[R-SIG-Mac] Which gfortran for Leopard?
cstrato
cstrato at aon.at
Mon Jan 25 23:34:35 CET 2010
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?
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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