[Phylobase-devl] [R-sig-phylo] Phylobase 0.4 Forge (installing issues in my old G4 powerBook)
Raul Sedano
milvago at gmail.com
Fri Mar 13 03:41:40 CET 2009
Thanks Brian,While your 4 steps did work in a Mac OSX 10.5, it did not work
on my old PPC 10.4.11. This is what I got from R (newest version) in my old
mac:
After a long process of installation 10.4.11. systems, this is just the last
part in red
ld: flag: -undefined dynamic_lookup can't be used with
MACOSX_DEPLOYMENT_TARGET environment variable set to: 10.1
/usr/bin/libtool: internal link edit command failed
make: *** [phylobase.so] Error 1
chmod: ** Removing
'/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase'
/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase/libs/ppc/*:
No such file or directory
ERROR: compilation failed for package 'phylobase'
The downloaded packages are in
/private/tmp/RtmpcBvRaE/downloaded_packages
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("phylobase", repos = "http://R-Forge.R-project.org", :
installation of package 'phylobase' had non-zero exit status
However, I was able to follow most of the Brian's four steps to remove
phylobase and then re-install it but source compilation failed. Can you guys
tell what is wrong with compilation? is this a issue just with OSX 10.4.11?
Raul Sedano
On Thu, Mar 12, 2009 at 3:13 PM, Brian O'Meara <bcomeara at nescent.org> wrote:
> 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
> ________________________________
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.r-forge.r-project.org/pipermail/phylobase-devl/attachments/20090312/714a6ddb/attachment-0001.htm
More information about the Phylobase-devl
mailing list