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:
> 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?
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?
Best regards
Christian
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,@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
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