This is XCode 3.0 with the updated gcc suite from the Apple developer
site. It sure seems to compile an awful lot before hitting this.
I wonder how to make this work with R. R has these 100s of packages,
many of which need to be compiled when installed.
Right now, at least on the Mac, R-2-7 itself supports/contains 4
architectures ( ppc, x86 each 32 and 64 bits ) and the compilers for
c, c++ and fortran need to match for above package installations
(those that need to be compiled). Until recently there were disastrous
bugs in the compilers for 64 bits (and other issues with gcc4.0, e.g.
when fortran was involved).
Sage rc1 seems to include R-2.6.1, this week's R-2.7 release will
replace R-2.6.2.
I have tried gcc-4.0.1 but on my system it will hang forever (might be
related to the broken X11 that ships with Leopard):
gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.3-i386-2.5/
Users/rob/Downloads/sage-3.0.rc1/spkg/build/python-2.5.2/src/Mac/
Modules/launch/_Launchmodule.o -L/Users/rob/Downloads/sage-3.0.rc1/
local/lib -L/usr/local/lib -o build/lib.macosx-10.3-i386-2.5/
_Launch.so -framework ApplicationServices
*** WARNING: renaming "_Launch" since importing it failed:
dlopen(build/lib.macosx-10.3-i386-2.5/_Launch.so, 2): Symbol not
found: __cg_png_create_info_struct
Referenced from: /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/ImageIO
Expected in: /usr/X11R6/lib/libPng.dylib
building '_CG' extension
creating build/temp.macosx-10.3-i386-2.5/Users/rob/Downloads/
sage-3.0.rc1/spkg/build/python-2.5.2/src/Mac/Modules/cg
gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-
madd -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -I/Users/
rob/Downloads/sage-3.0.rc1/spkg/build/python-2.5.2/src/./Include -I/
Users/rob/Downloads/sage-3.0.rc1/spkg/build/python-2.5.2/src/./Mac/
Include -I/Users/rob/Downloads/sage-3.0.rc1/local/include -I. -
IInclude -I./Include -I/usr/local/include -I/Users/rob/Downloads/
sage-3.0.rc1/spkg/build/python-2.5.2/src/Include -I/Users/rob/
Downloads/sage-3.0.rc1/spkg/build/python-2.5.2/src -c /Users/rob/
Downloads/sage-3.0.rc1/spkg/build/python-2.5.2/src/Mac/Modules/cg/
_CGmodule.c -o build/temp.macosx-10.3-i386-2.5/Users/rob/Downloads/
sage-3.0.rc1/spkg/build/python-2.5.2/src/Mac/Modules/cg/_CGmodule.o -
Wno-deprecated-declarations
gcc -bundle -undefined dynamic_lookup build/temp.macosx-10.3-i386-2.5/
Users/rob/Downloads/sage-3.0.rc1/spkg/build/python-2.5.2/src/Mac/
Modules/cg/_CGmodule.o -L/Users/rob/Downloads/sage-3.0.rc1/local/lib -
L/usr/local/lib -o build/lib.macosx-10.3-i386-2.5/_CG.so -framework
ApplicationServices
and it will never finish this step.
My hope is that I can literally use either R.app to work with R and
its libraries and Sage notebooks using the same version of R and
libraries. Maybe the way Sage works with Mathematica?
As MIchael suggested, 3.0.1 stuff!
Rob
On Apr 21, 2008, at 9:54 AM, William Stein wrote:
>
> On Mon, Apr 21, 2008 at 9:31 AM, Rob Goedman <[EMAIL PROTECTED]> wrote:
>> Hi,
>>
>> Brand new to Sage builds!
>>
>> On Mac OS 10.5.2, with:
>>
>> Robs-Intel:sage-3.0.rc0 rob$ gcc -v
>> Using built-in specs.
>> Target: i686-apple-darwin9
>> Configured with: /var/tmp/gcc_42/gcc_42-5531~1/src/configure --
>> disable-
>> checking -enable-werror --prefix=/usr --mandir=/usr/share/man --
>> enable-
>> languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/
>> s/
>> $/-4.2/ --with-gxx-include-dir=/usr/include/c++/4.0.0 --with-
>> slibdir=/
>> usr/lib --build=i686-apple-darwin9 --host=i686-apple-darwin9 --
>> target=i686-apple-darwin9
>> Thread model: posix
>> gcc version 4.2.1 (Apple Inc. build 5531)
> ^^^^^^^^^^^^^^^^^^^
>
> Which version of XCode is this? When did you get it?
> I'm sure your problem is that we haven't ported Sage to work
> with Apple's heavily hacked GCC-4.2.1.
>
> I've been building all my OS X code on all platforms using
> Apples GCC-4.0.1. I wasn't aware that they released GCC-4.2.1.
> My guess is that numerous things will have to be fixed to get
> Sage to build against APPLE-GCC-4.2.1. Your best bet
> is to install a binary or install an older XCode (with GCC-4.0.1)
> or wait until Sage supports GCC-4.2.1, which means 1-2 weeks
> (since obviously I'll upgrade and have to support the newer compiler).
>
> The compiler I use:
> bsd:~ was$ gcc -v
> Using built-in specs.
> Target: i686-apple-darwin9
> Configured with: /var/tmp/gcc/gcc-5465~16/src/configure
> --disable-checking -enable-werror --prefix=/usr --mandir=/share/man
> --enable-languages=c,objc,c++,obj-c++
> --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/
> --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib
> --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic
> --host=i686-apple-darwin9 --target=i686-apple-darwin9
> Thread model: posix
> gcc version 4.0.1 (Apple Inc. build 5465)
> bsd:~ was$
>
>
> -- William
>
>>
>> make gives below (summarized) error on 2.11, alpha6, rc0 and rc1.
>> Below attachment contains the complete rc1 install.log .
>>
>> If, as a quick test, the Mac specific '-fasm-blocks' flag is added in
>> the subdir cipher, make complains about the assembler code in the asm
>> block in poll_padlock.
>>
>> Do I have to disable ENABLE_PADLOCK_SUPPORT? If so, can I force the
>> sage make to use './configure -disable_padlock_support'?
>>
>> As this is not related to the upcoming Sage 3.0 release, I'm fine to
>> wait for a binary release, although ultimately I would like to be
>> able
>> to build sage myself.
>>
>> Thanks,
>> Rob
>>
>> ----------------------------------------------
>>
>> Making all in cipher
>> /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -
>> I. -
>> I.. -I../src -I../src -I/Users/rob/Downloads/sage-3.0.rc0/local/
>> include -I/Users/rob/Downloads/sage-3.0.rc0/local/include -g -O2 -
>> Wall
>> -Wpointer-arith -MT cipher.lo -MD -MP -MF .deps/cipher.Tpo -c -o
>> cipher.lo cipher.c
>> mkdir .libs
>> gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I../src -I/Users/rob/
>> Downloads/sage-3.0.rc0/local/include -I/Users/rob/Downloads/
>> sage-3.0.rc0/local/include -g -O2 -Wall -Wpointer-arith -MT
>> cipher.lo -
>> MD -MP -MF .deps/cipher.Tpo -c cipher.c -fno-common -DPIC -o .libs/
>> cipher.o
>> gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I../src -I/Users/rob/
>> Downloads/sage-3.0.rc0/local/include -I/Users/rob/Downloads/
>> sage-3.0.rc0/local/include -g -O2 -Wall -Wpointer-arith -MT
>> cipher.lo -
>> MD -MP -MF .deps/cipher.Tpo -c cipher.c -o cipher.o >/dev/null 2>&1
>> mv -f .deps/cipher.Tpo .deps/cipher.Plo
>> /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -
>> I. -
>> I.. -I../src -I../src -I/Users/rob/Downloads/sage-3.0.rc0/local/
>> include -I/Users/rob/Downloads/sage-3.0.rc0/local/include -g -O2 -
>> Wall
>> -Wpointer-arith -MT pubkey.lo -MD -MP -MF .deps/pubkey.Tpo -c -o
>> pubkey.lo pubkey.c
>> gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I../src -I/Users/rob/
>> Downloads/sage-3.0.rc0/local/include -I/Users/rob/Downloads/
>> sage-3.0.rc0/local/include -g -O2 -Wall -Wpointer-arith -MT
>> pubkey.lo -
>> MD -MP -MF .deps/pubkey.Tpo -c pubkey.c -fno-common -DPIC -o .libs/
>> pubkey.o
>>
>> ...
>>
>> gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I../src -I/Users/rob/
>> Downloads/sage-3.0.rc0/local/include -I/Users/rob/Downloads/
>> sage-3.0.rc0/local/include -g -O2 -Wall -Wpointer-arith -MT
>> random.lo -
>> MD -MP -MF .deps/random.Tpo -c random.c -fno-common -DPIC -o .libs/
>> random.o
>> gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I../src -I/Users/rob/
>> Downloads/sage-3.0.rc0/local/include -I/Users/rob/Downloads/
>> sage-3.0.rc0/local/include -g -O2 -Wall -Wpointer-arith -MT
>> random.lo -
>> MD -MP -MF .deps/random.Tpo -c random.c -o random.o >/dev/null 2>&1
>> mv -f .deps/random.Tpo .deps/random.Plo
>> /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -
>> I. -
>> I.. -I../src -I../src -I/Users/rob/Downloads/sage-3.0.rc0/local/
>> include -I/Users/rob/Downloads/sage-3.0.rc0/local/include -g -O2 -
>> Wall
>> -Wpointer-arith -MT rndhw.lo -MD -MP -MF .deps/rndhw.Tpo -c -o
>> rndhw.lo rndhw.c
>> gcc -DHAVE_CONFIG_H -I. -I.. -I../src -I../src -I/Users/rob/
>> Downloads/sage-3.0.rc0/local/include -I/Users/rob/Downloads/
>> sage-3.0.rc0/local/include -g -O2 -Wall -Wpointer-arith -MT
>> rndhw.lo -
>> MD -MP -MF .deps/rndhw.Tpo -c rndhw.c -fno-common -DPIC -o .libs/
>> rndhw.o
>> rndhw.c: In function 'poll_padlock':
>> rndhw.c:60: error: asm blocks not enabled, use `-fasm-blocks'
>> rndhw.c:60: error: expected identifier before '(' token
>> rndhw.c:60: confused by earlier errors, bailing out
>> make[4]: *** [rndhw.lo] Error 1
>> make[3]: *** [all-recursive] Error 1
>> make[2]: *** [all] Error 2
>> failed to build libgcrypt
>>
>> real 0m34.193s
>> user 0m17.394s
>> sys 0m14.601s
>> sage: An error occurred while installing libgcrypt-1.4.0.p1
>> Please email sage-devel http://groups.google.com/group/sage-devel
>> explaining the problem and send the relevant part of
>> of /Users/rob/Downloads/sage-3.0.rc0/install.log. Describe your
>> computer, operating system, etc.
>> If you want to try to fix the problem, yourself *don't* just cd to
>> /Users/rob/Downloads/sage-3.0.rc0/spkg/build/libgcrypt-1.4.0.p1 and
>> type 'make'.
>> Instead type "/Users/rob/Downloads/sage-3.0.rc0/sage -sh"
>> in order to set all environment variables correctly, then cd to
>> /Users/rob/Downloads/sage-3.0.rc0/spkg/build/libgcrypt-1.4.0.p1
>> (When you are done debugging, you can type "exit" to leave the
>> subshell.)
>> make[1]: *** [installed/libgcrypt-1.4.0.p1] Error 1
>>
>> real 15m9.941s
>> user 11m47.843s
>> sys 2m35.299s
>>
>> ---------------------------------------------------------------
>>
>>
>>
>>>
>>
>>
>>
>>
>
>
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washington
> http://wstein.org
>
> >
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