Re: [R-SIG-Mac] Which gfortran for Leopard?
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
Re: [R-SIG-Mac] Which gfortran for Leopard?
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:
Re: [R-SIG-Mac] Which gfortran for Leopard?
On Jan 26, 2010, at 15:24 PM, 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:
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?
This is probably because you are using the CRAN binary which is a universal
binary. Specifically this means that it will try to compile the package for
all architectures, which will fail because ROOT is only installed for one of
the architectures. This will happen for any package with C code you install
from source, try picking your favorite R package with C code (say,
preprocessCore), set options(pkgType = source) and install it using biocLite.
You will see several compilation runs.
There are a hack to fix this, and there may be an official way to compile a
package only for a specific architecture, which I don't know about.
The hack: inside (this is for 2.11)
/Library/Frameworks/R.framework/Versions/2.11/Resources/bin/exec/
you will see a list of subdirectories describing what architecture you have R
compiled for. If you remove all the other architectures aside from x86_64 it
might work. This might mess up your R.app though.
Alternatively you could compile R from source, only for one architecture. This
is what I do.
Kasper
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
Re: [R-SIG-Mac] Which gfortran for Leopard?
Hmm, I forgot about --arch. As Simon said, you should be able to do it by
R --arch=x86_64 --no-multiarch CMD INSTALL
My guess is that you need --no-multiarch, but I cannot experiment with this
where I sit.
Kasper
On Jan 26, 2010, at 15:57 PM, Kasper Daniel Hansen wrote:
On Jan 26, 2010, at 15:24 PM, 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:
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?
This is probably because you are using the CRAN binary which is a universal
binary. Specifically this means that it will try to compile the package for
all architectures, which will fail because ROOT is only installed for one of
the architectures. This will happen for any package with C code you install
from source, try picking your favorite R package with C code (say,
preprocessCore), set options(pkgType = source) and install it using
biocLite. You will see several compilation runs.
There are a hack to fix this, and there may be an official way to compile a
package only for a specific architecture, which I don't know about.
The hack: inside (this is for 2.11)
/Library/Frameworks/R.framework/Versions/2.11/Resources/bin/exec/
you will see a list of subdirectories describing what architecture you have R
compiled for. If you remove all the other architectures aside from x86_64 it
might work. This might mess up your R.app though.
Alternatively you could compile R from source, only for one architecture.
This is what I do.
Kasper
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
[R-SIG-Mac] Failed compile of cshapes package
Dear all, I have been submitting more recent versions of my cshapes package to CRAN. Whereas version 0.1-1 compiled just fine, all subsequent releases failed to do so, but only under OS X: http://cran.r-project.org/web/checks/check_results_cshapes.html This is weird, because * the example that triggered the OS X compilation error was not changed between 0.1-1 and now * this example has also been excluded from testing (using Not run:) Any suggestions of what I could do? Thanks! Nils -- Nils B. Weidmann Woodrow Wilson School Princeton University http://nils.weidmann.ws ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Which gfortran for Leopard?
On Jan 26, 2010, at 15:57 , Kasper Daniel Hansen wrote:
On Jan 26, 2010, at 15:24 PM, 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:
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?
This is probably because you are using the CRAN binary which is a
universal binary. Specifically this means that it will try to
compile the package for all architectures,
Nope - see above - it has a configure. He's simply running the wrong
architecture. With the proper binary
R --arch=x86_64 CMD INSTALL ...
will do the trick.
Cheers,
Simon
which will fail because ROOT is only installed for one of the
architectures. This will happen for any package with C code you
install from source, try picking your favorite R package with C code
(say, preprocessCore), set options(pkgType = source) and install
it using biocLite. You will see several compilation runs.
There are a hack to fix this, and there may be an official way to
compile a package only for a specific architecture, which I don't
know about.
The hack: inside (this is for 2.11)
/Library/Frameworks/R.framework/Versions/2.11/Resources/bin/exec/
you will see a list of subdirectories describing what architecture
you have R compiled for. If you remove all the other architectures
aside from x86_64 it might work. This might mess up your R.app
though.
Alternatively you could compile R from source, only for one
architecture. This is what I do.
Kasper
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
Re: [R-SIG-Mac] Which gfortran for Leopard?
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
Re: [R-SIG-Mac] Failed compile of cshapes package
On Jan 26, 2010, at 16:19 , Nils B. Weidmann wrote: Dear all, I have been submitting more recent versions of my cshapes package to CRAN. Whereas version 0.1-1 compiled just fine, all subsequent releases failed to do so, but only under OS X: http://cran.r-project.org/web/checks/check_results_cshapes.html This is weird, because * the example that triggered the OS X compilation error was not changed between 0.1-1 and now The issue is that you compiled it with too high target: java.lang.UnsupportedClassVersionError: Bad version number in .class file We only support JDK 1.5. Please use -target 1.5 when compiling your class files (they seem to not require 1.6 at all). * this example has also been excluded from testing (using Not run:) No, it's not -- the Not run is just your comment, it has no influence on the examples. Any suggestions of what I could do? See above. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
