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

cstrato cstrato at aon.at
Tue Jan 26 22:52:55 CET 2010


Dear Kasper, dear Simon,

Thank you both for your help, this was easier than I thought.

Since I had already installed "R-2.10.1.pkg" all I needed to do was:
$ R --arch=x86_64 --no-multiarch CMD INSTALL -l ~/Library/R/2.10/library 
xps_1.7.4.tar.gz
* installing *source* package 'xps' ...
checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... 
none needed
checking how to run the C preprocessor... gcc-4.2 -arch x86_64 -std=gnu99 -E
checking for gcc... (cached) gcc-4.2 -arch x86_64 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... (cached) yes
checking for gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... 
(cached) none needed
found ROOT version 5.24/00 in directory /Users/rabbitus/ROOT/root
** libs
** arch - x86_64

Now xps compiles for 64 bit and starting R with:
$ R --arch=x86_64
I am able to load my package:
 > library(xps)

Welcome to xps version 1.7.4
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2009 by Christian Stratowa


Now one final question remains, which is a question of a user of xps who 
has started the whole discussion since he has compiled ROOT as 64 bit 
and wanted to install xps using:
 > biocLite("xps", type = "source")
I assume that when I start R using "R --arch=x86_64" then every package 
is compiled as 64 bit automatically.

Best regards
Christian



Simon Urbanek wrote:
>
> On Jan 26, 2010, at 15:24 , cstrato wrote:
>
>> Dear Simon,
>>
>> Meanwhile I have tried to install xps:
>> $ R CMD INSTALL -l ~/Library/R/2.10/library xps_1.7.4.tar.gz
>> * installing *source* package 'xps' ...
>> checking for gcc... gcc-4.2 -arch i386 -std=gnu99
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g... yes
>> checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ANSI C... 
>> none needed
>> checking how to run the C preprocessor... gcc-4.2 -arch i386 
>> -std=gnu99 -E
>> checking for gcc... (cached) gcc-4.2 -arch i386 -std=gnu99
>> checking whether we are using the GNU C compiler... (cached) yes
>> checking whether gcc-4.2 -arch i386 -std=gnu99 accepts -g... (cached) 
>> yes
>> checking for gcc-4.2 -arch i386 -std=gnu99 option to accept ANSI C... 
>> (cached) none needed
>> found ROOT version 5.24/00 in directory /Users/rabbitus/ROOT/root
>> ** libs
>> ** arch - i386
>>
>> As you can see it compiles using the wrong architecture:
>
> Well, you're running the wrong architecture ... As I said when you 
> want to link, you have to use 64-bit.
>
>
>> > library(xps)
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared library 
>> '/Users/rabbitus/Library/R/2.10/library/xps/libs/i386/xps.so':
>> dlopen(/Users/rabbitus/Library/R/2.10/library/xps/libs/i386/xps.so, 
>> 6): no suitable image found.  Did find:
>>       /Users/rabbitus/Library/R/2.10/library/xps/libs/i386/xps.so: 
>> mach-o, but wrong architecture
>> Error: package/namespace load failed for 'xps'
>> >
>>
>> In my file "config.in" I have the following lines:
>> # See "Writing R Extensions"
>> : ${R_HOME=`R RHOME`}
>> if test -z "${R_HOME}"; then
>>  echo "could not determine R_HOME"
>>  exit 1
>> fi
>> CC=`"${R_HOME}/bin/R" CMD config CC`
>> CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
>> AC_PROG_CPP
>> AC_PROG_CC
>>
>> Thus I assume that I need to use 64 bit R so that the flags are set 
>> correctly. Is this correct?
>>
>
> You have to use 64-bit R if you want to link to a 64-bit program - as 
> I said.
>
>
>> If yes, can I use: 
>> http://r.research.att.com/R-GUI-5548-2.10-leopard-Leopard64.dmg
>> or do I need to build 64 bit R from source?
>>
>
> Neither - just pick it from CRAN - it's the first download in the 
> list. Note that you still have to run 64-bit R -- e.g. R --arch=x86_64
>
> Cheers,
> Simon
>
>
>
>>
>>
>> Simon Urbanek wrote:
>>> 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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