Body: <p>I use clustal() from library ape every now and then, but now it doesnt work...</p>
  <p>code:</p>
  <pre><code>sylvia.clus = clustal(sylvia.seq)
  </code></pre>
  <p>Error:</p>
  <pre><code>&gt; sh: /opt/X11/bin/clustalw2: Bad CPU type in executable cannot open
  &gt; file
  &gt; '/var/folders/46/vt_whvms133190kjmlx5gf4m0000gn/T//Rtmpa82i72/clustald5d11dadcdf.fas':
  &gt; No such file or directoryError in file(con, &quot;rb&quot;) : cannot open the
  &gt; connection
  </code></pre>
  <p>Is there any workaround? (I try reinstalling ape library, but I got the same error)</p>
  <p>Screenshot from Rstudio:
  <a href="https://i.sstatic.net/XiB88.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/XiB88.png" alt="enter image description here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-23T02:25:50.643Z
Comments.Text: Did you recently update the OS on your mac? Try opening running `xcode-select --install` and try your code again after you run that.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-23T02:27:03.910Z
Comments.Text: Also you could just open the XCode app on the Mac - it will "install additional components" and then your code might work fine. I do see that there was a recent update.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-23T11:40:53.240Z
Comments.Text: I get the error in Rstudio (I added screenshot).
Comments.UserDisplayName: Chicago1988
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-23T11:41:04.890Z
Comments.Text: I ran:    xcode-select --install   in the terminal and I get 'xcode-select: error: command line tools are already installed, use "Software Update" to install updates'
Comments.UserDisplayName: Chicago1988
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-23T23:38:02.100Z
Comments.Text: Did you try opening XCode the app?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-08T02:21:36.517Z
Comments.Text: re-install ape and clustalw?
Comments.UserDisplayName: user3479780
Tags: <r><phylogenetics>
Title: workaround for error: Bad CPU type in executable c
ThreadText: # workaround for error: Bad CPU type in executable c
  
  (Asked by: username_0 on 2020-08-22)
  
  I use clustal() from library ape every now and then, but now it doesnt work...
  
  code:
  
  ```
  sylvia.clus = clustal(sylvia.seq)
  
  ```
  
  Error:
  
  ```
  > sh: /opt/X11/bin/clustalw2: Bad CPU type in executable cannot open
  > file
  > '/var/folders/46/vt_whvms133190kjmlx5gf4m0000gn/T//Rtmpa82i72/clustald5d11dadcdf.fas':
  > No such file or directoryError in file(con, "rb") : cannot open the
  > connection
  
  ```
  
  Is there any workaround? (I try reinstalling ape library, but I got the same error)
  
  Screenshot from Rstudio:
  [![enter image description here](https://i.sstatic.net/XiB88.png)](https://i.sstatic.net/XiB88.png)
  
  **Tags:** r, phylogenetics
  
  > **Comments:**
  > **username_1**: Did you recently update the OS on your mac? Try opening running `xcode-select --install` and try your code again after you run that.  
  > **username_1**: Also you could just open the XCode app on the Mac - it will "install additional components" and then your code might work fine. I do see that there was a recent update.  
  > **username_0**: I get the error in Rstudio (I added screenshot).  
  > **username_0**: I ran:    xcode-select --install   in the terminal and I get 'xcode-select: error: command line tools are already installed, use "Software Update" to install updates'  
  > **username_1**: Did you try opening XCode the app?  
  > **username_2**: re-install ape and clustalw?  
  
  ---
  
  ## 0 answers
  
  