Build/check report for BioC 3.23 - BUILD results for TransView on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	3809
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BUILD results for TransView on nebbiolo1

To the developers/maintainers of the TransView package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TransView.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: TransView

Version: 1.53.1

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TransView

StartedAt: 2025-10-23 00:51:47 -0000 (Thu, 23 Oct 2025)

EndedAt: 2025-10-23 00:52:05 -0000 (Thu, 23 Oct 2025)

EllapsedTime: 18.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TransView
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* checking for file ‘TransView/DESCRIPTION’ ... OK
* preparing ‘TransView’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘TransView.Rnw’ using Sweave
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect,
    is.element, setdiff, setequal, union


Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated,
    aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq,
    get, grep, grepl, is.unsorted, lapply, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table,
    tapply, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Welcome to TransView version 1.53.1
Warning in fun(libname, pkgname) :
  Package 'TransView' is deprecated and will be removed
  from Bioconductor version 3.23

Attaching package: ‘TransView’

The following object is masked from ‘package:GenomicRanges’:

    pos

The following object is masked from ‘package:IRanges’:

    pos

The following object is masked from ‘package:BiocGenerics’:

    pos


Error: processing vignette 'TransView.Rnw' failed with diagnostics:
 chunk 3 (label = load_files) 
Error in library("pasillaBamSubset") : 
  there is no package called ‘pasillaBamSubset’

--- failed re-building ‘TransView.Rnw’

SUMMARY: processing the following file failed:
  ‘TransView.Rnw’

Error: Vignette re-building failed.
Execution halted