[R-SIG-Mac] [Rd] R 2.5.0 MAC OS X version
Weiwei Shi
helprhelp at gmail.com
Tue Jul 3 06:57:48 CEST 2007
Hi, there:
I am re-compiling Package supclust for some small modification for my
own purpose. After running "R CMD check", I got the following
messenge:
nicebaby:~/Documents/projects/R_customerized_packages wshi$ R CMD check supclust
* checking for working latex ...sh: line 1: latex: command not found
NO
* using log directory
'/Users/wshi/Documents/projects/R_customerized_packages/supclust.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'supclust/DESCRIPTION' ... OK
* this is package 'supclust' version '1.0-5'
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory 'supclust/src' contains object files.
* checking whether package 'supclust' can be installed ... ERROR
Installation failed.
See '/Users/wshi/Documents/projects/R_customerized_packages/supclust.Rcheck/00install.out'
for details.
The first one is about latex, I am going to install from office
tomorrow since my home internet is really slow to download that one;
The second is a warning about the source, and I am not sure how to
find the detailed warning messege;
The third one is the most serious one; check the detail and I found I
did not have
libgfortran.dylib and libgcc_s.10.4.dylib;
so I installed gfortran 4.2, as shown below:
nicebaby:~/Documents/projects/R_customerized_packages wshi$ gfortran --version
GNU Fortran (GCC) 4.2.0
Copyright (C) 2007 Free Software Foundation, Inc.
GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING
But splotlight still does not help me find the two files above;
So my third quesiton actually is, how to solve the problem. (For the
same slow internet reason, my xcode tool is still at 2.2.0 version.
But I assume it is not related since 2.4.0 might not include gfortran
either.
My mac os/x is 10.4.9
Please help!
Thanks,
Weiwei
On 5/30/07, Simon Urbanek <simon.urbanek at r-project.org> wrote:
> On May 30, 2007, at 10:44 AM, Recai Yucel wrote:
>
> > Right. I thought the problems might be obvious enough for MAC
> > users, probably not!
>
> How can "the problems" be obvious when most Mac users don't have
> any? ;) If it was that obvious, why would you ask? The answer would
> be on the list already...
>
>
> > I was mistaken with the GNU Fortran version, it is 4.0 as seen below.
>
> Not really, run gfortran --version to find out.
>
>
> > A specific example where I had problems is given below:
> >
> > When I try to install a package called lmm (which was installed
> > with no problem with the previous versions of R), I get the
> > following messages, specifically on the make, chmod, etc.
> >
>
> Just out of curiosity, why don't you just install it from CRAN in
> binary form as suggested? Just type in R: install.packages("lmm")
> That works without problems and saves you all the hassle...
>
> If you really insist on re-compiling the package yourself (you didn't
> even tell us what you are really doing), make sure you have all the
> necessary tools (Xcode 2.4.1 and GNU Fortran from the R distribution
> - see also http://r.research.att.com/tools/ ). From the output it
> appears as if your Fortran installation is broken.
>
> Cheers,
> Simon
>
>
> > *************************************
> > trying URL 'http://cran.us.r-project.org/src/contrib/lmm_0.3-4.tar.gz'
> > Content type 'application/x-tar' length 31471 bytes
> > opened URL
> > ==================================================
> > downloaded 30Kb
> >
> > WARNING: ignoring environment value of R_HOME
> > tar: Read 4096 bytes from -
> > * Installing *source* package 'lmm' ...
> > ** libs
> > ** arch - i386
> > gfortran-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> > -fPIC -g -O2 -march=nocona -c lmm.f -o lmm.o
> > gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -
> > dynamiclib
> > -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup
> > -single_module -multiply_defined suppress -L/usr/local/lib -o lmm.so
> > lmm.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.0 -lgfortran
> > -lgcc_s.10.4 -F/Library/Frameworks/R.framework/.. -framework R
> > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> > object: /usr/local/lib/libgfortran.dylib malformed object (unknown
> > load
> > command 4)
> > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> > object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown
> > load command 4)
> > ** arch - ppc
> > gfortran-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> > -fPIC -g -O2 -c lmm.f -o lmm.o
> > make: *** [lmm.so] Error 1
> > chmod:
> > /Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm/
> > libs/i386/*:
> > No such file or directory
> > gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99
> > -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup
> > -single_module -multiply_defined suppress -L/usr/local/lib -o lmm.so
> > lmm.o -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.0 -lgfortran
> > -lgcc_s.10.4 -lSystemStubs -F/Library/Frameworks/R.framework/..
> > -framework R
> >
> > The downloaded packages are in
> > /private/tmp/Rtmpe4c9Of/downloaded_packages
> > ** Removing
> > '/Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm'
> > ** Restoring previous
> > '/Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm'
> > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> > object: /usr/local/lib/libgfortran.dylib malformed object (unknown
> > load
> > command 4)
> > /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> > object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown
> > load command 4)
> > make: *** [lmm.so] Error 1
> > chmod:
> > /Library/Frameworks/R.framework/Versions/2.5/Resources/library/lmm/
> > libs/ppc/*:
> > No such file or directory
> > ERROR: compilation failed for package 'lmm'
> > *************************************
> >
> >
> >
> > Prof Brian Ripley wrote:
> >> And beyond that good advice, the mailing list for MacOS issues is
> >> R-sig-mac.
> >>
> >> Are you really using 'GNU Fortran 4.2.0' (which was released well
> >> after R 2.5.0), or some pre-release of it? Such details do matter.
> >>
> >>
> >> On Wed, 30 May 2007, Roy Mendelssohn wrote:
> >>
> >>> Hi Recal:
> >>>
> >>> To save you from some possible flames, it would probably help if you
> >>> describe what the problems are, with specific examples and some of
> >>> the relevant error messages. It would be difficult to for someone to
> >>> know if they are seeing similar problems without knowing what the
> >>> problems are.
> >>>
> >>> I believe such information is in the posting guides, which do
> >>> contain
> >>> good information on how to frame a question to the mail list that
> >>> will elicit useful responses.
> >>>
> >>> -Roy
> >>>
> >>>
> >>>
> >>>
> >>> On May 30, 2007, at 7:08 AM, Recai Yucel wrote:
> >>>
> >>>> Please accept my apologies if this was addressed before, I could
> >>>> not
> >>>> find any solution so I am posting my question here.
> >>>>
> >>>> I am having a lot of difficulties with installing and developing R
> >>>> packages with the latest version of R 2.5.0. I am using a MacBook
> >>>> Pro. I
> >>>> never had these problems with the previous versions of R. I
> >>>> think part
> >>>> of the problem is caused by the GNU Fortran 4.2.0 or my lack of
> >>>> knowledge...
> >>>>
> >>>> If anybody else had similar problems and found the solution, please
> >>>> let
> >>>> me know.
> >>>>
> >>>> Best.
> >>>>
> >>>> --
> >>>> Recai Yucel, Ph.D.
> >>>> Assistant Professor of Biostatistics
> >>>> Biostatistics and Epidemiology
> >>>> UMASS-Amherst
> >>
> >
> > --
> > Recai Yucel, Ph.D.
> > Assistant Professor of Biostatistics
> > Biostatistics and Epidemiology
> > UMASS-Amherst
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>
> _______________________________________________
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>
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
"Did you always know?"
"No, I did not. But I believed..."
---Matrix III
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