DESeq2 installation Error (ERROR: dependency ‘locfit’ is not available for package ‘DESeq2’)

Question

[tsomakiank]

Hello everybody! I am trying to install DESeq2 and I keep getting errors. At first I had about 10 errors regarding packages I couldnt install. The main problem of that was that I couldnt install RCurl. From searching I managed to install RCurl but I still get the bellow error.

install('DESeq2', lib = '/home/kostas/R/x86_64-pc-linux-gnu-library/3.6') 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.10 (BiocManager 1.30.17), R 3.6.3 (2020-02-29)
Installing package(s) 'DESeq2'
Warning: dependency ‘locfit’ is not available
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DESeq2_1.26.0.tar.gz'
Content type 'application/x-gzip' length 2060061 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

ERROR: dependency ‘locfit’ is not available for package ‘DESeq2’
* removing ‘/home/kostas/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmpvImMFF/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status

Answer 1

[Mensur Dlakic]

You are using an older R version (3.6.3) for which not all packages are available. I know that may sound ridiculous given that your R version is only a couple of years old, but I don't make the rules.

Here is what locfit page shows:

https://cran.r-project.org/web/packages/locfit/index.html

It seems that the latest locfit version requires R ≥ 4.1.0. It would appear that either versions 1.5-9.2 or 1.5-9.4 will be compatible with your R version, so maybe installing one of those ahead of DESeq2 will do the trick.

If you are into extreme makeovers, upgrading your R to the latest version could work as well.

[tsomakiank]

OOOh really! Thats whats the obvious and what got through my mind at first but taking under consideration that I just got into the field I thought that this is no way whats going on and that it has to do with some deeper R knowledge. Such a relief reading it now! Thanks a lot Mensur Dlakic !

Answer 2

[emalekos]

Extending Mensur's answer, here are previous releases of locfit: https://cran.r-project.org/src/contrib/Archive/locfit/

you can install in R with:

install.packages(URL-to-desired-version, repos=NULL, type="source")

install.packages("https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.4.tar.gz", repos=NULL, type="source")