<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">This error seems to have come up with another package (gee), and the solution is setting an environmental variable. See thread at <a href="https://stat.ethz.ch/pipermail/r-sig-mac/2008-October/005450.html">https://stat.ethz.ch/pipermail/r-sig-mac/2008-October/005450.html</a>>. Basically do Sys.setenv("MACOSX_DEPLOYMENT_TARGET"="10.4") so that it targets 10.4 rather than 10.1.<div><br></div><div>Brian<br><div><br></div><div><br><div><div>On Mar 12, 2009, at 10:41 PM, Raul Sedano wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">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></blockquote></div><br></div></div></body></html>