DYLD_FALLBACK_LIBRARY_PATH not set in R.app

2 messages · Dan Tenenbaum

Wed, Apr 10, 2013 3:38 PM #

Not sure if this is a bug or not, but there is different behavior
between R.app and command-line R as regards
DYLD_FALLBACK_LIBRARY_PATH.

If I start R.app and try and load the BioC package 'impute':

source('http://bioconductor.org/biocLite.R")
biocLite("impute")
library(impute)

I get:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/Library/Frameworks/R.framework.release/Versions/3.0/Resources/library/impute/libs/impute.so':
  dlopen(/Library/Frameworks/R.framework.release/Versions/3.0/Resources/library/impute/libs/impute.so,
6): Library not loaded: /usr/local/lib/libgfortran.2.dylib
  Referenced from:
/Library/Frameworks/R.framework.release/Versions/3.0/Resources/library/impute/libs/impute.so
  Reason: image not found
Error: package or namespace load failed for 'impute'

However, the package loads fine in command-line R.

I found that if I start R.app like this:

 export DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib
open /Applications/R.app

Then I can load the impute package.

So can R.app set this variable when it starts? Or is there another
solution I need to look at?

Thanks,
Dan

Dan Tenenbaum

Wed, Apr 10, 2013 6:05 PM #

On Wed, Apr 10, 2013 at 3:38 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:

It turns out that BioC was making packages incorrectly.

You can disregard this message.

Thanks,
Dan