I couldn't install DEseq2?

Question

[enginbozaba]

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

[cdastmalchi]

I'm having this same error when trying to install DESeq2 for R Version 3.6.1, even after adding sudo apt-get install libxml2 , sudo apt-get install libxml2-dev. I'm trying to install deseq2 via a Docker container, for which my Dockerfile looks like:

FROM r-base:3.6.1

WORKDIR /home

RUN apt-get update && \ 
    apt-get install -y \ 
        build-essential \ 
        gdb \ 
        git \ 
        jags \ 
        libcurl4-openssl-dev \ 
        libopenblas-base \ 
        libopenblas-dev \ 
        libssl-dev \     
        libssh2-1-dev \ 
        libxml2 \ 
        libxml2-dev \ 
        python-dev \ 
        python-pip \ 
        wget \
        sudo

RUN pip install awscli boto3

ENV PATH=$PATH:~/.local/bin/
ADD . /home/
ENV R_THREADS=30

And then once I run this container interactively and start an R session, I try to install deseq via:

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

BiocManager::install("DESeq2")

But I still get the dependency errors the poster of this question got:

ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/usr/local/lib/R/site-library/SummarizedExperiment’
ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
* removing ‘/usr/local/lib/R/site-library/ggplot2’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/usr/local/lib/R/site-library/annotate’
ERROR: dependency ‘ggplot2’ is not available for package ‘viridis’
* removing ‘/usr/local/lib/R/site-library/viridis’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/usr/local/lib/R/site-library/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/usr/local/lib/R/site-library/geneplotter’
ERROR: dependencies ‘ggplot2’, ‘latticeExtra’, ‘viridis’ are not available for package ‘Hmisc’
* removing ‘/usr/local/lib/R/site-library/Hmisc’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’, ‘ggplot2’, ‘Hmisc’ are not available for package ‘DESeq2’
* removing ‘/usr/local/lib/R/site-library/DESeq2’

[Ram]

You should ideally ask this as a new question and maybe point to this question in that new question. Given that you're using docker, I think the topic is different enough to warrant being a new thread.

Answer 1

[Ram]

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).

[enginbozaba]

As you said (sudo apt-get install libxml2 , sudo apt-get install libxml2-dev), the problem was solved. Thank you.:)

[ATpoint]

[cdastmalchi]

libxml2-dev is among the packages I install in my Dockerfile. I'll maybe just post this as a new question like you suggested.

Answer 2

[Nai]

sudo apt-get install libxml2-dev:

[Nai]

Reading package lists... Done Building dependency tree
Reading state information... Done libxml2-dev is already the newest version (2.9.3+dfsg1-1ubuntu0.7). 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.

When I am trying BiocManager::install("genefilter"). I am getting the following issue...

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

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

Bioconductor version 3.10 (BiocManager 1.30.16), R 3.6.3 (2020-02-29) Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'genefilter'

Kindly help me....If I don't use R without sudo then I get an error genefilter non zero exit status

[ATpoint]

Please open a new question, providing full code and the full error log. Please use the code option (botton 10101) to highlight code with markdown.