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Rafael
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@rafael-24147
Last seen 3.4 years ago
Hi guys, I'am trying to run a DE analysis for my PhD thesis. Trying to install 'DeSeq2' package in Rstudio server (Ubuntu 18.04.4 LTS). After update version 3.6 to 4.0, I am having several error messages when installing new packages. The messages is always something like "Package ‘#####’ was installed before R 4.0.0: please re-install it". I tried to add a new path to the new version 4.0, as shown in the output and sessionInfo(). When I tried to install Biocmanager again, I have the same massage "...please re-install it", after chosse "a" to update all packages.
Can someone help me?
'
> .libPaths()
[1] "/home/XXXX/R/x86_64-pc-linux-gnu-library/4.0"
[2] "/home/XXXX/R/x86_64-pc-linux-gnu-library/3.6"
[3] "/usr/local/lib/R/site-library"
[4] "/usr/lib/R/site-library"
[5] "/usr/lib/R/library"
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3 grid_4.0.3
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install(version = "3.12")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installation path not writeable, unable to update packages: foreign, spatial
Old packages: 'AnnotationDbi', 'BiocFileCache', 'biomaRt', 'Biostrings', 'GenomicFeatures',
'lubridate', 'recipes', 'Rsamtools', 'Rsubread', 'waldo'
Update all/some/none? [a/s/n]:
Hello James W. MacDonald !
I don't know what is a ".Renviron" and I don't know why I have 3 paths. How can I fix it?
When you said "setup", do you mean the server specs? What can I inform to help?
I tried to do what you said "z=dir..." but the same thing happened...
Thanks!
Well, the best way to find out what a .Renviron is would be to do a search. I just did one and there were a gazillion hits of people saying what they are and how you use them and all that stuff. That's really the best way to proceed; it's way faster than asking on a support site, and quite frankly that's the only way IMO that you will ever get even reasonably proficient with R.
Anyway, I work in a core facility and often need to use old versions of R to re-run old analyses where the collaborator doesn't want anything to change. So I have this in my .Renviron
And I am careful to use particular versions of R for particular versions of Bioconductor. So R-3.6.0 was for Bioc3.9, and R-3.6.1 was for Bioc3.10, and R-4.0.0 was for Bioc3.11, and R-4.0.2 is for the current release. Otherwise this paradigm won't work. And our sysadmin is nice enough to make symbolic links to the various installed R versions (how that might be helpful if you use Rstudio is unknown to me - I use emacs and ESS like God intended ;-D). Anyway in practice it looks like this:
You can also read the BiocManager vignette for more ideas.