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

Simon Urbanek simon.urbanek at r-project.org
Mon Jan 25 23:55:34 CET 2010 

On Jan 25, 2010, at 5:34 PM, cstrato wrote:

> Dear Simon,
> 
> Thank you, with this version I could finally compile ROOT as 64 bit.
> 
> Now I have one more question:
> When I do "R CMD Install xps.tar.gz" which now depends on 64 bit ROOT, do I need to install the 64 bit version of R or can I use the current R version?
> 

I have no idea since I don't know your package. If you *link* to ROOT then yes, you have to use 64-bit R to load 64-bit code. (Linking in itself can be quite interesting given the flags ROOT uses, so your journey may not end there ;)).

Cheers,
Simon



> Best regards
> Christian
> 
> 
> Simon Urbanek wrote:
>> 
>> On Jan 25, 2010, at 15:03 , cstrato wrote:
>> 
>>> 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.
>>> 
>> 
>> Oh ... that's a surprise - it should be there, sorry. Ok, so please use the more recent 5566 build:
>> http://r.research.att.com/tools/gfortran-4.2-5566-darwin9.tar.gz
>> 
>> that one has the x86_64 files - I checked:
>> ginaz:~$ curl -s -S http://r.research.att.com/tools/gfortran-4.2-5566-darwin9.tar.gz | tar fvtz - | grep gfortran.a
>> -rw-r--r-- root/wheel  3592608 2008-12-24 14:51:33 usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortran.a
>> -rw-r--r-- root/wheel  3870032 2008-12-24 14:51:33 usr/lib/gcc/powerpc-apple-darwin9/4.2.1/libgfortran.a
>> -rw-r--r-- root/wheel  5002152 2008-12-24 14:51:33 usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64/libgfortran.a
>> 
>> (Ideally you should install Xcode 3.1.2 for this since that is where the 5566 build comes from, but it will probably work even if the builds don't match perfectly).
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> 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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