I did:

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


I got the output and the installation

    BioC_mirror: https://bioconductor.org
    Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.6.0 (2019-04-26).
    Installing package(s) ‘DESeq2’
    also installing the dependencies ‘XML’, ‘annotate’, ‘genefilter’, ‘geneplotter’
    
    trying URL 'https://cloud.r-project.org/src/contrib/XML_3.98-1.19.tar.gz'
    Content type 'application/x-gzip' length 1600788 bytes (1.5 MB)
    ==================================================
    downloaded 1.5 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/annotate_1.58.0.tar.gz'
    Content type 'application/x-gzip' length 1867576 bytes (1.8 MB)
    ==================================================
    downloaded 1.8 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/genefilter_1.62.0.tar.gz'
    Content type 'application/x-gzip' length 1432307 bytes (1.4 MB)
    ==================================================
    downloaded 1.4 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/geneplotter_1.58.0.tar.gz'
    Content type 'application/x-gzip' length 1428691 bytes (1.4 MB)
    ==================================================
    downloaded 1.4 MB
    
    trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/DESeq2_1.20.0.tar.gz'
    Content type 'application/x-gzip' length 2059356 bytes (2.0 MB)
    ==================================================
    downloaded 2.0 MB
    
    * installing *source* package ‘XML’ ...
    ** package ‘XML’ successfully unpacked and MD5 sums checked
    ** using staged installation
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables... 
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking how to run the C preprocessor... gcc -E
    checking for sed... /bin/sed
    checking for pkg-config... /usr/bin/pkg-config
    checking for xml2-config... no
    Cannot find xml2-config
    ERROR: configuration failed for package ‘XML’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/XML’
    ERROR: dependency ‘XML’ is not available for package ‘annotate’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/annotate’
    ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
    ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
    ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/DESeq2’
    
    The downloaded source packages are in
    	‘/tmp/RtmpnoZO5Z/downloaded_packages’
    installation path not writeable, unable to update packages: boot, class,
      cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme,
      nnet, spatial, survival
    Warning messages:
    1: In install.packages(pkgs = doing, lib = lib, ...) :
      installation of package ‘XML’ had non-zero exit status
    2: In install.packages(pkgs = doing, lib = lib, ...) :
      installation of package ‘annotate’ had non-zero exit status
    3: In install.packages(pkgs = doing, lib = lib, ...) :
      installation of package ‘genefilter’ had non-zero exit status
    4: In install.packages(pkgs = doing, lib = lib, ...) :
      installation of package ‘geneplotter’ had non-zero exit status
    5: In install.packages(pkgs = doing, lib = lib, ...) :
      installation of package ‘DESeq2’ had non-zero exit status
    > if (!requireNamespace("BiocManager", quietly = TRUE))
    +   install.packages("BiocManager")
    > BiocManager::install("DESeq")
    Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
    Installing package(s) 'DESeq'
    also installing the dependencies ‘XML’, ‘annotate’, ‘genefilter’, ‘geneplotter’
    
    trying URL 'https://cloud.r-project.org/src/contrib/XML_3.98-1.19.tar.gz'
    Content type 'application/x-gzip' length 1600788 bytes (1.5 MB)
    ==================================================
    downloaded 1.5 MB
    
    trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/annotate_1.62.0.tar.gz'
    Content type 'application/x-gzip' length 1870418 bytes (1.8 MB)
    ==================================================
    downloaded 1.8 MB
    
    trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/genefilter_1.66.0.tar.gz'
    Content type 'application/x-gzip' length 1419350 bytes (1.4 MB)
    ==================================================
    downloaded 1.4 MB
    
    trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/geneplotter_1.62.0.tar.gz'
    Content type 'application/x-gzip' length 1435430 bytes (1.4 MB)
    ==================================================
    downloaded 1.4 MB
    
    trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/DESeq_1.36.0.tar.gz'
    Content type 'application/x-gzip' length 1692053 bytes (1.6 MB)
    ==================================================
    downloaded 1.6 MB
    
    * installing *source* package ‘XML’ ...
    ** package ‘XML’ successfully unpacked and MD5 sums checked
    ** using staged installation
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables... 
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking how to run the C preprocessor... gcc -E
    checking for sed... /bin/sed
    checking for pkg-config... /usr/bin/pkg-config
    checking for xml2-config... no
    Cannot find xml2-config
    ERROR: configuration failed for package ‘XML’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/XML’
    ERROR: dependency ‘XML’ is not available for package ‘annotate’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/annotate’
    ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
    ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’
    ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq’
    * removing ‘/home/engin/R/x86_64-pc-linux-gnu-library/3.6/DESeq’
    
    The downloaded source packages are in
    	‘/tmp/RtmpnoZO5Z/downloaded_packages’
    installation path not writeable, unable to update packages: boot, class,
      cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme,
      nnet, spatial, survival
    Warning messages:
    1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
      installation of package ‘XML’ had non-zero exit status
    2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
      installation of package ‘annotate’ had non-zero exit status
    3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
      installation of package ‘genefilter’ had non-zero exit status
    4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
      installation of package ‘geneplotter’ had non-zero exit status
    5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
      installation of package ‘DESeq’ had non-zero exit status



As the error message states, you're missing the package `xml2-config`. You can google how to install that (probably `libxml2-dev`) on your OS (if you're on Ubuntu/macOS, it should be easy with a package manager).