[R-SIG-Mac] Which gfortran for Leopard?
cstrato
cstrato at aon.at
Sat Jan 23 14:37:47 CET 2010
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
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?
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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