Hi, I am using the Bioconductor package BindingSiteFinder. However I want to use the latest version on BindingSiteFinder. I updated BiocManager to version 3.14 and also updated all packages (apart from Matrix for some reason). Still der BindingSiteFinder version is [Package BindingSiteFinder version 1.0.0 Index], while on the webpage it says the version that goes with Bioconductor 3.14 should be 1.4.0 (https://www.bioconductor.org/packages/release/bioc/html/BindingSiteFinder.html). How can I update the package to version 1.4.0?

See my code and session info below.

BiocManager::version()

[1] ‘3.14’

BiocManager::install()

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.1 (2021-08-10) Old packages: 'Matrix' Update all/some/none? [a/s/n]:

sessionInfo( )

R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.5.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] purrr_1.0.1 BindingSiteFinder_1.0.0 biomaRt_2.50.3 dplyr_1.0.10 GenomicFeatures_1.46.5 AnnotationDbi_1.56.2
[7] Biobase_2.54.0 knitr_1.41 rtracklayer_1.54.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0
[13] S4Vectors_0.32.4 BiocGenerics_0.40.0 ggplot2_3.4.0

loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_0.63.0 bit64_4.0.5 filelock_1.0.2 progress_1.2.2
[6] httr_1.4.4 tools_4.1.1 utf8_1.2.2 R6_2.5.1 DBI_1.1.3
[11] colorspace_2.0-3 withr_2.5.0 tidyselect_1.2.0 prettyunits_1.1.1 bit_4.0.5
[16] curl_5.0.0 compiler_4.1.1 cli_3.6.0 xml2_1.3.3 exomeCopy_1.40.0
[21] DelayedArray_0.20.0 labeling_0.4.2 scales_1.2.1 rappdirs_0.3.3 stringr_1.5.0
[26] digest_0.6.31 Rsamtools_2.10.0 rmarkdown_2.19 XVector_0.34.0 pkgconfig_2.0.3
[31] htmltools_0.5.4 MatrixGenerics_1.6.0 highr_0.10 dbplyr_2.3.0 fastmap_1.1.0
[36] rlang_1.0.6 rstudioapi_0.14 RSQLite_2.2.20 farver_2.1.1 BiocIO_1.4.0
[41] generics_0.1.3 BiocParallel_1.28.3 RCurl_1.98-1.9 magrittr_2.0.3 GenomeInfoDbData_1.2.7
[46] Matrix_1.4-1 Rcpp_1.0.9 munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.3
[51] stringi_1.7.12 yaml_2.3.6 MASS_7.3-58.1 SummarizedExperiment_1.24.0 zlibbioc_1.40.0
[56] BiocFileCache_2.2.1 grid_4.1.1 blob_1.2.3 parallel_4.1.1 crayon_1.5.2
[61] lattice_0.20-45 Biostrings_2.62.0 hms_1.1.2 KEGGREST_1.34.0 pillar_1.8.1
[66] rjson_0.2.21 XML_3.99-0.13 glue_1.6.2 evaluate_0.20 BiocManager_1.30.19
[71] png_0.1-8 vctrs_0.5.1 tweenr_2.0.2 gtable_0.3.1 polyclip_1.10-4
[76] tidyr_1.2.1 assertthat_0.2.1 cachem_1.0.6 xfun_0.36 ggforce_0.4.1
[81] restfulr_0.0.15 tibble_3.1.8 GenomicAlignments_1.30.0 memoise_2.0.1 ellipsis_0.3.2

The current version of Bioconductor is 3.16. You can see this at the top of the BindingSiteFinder page you linked to (https://www.bioconductor.org/packages/release/bioc/html/BindingSiteFinder.html). Near the top of the page navigation breadcrumbs read: Home >> Bioconductor 3.16 >> Software Packages >> BindingSiteFinder and then slightly lower down it has "Bioconductor version: Release (3.16)".

BindingSiteFinder version 1.0.0 is appropriate for Bioconductor 3.14 (https://www.bioconductor.org/packages/3.14/bioc/html/BindingSiteFinder.html), which is why you're ending up with that version.

If you run BiocManager::install(version = "3.16") it will hopefully update all your packages. You might need to update to R version 4.2 in order for this to work, as Bioconductor releases are tied to specific R versions.