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,@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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