Answers.Body: <p>You're using an outdated version of R. You can use the R 4.0 from <code>conda-forge</code> channel, just create an environment with <code>r-base</code> and then install <code>rpy2</code>, the latest version compatible with R 4.0 is available through <code>pip</code></p>
  <pre><code>conda create -n rpy2 -c conda-forge r-base
  conda activate rpy2
  pip install rpy2
  </code></pre>
  <p>Now you can use rpy2 with R 4.0 in your python code.</p>
  <pre><code>import rpy2.robjects as robjects
  robjects.r('install.packages(&quot;BiocManager&quot;, '
             'repos=&quot;http://cran.r-project.org&quot;)')
  robjects.r('BiocManager::install(&quot;seqLogo&quot;)')
  robjects.r('library(seqLogo)')
  </code></pre>
  <p>Remember deactivate your env with <code>conda deactivate</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-28T19:00:41.133Z
Answers.Text: Thank you so much this work! but when I do the same thing for "GenomicAlignments" package I get error:    
      raise embedded.RRuntimeError(_rinterface._geterrmessage())
  rpy2.rinterface_lib.embedded.RRuntimeError: Error in (new("nonstandardGenericFunction", .Data = function (expr, envir = parent.frame(),  : 
    object 'GenomicAlignments' not found
Answers.UserDisplayName: aBiologist
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-30T23:04:30.933Z
Answers.Text: I can't replicate you error. I did `robjects.r('BiocManager::install("GenomicAlignments")')` and then `robjects.r('library(GenomicAlignments)')` and it works.
Answers.UserDisplayName: zorbax
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-27T14:53:58.867Z
Answers.Text: I am unable to do this for pcalg (https://cran.r-project.org/web/packages/pcalg/pcalg.pdf). Can I see a minimal working example?
Answers.UserDisplayName: S_S
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-28T11:23:51.950Z
Answers.LastActivityDate: 2020-08-28T11:23:51.950Z
Answers.UserDisplayName: zorbax
Body: <p>I am running into an error when I tried to run the following lines of code, the <code>error</code> at line 3:</p>
  <pre><code>1 from rpy2.robjects.packages import importr
  2 base = importr('base')
  3 base.source(&quot;http://www.bioconductor.org/biocLite.R&quot;)
  4 biocinstaller = importr(&quot;BiocInstaller&quot;)
  5 biocinstaller.biocLite(&quot;seqLogo&quot;)
  </code></pre>
  <p><code>rpy2.rinterface_lib.embedded.RRuntimeError: Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install</code></p>
  <p>How can I use <code>BiocManager</code> installer instead of <code>biocLite </code> and reflect that on my code? I couldn't find any documentation or source that talk about this error from within Python.</p>
  <p>Thank you in advance</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-28T10:44:04.960Z
Comments.Text: you need upgrade your R base version.
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-28T12:59:43.053Z
Comments.Text: Definitely recommend installation via Conda as @zorbax points out. This normal stuff for installing rpy2 As a word of warning further errors with rpy2 are also normal and as a general rule of thumb rpy2 is a nightmare. For R's ggplot2 via rpy2 is outdated and will not import the full funcationality of the ggplot2 into Python3. This is irregular given have important ggplot2 is as a graphing package. After my experience I would use subprocessing into R rather than deal with rpy2 again
Comments.UserDisplayName: M__
Tags: <r><python><rpy2>
Title: Error When Using biocLite as an installer in rpy2 python library
ThreadText: # Error When Using biocLite as an installer in rpy2 python library
  
  (Asked by: username_0 on 2020-08-28)
  
  I am running into an error when I tried to run the following lines of code, the `error` at line 3:
  
  ```
  1 from rpy2.robjects.packages import importr
  2 base = importr('base')
  3 base.source("http://www.bioconductor.org/biocLite.R")
  4 biocinstaller = importr("BiocInstaller")
  5 biocinstaller.biocLite("seqLogo")
  
  ```
  
  `rpy2.rinterface_lib.embedded.RRuntimeError: Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install`
  
  How can I use `BiocManager` installer instead of `biocLite`  and reflect that on my code? I couldn't find any documentation or source that talk about this error from within Python.
  
  Thank you in advance
  
  **Tags:** r, python, rpy2
  
  > **Comments:**
  > **username_1**: you need upgrade your R base version.  
  > **username_2**: Definitely recommend installation via Conda as @username_1 points out. This normal stuff for installing rpy2 As a word of warning further errors with rpy2 are also normal and as a general rule of thumb rpy2 is a nightmare. For R's ggplot2 via rpy2 is outdated and will not import the full funcationality of the ggplot2 into Python3. This is irregular given have important ggplot2 is as a graphing package. After my experience I would use subprocessing into R rather than deal with rpy2 again  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-08-28. Score: 2
  
  You're using an outdated version of R. You can use the R 4.0 from `conda-forge` channel, just create an environment with `r-base` and then install `rpy2`, the latest version compatible with R 4.0 is available through `pip`
  
  ```
  conda create -n rpy2 -c conda-forge r-base
  conda activate rpy2
  pip install rpy2
  
  ```
  
  Now you can use rpy2 with R 4.0 in your python code.
  
  ```
  import rpy2.robjects as robjects
  robjects.r('install.packages("BiocManager", '
             'repos="http://cran.r-project.org")')
  robjects.r('BiocManager::install("seqLogo")')
  robjects.r('library(seqLogo)')
  
  ```
  
  Remember deactivate your env with `conda deactivate`.
  
  > **Comments:**
  > **username_0**: Thank you so much this work! but when I do the same thing for "GenomicAlignments" package I get error:         raise embedded.RRuntimeError(_rinterface._geterrmessage()) rpy2.rinterface_lib.embedded.RRuntimeError: Error in (new("nonstandardGenericFunction", .Data = function (expr, envir = parent.frame(),  :    object 'GenomicAlignments' not found  
  > **username_1**: I can't replicate you error. I did `robjects.r('BiocManager::install("GenomicAlignments")')` and then `robjects.r('library(GenomicAlignments)')` and it works.  
  > **username_3**: I am unable to do this for pcalg (https://cran.r-project.org/web/packages/pcalg/pcalg.pdf). Can I see a minimal working example?  
  
  ---
  
  