these errors are generated when I am doing what PPK suggested: Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29) Installation path not writeable, unable to update packages: nlme, spatial, survival

BiocManager::install("DESeq2") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29) Installing package(s) 'DESeq2' Warning: dependency ‘XML’ is not available also installing the dependencies ‘annotate’, ‘genefilter’, ‘geneplotter’

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz' Content type 'application/x-gzip' length 1873132 bytes (1.8 MB)

downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/genefilter_1.68.0.tar.gz' Content type 'application/x-gzip' length 1421076 bytes (1.4 MB)

downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/geneplotter_1.64.0.tar.gz' Content type 'application/x-gzip' length 1431450 bytes (1.4 MB)

downloaded 1.4 MB

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 ‘XML’ is not available for package ‘annotate’

• removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/annotate’ ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
• removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/genefilter’ ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
• removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’ ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
• removing ‘/home/nikolena/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’

The downloaded source packages are in ‘/tmp/RtmphLXrZb/downloaded_packages’ Installation path not writeable, unable to update packages: nlme, spatial, survival Warning messages: 1: In install.packages(...) : installation of package ‘annotate’ had non-zero exit status 2: In install.packages(...) : installation of package ‘genefilter’ had non-zero exit status 3: In install.packages(...) : installation of package ‘geneplotter’ had non-zero exit status 4: In install.packages(...) : installation of package ‘DESeq2’ had non-zero exit status

I have tried to instal XML and the other dependencies without success..

Bioconductor is a package management tool for R that allows you to install the appropriate package versions for your R version.

For R 3.6.3 you'll need Bioconductor 3.10:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.10")

Then you install DESeq2:

BiocManager::install("DESeq2")