Thanks Hervé! --t > On Oct 14, 2025, at 2:13 AM, Hervé Pagès <[email protected]> wrote: > > TxDb.Hsapiens.UCSC.hg19.knownGene 3.22.1 now available in BioC 3.22. With > this version: > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > isCircular(seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene))[c("chrM", "chrMT")] > # chrM chrMT > # TRUE TRUE > > Likely too late to have an impact on tomorrow's build report. But hopefully > the affected packages will go green again on Wednesday. > > Cheers, > > H. > >> On 13/10/2025 16:52, Hervé Pagès wrote: >> Hi Raymond, Tim, >> >> TxDb.Hsapiens.UCSC.hg19.knownGene got updated last week in BioC 3.22 to >> reflect the current state of UCSC track hg19.knownGene, but the new version >> of the package (3.22.0) does not carry the correct circularity flag for >> chrMT, only for chrM. This is on our end and will be addressed shortly. >> >> List of packages affected by this: annotatr, decompTumor2Sig, >> GenomicFeatures, gmapR, MutationalPatterns, OrganismDbi, ProteoDisco, and >> VariantTools. >> >> Sorry for the inconvenience. >> >> Best, >> H. >> >>> On 13/10/2025 07:24, Raymond Cavalcante wrote: >>> I'm sorry, I must have missed the moment where chrM and chrMT were both >>> included, or they always were and I didn't notice it. To put a finer point >>> on this issue, the seqinfo from Txdb is inconsistent with that from Seqinfo: >>> >>>> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene >>>> tx_gr = transcripts(txdb, columns = c('TXID','GENEID','TXNAME')) >>>> seqinfo(tx_gr)[c('chrM','chrMT')] >>> Seqinfo object with 2 sequences (1 circular) from hg19 genome: >>> seqnames seqlengths isCircular genome >>> chrM 16571 TRUE hg19 >>> chrMT 16569 FALSE hg19 >>> >>> chrMT is circular from Seqinfo but not from TxDb. >>> >>> Thanks, >>> Raymond >>> >>> -------------------- >>> Raymond Cavalcante, PhD >>> Bioinformatics Analyst >>> Epigenomics Core and Bioinformatics Core >>> Biomedical Research Core Facilities >>> University of Michigan Medical School >>> >>> [email protected] >>> [email protected] >>> >>> >>> On Sun, Oct 12, 2025 at 10:57 AM Tim Triche, Jr. <[email protected]> >>> wrote: >>> >>>> chrM is the broken old hg19 mitogenome >>>> >>>> chrMT is rCRS, same as hg38 chrM >>>> >>>> --t >>>> >>>>> On Oct 12, 2025, at 12:30 PM, Raymond Cavalcante <[email protected]> >>>> wrote: >>>>> Hi, >>>>> >>>>> I was testing the annotatr package after fixing the ggplot2 v4 stuff, >>>> but I >>>>> got an error in my vignette build and discovered what I think is an error >>>>> in the result of Seqinfo::seqinfo(genome = 'hg19'). >>>>> >>>>> There are two mitochondrial chromosomes for hg19. This causes some >>>>> downstream issues when merging hg19 GRanges. >>>>> >>>>>> Seqinfo::Seqinfo(genome='hg19')[c('chrM', 'chrMT')] >>>>> Seqinfo object with 2 sequences (2 circular) from hg19 genome: >>>>> seqnames seqlengths isCircular genome >>>>> chrM 16571 TRUE hg19 >>>>> chrMT 16569 TRUE hg19 >>>>> >>>>> I checked hg38 on a lark and it appears correct. >>>>> >>>>>> Seqinfo::Seqinfo(genome='hg38')[c('chrM', 'chrMT')] >>>>> Seqinfo object with 2 sequences (1 circular) from 2 genomes (hg38, NA): >>>>> seqnames seqlengths isCircular genome >>>>> chrM 16569 TRUE hg38 >>>>> chrMT NA NA <NA> >>>>> >>>>> I'm using 0.99.2 of Seqinfo in a Bioconductor devel Docker image. >>>>> >>>>> My session info: >>>>> >>>>>> devtools::session_info() >>>>> ─ Session info >>>>> >>>> ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── >>>>> setting value >>>>> version R version 4.5.1 (2025-06-13) >>>>> os Ubuntu 24.04.3 LTS >>>>> system x86_64, linux-gnu >>>>> ui X11 >>>>> language (EN) >>>>> collate en_US.UTF-8 >>>>> ctype en_US.UTF-8 >>>>> tz Etc/UTC >>>>> date 2025-10-12 >>>>> pandoc 3.8.1 @ /usr/bin/pandoc >>>>> quarto 1.7.32 @ /usr/local/bin/quarto >>>>> >>>>> ─ Packages >>>>> >>>> ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── >>>>> ! package * version date (UTC) lib source >>>>> abind 1.4-8 2024-09-12 [1] RSPM (R >>>>> 4.5.0) >>>>> AnnotationDbi * 1.71.1 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> AnnotationHub 3.99.6 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> VP annotatr * 1.35.1 2025-05-13 [?] >>>>> Bioconductor 3.22 (R 4.5.0) (on disk 1.35.0) >>>>> Biobase * 2.69.1 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> BiocFileCache 2.99.6 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> BiocGenerics * 0.55.3 2025-10-09 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> BiocIO 1.19.0 2025-04-15 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2.5.1 2025-09-10 [1] RSPM (R >>>>> 4.5.0) >>>>> DelayedArray 0.35.3 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> desc 1.4.3 2023-12-10 [1] RSPM (R >>>>> 4.5.0) >>>>> devtools 2.4.6 2025-10-03 [1] RSPM (R >>>>> 4.5.0) >>>>> dplyr 1.1.4 2023-11-17 [1] RSPM (R >>>>> 4.5.0) >>>>> ellipsis 0.3.2 2021-04-29 [1] RSPM (R >>>>> 4.5.0) >>>>> farver 2.1.2 2024-05-13 [1] RSPM (R >>>>> 4.5.0) >>>>> fastmap 1.2.0 2024-05-15 [1] RSPM (R >>>>> 4.5.0) >>>>> filelock 1.0.3 2023-12-11 [1] RSPM (R >>>>> 4.5.0) >>>>> fs 1.6.6 2025-04-12 [1] RSPM (R >>>>> 4.5.0) >>>>> generics * 0.1.4 2025-05-09 [1] RSPM (R >>>>> 4.5.0) >>>>> GenomeInfoDb 1.45.12 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> GenomicAlignments 1.45.4 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> GenomicFeatures * 1.61.6 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> GenomicRanges * 1.61.5 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> ggplot2 4.0.0 2025-09-11 [1] RSPM (R >>>>> 4.5.0) >>>>> glue 1.8.0 2024-09-30 [1] RSPM (R >>>>> 4.5.0) >>>>> gtable 0.3.6 2024-10-25 [1] RSPM (R >>>>> 4.5.0) >>>>> hms 1.1.3 2023-03-21 [1] RSPM (R >>>>> 4.5.0) >>>>> httr 1.4.7 2023-08-15 [1] RSPM (R >>>>> 4.5.0) >>>>> httr2 1.2.1 2025-07-22 [1] RSPM (R >>>>> 4.5.0) >>>>> IRanges * 2.43.5 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> jsonlite 2.0.0 2025-03-27 [1] RSPM (R >>>>> 4.5.0) >>>>> KEGGREST 1.49.2 2025-10-10 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> lattice 0.22-7 2025-04-02 [2] CRAN (R >>>>> 4.5.1) >>>>> lifecycle 1.0.4 2023-11-07 [1] RSPM (R >>>>> 4.5.0) >>>>> magrittr 2.0.4 2025-09-12 [1] RSPM (R >>>>> 4.5.0) >>>>> Matrix 1.7-4 2025-08-28 [1] RSPM (R >>>>> 4.5.0) >>>>> MatrixGenerics 1.21.0 2025-04-15 [1] >>>>> Bioconductor 3.22 (R 4.5.0) >>>>> matrixStats 1.5.0 2025-01-07 [1] RSPM (R >>>>> 4.5.0) >>>>> memoise 2.0.1 2021-11-26 [1] RSPM (R >>>>> 4.5.0) >>>>> org.Hs.eg.db * 3.22.0 2025-10-11 [1] >>>>> Bioconductor >>>>> pillar 1.11.1 2025-09-17 [1] RSPM (R >>>>> 4.5.0) >>>>> pkgbuild 1.4.8 2025-05-26 [1] RSPM (R >>>>> 4.5.0) >>>>> pkgconfig 2.0.3 2019-09-22 [1] RSPM (R >>>>> 4.5.0) >>>>> pkgload 1.4.1 2025-09-23 [1] RSPM (R >>>>> 4.5.0) >>>>> plyr 1.8.9 2023-10-02 [1] RSPM (R >>>>> 4.5.0) >>>>> png 0.1-8 2022-11-29 [1] RSPM (R >>>>> 4.5.0) >>>>> purrr 1.1.0 2025-07-10 [1] RSPM (R >>>>> 4.5.0) >>>>> R6 2.6.1 2025-02-15 [1] RSPM (R >>>>> 4.5.0) >>>>> rappdirs 0.3.3 2021-01-31 [1] RSPM (R >>>>> 4.5.0) >>>>> RColorBrewer 1.1-3 2022-04-03 [1] RSPM (R >>>>> 4.5.0) >>>>> Rcpp 1.1.0 2025-07-02 [1] RSPM (R >>>>> 4.5.0) >>>>> RCurl 1.98-1.17 2025-03-22 [1] RSPM (R >>>>> 4.5.0) >>>>> readr 2.1.5 2024-01-10 [1] RSPM (R >>>>> 4.5.0) >>>>> regioneR 1.41.3 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> remotes 2.5.0 2024-03-17 [1] RSPM (R >>>>> 4.5.0) >>>>> reshape2 1.4.4 2020-04-09 [1] RSPM (R >>>>> 4.5.0) >>>>> restfulr 0.0.16 2025-06-27 [1] RSPM (R >>>>> 4.5.1) >>>>> rjson 0.2.23 2024-09-16 [1] RSPM (R >>>>> 4.5.0) >>>>> rlang 1.1.6 2025-04-11 [1] RSPM (R >>>>> 4.5.0) >>>>> rprojroot 2.1.1 2025-08-26 [1] RSPM (R >>>>> 4.5.0) >>>>> Rsamtools 2.25.3 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> RSQLite 2.4.3 2025-08-20 [1] RSPM (R >>>>> 4.5.0) >>>>> rstudioapi 0.17.1 2024-10-22 [1] RSPM (R >>>>> 4.5.0) >>>>> rtracklayer * 1.69.1 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> S4Arrays 1.9.1 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> S4Vectors * 0.47.4 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> S7 0.2.0 2024-11-07 [1] RSPM (R >>>>> 4.5.0) >>>>> scales 1.4.0 2025-04-24 [1] RSPM (R >>>>> 4.5.0) >>>>> Seqinfo * 0.99.2 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> sessioninfo 1.2.3 2025-02-05 [1] RSPM (R >>>>> 4.5.0) >>>>> SparseArray 1.9.1 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> stringi 1.8.7 2025-03-27 [1] RSPM (R >>>>> 4.5.0) >>>>> stringr 1.5.2 2025-09-08 [1] RSPM (R >>>>> 4.5.0) >>>>> SummarizedExperiment 1.39.2 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> testthat * 3.2.3 2025-01-13 [1] RSPM (R >>>>> 4.5.0) >>>>> tibble 3.3.0 2025-06-08 [1] RSPM (R >>>>> 4.5.0) >>>>> tidyselect 1.2.1 2024-03-11 [1] RSPM (R >>>>> 4.5.0) >>>>> TxDb.Hsapiens.UCSC.hg19.knownGene * 3.22.0 2025-10-11 [1] >>>>> Bioconductor >>>>> tzdb 0.5.0 2025-03-15 [1] RSPM (R >>>>> 4.5.0) >>>>> UCSC.utils 1.5.0 2025-04-17 [1] >>>>> Bioconductor 3.22 (R 4.5.0) >>>>> usethis 3.2.1 2025-09-06 [1] RSPM (R >>>>> 4.5.0) >>>>> vctrs 0.6.5 2023-12-01 [1] RSPM (R >>>>> 4.5.0) >>>>> withr 3.0.2 2024-10-28 [1] RSPM (R >>>>> 4.5.0) >>>>> XML 3.99-0.19 2025-08-22 [1] RSPM (R >>>>> 4.5.0) >>>>> XVector 0.49.1 2025-10-07 [1] >>>>> Bioconductor 3.22 (R 4.5.1) >>>>> yaml 2.3.10 2024-07-26 [1] RSPM (R >>>>> 4.5.0) >>>>> >>>>> Thanks! >>>>> >>>>> -------------------- >>>>> Raymond Cavalcante, PhD >>>>> Bioinformatics Analyst >>>>> Epigenomics Core and Bioinformatics Core >>>>> Biomedical Research Core Facilities >>>>> University of Michigan Medical School >>>>> >>>>> [email protected] >>>>> [email protected] >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> [email protected] mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> [email protected] mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > -- > Hervé Pagès > > Bioconductor Core Team > [email protected] >
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