[Phylobase-devl] [R-sig-phylo] Phylobase 0.4 Forge (installing issues in my old G4 powerBook)

Brian O'Meara bcomeara at nescent.org
Thu Mar 12 21:00:22 CET 2009 

Well, using 10.4.11 on an intel mac, with developer tools installed,  
running R 2.8.1, and got the error when trying to load phylobase  
(install appeared to work, just error on load):

 > install.packages("phylobase",repos="http://R-Forge.R-project.org")
trying URL 'http://R-Forge.R-project.org/bin/macosx/universal/contrib/ 
2.8/phylobase_0.4.tgz'
Content type 'application/x-gzip' length 663910 bytes (648 Kb)
opened URL
==================================================
downloaded 648 Kb


The downloaded packages are in
	/tmp/RtmpFOnUD2/downloaded_packages

 > library(phylobase)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library '/Library/Frameworks/R.framework/ 
Resources/library/phylobase/libs/i386/phylobase.so':
   dlopen(/Library/Frameworks/R.framework/Resources/library/phylobase/ 
libs/i386/phylobase.so, 6): Symbol not found: _strtod$UNIX2003
   Referenced from: /Library/Frameworks/R.framework/Resources/library/ 
phylobase/libs/i386/phylobase.so
   Expected in: /usr/lib/libSystem.B.dylib

Error in library(phylobase) : .First.lib failed for 'phylobase'

So, it's not an issue of Raul not having developer tools (though I  
get a slightly different error, I'm assuming it is the same root  
cause). My error comes from the compiled version being made just for  
Mac OS 10.5, not cross-compiled for 10.4. My error persists when  
installing from source, though (after removing phylobase first), both  
from the 0.4 release and the trunk.

We've run through this before with phylobase, I think the fix  
involved a makefile, but I wonder how it got broken again.

Brian


On Mar 12, 2009, at 12:32 AM, Peter Cowan wrote:

> Raul,
>
> I'm CCing r-sig-phylo and the phylobase-dev list as other people  
> may be having the same problem.
>
> On Mar 11, 2009, at 8:10 PM, Raul Sedano wrote:
>
>> Hi Peter, thanks for your comments, I already tried your  
>> suggestion. This is
>> what I got when using install.packages("phylobase", repos="
>> http://R-Forge.R-project.org")
>> Error in library(phylobase) : .First.lib failed for 'phylobase'
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared library
>> '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/ 
>> phylobase/libs/ppc/phylobase.so':
>>  dlopen(/Library/Frameworks/R.framework/Versions/2.8/Resources/ 
>> library/phylobase/libs/ppc/phylobase.so,
>> 6): Symbol not found: __ZN8NxsBlock16GetImpliedBlocksEv
>>  Referenced from:
>> /Library/Frameworks/R.framework/Versions/2.8/Resources/library/ 
>> phylobase/libs/ppc/phylobase.so
>>  Expected in: dynamic lookup
>
> This should have worked.  It works for me, however I'm using 10.5  
> on an intel computer.  Guessing from the error message you're using  
> a PPC computer.
>
>> Any ideas to solve this? I though the problem was related to the  
>> lack of
>> compilers. I have tried multiple compilers including those you  
>> pointed
>> through the website.
>
> Well we know appear to have two problems, one is that the build  
> from R-forge doesn't work on your system (does any one on the list  
> have a PPC with Mac os X 10.4, to confirm this).  The other problem  
> is that it's not compiling either.
>
> Are you still getting the same errors even with the developer tools  
> installed?
>
> Peter
>
>
>> Raul Sedano
>>
>>
>>
>> On Wed, Mar 11, 2009 at 6:02 PM, Peter Cowan <pdc at berkeley.edu>  
>> wrote:
>>
>>> Raul,
>>>
>>> Yes, you need to have the full developer tools package installed for
>>> compiling to work.  It's installs a bunch of programs necessary  
>>> to build
>>> from source.  Out of curiosity, is there a reason why you're  
>>> trying to
>>> install from source?
>>>
>>> You should be able to install the package using the following  
>>> line in R:
>>>
>>> install.packages("phylobase", repos="http://R-Forge.R-project.org")
>>>
>>> Peter
>>>
>>>
>>>
>>> On Mar 11, 2009, at 5:10 PM, Raul Sedano wrote:
>>>
>>> Hey Peter, I got a different output from the terminal. Do you  
>>> have any
>>>> suggestion to correct this in my system? This might be the  
>>>> reason for my
>>>> current problem installing phylobase.Raul:~ Milvago$ Make
>>>> -bash: Make: command not found
>>>> Raul:~ Milvago$
>>>>
>>>> Should I use installers from Apple Developer Tools package to  
>>>> solve this
>>>> problem. Yes I did install gcc3.3 (but also tried gcc4.0)  
>>>> software from
>>>> the
>>>> Xcode Tools /Applications/Installers in my PowerBook.
>>>>
>>>> Thanks in advance,
>>>>
>>>> Raul Sedano
>>>>
>>>> On Wed, Mar 11, 2009 at 4:33 PM, Peter Cowan <pdc at berkeley.edu>  
>>>> wrote:
>>>>
>>>> Raul,
>>>>>
>>>>> When you say you installed the compilers in the R-FAQ, which  
>>>>> ones do you
>>>>> mean?  Did you install the tools individually or as the Apple  
>>>>> Developer
>>>>> Tools package?  For the mac the best guide to compliers for R  
>>>>> stuff, is
>>>>> here:
>>>>>
>>>>> <http://r.research.att.com/tools/>
>>>>>
>>>>> When you open the terminal and run the command "make" what do  
>>>>> you get?
>>>>>
>>>>> I see:
>>>>>
>>>>> Macintosh-7:~ peter$ make
>>>>> make: *** No targets specified and no makefile found.  Stop.
>>>>> Macintosh-7:~ peter$
>>>>>
>>>>> Peter
>>>>>
>>>>>
>>>>> On Mar 11, 2009, at 4:22 PM, Raul Sedano wrote:
>>>>>
>>>>> Hey,
>>>>>
>>>>>> First, I want to thanks Phylobase developers for such flexible
>>>>>> application,
>>>>>> I look forward to squeeze phylobase capabilities. However I  
>>>>>> need some
>>>>>> advice
>>>>>> to install Phylobase 0.4 (source) in my old G4/10.4/mac. I have
>>>>>> installed compilers as indicated in R-FAQ but still does not  
>>>>>> work. The
>>>>>> same
>>>>>> error show up  in multiple newer PowerBook machines. I got the  
>>>>>> following
>>>>>> R
>>>>>> "response" suggesting the lack of a Make command. I will  
>>>>>> appreciate any
>>>>>> comments in such basic topic.
>>>>>>
>>>>>> Raul Sedano
>>>>>>
>>>>>>
>>>>>>
>>>>>> trying URL '
>>>>>> http://r-forge.r-project.org/src/contrib/phylobase_0.4.tar.gz
>>>>>> '
>>>>>> Content type 'application/x-gzip' length 771914 bytes (753 Kb)
>>>>>> opened URL
>>>>>> ==================================================
>>>>>> downloaded 753 Kb
>>>>>>
>>>>>> WARNING: ignoring environment value of R_HOME
>>>>>> * Installing *source* package 'phylobase' ...
>>>>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1:  
>>>>>> make:
>>>>>> command
>>>>>> not found
>>>>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1:  
>>>>>> make:
>>>>>> command
>>>>>> not found
>>>>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1:  
>>>>>> make:
>>>>>> command
>>>>>> not found
>>>>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1:  
>>>>>> make:
>>>>>> command
>>>>>> not found
>>>>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1:  
>>>>>> make:
>>>>>> command
>>>>>> not found
>>>>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1:  
>>>>>> make:
>>>>>> command
>>>>>> not found
>>>>>> checking for g++... no
>>>>>> checking for c++... no
>>>>>> checking for gpp... no
>>>>>> checking for aCC... no
>>>>>> checking for CC... no
>>>>>> checking for cxx... no
>>>>>> checking for cc++... no
>>>>>> checking for cl... no
>>>>>> checking for FCC... no
>>>>>> checking for KCC... no
>>>>>> checking for RCC... no
>>>>>> checking for xlC_r... no
>>>>>> checking for xlC... no
>>>>>> checking for C++ compiler default output file name...  
>>>>>> configure: error:
>>>>>> C++
>>>>>> compiler cannot create executables
>>>>>> See `config.log' for more details.
>>>>>> ERROR: configuration failed for package 'phylobase'
>>>>>> ** Removing
>>>>>>
>>>>>> '/Library/Frameworks/R.framework/Versions/2.8/Resources/ 
>>>>>> library/phylobase'
>>>>>> ** Restoring previous
>>>>>>
>>>>>> '/Library/Frameworks/R.framework/Versions/2.8/Resources/ 
>>>>>> library/phylobase'
>>>>>>
>>>>>> The downloaded packages are in
>>>>>> /private/tmp/RtmpMpRHQe/downloaded_packages
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>      [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-sig-phylo mailing list
>>>>>> R-sig-phylo at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>
>
> _______________________________________________
> R-sig-phylo mailing list
> R-sig-phylo at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo


________________________________
Brian O'Meara
NESCent
Durham, NC
http://www.brianomeara.info
________________________________

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