I don't have sudo, my R version is 4.0.2, I can not use BiocManager::install, because it notices me the version is not compatible. However, I can not degrade the Bioconductor version. Here is the problem capture:
>BiocManager::install()
Error: Bioconductor version '3.14' requires R version '4.1'; use
`BiocManager::install(version = '3.12')` with R version 4.0; see
https://bioconductor.org/install
>BiocManager::install(version = '3.12')
Downgrade 185 packages to Bioconductor version '3.12'? [y/n]:y
# download and install 185 packages
The downloaded source packages are in
‘/tmp/Rtmp7zU440/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to
re-install: 'BiocVersion'
2: package(s) not installed when version(s) same as current; use `force = TRUE` to
re-install: 'annotate' [... truncated]
3: In .inet_warning(msg) :
installation of package ‘clusterProfiler’ had non-zero exit status
>BiocManager::install()
Error: Bioconductor version '3.14' requires R version '4.1'; use
`BiocManager::install(version = '3.12')` with R version 4.0; see
https://bioconductor.org/install
>BiocManager::install(version = '3.12')
Downgrade 185 packages to Bioconductor version '3.12'? [y/n]:n
Error: Bioconductor version not changed by 'install()'
sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.3
Matrix products: default
BLAS: /home/a/a_local/lib/R/lib/libRblas.so
LAPACK: /home/a/a_local/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_HK.UTF-8 LC_COLLATE=en_HK.UTF-8
[5] LC_MONETARY=en_HK.UTF-8 LC_MESSAGES=en_HK.UTF-8
[7] LC_PAPER=en_HK.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2
Downgrade packages take me half an hour each time but do nothing, and I have been unable to use BiocManager::install()
, may I know what I should do? Thanks in advance.
You should use a new directory via e.g. libPaths() and not forcefully overwrite dozens of existing packages, imo.