Computational Mathematics

Adventures in Computing, Statistics, and R

R and RStudio incompatibility with Yosemite Mac OS X 10.10

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There is currently a bug (or feature?) in the current version of Yosemite (OS X 10.10) that messes with the passing of environmental variables to programs launched from Finder (as pointed out by Adam Maxwell).

Notably, this means that PATH variables are not passed properly to R.app or RStudio.app. You may end up seeing errors such as the following:

Error in system("pdflatex", intern = TRUE) : error in running command
sh: pdflatex: command not found

Error in system("convert", intern = TRUE) : error in running command
sh: convert: command not found

Until Apple releases a fix to this, the easy workaround is to launch the desired application from the command-line (terminal).

For example to launch R, you can instead run

/Applications/R.app/Contents/MacOS/R

And for RStudio, you can run

/Applications/RStudio.app/Contents/MacOS/RStudio

Let’s hope Apple releases a fix soon.

Dreamweaver SFTP error – New SSH host key fix

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I use Dreamweaver (CS4) to maintain my personal homepage and synchronize my files to my department’s webserver over SFTP (FTP over SSH that is).  A few months ago, our server got updated and Dreamweaver could no longer connect via SFTP.  I was getting the following error:

An FTP error occured – cannot make connection to host.

I figured it that perhaps SFTP wasn’t running on the server or maybe the port had changed.  But a quick check through the sftp command line confirmed that indeed the process was still working.

It turns out that server reset had created a new SSH host key and the local fingerprint stored by Dreamweaver was not updated.  It’s strange because most other applications will inform you of the new host key and prompt you to overwrite the old fingerprint.  For Dreamweaver, you have to manually delete the ssh_hosts file in

~/Library/Application Support/Adobe/Dreamweaver CS4/en_US/Configuration

or at least delete the row corresponding to the server in question.

I also read this blog post that claims older versions of Dreamweaver had this support, but it was taken out for some mysterious reason.