[R-SIG-Mac] Which gfortran for Leopard?

Kasper Daniel Hansen khansen at stat.berkeley.edu
Sat Jan 23 16:31:19 CET 2010 

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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