Multiple platform build/check report for BioC 3.22 - BUILD results for DominoEffect on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4810
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4528
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4493
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*

BUILD results for DominoEffect on nebbiolo2

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

Version: 1.29.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DominoEffect

StartedAt: 2025-06-18 17:20:22 -0400 (Wed, 18 Jun 2025)

EndedAt: 2025-06-18 17:21:43 -0400 (Wed, 18 Jun 2025)

EllapsedTime: 81.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DominoEffect
###
##############################################################################
##############################################################################


* checking for file ‘DominoEffect/DESCRIPTION’ ... OK
* preparing ‘DominoEffect’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Vignette.Rmd’ using rmarkdown
trying URL 'http://www.uniprot.org/uniprot/P50148.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/P29992.fasta'
Content type 'text/plain;format=fasta' length 483 bytes
==================================================
downloaded 483 bytes

trying URL 'http://www.uniprot.org/uniprot/O75533.fasta'
Content type 'text/plain;format=fasta' length 1421 bytes
==================================================
downloaded 1421 bytes

trying URL 'http://www.uniprot.org/uniprot/Q9NR22.fasta'
Content type 'text/plain;format=fasta' length 505 bytes
==================================================
downloaded 505 bytes

trying URL 'http://www.uniprot.org/uniprot/O96017.fasta'
Content type 'text/plain;format=fasta' length 655 bytes
==================================================
downloaded 655 bytes


Quitting from Vignette.Rmd:60-63 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.call_fun_in_pwalign()`:
! pattern() has moved from Biostrings to the pwalign package, and is formally
  defunct in Biostrings >= 2.77.1. Please call pwalign::pattern() to get rid of
  this error.
---
Backtrace:
    ▆
 1. └─DominoEffect::DominoEffect(...)
 2.   └─DominoEffect::map_to_func_elem(results, write_to_file, ens_release = ens_release)
 3.     └─DominoEffect::align_to_unip(ens.seq, uni.seq, ensembl_mut_position)
 4.       ├─base::grep("-", pattern(alignment.subseq[1]))
 5.       │ └─base::is.factor(x)
 6.       └─Biostrings::pattern(alignment.subseq[1])
 7.         └─Biostrings:::.call_fun_in_pwalign("pattern", ...)
 8.           └─base::.Defunct(msg = wmsg(msg))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
pattern() has moved from Biostrings to the pwalign package, and is formally
  defunct in Biostrings >= 2.77.1. Please call pwalign::pattern() to get rid of
  this error.
--- failed re-building ‘Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted