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

Peter Cowan pdc at berkeley.edu
Thu Mar 12 22:54:11 CET 2009 

On Mar 12, 2009, at 1:00 PM, Brian O'Meara wrote:

> 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.

How can you tell it is due to the 10.4/10.5 difference.  I'm no  
expert, but I would have guessed that they wouldn't differ when it  
comes to building R packages.

Brian when you run

install.packages("phylobase",repos="http://R-Forge.R-project.org",  
type='source')

Do you get any errors?  Or is it when loading the package?

Is this email helpful here:

<http://lists.r-forge.r-project.org/pipermail/phylobase-devl/2008-July/000192.html 
 >

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

This might add impetus to update NCL, I think that the building  
process might have been improved.

peter

>
> 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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