[R-SIG-Mac] vegan failed to load under Mac OS X Mavericks

[Marc Schwartz]

That is actually referenced in the R Installation and Administration Manual:

  http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X

The second paragraph in that section:

"You may also need to install an X sub-system (or you will need to configure using option --without-x): X is part of the standard OS X distribution in versions prior to Mountain Lion, but not always installed. For Mountain Lion and later, see http://xquartz.macosforge.org/. (Note that XQuartz will likely need to be re-installed after an OS upgrade.)"


Regards,

Marc Schwartz


> On Jan 8, 2015, at 7:24 AM, Pedro Gomes <pagomes at bio.uminho.pt> wrote:
> 
> Problem solved after re-installation of X-Quartz. It seems some libraries were missing after the last update (I don’t know if its R fault or Yosemite operating system update)
> 
> thanks anyway
> 
> regards
> 
> Pedro
> 
> 
>> On 08/01/2015, at 11:54, Jari Oksanen <jari.oksanen at oulu.fi> wrote:
>> 
>> Howdy,
>> 
>> This is not a vegan issue: see this mailing list about the problems other people had with tcltk (tcltk is the key issue).
>> 
>> Next version of vegan can be loaded without tcltk and there should be patched versions of R-for-Mac that do not suffer with this problem. The next version of vegan can be obtained from http://r-forge.r-project.og/, <http://r-forge.r-project.og/,> but it no longer provides Mac binaries. For patched versions of R, see other messages in this mailing list.
>> 
>> Cheers, Jari Oksanen
>> From: R-SIG-Mac <r-sig-mac-bounces at r-project.org <mailto:r-sig-mac-bounces at r-project.org>> on behalf of Pedro Gomes <pagomes at bio.uminho.pt <mailto:pagomes at bio.uminho.pt>>
>> Sent: 18 December 2014 23:52
>> To: r-sig-mac at r-project.org <mailto:r-sig-mac at r-project.org>
>> Subject: [R-SIG-Mac] vegan failed to load under Mac OS X Mavericks
>> 
>> Hi
>> 
>> When trying to load Vegan in R 3.1.2 under under Mac OS X Mavericks I get the following error. Any idea why?
>> 
>> "starting httpd help server ... done
>> Error : .onLoad failed in loadNamespace() for 'tcltk', details:
>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so':
>>  dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /usr/X11/lib/libXft.2.dylib
>>  Referenced from: /usr/local/lib/libtk8.6.dylib
>>  Reason: image not found
>> In addition: Warning message:
>> running command ''otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 69 
>> Error: package or namespace load failed for ‘vegan’
>> 
>> Agreeing to the Xcode/iOS license requires admin privileges, please re-run as root via sudo."
>> 
>> regards
>> 
>> Pedro Gomes