I've recently updated my R to the newest version (3.6.1) and updated all my packages. However, one of the functions which previously worked perfectly fine, now produces an error, as the GO.db package is not available. For some reason I cannot install the GO.db package, I've tried multiple things and visited other webpages for problems with this package. So, I have compatible Rtools (v3.5) and RSQLite (which seemed to give problems with other people, e.g. https://www.biostars.org/p/133369/. So, when I run BiocManager::install("GO.db") I get the following error.
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05) Installing package(s) 'GO.db' cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/bin/windows/contrib/3.6/PACKAGES.rds': HTTP status was '404 Not Found'cannot open URL 'https://bioconductor.org/packages/3.9/workflows/bin/windows/contrib/3.6/PACKAGES.rds': HTTP status was '404 Not Found'installing the source package �GO.db� trying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GO.db_3.8.2.tar.gz' Content type 'application/x-gzip' length 31820866 bytes (30.3 MB) downloaded 30.3 MB * installing *source* package 'GO.db' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in findpack(package, lib.loc) : there is no package called 'GO.db' Calls: <Anonymous> -> findpack Execution halted ERROR: lazy loading failed for package 'GO.db'
I subsequently tried to install the package by downloading GO.db_3.8.2.tar.gz to my local computer, and then install from source, which also didn't work. I'm a bit at a loss now, and would very much appreciate any help!
> sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale:  LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252  LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C  LC_TIME=Dutch_Netherlands.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  devtools_2.1.0 usethis_1.5.1 loaded via a namespace (and not attached):  Rcpp_1.0.1 rstudioapi_0.10 knitr_1.23 magrittr_1.5  pkgload_1.0.2 tidyselect_0.2.5 R6_2.4.0 rlang_0.4.0  dplyr_0.8.3 tools_3.6.1 pkgbuild_1.0.3 xfun_0.8  sessioninfo_1.1.1 cli_1.1.0 withr_2.1.2 remotes_2.1.0  rprojroot_1.3-2 assertthat_0.2.1 digest_0.6.20 tibble_2.1.3  crayon_1.3.4 processx_3.4.1 BiocManager_1.30.4 purrr_0.3.2  callr_3.3.1 fs_1.3.1 ps_1.3.0 testthat_2.1.1  memoise_1.1.0 glue_1.3.1 compiler_3.6.1 pillar_1.4.2  backports_1.1.4 desc_1.2.0 prettyunits_1.0.2 pkgconfig_2.0.2