[R-SIG-Mac] Which gfortran for Leopard?
cstrato
cstrato at aon.at
Sun Jan 24 21:28:11 CET 2010
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"
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 $(F77) -m64 -print-file-name=libgfortranbegin.a)
the error disappeared, and I could finish the compilation.
However, now I got a link-error:
ld warning: in /usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortranbegin.a,
file is not of required architecture
Undefined symbols:
"_main", referenced from:
start in crt1.10.5.o
I am not sure what this error means since Makefile.macosx64 contains:
F77FLAGS = -m64 -std=legacy
Could it be that libgfortranbegin.a can only be used for 32bit compilation?
Furthermore, I still have the question (and hopefully Simon will answer it):
Why does gfortran-4.2-5564-darwin9.tar.gz not contain any
libgfortran.dylib files?
Interestingly, when googling "/usr/lib/libgfortran.dylib" I get the
answer that NO results were found, while googling
"/usr/local/lib/libgfortran.dylib" gives many results. Thus it seems
that there will never be any libgfortran.dylib in "/usr/lib/"!? I must
admit that I do not understand this issue.
Best regards
Christian
Kasper Daniel Hansen wrote:
> On Jan 23, 2010, at 8:37 AM, cstrato wrote:
>
>
>> Dear Kasper,
>>
>> Thank you for your suggestion, I did indeed use gcc 4.0.
>> Since gcc_select does no longer exist on Leopard I had to do:
>> cd /usr/bin
>> sudo ln -s gcc-4.2 gcc
>> sudo ln -s g++-4.2 g++
>> sudo ln -s gcov-4.2 gcov
>>
>
> I am not sure this is advisable in general. When I compile stuff with gcc-4.2 I usually explicitly set
> CC=/usr/bin/gcc-4.2
> when I run configure. For example, my entire configure line for R on my macbook is
> ../${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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
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>>>> R-SIG-Mac at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>>
>>>
>>>
>
>
>
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