From f352115dc28250ec55a433f81b3195e8df5a65f2 Mon Sep 17 00:00:00 2001 From: Chen Ying Date: Mon, 2 Feb 2026 10:43:32 +0800 Subject: [PATCH 1/4] Bump version to 3.13.2 and update author emails Updated version number and author emails in DESCRIPTION file. --- DESCRIPTION | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b0280eff..8e87d978 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,15 +1,15 @@ Package: bambu Type: Package Title: Context-Aware Transcript Quantification from Long Read RNA-Seq data -Version: 3.13.1 +Version: 3.13.2 Authors@R: c(person("Ying", "Chen", role = c("cre","aut"), - email = "chen_ying@gis.a-star.edu.sg"), + email = "chen_ying@a-star.edu.sg"), person("Andre", "Sim", role = "aut", - email = "andre_sim@gis.a-star.edu.sg"), + email = "andre_sim@a-star.edu.sg"), person("Yuk Kei", "Wan", role = "aut", - email = "Wan_Yuk_Kei@gis.a-star.edu.sg"), + email = "Wan_Yuk_Kei@a-star.edu.sg"), person("Jonathan", "Goeke", role = "aut", - email = "gokej@gis.a-star.edu.sg")) + email = "gokej@a-star.edu.sg")) Description: bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and From caff79a4c9ea935ac0a8f64b026a430e37527e1a Mon Sep 17 00:00:00 2001 From: Chen Ying Date: Mon, 2 Feb 2026 13:17:07 +0800 Subject: [PATCH 2/4] Fix email address for Jonathan Goeke Updated email address for Jonathan Goeke in DESCRIPTION file. --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8e87d978..861e77b3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,7 @@ Authors@R: c(person("Ying", "Chen", role = c("cre","aut"), person("Yuk Kei", "Wan", role = "aut", email = "Wan_Yuk_Kei@a-star.edu.sg"), person("Jonathan", "Goeke", role = "aut", - email = "gokej@a-star.edu.sg")) + email = "Jonathan_GOEKE@a-star.edu.sg")) Description: bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and From 8dbc3193067efef64281e22dd6f629cdf4969cd2 Mon Sep 17 00:00:00 2001 From: jonathangoeke <10560051+jonathangoeke@users.noreply.github.com> Date: Wed, 2 Sep 2026 09:53:26 +0800 Subject: [PATCH 3/4] Fix bambu requiring internet access when given a local FASTA genome path 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 --- R/bambu_utilityFunctions.R | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/R/bambu_utilityFunctions.R b/R/bambu_utilityFunctions.R index ef78e8f3..2152e264 100644 --- a/R/bambu_utilityFunctions.R +++ b/R/bambu_utilityFunctions.R @@ -147,11 +147,16 @@ checkInputs <- function(annotations, reads, readClass.outputDir, genomeSequence) checkInputSequence <- function(genomeSequence) { if (is.null(genomeSequence)) stop("Reference genome sequence is missing, please provide fasta file or BSgenome name, see available.genomes()") + if (is.character(genomeSequence) && !file.exists(genomeSequence)) { + isBSgenomeName <- tryCatch( + genomeSequence %in% BSgenome::available.genomes(), + error = function(cond) FALSE) + if (isBSgenomeName) { + genomeSequence <- BSgenome::getBSgenome(genomeSequence) + return(genomeSequence) + } + } if(is.character(genomeSequence)){ - if (genomeSequence %in% BSgenome::available.genomes()) { - genomeSequence <- BSgenome::getBSgenome(genomeSequence) - return(genomeSequence) - } tryCatch( { if (.Platform$OS.type == "windows") { From 216363b37e484fb59cf3fc971ffbe08a3d2edd39 Mon Sep 17 00:00:00 2001 From: Chen Ying Date: Thu, 1 Oct 2026 16:25:17 +0800 Subject: [PATCH 4/4] temporarily disable the plotBambu for plot annotations in vignettes and unit test functions --- tests/testthat/test_plotBambu.R | 6 +++--- vignettes/bambu.Rmd | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/testthat/test_plotBambu.R b/tests/testthat/test_plotBambu.R index 54f8178a..7e1d7d52 100644 --- a/tests/testthat/test_plotBambu.R +++ b/tests/testthat/test_plotBambu.R @@ -11,8 +11,8 @@ test_that("visualization for transcript expression is successful", { # case 1: no group.variable provided expect_is(plotBambu(seCombined, type = "heatmap"), "Heatmap") expect_true(ggplot2::is.ggplot(plotBambu(seCombined, type = "pca"))) - expect_is(plotBambu(seCombined, type = "annotation", gene_id = unique(rowData(seCombined)$GENEID)[c(4, 6)]), "list") - expect_is(plotBambu(seCombined, type = "annotation", transcript_id = rownames(seCombined)[c(4, 6)]), "grob") + #expect_is(plotBambu(seCombined, type = "annotation", gene_id = unique(rowData(seCombined)$GENEID)[c(4, 6)]), "list") + #expect_is(plotBambu(seCombined, type = "annotation", transcript_id = rownames(seCombined)[c(4, 6)]), "grob") # case 2: group.variable is provided @@ -31,7 +31,7 @@ test_that("visualization for gene expression is successful", { # case 1: no group.variable provided expect_is(plotBambu(seCombinedGeneExpected, type = "heatmap"), "Heatmap") expect_true(ggplot2::is.ggplot(plotBambu(seCombinedGeneExpected, type = "pca"))) - expect_is(plotBambu(seCombinedGeneExpected, type = "annotation", gene_id = rownames(seCombinedGeneExpected)[c(4, 6)]), "grob") + #expect_is(plotBambu(seCombinedGeneExpected, type = "annotation", gene_id = rownames(seCombinedGeneExpected)[c(4, 6)]), "grob") # case 2: group.variable is provided colData(seCombinedGeneExpected)$groupVar <- c("group1", "group2") diff --git a/vignettes/bambu.Rmd b/vignettes/bambu.Rmd index 460da8b2..693e763b 100644 --- a/vignettes/bambu.Rmd +++ b/vignettes/bambu.Rmd @@ -235,7 +235,7 @@ a function to visualise the extended annotation and expression estimation for individual genes. Here we look at gene ENSG00000099968 and visualise the transcript coordinates for annotated and novel isoforms and expression levels for these isoforms across all samples. -```{r, fig.width = 8, fig.height = 10} +```{r, fig.width = 8, fig.height = 10, eval = FALSE} plotBambu(se.multiSample, type = "annotation", gene_id = "ENSG00000099968") ```