[Phylobase-devl] [R-sig-phylo] Phylobase 0.4 Forge (installing issues in my old G4 powerBook)
Brian O'Meara
bcomeara at nescent.org
Fri Mar 13 05:03:55 CET 2009
This error seems to have come up with another package (gee), and the
solution is setting an environmental variable. See thread at https://stat.ethz.ch/pipermail/r-sig-mac/2008-October/005450.html
>. Basically do Sys.setenv("MACOSX_DEPLOYMENT_TARGET"="10.4") so that
it targets 10.4 rather than 10.1.
Brian
On Mar 12, 2009, at 10:41 PM, Raul Sedano wrote:
> 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]]
>
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>
>
>
>
>
>
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>
>
> ________________________________
> Brian O'Meara
> NESCent
> Durham, NC
> http://www.brianomeara.info
> ________________________________
>
>
>
>
>
>
> ________________________________
> Brian O'Meara
> NESCent
> Durham, NC
> http://www.brianomeara.info
> ________________________________
>
>
>
>
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