When I try to install the gtf for hg38
BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
I get the following error:
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'TxDb.Hsapiens.UCSC.hg38.knownGene'
Error in readRDS(dest) : error reading from connection
Per https://stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I ran
```> BiocManager::install("BiocVersion")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories: CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories: CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) 'TxDb.Hsapiens.UCSC.hg38.knownGene' Error in readRDS(dest) : error reading from connection
getOption("repos") CRAN "https://cran.rstudio.com/" attr(,"RStudio") [1] TRUE BioManager::repositories() Error in loadNamespace(x) : there is no package called 'BioManager' BiocManager::repositories() 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories: CRAN: https://cran.rstudio.com/
BioCsoft BioCann
"https://bioconductor.org/packages/3.14/bioc" "https://bioconductor.org/packages/3.14/data/annotation"
BioCexp BioCworkflows
"https://bioconductor.org/packages/3.14/data/experiment" "https://bioconductor.org/packages/3.14/workflows" BioCbooks CRAN "https://bioconductor.org/packages/3.14/books" "https://cran.rstudio.com/"
But the installation still does not work.
sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6.4
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] GenomicFeatures_1.46.5 AnnotationDbi_1.56.2 Biobase_2.54.0 BiocManager_1.30.16 Rsamtools_2.10.0
[6] Biostrings_2.62.0 XVector_0.34.0 ATACseqQC_1.18.0 preseqR_4.0.0 SeuratObject_4.0.4
[11] Seurat_4.1.0 data.table_1.14.2 ggplot2_3.3.5 viridisLite_0.4.0 GenomicRanges_1.46.1
[16] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0 SnapATAC_1.0.0
[21] rhdf5_2.38.1 Matrix_1.4-0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.24 tidyselect_1.1.2 RSQLite_2.2.10
[5] htmlwidgets_1.5.4 grid_4.1.2 BiocParallel_1.28.3 Rtsne_0.15
[9] munsell_0.5.0 codetools_0.2-18 ica_1.0-2 future_1.24.0
[13] miniUI_0.1.1.1 misc3d_0.9-1 withr_2.5.0 spatstat.random_2.1-0
[17] colorspace_2.0-3 filelock_1.0.2 knitr_1.37 rstudioapi_0.13
[21] ROCR_1.0-11 tensor_1.5 motifStack_1.38.0 listenv_0.8.0
[25] MatrixGenerics_1.6.0 GenomeInfoDbData_1.2.7 polyclip_1.10-0 bit64_4.0.5
[29] parallelly_1.30.0 vctrs_0.3.8 ChIPpeakAnno_3.28.1 generics_0.1.2
[33] lambda.r_1.2.4 xfun_0.30 BiocFileCache_2.2.1 randomForest_4.7-1
[37] regioneR_1.26.1 R6_2.5.1 doParallel_1.0.17 locfit_1.5-9.5
[41] AnnotationFilter_1.18.0 cachem_1.0.6 bitops_1.0-7 rhdf5filters_1.6.0
[45] spatstat.utils_2.3-0 DelayedArray_0.20.0 assertthat_0.2.1 promises_1.2.0.1
[49] BiocIO_1.4.0 scales_1.1.1 gtable_0.3.0 globals_0.14.0
[53] goftest_1.2-3 ensembldb_2.18.3 rlang_1.0.2 splines_4.1.2
[57] rtracklayer_1.54.0 lazyeval_0.2.2 spatstat.geom_2.3-2 yaml_2.3.5
[61] reshape2_1.4.4 abind_1.4-5 httpuv_1.6.5 RBGL_1.70.0
[65] tools_4.1.2 tcltk_4.1.2 GenomicScores_2.6.0 ellipsis_0.3.2
[69] spatstat.core_2.4-0 jquerylib_0.1.4 RColorBrewer_1.1-2 ggridges_0.5.3
[73] polynom_1.4-0 Rcpp_1.0.8.2 plyr_1.8.6 progress_1.2.2
[77] zlibbioc_1.40.0 purrr_0.3.4 RCurl_1.98-1.6 prettyunits_1.1.1
[81] rpart_4.1.16 deldir_1.0-6 pbapply_1.5-0 viridis_0.6.2
[85] cowplot_1.1.1 zoo_1.8-9 SummarizedExperiment_1.24.0 ggrepel_0.9.1
[89] cluster_2.1.2 magrittr_2.0.2 futile.options_1.0.1 scattermore_0.8
[93] lmtest_0.9-39 RANN_2.6.1 ProtGenerics_1.26.0 fitdistrplus_1.1-8
[97] matrixStats_0.61.0 hms_1.1.1 patchwork_1.1.1 mime_0.12
[101] evaluate_0.15 xtable_1.8-4 XML_3.99-0.9 VennDiagram_1.7.1
[105] gridExtra_2.3 biomaRt_2.50.3 compiler_4.1.2 tibble_3.1.6
[109] KernSmooth_2.23-20 crayon_1.5.0 htmltools_0.5.2 mgcv_1.8-39
[113] later_1.3.0 snow_0.4-4 tidyr_1.2.0 DBI_1.1.2
[117] formatR_1.11 dbplyr_2.1.1 rappdirs_0.3.3 MASS_7.3-55
[121] ade4_1.7-18 cli_3.2.0 parallel_4.1.2 igraph_1.2.11
[125] pkgconfig_2.0.3 bigmemory.sri_0.1.3 GenomicAlignments_1.30.0 plotly_4.10.0
[129] spatstat.sparse_2.1-0 InteractionSet_1.22.0 xml2_1.3.3 foreach_1.5.2
[133] bslib_0.3.1 multtest_2.50.0 stringr_1.4.0 digest_0.6.29
[137] sctransform_0.3.3 RcppAnnoy_0.0.19 graph_1.72.0 spatstat.data_2.1-2
[141] rmarkdown_2.13 leiden_0.3.9 uwot_0.1.11 edgeR_3.36.0
[145] curl_4.3.2 restfulr_0.0.13 shiny_1.7.1 rjson_0.2.21
[149] lifecycle_1.0.1 nlme_3.1-155 jsonlite_1.8.0 Rhdf5lib_1.16.0
[153] futile.logger_1.4.3 bigmemory_4.5.36 limma_3.50.1 BSgenome_1.62.0
[157] fansi_1.0.2 pillar_1.7.0 lattice_0.20-45 KEGGREST_1.34.0
[161] fastmap_1.1.0 httr_1.4.2 survival_3.3-1 interactiveDisplayBase_1.32.0
[165] glue_1.6.2 png_0.1-7 iterators_1.0.14 BiocVersion_3.14.0
[169] plot3D_1.4 bit_4.0.4 HDF5Array_1.22.1 stringi_1.7.6
[173] sass_0.4.0 blob_1.2.2 AnnotationHub_3.2.2 doSNOW_1.0.20
[177] memoise_2.0.1 dplyr_1.0.8 irlba_2.3.5 future.apply_1.8.1
```
