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,@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@stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>
>>
>>
>>
>
>
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