[R-SIG-Mac] Which gfortran for Leopard?
Simon Urbanek
simon.urbanek at r-project.org
Tue Jan 26 22:23:43 CET 2010
On Jan 26, 2010, at 15:57 , Kasper Daniel Hansen wrote:
> On Jan 26, 2010, at 15:24 PM, 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:
>>> 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?
>
> This is probably because you are using the CRAN binary which is a
> universal binary. Specifically this means that it will try to
> compile the package for all architectures,
Nope - see above - it has a configure. He's simply running the wrong
architecture. With the proper binary
R --arch=x86_64 CMD INSTALL ...
will do the trick.
Cheers,
Simon
> which will fail because ROOT is only installed for one of the
> architectures. This will happen for any package with C code you
> install from source, try picking your favorite R package with C code
> (say, preprocessCore), set options(pkgType = "source") and install
> it using biocLite. You will see several compilation runs.
>
> There are a hack to fix this, and there may be an official way to
> compile a package only for a specific architecture, which I don't
> know about.
>
> The hack: inside (this is for 2.11)
> /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/exec/
> you will see a list of subdirectories describing what architecture
> you have R compiled for. If you remove all the other architectures
> aside from x86_64 it might work. This might mess up your R.app
> though.
>
> Alternatively you could compile R from source, only for one
> architecture. This is what I do.
>
> Kasper
>
>
>> 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?
>>
>> Best regards
>> Christian
>>
>>
>> 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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