Dima,
It looks like it is getting set pretty early, so I'm just posting here
the beginning of the install.log, rather than the whole huge file.
But it sounds to me that somehow the problem is that "make clean"
leaves too much behind. For instance, it seems to want to start
building r right away, even though I would think it would start with a
fresh compile.
Jon
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
SAGENB=sagenb-0.8.10
GD=gd-2.0.35.p5
CONWAY=conway_polynomials-0.2
CLIQUER=cliquer-1.2.p7
MANPATH=/usr/share/man:/usr/local/share/man:/Library/TeX/
Distributions/.DefaultT
eX/Contents/Man:/usr/X11/man
READLINE=readline-6.1
JINJA2=jinja2-2.5.5
SAGE_LOGS=/Users/jtyard/test/sage-4.6.1/spkg/logs
PEXPECT=pexpect-2.0.p4
F2C=f2c-20070816.p2
TERM_PROGRAM=Apple_Terminal
MATPLOTLIB=matplotlib-1.0.0.p0
G2RED=genus2reduction-0.3.p8
LIBM4RI=libm4ri-20100701.p1
SAGE_BZIP2=bzip2-1.0.5
TERM=xterm-color
SHELL=/bin/bash
CYTHON=cython-0.13.p1
MAKEFLAGS=
TMPDIR=/var/folders/5g/5gZAKtBmGPW3YZx94BmD3++++TM/-Tmp-/
SQLALCHEMY=sqlalchemy-0.5.8
DOCUTILS=docutils-0.5.p0
Apple_PubSub_Socket_Render=/tmp/launch-GGQ5RD/Render
ZNPOLY=zn_poly-0.9.p5
WEAVE=weave-0.4.9.p0
SYMMETRICA=symmetrica-2.0.p5
GIVARO=givaro-3.2.13rc2.p2
TERM_PROGRAM_VERSION=240.2
SAGETEX=sagetex-2.2.5
MPFR=mpfr-2.4.2
SYMPY=sympy-0.6.4.p0
POLYTOPES_DB=polytopes_db-20100210
OLDPWD=/Users/jtyard/test/sage-4.6.1
EXAMPLES=examples-4.6.1
ATLAS=atlas-3.8.3.p16
PREREQ=prereq-0.7
DIR=dir-0.1
TACHYON=tachyon-0.98beta.p11
SCIPY_SANDBOX=scipy_sandbox-20071020.p7
MPFI=mpfi-1.3.4-cvs20071125.p8
MERCURIAL=mercurial-1.6.4.p0
CDDLIB=cddlib-094f.p8
DOT_SAGE=/Users/jtyard/.sage
ECLIB=eclib-20100711
USER=jtyard
R=r-2.10.1.p4
SPHINX=sphinx-1.0.4.p5
COMMAND_MODE=unix2003
LIBGCRYPT=libgcrypt-1.4.4.p3
CVXOPT=cvxopt-1.1.3
BOEHM_GC=boehm_gc-7.1.p6
TERMCAP=termcap-1.3.1.p1
MPIR=mpir-1.2.2.p2
SSH_AUTH_SOCK=/tmp/launch-Cq1ACl/Listeners
ZODB=zodb3-3.7.0.p4
GRAPHS=graphs-20070722.p1
ICONV=iconv-1.13.1.p3
__CF_USER_TEXT_ENCODING=0x1F6:0:0
ECL=ecl-10.4.1
CEPHES=cephes-2.8
SAGE_LOCAL=/Users/jtyard/test/sage-4.6.1/local
MAKELEVEL=1
SAGE_SCRIPTS=sage_scripts-4.6.1
ECM=ecm-6.2.1.p2
TWISTED=twisted-9.0.p2
RUBIKS=rubiks-20070912.p12
FREETYPE=freetype-2.3.5.p3
MFLAGS=
PYGMENTS=pygments-1.3.1.p0
GAP=gap-4.4.12.p4
PATH=/Users/jtyard/test/sage-4.6.1:/Users/jtyard/test/sage-4.6.1/local/
bin:/User
s/jtyard/sage-4.6:/usr/bin:/bin:/usr/sbin:/sbin:/Users/jtyard:/usr/
local/bin:/us
r/texbin:/usr/X11/bin
IML=iml-1.0.1.p13
LAPACK=lapack-20071123.p2
EXTCODE=extcode-4.6.1
BLAS=blas-20070724
ZLIB=zlib-1.2.5
SINGULAR=singular-3-1-1-4.p3
GNUTLS=gnutls-2.2.1.p5
POLYBORI=polybori-0.6.4.p6
LIBGPG_ERROR=libgpg_error-1.6.p3
PWD=/Users/jtyard/test/sage-4.6.1/spkg
LCALC=lcalc-20100428-1.23.p5
SCONS=scons-1.2.0
LINBOX=linbox-1.1.6.p3
OPENCDK=opencdk-0.6.6.p5
LANG=en_US.UTF-8
FLINTQS=flintqs-20070817.p5
GDMODULE=gdmodule-0.56.p7
SCIPY=scipy-0.8
GFAN=gfan-0.4plus.p1
SAGE_ROOT=/Users/jtyard/test/sage-4.6.1
SAGE=sage-4.6.1
RATPOINTS=ratpoints-2.1.3.p1
NUMPY=numpy-1.5.0
FIDUCIAL_DIRECTORY=/Users/jtyard/fiducials
PARI=pari-2.4.3.alpha.p0
PATCH=patch-2.5.9
GLPK=glpk-4.44
PALP=palp-1.1.p3
SHLVL=4
HOME=/Users/jtyard
PYCRYPTO=pycrypto-2.1.0
GSL=gsl-1.14
PYTHON_GNUTLS=python_gnutls-1.1.4.p7
DROPBOX=/Users/meagenharriman/Dropbox
IPYTHON=ipython-0.9.1.p0
FLINT=flint-1.5.0.p5
PYTHONPATH=/Users/jtyard/test/sage-4.6.1/local
LOGNAME=jtyard
SQLITE=sqlite-3.6.22
MPMATH=mpmath-0.15
NTL=ntl-5.4.2.p12
FORTRAN=fortran-20100629
PIL=pil-1.1.6.p4
SYMPOW=sympow-1.018.1.p8
PYNAC=pynac-0.2.1
MAXIMA=maxima-5.22.1
FPLLL=libfplll-3.0.12.p1
DISPLAY=/tmp/launch-FaNKeD/:0
SETUPTOOLS=setuptools-0.6c9.p0
MOIN=moin-1.9.1.p1
ELLIPTIC_CURVES=elliptic_curves-0.1
BOOST_CROPPED=boost-cropped-1.34.1
SECURITYSESSIONID=26c06c0
PYTHON=python-2.6.4.p9
NETWORKX=networkx-1.2.p1
LIBPNG=libpng-1.2.35.p2
_=/usr/bin/env
***********************************************
/Users/jtyard/test/sage-4.6.1/spkg/pipestatus "sage-spkg $
{SAGE_SPKG_OPTS} r-2.1
0.1.p4 2>&1" "tee -a /Users/jtyard/test/sage-4.6.1/spkg/logs/
r-2.10.1.p4.log"
Warning: Attempted to overwrite SAGE_ROOT environment variable
Detected SAGE64 flag
Building Sage on OS X in 64-bit mode
r-2.10.1.p4
Machine:
Darwin Megatron.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT
2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
Deleting directories from past builds of previous/current versions of
r-2.10.1.p
4
Extracting package /Users/jtyard/test/sage-4.6.1/spkg/standard/
r-2.10.1.p4.spkg
...
-rw-r--r--@ 1 jtyard staff 17013408 Sep 25 16:30 /Users/jtyard/test/
sage-4.6.1
/spkg/standard/r-2.10.1.p4.spkg
Finished extraction
****************************************************
Host system
uname -a:
Darwin Megatron.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT
2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
****************************************************
****************************************************
CC Version
gcc -v
Using built-in specs.
Target: i686-apple-darwin9
Configured with: /var/tmp/gcc/gcc-5493~1/src/configure --disable-
checking -enabl
e-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c+
+,obj-c++
--program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-
dir=/includ
e/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 5493)
****************************************************
Building R 64 bit.
Copying fake java and javac compiler on OSX
Configuring R for OSX
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf...
On Jan 29, 8:39 pm, Dima Pasechnik <dimp...@gmail.com> wrote:
> It would be useful if you put the complete install.log somewhere, so
> that one could see where the 64-bit setting comes from...
>
> On Jan 29, 7:02 am, Jon Yard <jty...@gmail.com> wrote:
>
>
>
>
>
>
>
> > Hello,
>
> > I am having trouble building sage 4.6.1 on an iMac8,1 (2.4 GHz Intel Core 2
> > Duo) running OS X 10.5.8. Below is the last relevant output from the
> > compilation. Any help would be appreciated.
>
> > Thanks,
> > Jon
>
> > gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined
> > dynamic_lookup -single_module -multiply_defined suppress
> > -L/Users/jtyard/sage-4.6.1/local/lib/ -m64 -o grDevices.so chull.o devNull.o
> > devPicTeX.o devPS.o devQuartz.o init.o qdBitmap.o qdPDF.o qdCocoa.o
> > -framework AppKit -L../../../../lib -lR -dylib_file
> > libRblas.dylib:../../../../lib/libRblas.dylib -Wl,-framework
> > -Wl,CoreFoundation
> > ld warning: in qdCocoa.o, file is not of required architecture
> > make[8]: `Makedeps' is up to date.
> > mkdir ../../../../library/grDevices/libs
> > building package 'graphics'
> > mkdir ../../../library/graphics
> > mkdir ../../../library/graphics/R
> > mkdir ../../../library/graphics/po
> > Error in dyn.load(file, DLLpath = DLLpath, ...) :
> > unable to load shared library
> > '/Users/jtyard/sage-4.6.1/spkg/build/r-2.10.1.p4/src/library/grDevices/libs
> > /grDevices.so':
> >
> > dlopen(/Users/jtyard/sage-4.6.1/spkg/build/r-2.10.1.p4/src/library/grDevice
> > s/libs/grDevices.so,
> > 6): Symbol not found: _QuartzCocoa_DeviceCreate
> > Referenced from:
> > /Users/jtyard/sage-4.6.1/spkg/build/r-2.10.1.p4/src/library/grDevices/libs/
> > grDevices.so
> > Expected in: dynamic lookup
> > Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam ->
> > dyn.load
> > Execution halted
> > make[6]: *** [mklazy] Error 1
> > make[5]: *** [all] Error 2
> > make[4]: *** [R] Error 1
> > make[3]: *** [R] Error 1
> > make[2]: *** [R] Error 1
> > Error building R.
>
> > real 3m59.617s
> > user 2m54.940s
> > sys 0m39.710s
> > sage: An error occurred while installing r-2.10.1.p4
> > Please email sage-develhttp://groups.google.com/group/sage-develexplaining
> > the problem and send the relevant part of of
> > /Users/jtyard/sage-4.6.1/install.log. Describe your computer, operating
> > system, etc.
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