Indeed, thank you! -------------------- Raymond Cavalcante, PhD Bioinformatics Analyst Epigenomics Core and Bioinformatics Core Biomedical Research Core Facilities University of Michigan Medical School
[email protected] [email protected] On Tue, Oct 14, 2025 at 4:48 AM Tim Triche, Jr. <[email protected]> wrote: > 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 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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] > > > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
