Thanks Brian,<div>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:<br></div><div><br></div><div>After a long process of installation 10.4.11. systems, this is just the last part in red</div>
<div><br></div><div><div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">ld: flag: -undefined dynamic_lookup can't be used with MACOSX_DEPLOYMENT_TARGET environment variable set to: 10.1</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">/usr/bin/libtool: internal link edit command failed</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">make: *** [phylobase.so] Error 1</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">chmod: ** Removing '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase'</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase/libs/ppc/*: No such file or directory</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">ERROR: compilation failed for package 'phylobase'</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);"><br>
</span></div><div><div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">The downloaded packages are in</span></div><div><span class="Apple-tab-span" style="white-space:pre"><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);"> </span></span><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">/private/tmp/RtmpcBvRaE/downloaded_packages</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">Updating HTML index of packages in '.Library'</span></div><div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">Warning message:</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);">In install.packages("phylobase", repos = "<a href="http://R-Forge.R-project.org">http://R-Forge.R-project.org</a>", :</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 0, 0);"> installation of package 'phylobase' had non-zero exit status</span></div></div><div><br></div><div>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?</div>
<div><br></div><div>Raul Sedano</div><div><br></div><br><div class="gmail_quote">On Thu, Mar 12, 2009 at 3:13 PM, Brian O'Meara <span dir="ltr"><<a href="mailto:bcomeara@nescent.org">bcomeara@nescent.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Thanks, Peter and Roland, for your emails. Installing from source with install.packages("phylobase",repos="<a href="http://R-Forge.R-" target="_blank">http://R-Forge.R-</a><a href="http://project.org" target="_blank">project.org</a>", 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 <<a href="http://snipurl.com/crosscompile" target="_blank">http://snipurl.com/crosscompile</a>>).<br>
<br>
So, Raul, if you 1) Quit R, 2) Run "R CMD REMOVE phylobase" in Terminal, 3) type "install.packages("phylobase",repos="<a href="http://R-" target="_blank">http://R-</a><a href="http://Forge.R-project.org" target="_blank">Forge.R-project.org</a>", type='source')" in R, 4) type "library(phylobase)", does everything work?<br>
<font color="#888888">
<br>
Brian</font><div class="im"><br>
<br>
<br>
On Mar 12, 2009, at 5:54 PM, Peter Cowan wrote:<br>
<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Mar 12, 2009, at 1:00 PM, Brian O'Meara wrote:<br>
<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
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):<br>
<br>
> install.packages("phylobase",repos="<a href="http://R-Forge.R-project.org" target="_blank">http://R-Forge.R-project.org</a>")<br>
trying URL '<a href="http://R-Forge.R-project.org/bin/macosx/universal/" target="_blank">http://R-Forge.R-project.org/bin/macosx/universal/</a>contrib/2.8/phylobase_0.4.tgz'<br>
Content type 'application/x-gzip' length 663910 bytes (648 Kb)<br>
opened URL<br>
==================================================<br>
downloaded 648 Kb<br>
<br>
<br>
The downloaded packages are in<br>
/tmp/RtmpFOnUD2/downloaded_packages<br>
<br>
> library(phylobase)<br>
Error in dyn.load(file, DLLpath = DLLpath, ...) :<br>
unable to load shared library '/Library/Frameworks/R.framework/Resources/library/phylobase/libs/i386/phylobase.so':<br>
dlopen(/Library/Frameworks/R.framework/Resources/library/phylobase/libs/i386/phylobase.so, 6): Symbol not found:<br></div><div><div></div><div class="h5">
Referenced from: /Library/Frameworks/R.framework/Resources/library/phylobase/libs/i386/phylobase.so<br>
Expected in: /usr/lib/libSystem.B.dylib<br>
<br>
Error in library(phylobase) : .First.lib failed for 'phylobase'<br>
<br>
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.<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
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.<br>
<br>
Brian when you run<br>
<br>
install.packages("phylobase",repos="<a href="http://R-Forge.R-project.org" target="_blank">http://R-Forge.R-project.org</a>", type='source')<br>
<br>
Do you get any errors? Or is it when loading the package?<br>
<br>
Is this email helpful here:<br>
<br>
<<a href="http://lists.r-forge.r-project.org/pipermail/phylobase-devl/2008-" target="_blank">http://lists.r-forge.r-project.org/pipermail/phylobase-devl/2008-</a>July/000192.html><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
We've run through this before with phylobase, I think the fix involved a makefile, but I wonder how it got broken again.<br>
</blockquote>
<br>
This might add impetus to update NCL, I think that the building process might have been improved.<br>
<br>
peter<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Brian<br>
<br>
<br>
On Mar 12, 2009, at 12:32 AM, Peter Cowan wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Raul,<br>
<br>
I'm CCing r-sig-phylo and the phylobase-dev list as other people may be having the same problem.<br>
<br>
On Mar 11, 2009, at 8:10 PM, Raul Sedano wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Peter, thanks for your comments, I already tried your suggestion. This is<br>
what I got when using install.packages("phylobase", repos="<br>
<a href="http://R-Forge.R-project.org" target="_blank">http://R-Forge.R-project.org</a>")<br>
Error in library(phylobase) : .First.lib failed for 'phylobase'<br>
Error in dyn.load(file, DLLpath = DLLpath, ...) :<br>
unable to load shared library<br>
'/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase/libs/ppc/phylobase.so':<br>
dlopen(/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase/libs/ppc/phylobase.so,<br>
6): Symbol not found: __ZN8NxsBlock16GetImpliedBlocksEv<br>
Referenced from:<br>
/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase/libs/ppc/phylobase.so<br>
Expected in: dynamic lookup<br>
</blockquote>
<br>
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.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Any ideas to solve this? I though the problem was related to the lack of<br>
compilers. I have tried multiple compilers including those you pointed<br>
through the website.<br>
</blockquote>
<br>
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.<br>
<br>
Are you still getting the same errors even with the developer tools installed?<br>
<br>
Peter<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Raul Sedano<br>
<br>
<br>
<br>
On Wed, Mar 11, 2009 at 6:02 PM, Peter Cowan <<a href="mailto:pdc@berkeley.edu" target="_blank">pdc@berkeley.edu</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Raul,<br>
<br>
Yes, you need to have the full developer tools package installed for<br>
compiling to work. It's installs a bunch of programs necessary to build<br>
from source. Out of curiosity, is there a reason why you're trying to<br>
install from source?<br>
<br>
You should be able to install the package using the following line in R:<br>
<br>
install.packages("phylobase", repos="<a href="http://R-Forge.R-" target="_blank">http://R-Forge.R-</a><a href="http://project.org" target="_blank">project.org</a>")<br>
<br>
Peter<br>
<br>
<br>
<br>
On Mar 11, 2009, at 5:10 PM, Raul Sedano wrote:<br>
<br>
Hey Peter, I got a different output from the terminal. Do you have any<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
suggestion to correct this in my system? This might be the reason for my<br>
current problem installing phylobase.Raul:~ Milvago$ Make<br>
-bash: Make: command not found<br>
Raul:~ Milvago$<br>
<br>
Should I use installers from Apple Developer Tools package to solve this<br>
problem. Yes I did install gcc3.3 (but also tried gcc4.0) software from<br>
the<br>
Xcode Tools /Applications/Installers in my PowerBook.<br>
<br>
Thanks in advance,<br>
<br>
Raul Sedano<br>
<br>
On Wed, Mar 11, 2009 at 4:33 PM, Peter Cowan <<a href="mailto:pdc@berkeley.edu" target="_blank">pdc@berkeley.edu</a>> wrote:<br>
<br>
Raul,<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
When you say you installed the compilers in the R-FAQ, which ones do you<br>
mean? Did you install the tools individually or as the Apple Developer<br>
Tools package? For the mac the best guide to compliers for R stuff, is<br>
here:<br>
<br>
<<a href="http://r.research.att.com/tools/" target="_blank">http://r.research.att.com/tools/</a>><br>
<br>
When you open the terminal and run the command "make" what do you get?<br>
<br>
I see:<br>
<br>
Macintosh-7:~ peter$ make<br>
make: *** No targets specified and no makefile found. Stop.<br>
Macintosh-7:~ peter$<br>
<br>
Peter<br>
<br>
<br>
On Mar 11, 2009, at 4:22 PM, Raul Sedano wrote:<br>
<br>
Hey,<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
First, I want to thanks Phylobase developers for such flexible<br>
application,<br>
I look forward to squeeze phylobase capabilities. However I need some<br>
advice<br>
to install Phylobase 0.4 (source) in my old G4/10.4/mac. I have<br>
installed compilers as indicated in R-FAQ but still does not work. The<br>
same<br>
error show up in multiple newer PowerBook machines. I got the following<br>
R<br>
"response" suggesting the lack of a Make command. I will appreciate any<br>
comments in such basic topic.<br>
<br>
Raul Sedano<br>
<br>
<br>
<br>
trying URL '<br>
<a href="http://r-forge.r-project.org/src/contrib/phylobase_0.4.tar.gz" target="_blank">http://r-forge.r-project.org/src/contrib/phylobase_0.4.tar.gz</a><br>
'<br>
Content type 'application/x-gzip' length 771914 bytes (753 Kb)<br>
opened URL<br>
==================================================<br>
downloaded 753 Kb<br>
<br>
WARNING: ignoring environment value of R_HOME<br>
* Installing *source* package 'phylobase' ...<br>
/Library/Frameworks/R.framework/Resources/bin/config: line 1: make:<br>
command<br>
not found<br>
/Library/Frameworks/R.framework/Resources/bin/config: line 1: make:<br>
command<br>
not found<br>
/Library/Frameworks/R.framework/Resources/bin/config: line 1: make:<br>
command<br>
not found<br>
/Library/Frameworks/R.framework/Resources/bin/config: line 1: make:<br>
command<br>
not found<br>
/Library/Frameworks/R.framework/Resources/bin/config: line 1: make:<br>
command<br>
not found<br>
/Library/Frameworks/R.framework/Resources/bin/config: line 1: make:<br>
command<br>
not found<br>
checking for g++... no<br>
checking for c++... no<br>
checking for gpp... no<br>
checking for aCC... no<br>
checking for CC... no<br>
checking for cxx... no<br>
checking for cc++... no<br>
checking for cl... no<br>
checking for FCC... no<br>
checking for KCC... no<br>
checking for RCC... no<br>
checking for xlC_r... no<br>
checking for xlC... no<br>
checking for C++ compiler default output file name... configure: error:<br>
C++<br>
compiler cannot create executables<br>
See `config.log' for more details.<br>
ERROR: configuration failed for package 'phylobase'<br>
** Removing<br>
<br>
'/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase'<br>
** Restoring previous<br>
<br>
'/Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase'<br>
<br>
The downloaded packages are in<br>
/private/tmp/RtmpMpRHQe/downloaded_packages<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
[[alternative HTML version deleted]]<br>
</blockquote>
<br>
_______________________________________________<br>
R-sig-phylo mailing list<br>
<a href="mailto:R-sig-phylo@r-project.org" target="_blank">R-sig-phylo@r-project.org</a><br>
<a href="https://stat.ethz.ch/mailman/listinfo/r-sig-phylo" target="_blank">https://stat.ethz.ch/mailman/listinfo/r-sig-phylo</a><br>
<br>
<br>
</blockquote>
<br>
<br>
</blockquote></blockquote>
<br>
</blockquote></blockquote>
<br>
_______________________________________________<br>
R-sig-phylo mailing list<br>
<a href="mailto:R-sig-phylo@r-project.org" target="_blank">R-sig-phylo@r-project.org</a><br>
<a href="https://stat.ethz.ch/mailman/listinfo/r-sig-phylo" target="_blank">https://stat.ethz.ch/mailman/listinfo/r-sig-phylo</a><br>
</blockquote>
<br>
<br>
________________________________<br>
Brian O'Meara<br>
NESCent<br>
Durham, NC<br>
<a href="http://www.brianomeara.info" target="_blank">http://www.brianomeara.info</a><br>
________________________________<br>
<br>
<br>
<br>
</blockquote>
<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
<br>
________________________________<br>
Brian O'Meara<br>
NESCent<br>
Durham, NC<br>
<a href="http://www.brianomeara.info" target="_blank">http://www.brianomeara.info</a><br>
________________________________<br>
<br>
<br>
<br>
</div></div></blockquote></div><br></div>