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I tried to install gviz in a conda environment, but that library seems to be incompatible to python and r. I tried to setup a clean environment using 

conda create -n r -c conda-forge r-essentials jupyter

and then add the library with:

source activate r
conda install -c bioconda bioconductor-gviz

getting

UnsatisfiableError: The following specifications were found to be in conflict: - atk

I remove atk, but now I get:

UnsatisfiableError: The following specifications were found to be in conflict: - bioconductor-gviz - r-bindr

Does anyone manage to use gviz from within an jupyter notebook?

I also tried to install gviz from a running R-notebook with:

install.package('gviz')

Warning in install.packages : package ‘gviz’ is not available (for R version 3.4.3)

Same when I try 'bioconductor-gviz'.

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    $\begingroup$ The package is from Bioconductor, from the version you are using you should use:BiocInstall::biocLite("gviz") to be able to install it from R terminal $\endgroup$
    – llrs
    Jan 7, 2019 at 13:37
  • $\begingroup$ Not sure what that means. $\endgroup$
    – Soerendip
    Jan 7, 2019 at 14:02
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    $\begingroup$ That to install a package from Bioconductor you need to use a different command (not install.package), but the one I provided $\endgroup$
    – llrs
    Jan 7, 2019 at 15:45
  • $\begingroup$ It does not seem to be an accepted command though.Error in loadNamespace(name) : there is no package called ‘BiocInstall’ $\endgroup$
    – Soerendip
    Jan 7, 2019 at 16:22

3 Answers 3

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Did you try following the installation instructions?

Try this in R:

source("https://bioconductor.org/biocLite.R")
BiocInstaller::biocLite(c("Gviz"))
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  • $\begingroup$ Nope, I did not know, each package has its own way of installation. But the first line here was what I was missing. $\endgroup$
    – Soerendip
    Jan 9, 2019 at 19:28
  • $\begingroup$ All Bioconductor packages are installed the same way. Though in general, reading the software documentation before use is always a good idea. They've changed the command from my answer a bit for R 3.5 and later (see Alex's answer), but for R < 3.5, this is the general way to install any Biocondoctor package. $\endgroup$
    – Jared Andrews
    Jan 10, 2019 at 21:38
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# Install the BiocManager package first
install.packages("BiocManager") 
library("BiocManager")

# Then install the Gviz package
BiocManager::install("Gviz")
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Use BiocManager::install()

# Code
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Gviz", version = "3.8")

However, If R < 3.5.0 , please use the following for installing Bioconductor packages.

BiocInstaller::biocLite("Gviz")
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