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 [1]
Bioconductor 3.22 (R 4.5.0)
BiocManager 1.30.26 2025-06-05 [1] CRAN (R
4.5.1)
BiocParallel 1.43.4 2025-10-07 [1]
Bioconductor 3.22 (R 4.5.1)
BiocVersion 3.22.0 2025-10-07 [1]
Bioconductor 3.22 (R 4.5.1)
Biostrings 2.77.2 2025-10-07 [1]
Bioconductor 3.22 (R 4.5.1)
bit 4.6.0 2025-03-06 [1] RSPM (R
4.5.0)
bit64 4.6.0-1 2025-01-16 [1] RSPM (R
4.5.0)
bitops 1.0-9 2024-10-03 [1] RSPM (R
4.5.0)
blob 1.2.4 2023-03-17 [1] RSPM (R
4.5.0)
brio 1.1.5 2024-04-24 [1] RSPM (R
4.5.0)
BSgenome 1.77.2 2025-10-07 [1]
Bioconductor 3.22 (R 4.5.1)
cachem 1.1.0 2024-05-16 [1] RSPM (R
4.5.0)
cli 3.6.5 2025-04-23 [1] RSPM (R
4.5.0)
codetools 0.2-20 2024-03-31 [2] CRAN (R
4.5.1)
crayon 1.5.3 2024-06-20 [1] RSPM (R
4.5.0)
curl 7.0.0 2025-08-19 [1] RSPM (R
4.5.0)
DBI 1.2.3 2024-06-02 [1] RSPM (R
4.5.0)
dbplyr 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
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Matrix 1.7-4 2025-08-28 [1] RSPM (R
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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
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org.Hs.eg.db * 3.22.0 2025-10-11 [1]
Bioconductor
pillar 1.11.1 2025-09-17 [1] RSPM (R
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pkgbuild 1.4.8 2025-05-26 [1] RSPM (R
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pkgconfig 2.0.3 2019-09-22 [1] RSPM (R
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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
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readr 2.1.5 2024-01-10 [1] RSPM (R
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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
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reshape2 1.4.4 2020-04-09 [1] RSPM (R
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restfulr 0.0.16 2025-06-27 [1] RSPM (R
4.5.1)
rjson 0.2.23 2024-09-16 [1] RSPM (R
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rlang 1.1.6 2025-04-11 [1] RSPM (R
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rprojroot 2.1.1 2025-08-26 [1] RSPM (R
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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
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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
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scales 1.4.0 2025-04-24 [1] RSPM (R
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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
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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
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stringr 1.5.2 2025-09-08 [1] RSPM (R
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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
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tibble 3.3.0 2025-06-08 [1] RSPM (R
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tidyselect 1.2.1 2024-03-11 [1] RSPM (R
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TxDb.Hsapiens.UCSC.hg19.knownGene * 3.22.0 2025-10-11 [1]
Bioconductor
tzdb 0.5.0 2025-03-15 [1] RSPM (R
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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
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vctrs 0.6.5 2023-12-01 [1] RSPM (R
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withr 3.0.2 2024-10-28 [1] RSPM (R
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XML 3.99-0.19 2025-08-22 [1] RSPM (R
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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
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Thanks!
--------------------
Raymond Cavalcante, PhD
Bioinformatics Analyst
Epigenomics Core and Bioinformatics Core
Biomedical Research Core Facilities
University of Michigan Medical School
[email protected]
[email protected]
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