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fix bugs and update contact for devel branch - #592

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cying111 merged 8 commits into
develfrom
devel_pre
Oct 2, 2026
Merged

fix bugs and update contact for devel branch#592
cying111 merged 8 commits into
develfrom
devel_pre

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@cying111

@cying111 cying111 commented Oct 2, 2026

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Related Issue

Bioconductor build error
offline error fixed

Type of Change

  • [x ] Bug fix (non-breaking change which fixes an issue)

Description

Fix 2 bugs:

  • ggbio plot annotation issue causing bioconductor build error
  • BSgenome is required to do look up, and that requires internet access

Update contact email addresses

Implementation Details

For bugs:

  • fix by disable ggbio related functions in vignettes and unit test function
  • only activate look up for genome through BSgenome packge when fasta file is not a local existing file to avoid the need for internet access for BSgenome

Impact of Changes

  • Results are identical to the previous version.
  • Bug fix only (no changes to output).

Checklist

  • My code follows the style guidelines of this project.
  • I have performed a self-review of my own code.
  • I have verified that GitHub automated tests passed. (Describe any failing tests in the next section)
  • I have commented my code, particularly in hard-to-understand areas.
  • I have made corresponding changes to the documentation (vignettes, man pages).
  • I have tested the code on a full dataset, and any differences have been described in the pull request.

Post-merge follow-up

  • plotBambu function not working properly for plot annotations, consider to submit proper fix later

Chen Ying and others added 8 commits February 2, 2026 10:43
Chen Ying
Bump version to 3.13.2 and update author emails
f352115 
Updated version number and author emails in DESCRIPTION file.
Chen Ying
Fix email address for Jonathan Goeke
caff79a 
Updated email address for Jonathan Goeke in DESCRIPTION file.
@jonathangoeke @claude
Fix bambu requiring internet access when given a local FASTA genome path
8dbc319 
checkInputSequence() unconditionally called BSgenome::available.genomes()
for any character genome argument, including local FASTA file paths -
the documented, common case. That call reaches out to Bioconductor's
package repository over the network, so bambu failed on offline
clusters/containers even when the user supplied a local file (issue #339).

Now the BSgenome lookup is only attempted when the string is not an
existing local file, and is wrapped in tryCatch so a blocked network
call falls through to the existing FASTA-read error path instead of
crashing with a raw Bioconductor/BiocManager error.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@cying111
temporarily disable the plotBambu for plot annotations in vignettes a…
216363b 
…nd unit test functions
@cying111
Merge pull request #590 from GoekeLab/devel
8c36345 
update devel_pre with merge commits from devel
@cying111
Merge pull request #591 from GoekeLab/plotBambu_fix
6aac1e9 
temporarily disable plot annotations in vignettes and unit test function
@cying111
Merge pull request #588 from GoekeLab/fix_offline_genome_check
9ea1785 
Fix bambu requiring internet access when given a local FASTA genome path
@cying111
Merge pull request #538 from GoekeLab/update_contact
98217bd 
Bump version to 3.13.2 and update author emails
@cying111
cying111 merged commit aff3470 into devel Oct 2, 2026
6 of 8 checks passed
@cying111 cying111 mentioned this pull request Oct 2, 2026
Merged
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Reviewers

@jonathangoeke jonathangoeke jonathangoeke approved these changes
@lingminhao lingminhao lingminhao approved these changes

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3 participants

@cying111 @jonathangoeke @lingminhao