Answers.Body: <p>Did you try following the <a href="https://bioconductor.org/packages/release/bioc/html/Gviz.html" rel="nofollow noreferrer">installation instructions</a>?</p>
  
  <p>Try this in R:</p>
  
  <pre><code>source("https://bioconductor.org/biocLite.R")
  BiocInstaller::biocLite(c("Gviz"))
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-09T19:28:43.693Z
Answers.Text: Nope, I did not know, each package has its own way of installation. But the first line here was what I was missing.
Answers.UserDisplayName: Soerendip
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-10T21:38:06.483Z
Answers.Text: 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.
Answers.UserDisplayName: Jared Andrews
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-07T20:30:18.450Z
Answers.LastActivityDate: 2019-01-07T20:30:18.450Z
Answers.UserDisplayName: Jared Andrews
Answers.Body: <pre><code># Install the BiocManager package first
  install.packages("BiocManager") 
  library("BiocManager")
  
  # Then install the Gviz package
  BiocManager::install("Gviz")
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-08T21:14:16.540Z
Answers.LastActivityDate: 2019-01-09T17:21:51.807Z
Answers.LastEditDate: 2019-01-09T17:21:51.807Z
Answers.UserDisplayName: Aedin
Answers.Body: <p>Use BiocManager::install()</p>
  
  <pre><code># Code
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("Gviz", version = "3.8")
  </code></pre>
  
  <p>However, If R &lt; 3.5.0 , please use the following for installing Bioconductor packages.</p>
  
  <pre><code>BiocInstaller::biocLite("Gviz") 
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-09T13:06:13.280Z
Answers.LastActivityDate: 2019-01-09T13:06:13.280Z
Answers.UserDisplayName: Alex Yahiaoui Martinez
Body: <p>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 </p>
  
  <pre><code>conda create -n r -c conda-forge r-essentials jupyter
  </code></pre>
  
  <p>and then add the library with:</p>
  
  <pre><code>source activate r
  conda install -c bioconda bioconductor-gviz
  </code></pre>
  
  <p>getting </p>
  
  <blockquote>
    <p>UnsatisfiableError: The following specifications were found to be in conflict:
      - atk</p>
  </blockquote>
  
  <p>I remove atk, but now I get:</p>
  
  <blockquote>
    <p>UnsatisfiableError: The following specifications were found to be in conflict:
      - bioconductor-gviz
      - r-bindr</p>
  </blockquote>
  
  <p>Does anyone manage to use gviz from within an jupyter notebook?</p>
  
  <p>I also tried to install gviz from a running R-notebook with:</p>
  
  <pre><code>install.package('gviz')
  </code></pre>
  
  <blockquote>
    <p>Warning in install.packages :
      package ‘gviz’ is not available (for R version 3.4.3)</p>
  </blockquote>
  
  <p>Same when I try 'bioconductor-gviz'.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-07T13:37:24.853Z
Comments.Text: 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
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-07T14:02:18.523Z
Comments.Text: Not sure what that means.
Comments.UserDisplayName: Soerendip
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-07T15:45:32.253Z
Comments.Text: That to install a package from Bioconductor you need to use a different command (not `install.package`), but the one I provided
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-07T16:22:59.680Z
Comments.Text: It does not seem to be an accepted command though.Error in `loadNamespace(name) : there is no package called ‘BiocInstall’`
Comments.UserDisplayName: Soerendip
Tags: <bioconductor><gviz><bioconda><jupyter>
Title: How can I install bioconductor-gviz and use it in jupyter notebook?
ThreadText: # How can I install bioconductor-gviz and use it in jupyter notebook?
  
  (Asked by: username_0 on 2019-01-07)
  
  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'.
  
  **Tags:** bioconductor, gviz, bioconda, jupyter
  
  > **Comments:**
  > **username_1**: 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  
  > **username_0**: Not sure what that means.  
  > **username_1**: That to install a package from Bioconductor you need to use a different command (not `install.package`), but the one I provided  
  > **username_0**: It does not seem to be an accepted command though.Error in `loadNamespace(name) : there is no package called ‘BiocInstall’`  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2019-01-07. Score: 3 | Accepted answer
  
  Did you try following the [installation instructions](https://bioconductor.org/packages/release/bioc/html/Gviz.html)?
  
  Try this in R:
  
  ```
  source("https://bioconductor.org/biocLite.R")
  BiocInstaller::biocLite(c("Gviz"))
  
  ```
  
  > **Comments:**
  > **username_0**: Nope, I did not know, each package has its own way of installation. But the first line here was what I was missing.  
  > **username_2**: 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 username_4's answer), but for R < 3.5, this is the general way to install any Biocondoctor package.  
  
  ---
  
  ### Answer by username_3 on 2019-01-08. Score: 4
  
  ```
  # Install the BiocManager package first
  install.packages("BiocManager") 
  library("BiocManager")
  
  # Then install the Gviz package
  BiocManager::install("Gviz")
  
  ```
  
  
  ---
  
  ### Answer by username_4 on 2019-01-09. Score: 1
  
  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") 
  
  ```
  
  
  ---
  
  