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

[Peter Cowan]

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
>>>>>
>>>>>
>>>>
>>>>
>>