<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>

CC BY-SA 4.0
2020-08-23T02:25:50.643Z
Did you recently update the OS on your mac? Try opening running `xcode-select --install` and try your code again after you run that.
Ram RS
CC BY-SA 4.0
2020-08-23T02:27:03.910Z
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.
Ram RS
CC BY-SA 4.0
2020-08-23T11:40:53.240Z
I get the error in Rstudio (I added screenshot).
Chicago1988
CC BY-SA 4.0
2020-08-23T11:41:04.890Z
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'
Chicago1988
CC BY-SA 4.0
2020-08-23T23:38:02.100Z
Did you try opening XCode the app?
Ram RS
CC BY-SA 4.0
2020-09-08T02:21:36.517Z
re-install ape and clustalw?
user3479780
<r><phylogenetics>
workaround for error: Bad CPU type in executable c
# 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:

**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

