[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 23:13:58 CET 2009
Thanks, Peter and Roland, for your emails. Installing from source
with install.packages("phylobase",repos="http://R-Forge.R-
project.org", type='source') worked. I think my problem earlier was
that while I was using "R CMD REMOVE phylobase", I didn't restart R
between attempted installs or unload and then load phylobase, so the
version being used was never updated in memory. Peter, the reason I
suspected a 10.4/10.5 was that my particular error, based on googling
for it, occurs with code compiled on 10.5 without explicitly also
being compiled for 10.4 (i.e., see <http://snipurl.com/crosscompile>).
So, Raul, if you 1) Quit R, 2) Run "R CMD REMOVE phylobase" in
Terminal, 3) type "install.packages("phylobase",repos="http://R-
Forge.R-project.org", type='source')" in R, 4) type "library
(phylobase)", does everything work?
Brian
On Mar 12, 2009, at 5:54 PM, Peter Cowan wrote:
> 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:
>> 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
>> ________________________________
>>
>>
>>
>
________________________________
Brian O'Meara
NESCent
Durham, NC
http://www.brianomeara.info
________________________________
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