Which gfortran for Leopard?

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