[R-SIG-Mac] Which gfortran for Leopard?
cstrato
cstrato at aon.at
Fri Jan 29 19:49:10 CET 2010
Dear Simon,
As a subscriber to RootTalk I have just received the following mail:
http://root.cern.ch/root/roottalk/roottalk10/0122.html
As you see there are other Mac users of ROOT who do not want to use fink
but another gfortran compiler.
I seems that besides gfortran from your website, the following gfortran
can also be used:
http://www.macresearch.org/gfortran-leopard
My question now is:
Can gfortran from macresearch also be used to compile R 32 bit and 64 bit?
Best regards
Christian
cstrato wrote:
> Dear Kasper, dear Simon,
>
> Thank you both for your help, this was easier than I thought.
>
> Since I had already installed "R-2.10.1.pkg" all I needed to do was:
> $ R --arch=x86_64 --no-multiarch CMD INSTALL -l
> ~/Library/R/2.10/library xps_1.7.4.tar.gz
> * installing *source* package 'xps' ...
> checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
> checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI
> C... none needed
> checking how to run the C preprocessor... gcc-4.2 -arch x86_64
> -std=gnu99 -E
> checking for gcc... (cached) gcc-4.2 -arch x86_64 -std=gnu99
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g...
> (cached) yes
> checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI
> C... (cached) none needed
> found ROOT version 5.24/00 in directory /Users/rabbitus/ROOT/root
> ** libs
> ** arch - x86_64
>
> Now xps compiles for 64 bit and starting R with:
> $ R --arch=x86_64
> I am able to load my package:
> > library(xps)
>
> Welcome to xps version 1.7.4
> an R wrapper for XPS - eXpression Profiling System
> (c) Copyright 2001-2009 by Christian Stratowa
>
>
> Now one final question remains, which is a question of a user of xps
> who has started the whole discussion since he has compiled ROOT as 64
> bit and wanted to install xps using:
> > biocLite("xps", type = "source")
> I assume that when I start R using "R --arch=x86_64" then every
> package is compiled as 64 bit automatically.
>
> Best regards
> Christian
>
>
>
> Simon Urbanek wrote:
>>
>> On Jan 26, 2010, at 15:24 , cstrato wrote:
>>
>>> Dear Simon,
>>>
>>> Meanwhile I have tried to install xps:
>>> $ R CMD INSTALL -l ~/Library/R/2.10/library xps_1.7.4.tar.gz
>>> * installing *source* package 'xps' ...
>>> checking for gcc... gcc-4.2 -arch i386 -std=gnu99
>>> checking for C compiler default output file name... a.out
>>> checking whether the C compiler works... yes
>>> checking whether we are cross compiling... no
>>> checking for suffix of executables...
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g... yes
>>> checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ANSI
>>> C... none needed
>>> checking how to run the C preprocessor... gcc-4.2 -arch i386
>>> -std=gnu99 -E
>>> checking for gcc... (cached) gcc-4.2 -arch i386 -std=gnu99
>>> checking whether we are using the GNU C compiler... (cached) yes
>>> checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g...
>>> (cached) yes
>>> checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ANSI
>>> C... (cached) none needed
>>> found ROOT version 5.24/00 in directory /Users/rabbitus/ROOT/root
>>> ** libs
>>> ** arch - i386
>>>
>>> As you can see it compiles using the wrong architecture:
>>
>> Well, you're running the wrong architecture ... As I said when you
>> want to link, you have to use 64-bit.
>>
>>
>>> > library(xps)
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library
>>> '/Users/rabbitus/Library/R/2.10/library/xps/libs/i386/xps.so':
>>> dlopen(/Users/rabbitus/Library/R/2.10/library/xps/libs/i386/xps.so,
>>> 6): no suitable image found. Did find:
>>> /Users/rabbitus/Library/R/2.10/library/xps/libs/i386/xps.so:
>>> mach-o, but wrong architecture
>>> Error: package/namespace load failed for 'xps'
>>> >
>>>
>>> In my file "config.in" I have the following lines:
>>> # See "Writing R Extensions"
>>> : ${R_HOME=`R RHOME`}
>>> if test -z "${R_HOME}"; then
>>> echo "could not determine R_HOME"
>>> exit 1
>>> fi
>>> CC=`"${R_HOME}/bin/R" CMD config CC`
>>> CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
>>> AC_PROG_CPP
>>> AC_PROG_CC
>>>
>>> Thus I assume that I need to use 64 bit R so that the flags are set
>>> correctly. Is this correct?
>>>
>>
>> You have to use 64-bit R if you want to link to a 64-bit program - as
>> I said.
>>
>>
>>> If yes, can I use:
>>> http://r.research.att.com/R-GUI-5548-2.10-leopard-Leopard64.dmg
>>> or do I need to build 64 bit R from source?
>>>
>>
>> Neither - just pick it from CRAN - it's the first download in the
>> list. Note that you still have to run 64-bit R -- e.g. R --arch=x86_64
>>
>> Cheers,
>> Simon
>>
>>
>>
>>>
>>>
>>> Simon Urbanek wrote:
>>>> On Jan 25, 2010, at 5:34 PM, cstrato wrote:
>>>>
>>>>
>>>>> Dear Simon,
>>>>>
>>>>> Thank you, with this version I could finally compile ROOT as 64 bit.
>>>>>
>>>>> Now I have one more question:
>>>>> When I do "R CMD Install xps.tar.gz" which now depends on 64 bit
>>>>> ROOT, do I need to install the 64 bit version of R or can I use
>>>>> the current R version?
>>>>>
>>>>>
>>>>
>>>> I have no idea since I don't know your package. If you *link* to
>>>> ROOT then yes, you have to use 64-bit R to load 64-bit code.
>>>> (Linking in itself can be quite interesting given the flags ROOT
>>>> uses, so your journey may not end there ;)).
>>>>
>>>> Cheers,
>>>> Simon
>>>>
>>>>
>>>>
>>>>
>>>>> Best regards
>>>>> Christian
>>>>>
>>>>>
>>>>> Simon Urbanek wrote:
>>>>>
>>>>>> On Jan 25, 2010, at 15:03 , cstrato wrote:
>>>>>>
>>>>>>
>>>>>>> Dear Simon,
>>>>>>>
>>>>>>> Thank you for your suggestions, which I have just tried. Sadly
>>>>>>> the error remains the same.
>>>>>>>
>>>>>>> The problem seems to be that for some reason
>>>>>>> "gfortran-4.2-5564-darwin9.tar.gz" does not have a
>>>>>>> "/usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64" directory
>>>>>>> containing libgfortranbegin.a. For this reason the 64 bit
>>>>>>> version of libgfortranbegin.a is not installed in the
>>>>>>> corresponding directory x86_64 which contains only libgcc.a etc.
>>>>>>>
>>>>>>>
>>>>>> Oh ... that's a surprise - it should be there, sorry. Ok, so
>>>>>> please use the more recent 5566 build:
>>>>>> http://r.research.att.com/tools/gfortran-4.2-5566-darwin9.tar.gz
>>>>>>
>>>>>> that one has the x86_64 files - I checked:
>>>>>> ginaz:~$ curl -s -S
>>>>>> http://r.research.att.com/tools/gfortran-4.2-5566-darwin9.tar.gz
>>>>>> | tar fvtz - | grep gfortran.a
>>>>>> -rw-r--r-- root/wheel 3592608 2008-12-24 14:51:33
>>>>>> usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortran.a
>>>>>> -rw-r--r-- root/wheel 3870032 2008-12-24 14:51:33
>>>>>> usr/lib/gcc/powerpc-apple-darwin9/4.2.1/libgfortran.a
>>>>>> -rw-r--r-- root/wheel 5002152 2008-12-24 14:51:33
>>>>>> usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64/libgfortran.a
>>>>>>
>>>>>> (Ideally you should install Xcode 3.1.2 for this since that is
>>>>>> where the 5566 build comes from, but it will probably work even
>>>>>> if the builds don't match perfectly).
>>>>>>
>>>>>> Cheers,
>>>>>> Simon
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> You can see this by double-clicking on
>>>>>>> "gfortran-4.2-5564-darwin9.tar.gz" when located in some directory.
>>>>>>>
>>>>>>> In contrast, "gfortran-4.2.3.dmg" did install libgfortranbegin.a
>>>>>>> in the "/usr/local/lib/gcc/i686-apple-darwin9/4.2.1/x86_64"
>>>>>>> directory.
>>>>>>>
>>>>>>> Could you please check or tell me what the reason might be?
>>>>>>>
>>>>>>> I have installed it using:
>>>>>>> $ gunzip gfortran-4.2-5564-darwin9.tar.gz
>>>>>>> $ sudo tar -xvf gfortran-4.2-5564-darwin9.tar -C /
>>>>>>>
>>>>>>> Best regards
>>>>>>> Christian
>>>>>>>
>>>>>>>
>>>>>>> Simon Urbanek wrote:
>>>>>>>
>>>>>>>> On Jan 24, 2010, at 3:28 PM, cstrato wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Dear Kasper,
>>>>>>>>>
>>>>>>>>> You are right. Since ROOT supports the CC, CXX, F77 and LD
>>>>>>>>> flags I did:
>>>>>>>>> ./configure macosx64 --with-cxx="/usr/bin/g++-4.2 -arch
>>>>>>>>> x86_64" --with-f77="/usr/bin/gfortran-4.2 -arch x86_64"
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> You don't really need the override - it works without and they
>>>>>>>> add -m64 anyway so the -arch gets essentially ignored.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> The error was still the same:
>>>>>>>>> i686-apple-darwin9-g++-4.2.1: libgfortran.dylib: No such file
>>>>>>>>> or directory
>>>>>>>>>
>>>>>>>>> However, when I replaced in the Makefile.macosx64:
>>>>>>>>> F77LIBS := $(shell $(F77) -m64
>>>>>>>>> -print-file-name=libgfortran.dylib)
>>>>>>>>> F77LIBS += $(shell $(F77) -m64
>>>>>>>>> -print-file-name=libgfortranbegin.a)
>>>>>>>>> with:
>>>>>>>>> F77LIBS := $(shell $(F77) -m64
>>>>>>>>> -print-file-name=libgfortranbegin.a)
>>>>>>>>>
>>>>>>>>>
>>>>>>>> You found the right spot but your fix is wrong - just remove
>>>>>>>> the two lines, they are superfluous and only cause trouble.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> the error disappeared, and I could finish the compilation.
>>>>>>>>>
>>>>>>>>> However, now I got a link-error:
>>>>>>>>> ld warning: in
>>>>>>>>> /usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortranbegin.a, file
>>>>>>>>> is not of required architecture
>>>>>>>>> Undefined symbols:
>>>>>>>>> "_main", referenced from:
>>>>>>>>> start in crt1.10.5.o
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> Your'e getting the 32-bit version (of the wrong file - see
>>>>>>>> above). It should really be ../4.2.1/x86_64/lib...
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> I am not sure what this error means since Makefile.macosx64
>>>>>>>>> contains:
>>>>>>>>> F77FLAGS = -m64 -std=legacy
>>>>>>>>>
>>>>>>>>> Could it be that libgfortranbegin.a can only be used for 32bit
>>>>>>>>> compilation?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> No, you're picking the wrong one - there is one for each
>>>>>>>> architecture.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Furthermore, I still have the question (and hopefully Simon
>>>>>>>>> will answer it):
>>>>>>>>> Why does gfortran-4.2-5564-darwin9.tar.gz not contain any
>>>>>>>>> libgfortran.dylib files?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> Because it's using a static library.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Interestingly, when googling "/usr/lib/libgfortran.dylib" I
>>>>>>>>> get the answer that NO results were found, while googling
>>>>>>>>> "/usr/local/lib/libgfortran.dylib" gives many results. Thus it
>>>>>>>>> seems that there will never be any libgfortran.dylib in
>>>>>>>>> "/usr/lib/"!?
>>>>>>>>>
>>>>>>>>>
>>>>>>>> Nope - OS X has no Fortran by default.
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Simon
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> I must admit that I do not understand this issue.
>>>>>>>>>
>>>>>>>>> Best regards
>>>>>>>>> Christian
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Kasper Daniel Hansen wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> On Jan 23, 2010, at 8:37 AM, cstrato wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Dear Kasper,
>>>>>>>>>>>
>>>>>>>>>>> Thank you for your suggestion, I did indeed use gcc 4.0.
>>>>>>>>>>> Since gcc_select does no longer exist on Leopard I had to do:
>>>>>>>>>>> cd /usr/bin
>>>>>>>>>>> sudo ln -s gcc-4.2 gcc
>>>>>>>>>>> sudo ln -s g++-4.2 g++
>>>>>>>>>>> sudo ln -s gcov-4.2 gcov
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> I am not sure this is advisable in general. When I compile
>>>>>>>>>> stuff with gcc-4.2 I usually explicitly set
>>>>>>>>>> CC=/usr/bin/gcc-4.2
>>>>>>>>>> when I run configure. For example, my entire configure line
>>>>>>>>>> for R on my macbook is
>>>>>>>>>> ../${SRCDIR}/configure SHELL='/bin/bash' \
>>>>>>>>>> CC="/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99" \
>>>>>>>>>> CFLAGS="-g -O2 -std=gnu99 -march=nocona" \
>>>>>>>>>> CXX="/usr/bin/g++-4.2 -arch x86_64" \
>>>>>>>>>> CXXFLAGS="-g -O2 -march=nocona" \
>>>>>>>>>> OBJC="/usr/bin/gcc-4.2 -arch x86_64" \
>>>>>>>>>> F77="/usr/bin/gfortran-4.2 -arch x86_64" \
>>>>>>>>>> FFLAGS="-g -O2 -march=nocona" \
>>>>>>>>>> FC="/usr/bin/gfortran-4.2 -arch x86_64" \
>>>>>>>>>> FCFLAGS="-g -O2 -march=nocona" \
>>>>>>>>>> --x-includes=/usr/X11/include
>>>>>>>>>> --x-libraries=/usr/X11/lib \
>>>>>>>>>> --with-system-zlib \
>>>>>>>>>> --with-blas='-framework vecLib' --with-lapack
>>>>>>>>>> Of course this requires that ROOT uses the CC/CFLAGS macros,
>>>>>>>>>> but that should be pretty standard if it uses autoconf.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Sadly, compiling ROOT resulted still in the same error:
>>>>>>>>>>> i686-apple-darwin9-g++-4.2.1: libgfortran.dylib: No such
>>>>>>>>>>> file or directory
>>>>>>>>>>>
>>>>>>>>>>> When I check the location for gfortran-4.2.3.dmg I get:
>>>>>>>>>>> $ cd
>>>>>>>>>>> /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../../x86_64
>>>>>>>>>>> $ ls -al
>>>>>>>>>>> total 32
>>>>>>>>>>> drwxrwxr-x 6 root wheel 204 Jan 21 20:26 .
>>>>>>>>>>> drwxr-xr-x 35 root wheel 1190 Jan 21 20:26 ..
>>>>>>>>>>> lrwxr-xr-x 1 root wheel 26 Jan 21 20:26
>>>>>>>>>>> libgfortran.2.0.0.dylib -> ../libgfortran.2.0.0.dylib
>>>>>>>>>>> lrwxr-xr-x 1 root wheel 23 Jan 21 20:26
>>>>>>>>>>> libgfortran.2.dylib -> libgfortran.2.0.0.dylib
>>>>>>>>>>> lrwxr-xr-x 1 root wheel 16 Jan 21 20:26 libgfortran.a
>>>>>>>>>>> -> ../libgfortran.a
>>>>>>>>>>> lrwxr-xr-x 1 root wheel 23 Jan 21 20:26
>>>>>>>>>>> libgfortran.dylib -> libgfortran.2.0.0.dylib
>>>>>>>>>>>
>>>>>>>>>>> This means that /usr/local/bin does contain
>>>>>>>>>>> libgfortran.dylib whereas /usr/bin does not contain any of
>>>>>>>>>>> these files or links.
>>>>>>>>>>> Does this mean that gfortran-4.2.3.dmg does contain these
>>>>>>>>>>> file for libgfortran.dylib while
>>>>>>>>>>> gfortran-4.2-5564-darwin9.tar.gz does not contain these files?
>>>>>>>>>>> How do I get libgfortran.dylib?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> Simon might be able to answer this better, but the general
>>>>>>>>>> idea is that the
>>>>>>>>>>
>>>>>>>>>>> gfortran-4.2-5564-darwin9.tar.gz
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> installs into /usr/bin
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> gfortran-4.2.3.dmg
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> installs into /usr/local/bin. There is some logic here, the
>>>>>>>>>> way I think about it is that the former is a direct extension
>>>>>>>>>> of the Apple build.
>>>>>>>>>>
>>>>>>>>>> I would start from scratch, which means remove all traces of
>>>>>>>>>> both gfortrans, install the 5564-tarball and then set the
>>>>>>>>>> various macros as I have set it above for R (your exact
>>>>>>>>>> values may of course be different depending on what machine
>>>>>>>>>> etc. you are using).
>>>>>>>>>>
>>>>>>>>>> Kasper
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> BTW, I must apologize to Simon. On his website he lists the
>>>>>>>>>>> commands how to install gfortran.tar.gz, but in the Tiger
>>>>>>>>>>> section, so I did miss it. Nevertheless it would still be
>>>>>>>>>>> helpful for Mac users to know how to uninstall it:
>>>>>>>>>>> $ tar -tf gfortran.tar | sort -r | (cd /; xargs -p -n 1 rm -d)
>>>>>>>>>>>
>>>>>>>>>>> Best regards
>>>>>>>>>>> Christian
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Kasper Daniel Hansen wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Remember that Apple has two version of GCC on Leopard: 4.0
>>>>>>>>>>>> and 4.2. You are using 4.0, you might want to switch to
>>>>>>>>>>>> 4.2. In Tiger there used to be gcc_select (or select_gcc)
>>>>>>>>>>>> that let you choose between 3.x and 4.0, I don't remember
>>>>>>>>>>>> if that is still around on Leopard.
>>>>>>>>>>>>
>>>>>>>>>>>> The error seems to indicate that you need 4.2 in order to
>>>>>>>>>>>> use Simon's gfortran.
>>>>>>>>>>>>
>>>>>>>>>>>> Kasper
>>>>>>>>>>>>
>>>>>>>>>>>> On Jan 22, 2010, at 16:04 PM, cstrato wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Dear Simon,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for this information.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Now I have installed gfortran-4.2-5564-darwin9.tar.gz on
>>>>>>>>>>>>> Leopard and tried to compile ROOT again, but this time I
>>>>>>>>>>>>> got the following error:
>>>>>>>>>>>>> g++ -dynamiclib -single_module -undefined dynamic_lookup
>>>>>>>>>>>>> -install_name @rpath/libminicern.so -O2 -m64 -o
>>>>>>>>>>>>> lib/libminicern.so misc/minicern/src/cernlib.o -ldl
>>>>>>>>>>>>> misc/minicern/src/hbook.o misc/minicern/src/kernlib.o
>>>>>>>>>>>>> misc/minicern/src/zebra.o libgfortran.dylib
>>>>>>>>>>>>> /usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortranbegin.a
>>>>>>>>>>>>> i686-apple-darwin9-g++-4.0.1: libgfortran.dylib: No such
>>>>>>>>>>>>> file or directory
>>>>>>>>>>>>>
>>>>>>>>>>>>> I know that this is not necessarily an R-related question
>>>>>>>>>>>>> but I would greatly appreciate your help if possible (at
>>>>>>>>>>>>> least it is a Mac- and somehow a BioC-related question).
>>>>>>>>>>>>>
>>>>>>>>>>>>> When I have tried to compile ROOT with gfortran-4.2.3.dmg
>>>>>>>>>>>>> I got the following error:
>>>>>>>>>>>>> gfortran -O2 -m64 -o bin/g2root main/src/g2root.o -Llib
>>>>>>>>>>>>> lib/libminicern.so
>>>>>>>>>>>>> /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../../x86_64/libgfortran.dylib
>>>>>>>>>>>>> /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64/libgfortranbegin.a
>>>>>>>>>>>>> -lm -Wl,-rpath, at loader_path/../lib -pthread -ldl
>>>>>>>>>>>>> ld: -rpath can only be used when targeting Mac OS X 10.5
>>>>>>>>>>>>> or later
>>>>>>>>>>>>>
>>>>>>>>>>>>> As you can see gfortran-4.2.3 could find libgfortran.dylib
>>>>>>>>>>>>> at:
>>>>>>>>>>>>> /usr/local/lib/gcc/i686-apple-darwin8/4.2.3/../../../x86_64/libgfortran.dylib
>>>>>>>>>>>>> while gfortran-4.2.4 could not find libgfortran.dylib.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thus maybe I did make a mistake when installing
>>>>>>>>>>>>> gfortran-4.2.4. Here is what I did:
>>>>>>>>>>>>> $ gunzip gfortran-4.2-5564-darwin9.tar.gz
>>>>>>>>>>>>> $ sudo tar -xvf gfortran-4.2-5564-darwin9.tar -C /
>>>>>>>>>>>>> $ sudo ln -s /usr/bin/gfortran-4.2 /usr/bin/gfortran
>>>>>>>>>>>>>
>>>>>>>>>>>>> Do you know what I need to do so that libgfortran.dylib
>>>>>>>>>>>>> can be found?
>>>>>>>>>>>>>
>>>>>>>>>>>>> P.S.:Since many Mac users are no Unix experts please allow
>>>>>>>>>>>>> me to suggest to place on your website the commands to
>>>>>>>>>>>>> install/uninstall gfortran. I have found the following
>>>>>>>>>>>>> website, which told me how to install gfortran and how I
>>>>>>>>>>>>> could uninstall it:
>>>>>>>>>>>>> http://www.webmo.net/support/fortran_osx.html
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you in advance.
>>>>>>>>>>>>> Best regards
>>>>>>>>>>>>> Christian
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Simon Urbanek wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Jan 21, 2010, at 15:56 , cstrato wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Dear Simon,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> One more question:
>>>>>>>>>>>>>>> I have just unzipped gfortran-4.2-5564-darwin9.tar.gz.
>>>>>>>>>>>>>>> The version gives:
>>>>>>>>>>>>>>> Using built-in specs.
>>>>>>>>>>>>>>> Target: i686-apple-darwin9
>>>>>>>>>>>>>>> Configured with:
>>>>>>>>>>>>>>> /Builds/gcc/gcc_42-5564/build/obj/src/configure
>>>>>>>>>>>>>>> --disable-checking --enable-werror --prefix=/usr
>>>>>>>>>>>>>>> --mandir=/usr/share/man
>>>>>>>>>>>>>>> --enable-languages=c,objc,c++,obj-c++,fortran
>>>>>>>>>>>>>>> --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/
>>>>>>>>>>>>>>> --with-gxx-include-dir=/usr/include/c++/4.0.0
>>>>>>>>>>>>>>> --with-slibdir=/usr/lib --build=i686-apple-darwin9
>>>>>>>>>>>>>>> --host=i686-apple-darwin9 --target=i686-apple-darwin9
>>>>>>>>>>>>>>> Thread model: posix
>>>>>>>>>>>>>>> gcc version 4.2.1 (Apple Inc. build 5564)
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> This means that this version seems to be older than the
>>>>>>>>>>>>>>> one I am using now?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> No, that is GNU Fortran 4.2.4 that I was referring to.
>>>>>>>>>>>>>> The "gcc version 4.2.1" comes from Apple's Xcode 3.1
>>>>>>>>>>>>>> gcc-4.2 branch since that is what they define - it just
>>>>>>>>>>>>>> adds Fortran support to the existing gcc 4.2.1 branch of
>>>>>>>>>>>>>> Apple that you installed as Xcode. However, the Fortran
>>>>>>>>>>>>>> part is merged from the GNU Fortran 4.2.4 release - hence
>>>>>>>>>>>>>> I refer to it as 4.2.4.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>> Simon
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Simon Urbanek wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Jan 21, 2010, at 14:47 , cstrato wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Dear all,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I have the following problem:
>>>>>>>>>>>>>>>>> My Bioconductor package xps requires both R and ROOT,
>>>>>>>>>>>>>>>>> whereby I compile ROOT usually from source. Until now
>>>>>>>>>>>>>>>>> this has not been a problem since I do all my
>>>>>>>>>>>>>>>>> development on Tiger. However, now I wanted to compile
>>>>>>>>>>>>>>>>> ROOT on Leopard but failed since my gfortran compiler
>>>>>>>>>>>>>>>>> is too old, see:
>>>>>>>>>>>>>>>>> http://root.cern.ch/phpBB2/viewtopic.php?t=9721&sid=003b01ddb64f33dbe0c74651ee089c34
>>>>>>>>>>>>>>>>> To solve the problem I should upgrade to the latest
>>>>>>>>>>>>>>>>> version coming with gcc-4.4 in Fink.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I would advise against that - using gcc from Fink
>>>>>>>>>>>>>>>> usually calls for a disaster. The real solution is to
>>>>>>>>>>>>>>>> fix their flags, but that's another story ...
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thus my question is:
>>>>>>>>>>>>>>>>> Can I also use this version for R or do I need to use
>>>>>>>>>>>>>>>>> the version downloaded from att?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I would recommend using the Leopard gfortran 4.2.4 for
>>>>>>>>>>>>>>>> Xcode 3.1.x from the Mac devel page
>>>>>>>>>>>>>>>> http://r.research.att.com/tools/
>>>>>>>>>>>>>>>> which I assume is what you meant by the latter.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>> Simon
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>>>> R-SIG-Mac at stat.math.ethz.ch
>>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>
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