<span class="Apple-style-span" style="font-family: Times; font-size: 16px; "><pre>Dear Peter, Brian & Mark
Thanks for taking your time and your comments. Compilation process now seems to be targeting OSX 10.4 after <span class="Apple-style-span" style="border-collapse: collapse; font-family: arial; font-size: 13px; white-space: normal; ">Sys.setenv("MACOSX_DEPLOYMENT_TARGET"="10.4"). <span class="Apple-style-span" style="border-collapse: separate; font-family: -webkit-monospace; font-size: 16px; white-space: pre; ">However after all the compilation faile.</span></span></pre>
<pre></pre><pre>This red labeled output</pre><pre><span class="Apple-style-span" style="color: rgb(255, 0, 0);">ld: /Library/Frameworks/R.framework/../R.framework/R load command 14 unknown cmd field
/usr/bin/libtool: internal link edit command failed
make: *** [phylobase.so] Error 1
chmod: /Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase/libs/ppc/*: No such file or directory
ERROR: compilation failed for package 'phylobase'</span></pre><pre>I also noticed red labeled lines during initial stage of compilation as:</pre><pre><span class="Apple-style-span" style="color: rgb(255, 0, 0);">nxscharactersblock.cpp: In member function `virtual bool NxsCharactersBlock::HandleNextState(NxsToken&, unsigned int, unsigned int)':
nxscharactersblock.cpp:1412: warning: passing 'const double' for converting 1 of 'std::vector<_Tp, _Alloc>::vector(size_t) [with _Tp = double, _Alloc = std::allocator<double>]'</span></pre><pre>
I already compiled phylobase in a newer OSX 10.5. However, I will appreciate if you can help to make this old Power Book G4 to rock with phylobase.</pre><pre>Raul Sedano</pre></span><br><div class="gmail_quote">On Fri, Mar 13, 2009 at 6:11 AM, Mark Holder <span dir="ltr"><<a href="mailto:mtholder@ku.edu">mtholder@ku.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi,<br>
Take this with a grain of salt, because I've never done any development in R, but...<br>
<br>
I should be possible to compile and install NCL into a location on your system's LD_LIBRARY_PATH ( the DYLD_LIBRARY_PATH on Mac), such that phylobase picks up NCL from that location. (note that LD_LIBRARY_PATH and DYLD_LIBRARY_PATH are environmental variables that can be set in your environment if you install in "non-standard" locations, if you install to /usr or /usr/local you usually do not have to set any variables).<br>
<br>
You'd have to make sure that you install a version of NCL that has all of the functions that phylobase uses, but that should not be hard to do (I'd pull the NCL out of the phylobase distribution, if I were trying this).<br>
<br>
If NCL itself (outside of phylobase) won't build on your PPC, then I should be able to help you with that.<br>
<br>
Perhaps a more experienced R user can chime in on whether installing to a system location is going to cause problem for an R package.<br>
<br>
<br>
All the best,<br>
Mark<div><div></div><div class="h5"><br>
<br>
<br>
<br>
<br>
On Mar 12, 2009, at 11:03 PM, Brian O'Meara wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This error seems to have come up with another package (gee), and the<br>
solution is setting an environmental variable. See thread at <a href="https://stat.ethz.ch/pipermail/r-sig-mac/2008-October/005450.html" target="_blank">https://stat.ethz.ch/pipermail/r-sig-mac/2008-October/005450.html</a><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
. Basically do Sys.setenv("MACOSX_DEPLOYMENT_TARGET"="10.4") so that<br>
</blockquote>
it targets 10.4 rather than 10.1.<br>
<br>
Brian<br>
<br>
<br>
On Mar 12, 2009, at 10:41 PM, Raul Sedano wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks Brian,<br>
While your 4 steps did work in a Mac OSX 10.5, it did not work on my<br>
old PPC 10.4.11. This is what I got from R (newest version) in my<br>
old mac:<br>
<br>
After a long process of installation 10.4.11. systems, this is just<br>
the last part in red<br>
<br>
ld: flag: -undefined dynamic_lookup can't be used with<br>
MACOSX_DEPLOYMENT_TARGET environment variable set to: 10.1<br>
/usr/bin/libtool: internal link edit command failed<br>
make: *** [phylobase.so] Error 1<br>
chmod: ** Removing '/Library/Frameworks/R.framework/Versions/2.8/<br>
Resources/library/phylobase'<br>
/Library/Frameworks/R.framework/Versions/2.8/Resources/library/<br>
phylobase/libs/ppc/*: No such file or directory<br>
ERROR: compilation failed for package 'phylobase'<br>
<br>
The downloaded packages are in<br>
/private/tmp/RtmpcBvRaE/downloaded_packages<br>
Updating HTML index of packages in '.Library'<br>
Warning message:<br>
In install.packages("phylobase", repos = "<a href="http://R-Forge.R-" target="_blank">http://R-Forge.R-</a><br>
<a href="http://project.org" target="_blank">project.org</a>", :<br>
installation of package 'phylobase' had non-zero exit status<br>
<br>
However, I was able to follow most of the Brian's four steps to<br>
remove phylobase and then re-install it but source compilation<br>
failed. Can you guys tell what is wrong with compilation? is this a<br>
issue just with OSX 10.4.11?<br>
<br>
Raul Sedano<br>
<br>
<br>
On Thu, Mar 12, 2009 at 3:13 PM, Brian O'Meara<br>
<<a href="mailto:bcomeara@nescent.org" target="_blank">bcomeara@nescent.org</a>> wrote:<br>
Thanks, Peter and Roland, for your emails. Installing from source<br>
with install.packages("phylobase",repos="<a href="http://R-Forge.R-" target="_blank">http://R-Forge.R-</a><br>
<a href="http://project.org" target="_blank">project.org</a>", type='source') worked. I think my problem earlier was<br>
that while I was using "R CMD REMOVE phylobase", I didn't restart R<br>
between attempted installs or unload and then load phylobase, so the<br>
version being used was never updated in memory. Peter, the reason I<br>
suspected a 10.4/10.5 was that my particular error, based on<br>
googling for it, occurs with code compiled on 10.5 without<br>
explicitly also being compiled for 10.4 (i.e., see <<a href="http://snipurl.com/crosscompile" target="_blank">http://snipurl.com/crosscompile</a><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
).<br>
</blockquote>
<br>
So, Raul, if you 1) Quit R, 2) Run "R CMD REMOVE phylobase" in<br>
Terminal, 3) type "install.packages("phylobase",repos="<a href="http://R-Forge.R-project.org" target="_blank">http://R-Forge.R-project.org</a><br>
", type='source')" in R, 4) type "library(phylobase)", does<br>
everything work?<br>
<br>
Brian<br>
<br>
<br>
<br>
On Mar 12, 2009, at 5:54 PM, Peter Cowan wrote:<br>
<br>
On Mar 12, 2009, at 1:00 PM, Brian O'Meara wrote:<br>
<br>
Well, using 10.4.11 on an intel mac, with developer tools installed,<br>
running R 2.8.1, and got the error when trying to load phylobase<br>
(install appeared to work, just error on load):<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
install.packages("phylobase",repos="<a href="http://R-Forge.R-project.org" target="_blank">http://R-Forge.R-project.org</a>")<br>
</blockquote>
trying URL '<a href="http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.8/phylobase_0.4.tgz" target="_blank">http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.8/phylobase_0.4.tgz</a>'<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>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
library(phylobase)<br>
</blockquote>
Error in dyn.load(file, DLLpath = DLLpath, ...) :<br>
unable to load shared library '/Library/Frameworks/R.framework/<br>
Resources/library/phylobase/libs/i386/phylobase.so':<br>
dlopen(/Library/Frameworks/R.framework/Resources/library/phylobase/<br>
libs/i386/phylobase.so, 6): Symbol not found:<br>
Referenced from: /Library/Frameworks/R.framework/Resources/library/<br>
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<br>
get a slightly different error, I'm assuming it is the same root<br>
cause). My error comes from the compiled version being made just for<br>
Mac OS 10.5, not cross-compiled for 10.4. My error persists when<br>
installing from source, though (after removing phylobase first),<br>
both from the 0.4 release and the trunk.<br>
<br>
How can you tell it is due to the 10.4/10.5 difference. I'm no<br>
expert, but I would have guessed that they wouldn't differ when it<br>
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>",<br>
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-July/000192.html" target="_blank">http://lists.r-forge.r-project.org/pipermail/phylobase-devl/2008-July/000192.html</a><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
</blockquote>
<br>
We've run through this before with phylobase, I think the fix<br>
involved a makefile, but I wonder how it got broken again.<br>
<br>
This might add impetus to update NCL, I think that the building<br>
process might have been improved.<br>
<br>
peter<br>
<br>
<br>
Brian<br>
<br>
<br>
On Mar 12, 2009, at 12:32 AM, Peter Cowan wrote:<br>
<br>
Raul,<br>
<br>
I'm CCing r-sig-phylo and the phylobase-dev list as other people may<br>
be having the same problem.<br>
<br>
On Mar 11, 2009, at 8:10 PM, Raul Sedano wrote:<br>
<br>
Hi Peter, thanks for your comments, I already tried your suggestion.<br>
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/<br>
phylobase/libs/ppc/phylobase.so':<br>
dlopen(/Library/Frameworks/R.framework/Versions/2.8/Resources/<br>
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/<br>
phylobase/libs/ppc/phylobase.so<br>
Expected in: dynamic lookup<br>
<br>
This should have worked. It works for me, however I'm using 10.5 on<br>
an intel computer. Guessing from the error message you're using a<br>
PPC computer.<br>
<br>
Any ideas to solve this? I though the problem was related to the<br>
lack of<br>
compilers. I have tried multiple compilers including those you pointed<br>
through the website.<br>
<br>
Well we know appear to have two problems, one is that the build from<br>
R-forge doesn't work on your system (does any one on the list have a<br>
PPC with Mac os X 10.4, to confirm this). The other problem is that<br>
it's not compiling either.<br>
<br>
Are you still getting the same errors even with the developer tools<br>
installed?<br>
<br>
Peter<br>
<br>
<br>
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>
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<br>
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<br>
in R:<br>
<br>
install.packages("phylobase", repos="<a href="http://R-Forge.R-project.org" target="_blank">http://R-Forge.R-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>
suggestion to correct this in my system? This might be the reason<br>
for my<br>
current problem installing phylobase.Raul:~ Milvago$ Make<br>
-bash: Make: command not found<br>
Raul:~ Milvago$<br>
<br>
Should I use installers from Apple Developer Tools package to solve<br>
this<br>
problem. Yes I did install gcc3.3 (but also tried gcc4.0) software<br>
from<br>
the<br>
Xcode Tools /Applications/Installers in my PowerBook.<br>
<br>
Thanks in advance,<br>
<br>
Raul Sedano<br>
<br>
On Wed, Mar 11, 2009 at 4:33 PM, Peter Cowan <<a href="mailto:pdc@berkeley.edu" target="_blank">pdc@berkeley.edu</a>> wrote:<br>
<br>
Raul,<br>
<br>
When you say you installed the compilers in the R-FAQ, which ones do<br>
you<br>
mean? Did you install the tools individually or as the Apple<br>
Developer<br>
Tools package? For the mac the best guide to compliers for R stuff,<br>
is<br>
here:<br>
<br>
<<a href="http://r.research.att.com/tools/" target="_blank">http://r.research.att.com/tools/</a>><br>
<br>
When you open the terminal and run the command "make" what do you get?<br>
<br>
I see:<br>
<br>
Macintosh-7:~ peter$ 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>
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<br>
following<br>
R<br>
"response" suggesting the lack of a Make command. I will appreciate<br>
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:<br>
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/<br>
phylobase'<br>
** Restoring previous<br>
<br>
'/Library/Frameworks/R.framework/Versions/2.8/Resources/library/<br>
phylobase'<br>
<br>
The downloaded packages are in<br>
/private/tmp/RtmpMpRHQe/downloaded_packages<br>
<br>
<br>
<br>
[[alternative HTML version deleted]]<br>
<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>
<br>
<br>
<br>
<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>
________________________________<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>
<br>
<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>
<br>
</blockquote>
<br>
<br>
[[alternative HTML version deleted]]<br>
<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></div></div>
Mark Holder<br>
<br>
<a href="mailto:mtholder@ku.edu" target="_blank">mtholder@ku.edu</a><br>
<a href="http://www.people.ku.edu/~mtholder/" target="_blank">http://www.people.ku.edu/~mtholder/</a><br>
<br>
==============================================<br>
Department of Ecology and Evolutionary Biology<br>
University of Kansas<br>
6031 Haworth Hall<br>
1200 Sunnyside Avenue<br>
Lawrence, Kansas 66045<br>
<br>
lab phone: 785.864.5789<br>
<br>
fax (shared): 785.864.5860<br>
==============================================<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
</blockquote></div><br>