[Bioc-devel] glitches with releaseName() and seqlevelsStyle()

[Robert Castelo]

hi,

i've found the following glitches with 'releaseName()' and 
'seqlevelsStyle()', i guess due to recent changes in BSgenome and 
GenomeInfoDb, which is why i'm cc'ing Hervé ;)

===========BioC release 3.11 everything OK=============
library(BSgenome.Hsapiens.UCSC.hg19)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

releaseName(Hsapiens)
[1] "Genome Reference Consortium GRCh37.p13"
releaseName(as(Hsapiens, "GenomeDescription"))
[1] "Genome Reference Consortium GRCh37.p13"

seqlevelsStyle(txdb)
[1] "UCSC"
seqlevelsStyle(txdb) <- "NCBI"
seqlevelsStyle(txdb)
[1] "NCBI"    "Ensembl"
head(seqlengths(txdb))
         1         2         3         4         5 6
249250621 243199373 198022430 191154276 180915260 171115067
=======================================================

============BioC devel 3.12 inconsistencies============
library(BSgenome.Hsapiens.UCSC.hg19)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

releaseName(Hsapiens)
Error in (function (classes, fdef, mtable)  :
   unable to find an inherited method for function ‘releaseName’ for 
signature ‘"BSgenome"’
releaseName(as(Hsapiens, "GenomeDescription"))
[1] NA

seqlevelsStyle(txdb)
[1] "UCSC"
seqlevelsStyle(txdb) <- "NCBI"
seqlevelsStyle(txdb)
[1] "NCBI" "UCSC"
head(seqlengths(txdb))
         1         2         3         4         5 6
249250621 243199373 198022430 191154276 180915260 171115067
========================================================

in the case of 'releaseName()' i interpret that the method has become 
defunct for 'BSgenome' objects, but i think it should give a sensible 
result with a 'GenomeDescription' object, so something may be going 
wrong with the coercion from 'BSgenome' to 'GenomeDescription'.

in the case of 'seqlevelsStyle()', while the change of style seems to 
happen, i don't see how the style can be simultaneously NCBI and UCSC.

below my session information for the BioC devel 3.12 version.

thanks!!

robert.

sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
  [2] GenomicFeatures_1.41.2
  [3] AnnotationDbi_1.51.3
  [4] Biobase_2.49.0
  [5] BSgenome.Hsapiens.UCSC.hg19_1.4.3
  [6] BSgenome_1.57.5
  [7] rtracklayer_1.49.5
  [8] Biostrings_2.57.2
  [9] XVector_0.29.3
[10] GenomicRanges_1.41.6
[11] GenomeInfoDb_1.25.10
[12] IRanges_2.23.10
[13] S4Vectors_0.27.12
[14] BiocGenerics_0.35.4
[15] BiocManager_1.30.10

loaded via a namespace (and not attached):
  [1] SummarizedExperiment_1.19.6 progress_1.2.2
  [3] tidyselect_1.1.0 purrr_0.3.4
  [5] lattice_0.20-41 generics_0.0.2
  [7] vctrs_0.3.1 BiocFileCache_1.13.1
  [9] blob_1.2.1 XML_3.99-0.4
[11] rlang_0.4.6 pillar_1.4.4
[13] glue_1.4.1 DBI_1.1.0
[15] rappdirs_0.3.1 BiocParallel_1.23.2
[17] bit64_0.9-7.1 dbplyr_1.4.4
[19] matrixStats_0.56.0 GenomeInfoDbData_1.2.3
[21] lifecycle_0.2.0 stringr_1.4.0
[23] zlibbioc_1.35.0 memoise_1.1.0
[25] biomaRt_2.45.2 curl_4.3
[27] Rcpp_1.0.4.6 openssl_1.4.1
[29] DelayedArray_0.15.7 bit_1.1-15.2
[31] Rsamtools_2.5.3 hms_0.5.3
[33] askpass_1.1 digest_0.6.25
[35] stringi_1.4.6 dplyr_1.0.0
[37] grid_4.0.0 tools_4.0.0
[39] bitops_1.0-6 magrittr_1.5
[41] RCurl_1.98-1.2 RSQLite_2.2.0
[43] tibble_3.0.1 crayon_1.3.4
[45] pkgconfig_2.0.3 ellipsis_0.3.1
[47] Matrix_1.2-18 prettyunits_1.1.1
[49] assertthat_0.2.1 httr_1.4.1
[51] R6_2.4.1 GenomicAlignments_1.25.3
[53] compiler_4.0.0