I am trying to install the trackViewer package in R, following the instructions on the Bioconductor websites https://www.bioconductor.org/packages/devel/bioc/vignettes/trackViewer/inst/doc/trackViewer.html. https://bioconductor.org/packages/release/bioc/html/trackViewer.html
Every time I run the code
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("trackViewer")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Gviz")
I get this error
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'Gviz'
I'm not sure how to circumvent this. I am ultimately looking to create a lollipop plot to showcase mutations in a gene of interest with annotations.
I would appreciate any help with this.
Session info:
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] Rcpp_1.0.9 GenomicRanges_1.48.0 GenomeInfoDb_1.32.3 IRanges_2.30.0
[5] S4Vectors_0.34.0 BiocGenerics_0.42.0 BiocManager_1.30.18
loaded via a namespace (and not attached):
[1] MatrixGenerics_1.8.1 Biobase_2.56.0 httr_1.4.3
[4] bit64_4.0.5 assertthat_0.2.1 BiocFileCache_2.4.0
[7] blob_1.2.3 BSgenome_1.64.0 GenomeInfoDbData_1.2.8
[10] Rsamtools_2.12.0 yaml_2.3.5 progress_1.2.2
[13] pillar_1.8.0 RSQLite_2.2.16 lattice_0.20-45
[16] glue_1.6.2 digest_0.6.29 RColorBrewer_1.1-3
[19] XVector_0.36.0 colorspace_2.0-3 htmltools_0.5.3
[22] Matrix_1.4-1 XML_3.99-0.10 pkgconfig_2.0.3
[25] biomaRt_2.52.0 zlibbioc_1.42.0 purrr_0.3.4
[28] scales_1.2.0 BiocParallel_1.30.3 tibble_3.1.8
[31] KEGGREST_1.36.3 generics_0.1.3 ellipsis_0.3.2
[34] cachem_1.0.6 SummarizedExperiment_1.26.1 GenomicFeatures_1.48.3
[37] cli_3.3.0 magrittr_2.0.3 crayon_1.5.1
[40] memoise_2.0.1 fansi_1.0.3 xml2_1.3.3
[43] tools_4.2.1 prettyunits_1.1.1 hms_1.1.1
[46] BiocIO_1.6.0 lifecycle_1.0.1 matrixStats_0.62.0
[49] stringr_1.4.0 munsell_0.5.0 DelayedArray_0.22.0
[52] AnnotationDbi_1.58.0 Biostrings_2.64.0 compiler_4.2.1
[55] rlang_1.0.4 RCurl_1.98-1.8 rstudioapi_0.13
[58] rjson_0.2.21 rappdirs_0.3.3 htmlwidgets_1.5.4
[61] bitops_1.0-7 restfulr_0.0.15 codetools_0.2-18
[64] DBI_1.1.3 curl_4.3.2 R6_2.5.1
[67] GenomicAlignments_1.32.1 dplyr_1.0.9 rtracklayer_1.56.1
[70] fastmap_1.1.0 bit_4.0.4 utf8_1.2.2
[73] filelock_1.0.2 stringi_1.7.8 parallel_4.2.1
[76] vctrs_0.4.1 png_0.1-7 dbplyr_2.2.1
[79] tidyselect_1.1.2
Here warning message suggests that latest version of the package is already installed and if you want to reinstall the package then use force=TRUE like this :
BiocManager::install("Gviz", force = TRUE)