[R-SIG-Mac] Which gfortran for Leopard?
cstrato
cstrato at aon.at
Mon Jan 25 21:03:27 CET 2010
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.
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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