 | 1.426 | |
dotplot | 1.236 | 0.011 | 1.247 | |
filterByCoverage | 0.873 | 0.001 | 0.874 | |
filterByEventId | 0.790 | 0.002 | 0.792 | |
geneEvents | 0.764 | 0.019 | 0.782 | |
granges-Maser-method | 0.549 | 0.001 | 0.551 | |