Hi all,
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!
Best, Quinten
> 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:
[1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.1.0 usethis_1.5.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 rstudioapi_0.10 knitr_1.23 magrittr_1.5
[5] pkgload_1.0.2 tidyselect_0.2.5 R6_2.4.0 rlang_0.4.0
[9] dplyr_0.8.3 tools_3.6.1 pkgbuild_1.0.3 xfun_0.8
[13] sessioninfo_1.1.1 cli_1.1.0 withr_2.1.2 remotes_2.1.0
[17] rprojroot_1.3-2 assertthat_0.2.1 digest_0.6.20 tibble_2.1.3
[21] crayon_1.3.4 processx_3.4.1 BiocManager_1.30.4 purrr_0.3.2
[25] callr_3.3.1 fs_1.3.1 ps_1.3.0 testthat_2.1.1
[29] memoise_1.1.0 glue_1.3.1 compiler_3.6.1 pillar_1.4.2
[33] backports_1.1.4 desc_1.2.0 prettyunits_1.0.2 pkgconfig_2.0.2
Are there other versions of GO.db already installed (
"GO.db" %in% rownames(installed.packages())? If so remove them withremove.packages("GO.db").Is the temporary directory
tempdir()on a network share or in a location with a space in the path name?Dear Martin,
Thanks for your extremely quick reply
GO.db has not been installed yet (only GOstats). tempdir() is on the C:: drive of the PC, and no space in present in the path name, see below
Not all of these packages could be successfully updated. Could this be related to GO.db (even though it does not seem to pop up in the error message)? Or something completely different?
Best, Quinten