Michael Maibaum
2002-Oct-18 19:16 UTC
[R] Building R on Mac OS X-"dumping methods" problem
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I am trying to create a darwinports package for R, but I cannot get R
to compile on Mac OSX 10.2.
I have install g77 which seems fine. R compiles without problems until
it reaches
dumping R code in package 'methods'
Error in .Call("R_initialize_methods_metadata", table, PACKAGE =
"methods") :
.Call function name not in load table
Execution halted
gnumake[4]: *** [../../../library/methods/R/all.rda] Error 1
my configure environment is
FFLAGS="-O3 -funroll-all-loops" LDFLAGS="-L/opt/local/lib/"
\
CPPFLAGS="-I/opt/local/include/"
configure.args --without-gnome --enable-R-shlib
- --mandir='/opt/local/share/man' \
--with-tcl-config=/System/Library/Tcl/8.3/tclConfig.sh \
-C --without-blas
any suggestions? THis is essentially identical to the way fink builds R
so...?
thanks
Michael
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This was an error we had about half a year ago when building R on OS X. Which gcc ? Which R ? Which g77 ? Are you sure you are building from a clean install (not installed over a previous version) ? --- Jan On Friday, October 18, 2002, at 12:16 PM, Michael Maibaum wrote:> -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > I am trying to create a darwinports package for R, but I cannot get R > to compile on Mac OSX 10.2. > > I have install g77 which seems fine. R compiles without problems until > it reaches > > > dumping R code in package 'methods' > Error in .Call("R_initialize_methods_metadata", table, PACKAGE = > "methods") : > .Call function name not in load table > Execution halted > gnumake[4]: *** [../../../library/methods/R/all.rda] Error 1 > > > my configure environment is > FFLAGS="-O3 -funroll-all-loops" LDFLAGS="-L/opt/local/lib/" \ > CPPFLAGS="-I/opt/local/include/" > > configure.args --without-gnome --enable-R-shlib - > --mandir='/opt/local/share/man' \ > --with-tcl-config=/System/Library/Tcl/8.3/tclConfig.sh \ > -C --without-blas > > any suggestions? THis is essentially identical to the way fink builds > R so...? > > thanks > > Michael > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.7 (Darwin) > > iD8DBQE9sF32ilk3LUlIL0MRAoz1AJ9EQbLFSYAWualuWJDiyvGuA9oc1ACgwQLY > 7PQtpox/Dxtw5oN7OLRcMvs> =FzYj > -----END PGP SIGNATURE----- > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > .-.-.-.-.- > r-help mailing list -- Read > http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html > Send "info", "help", or "[un]subscribe" > (in the "body", not the subject !) To: > r-help-request at stat.math.ethz.ch > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ > ._._._._ > >==Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu homepage: http://gifi.stat.ucla.edu ------------------------------------------------------------------------ ------------------------- No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au ------------------------------------------------------------------------ ------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
I don't think I can help debug your problem with specific suggestions, but I can say that a after a default configure R compiles successfully in 10.2. Albeit, with various additional libraries installed from fink (dlcompat readline g77 ncurses pcre bzip2 tcltk atlas) Presumably, then, your problem results from one of the non-default args you have supplied to configure, or perhaps the absence of one of those other packages, or maybe a difference between the darwinports version of one of them and fink's version. I hope this helps at least a little! -Don At 12:16 PM -0700 10/18/02, Michael Maibaum wrote:>-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > > >I am trying to create a darwinports package for R, but I cannot get >R to compile on Mac OSX 10.2. > >I have install g77 which seems fine. R compiles without problems >until it reaches > > >dumping R code in package 'methods' >Error in .Call("R_initialize_methods_metadata", table, PACKAGE = "methods") : > .Call function name not in load table >Execution halted >gnumake[4]: *** [../../../library/methods/R/all.rda] Error 1 > > >my configure environment is > FFLAGS="-O3 -funroll-all-loops" LDFLAGS="-L/opt/local/lib/" \ > CPPFLAGS="-I/opt/local/include/" > >configure.args --without-gnome --enable-R-shlib - >--mandir='/opt/local/share/man' \ > > --with-tcl-config=/System/Library/Tcl/8.3/tclConfig.sh \ > -C --without-blas > >any suggestions? THis is essentially identical to the way fink builds R so...? > >thanks > >Michael >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.0.7 (Darwin) > >iD8DBQE9sF32ilk3LUlIL0MRAoz1AJ9EQbLFSYAWualuWJDiyvGuA9oc1ACgwQLY >7PQtpox/Dxtw5oN7OLRcMvs>=FzYj >-----END PGP SIGNATURE----- > >-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- >r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html >Send "info", "help", or "[un]subscribe" >(in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch >_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._-- -------------------------------------- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA -------------------------------------- -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
I have also had the same problem in trying to get R to build on MacOS X.
dumping R code in package 'methods'
Error in .Call("R_initialize_methods_metadata", table, PACKAGE =
"methods") :
.Call function name not in load table
Execution halted
OS 10.2.1
gcc 3.1 --supplied by apple
g77 GNU Fortran (GCC 3.1 20020420 (prerelease))
./configure --with-aqua --without-x --enable-R-shlib CPPFLAGS=''
which gives
R is now configured for powerpc-apple-darwin6.1
Source directory: .
Installation directory: /usr/local
C compiler: gcc -g -O2
C++ compiler: g++ -g -O2
Fortran compiler: g77 -g -O2
X11 support: no
Gnome support: no
Tcl/Tk support: no
Readline support: no
R profiling support: yes
R as a shared library: yes
Recommended packages: no
I have used a number of differing configurations all without success.
./configure
./configure --with-x
./configure --with-aqua --without-x
I used have darwinports instead of fink to get dlcompat.
I don't think darwinports current has a g77 for instllation. I got mine
from http://gravity.psu.edu/~khanna/g77v3-bin.tar.gz .
I build without atlas or tcltk.
Why do you need to get a curses lib and bzip2, there are already
versions installed in 10.2?
The cvs version of fink for 10.2 always kernel panics my machine during
the apt compile, so I have not been able to use fink.
I had the same error on a solaris box (2.6) which resolved when gcc was
upgraded to 3.3.
-Tom
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I have done some more homework.
I am running macos X 10.2.1 on a G3 700MHz ibook.
Developer tool July 2002 with August update.
I get R by rsync. I have tried all three version released, pathched and
devel and get the same problem with all of them.
If I run nm on methods.so, I get:
$nm methods.so |grep R_initialize
00002db8 T _R_initialize_methods_metadata
It is present but, is the leading underscore significant?
There is no 'ldd' on darwin but otool -L is the same I think. It gives
the same output.
$otool -L methods.so
methods.so:
/usr/local/lib/R/bin/libR.dylib (compatibility version 0.0.0,
current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 60.2.0)
This is a curious result since there is not currently a library at
/usr/local/lib/R/bin/libR.dylib since I have not install yet.
I did do a partial install and it made no difference.
If I look for libraries in R.bin, I get the following result and it
looks OK to me. Likewise it is identical for the dynamic library
libR.dylib. It is finding the dlcompat libdl, using the system ncurses,
libc and libz library.
$otool -L R.bin
R.bin:
/System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
(compatibility version 2.0.0, current version 122.0.0)
/opt/local/lib/libdl.1.dylib (compatibility version 1.0.0,
current version 1.0.0)
/usr/lib/libncurses.5.dylib (compatibility version 5.0.0,
current version 5.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
current version 60.2.0)
/usr/lib/libz.1.1.3.dylib (compatibility version 1.0.0, current
version 1.1.3)
In the R.bin, I looked for Call routine
$nm R.bin|grep Call
00002bd8 T _R_addCallRoutine
00071988 T _R_addTaskCallback
00071624 T _R_getTaskCallbackNames
000715c0 T _R_removeTaskCallback
00071810 T _R_taskCallbackRoutine
000860e8 T _RecordGraphicsCall
000712a4 T _Rf_addTaskCallback
00002c34 T _Rf_freeCallSymbol
000032c8 T _Rf_lookupRegisteredCallSymbol
00071480 T _Rf_removeTaskCallbackByIndex
000713a0 T _Rf_removeTaskCallbackByName
0005544c t _assignCall
00012ccc T _baseCallback
00085038 t _makeErrorCall
0005533c t _replaceCall
Does this look right?
I tested another .Call interface by running R and then loading library
ctest. ansari uses a library call and I got this result for
example(ansari.test).
...
Warning message:
Cannot compute exact p-value with ties in: ansari.test.default(ramsay,
jung.parekh)
Error in .C("pansari", as.integer(length(q)), p = as.double(q),
as.integer(m), :
C/Fortran function name not in load table
Looks like this is not just a problem in metheds.so.
Could the configure process be going wrong? The R.bin seems
to work OK but it cannot load external dynamic libraries.
Regards Tom
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