configure on mac

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configure on mac

Roger Koenker-2
I'm having trouble making yesterday's R-devel on my macs.

./configure seems fine, but eventually in make I get:

gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -L/
usr/local/lib -install_name libR.dylib -compatibility_version 2.4.0  -
current_version 2.4.0  -headerpad_max_install_names -o libR.dylib  
Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o  
RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o  
builtin.o character.o coerce.o colors.o complex.o connections.o  
context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o  
dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o  
eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o  
identical.o internet.o iosupport.o lapack.o list.o localecharset.o  
logic.o main.o mapply.o match.o memory.o model.o names.o objects.o  
optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o  
plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o  
qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o  
scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o  
startup.o subassign.o subscript.o subset.o summary.o sysutils.o  
unique.o util.o version.o vfonts.o xxxpr.o   `ls ../appl/*.o ../nmath/
*.o ../unix/*.o  2>/dev/null|grep -v /ext-` -framework vecLib -
lgfortran -lgcc_s -lSystemStubs -lmx -lSystem  ../extra/zlib/
libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  -lintl -
liconv -Wl,-framework -Wl,CoreFoundation -lreadline  -lm -liconv
/usr/bin/libtool: unknown option character `m' in: -macosx_version_min
Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile
[,dirname]] [-arch_only arch] [-sacLT]
Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile
[,dirname]] [-arch_only arch] [-o output] [-install_name name] [-
compatibility_version #] [-current_version #] [-seg1addr 0x#] [-
segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-seg_addr_table  
<filename>] [-seg_addr_table_filename <file_system_path>] [-all_load]  
[-noall_load]
make[3]: *** [libR.dylib] Error 1
make[2]: *** [R] Error 2
make[1]: *** [R] Error 1
make: *** [R] Error 1

This was ok  as of my last build which was:

 > version
                _
platform       powerpc-apple-darwin8.7.0
arch           powerpc
os             darwin8.7.0
system         powerpc, darwin8.7.0
status         Under development (unstable)
major          2
minor          4.0
year           2006
month          07
day            28
svn rev        38710
language       R
version.string R version 2.4.0 Under development (unstable)  
(2006-07-28 r38710)

url:    www.econ.uiuc.edu/~roger                Roger Koenker
email   [hidden email]                       Department of Economics
vox:    217-333-4558                            University of Illinois
fax:    217-244-6678                            Champaign, IL 61820

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Re: configure on mac

Prof Brian Ripley
I gather you need to update your Xtools: others have had similar problems.
(If they are online you will no doubt get more complete information.)

On Sat, 12 Aug 2006, roger koenker wrote:

> I'm having trouble making yesterday's R-devel on my macs.
>
> ./configure seems fine, but eventually in make I get:
>
> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
> dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -L/
> usr/local/lib -install_name libR.dylib -compatibility_version 2.4.0  -
> current_version 2.4.0  -headerpad_max_install_names -o libR.dylib  
> Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o  
> RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o  
> builtin.o character.o coerce.o colors.o complex.o connections.o  
> context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o  
> dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o  
> eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o  
> identical.o internet.o iosupport.o lapack.o list.o localecharset.o  
> logic.o main.o mapply.o match.o memory.o model.o names.o objects.o  
> optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o  
> plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o  
> qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o  
> scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o  
> startup.o subassign.o subscript.o subset.o summary.o sysutils.o  
> unique.o util.o version.o vfonts.o xxxpr.o   `ls ../appl/*.o ../nmath/
> *.o ../unix/*.o  2>/dev/null|grep -v /ext-` -framework vecLib -
> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem  ../extra/zlib/
> libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  -lintl -
> liconv -Wl,-framework -Wl,CoreFoundation -lreadline  -lm -liconv
> /usr/bin/libtool: unknown option character `m' in: -macosx_version_min
> Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile
> [,dirname]] [-arch_only arch] [-sacLT]
> Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile
> [,dirname]] [-arch_only arch] [-o output] [-install_name name] [-
> compatibility_version #] [-current_version #] [-seg1addr 0x#] [-
> segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-seg_addr_table  
> <filename>] [-seg_addr_table_filename <file_system_path>] [-all_load]  
> [-noall_load]
> make[3]: *** [libR.dylib] Error 1
> make[2]: *** [R] Error 2
> make[1]: *** [R] Error 1
> make: *** [R] Error 1
>
> This was ok  as of my last build which was:
>
>  > version
>                 _
> platform       powerpc-apple-darwin8.7.0
> arch           powerpc
> os             darwin8.7.0
> system         powerpc, darwin8.7.0
> status         Under development (unstable)
> major          2
> minor          4.0
> year           2006
> month          07
> day            28
> svn rev        38710
> language       R
> version.string R version 2.4.0 Under development (unstable)  
> (2006-07-28 r38710)
>
> url:    www.econ.uiuc.edu/~roger                Roger Koenker
> email   [hidden email]                       Department of Economics
> vox:    217-333-4558                            University of Illinois
> fax:    217-244-6678                            Champaign, IL 61820
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: configure on mac

Robert Gentleman
Hi,
  I think Simon and Stefano are both off line for a little while. I can
confirm that an upgrade of Xcode to either 2.3 or the very recent 2.4 is
needed in most cases, either seems to work so probably 2.4 is the better
choice.

   best wishes
     Robert


Prof Brian Ripley wrote:

> I gather you need to update your Xtools: others have had similar problems.
> (If they are online you will no doubt get more complete information.)
>
> On Sat, 12 Aug 2006, roger koenker wrote:
>
>> I'm having trouble making yesterday's R-devel on my macs.
>>
>> ./configure seems fine, but eventually in make I get:
>>
>> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
>> dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -L/
>> usr/local/lib -install_name libR.dylib -compatibility_version 2.4.0  -
>> current_version 2.4.0  -headerpad_max_install_names -o libR.dylib  
>> Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o  
>> RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o  
>> builtin.o character.o coerce.o colors.o complex.o connections.o  
>> context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o  
>> dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o  
>> eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o  
>> identical.o internet.o iosupport.o lapack.o list.o localecharset.o  
>> logic.o main.o mapply.o match.o memory.o model.o names.o objects.o  
>> optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o  
>> plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o  
>> qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o  
>> scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o  
>> startup.o subassign.o subscript.o subset.o summary.o sysutils.o  
>> unique.o util.o version.o vfonts.o xxxpr.o   `ls ../appl/*.o ../nmath/
>> *.o ../unix/*.o  2>/dev/null|grep -v /ext-` -framework vecLib -
>> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem  ../extra/zlib/
>> libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  -lintl -
>> liconv -Wl,-framework -Wl,CoreFoundation -lreadline  -lm -liconv
>> /usr/bin/libtool: unknown option character `m' in: -macosx_version_min
>> Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile
>> [,dirname]] [-arch_only arch] [-sacLT]
>> Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile
>> [,dirname]] [-arch_only arch] [-o output] [-install_name name] [-
>> compatibility_version #] [-current_version #] [-seg1addr 0x#] [-
>> segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-seg_addr_table  
>> <filename>] [-seg_addr_table_filename <file_system_path>] [-all_load]  
>> [-noall_load]
>> make[3]: *** [libR.dylib] Error 1
>> make[2]: *** [R] Error 2
>> make[1]: *** [R] Error 1
>> make: *** [R] Error 1
>>
>> This was ok  as of my last build which was:
>>
>>  > version
>>                 _
>> platform       powerpc-apple-darwin8.7.0
>> arch           powerpc
>> os             darwin8.7.0
>> system         powerpc, darwin8.7.0
>> status         Under development (unstable)
>> major          2
>> minor          4.0
>> year           2006
>> month          07
>> day            28
>> svn rev        38710
>> language       R
>> version.string R version 2.4.0 Under development (unstable)  
>> (2006-07-28 r38710)
>>
>> url:    www.econ.uiuc.edu/~roger                Roger Koenker
>> email   [hidden email]                       Department of Economics
>> vox:    217-333-4558                            University of Illinois
>> fax:    217-244-6678                            Champaign, IL 61820
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>

--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
[hidden email]

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Re: configure on mac

stefano iacus
In reply to this post by Roger Koenker-2
Hi Roger,
due to latest change in the build scripts, you need to get the latest  
apple dev tools to correctly build r-devel. In particular, libtool  
needs to be updated. This is contained in the latest apple dev (XCode  
2.3 as other mentioned) on apple developer web site.
stefano

On 12/ago/06, at 18:56, roger koenker wrote:

> I'm having trouble making yesterday's R-devel on my macs.
>
> ./configure seems fine, but eventually in make I get:
>
> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined
> dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -L/
> usr/local/lib -install_name libR.dylib -compatibility_version 2.4.0  -
> current_version 2.4.0  -headerpad_max_install_names -o libR.dylib
> Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o
> RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o
> builtin.o character.o coerce.o colors.o complex.o connections.o
> context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o
> dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o
> eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o
> identical.o internet.o iosupport.o lapack.o list.o localecharset.o
> logic.o main.o mapply.o match.o memory.o model.o names.o objects.o
> optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o
> plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o
> qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o
> scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o
> startup.o subassign.o subscript.o subset.o summary.o sysutils.o
> unique.o util.o version.o vfonts.o xxxpr.o   `ls ../appl/*.o ../nmath/
> *.o ../unix/*.o  2>/dev/null|grep -v /ext-` -framework vecLib -
> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem  ../extra/zlib/
> libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  -lintl -
> liconv -Wl,-framework -Wl,CoreFoundation -lreadline  -lm -liconv
> /usr/bin/libtool: unknown option character `m' in: -macosx_version_min
> Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile
> [,dirname]] [-arch_only arch] [-sacLT]
> Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile
> [,dirname]] [-arch_only arch] [-o output] [-install_name name] [-
> compatibility_version #] [-current_version #] [-seg1addr 0x#] [-
> segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-seg_addr_table
> <filename>] [-seg_addr_table_filename <file_system_path>] [-all_load]
> [-noall_load]
> make[3]: *** [libR.dylib] Error 1
> make[2]: *** [R] Error 2
> make[1]: *** [R] Error 1
> make: *** [R] Error 1
>
> This was ok  as of my last build which was:
>
>> version
>                 _
> platform       powerpc-apple-darwin8.7.0
> arch           powerpc
> os             darwin8.7.0
> system         powerpc, darwin8.7.0
> status         Under development (unstable)
> major          2
> minor          4.0
> year           2006
> month          07
> day            28
> svn rev        38710
> language       R
> version.string R version 2.4.0 Under development (unstable)
> (2006-07-28 r38710)
>
> url:    www.econ.uiuc.edu/~roger                Roger Koenker
> email   [hidden email]                       Department of  
> Economics
> vox:    217-333-4558                            University of Illinois
> fax:    217-244-6678                            Champaign, IL 61820
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: configure on mac

RKoenker
Yes,  upgrading to Xcode 2.4  worked perfectly.  Thanks to all.

url:    www.econ.uiuc.edu/~roger            Roger Koenker
email    [hidden email]            Department of Economics
vox:     217-333-4558                University of Illinois
fax:       217-244-6678                Champaign, IL 61820


On Aug 14, 2006, at 8:07 AM, stefano iacus wrote:

> Hi Roger,
> due to latest change in the build scripts, you need to get the  
> latest apple dev tools to correctly build r-devel. In particular,  
> libtool needs to be updated. This is contained in the latest apple  
> dev (XCode 2.3 as other mentioned) on apple developer web site.
> stefano
>
> On 12/ago/06, at 18:56, roger koenker wrote:
>
>> I'm having trouble making yesterday's R-devel on my macs.
>>
>> ./configure seems fine, but eventually in make I get:
>>
>> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined
>> dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib  
>> -L/
>> usr/local/lib -install_name libR.dylib -compatibility_version  
>> 2.4.0  -
>> current_version 2.4.0  -headerpad_max_install_names -o libR.dylib
>> Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o
>> RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o
>> builtin.o character.o coerce.o colors.o complex.o connections.o
>> context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o
>> dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o
>> eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o
>> identical.o internet.o iosupport.o lapack.o list.o localecharset.o
>> logic.o main.o mapply.o match.o memory.o model.o names.o objects.o
>> optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o
>> plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o
>> qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o
>> scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o
>> startup.o subassign.o subscript.o subset.o summary.o sysutils.o
>> unique.o util.o version.o vfonts.o xxxpr.o   `ls ../appl/*.o ../
>> nmath/
>> *.o ../unix/*.o  2>/dev/null|grep -v /ext-` -framework vecLib -
>> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem  ../extra/zlib/
>> libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  -lintl -
>> liconv -Wl,-framework -Wl,CoreFoundation -lreadline  -lm -liconv
>> /usr/bin/libtool: unknown option character `m' in: -
>> macosx_version_min
>> Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile
>> [,dirname]] [-arch_only arch] [-sacLT]
>> Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile
>> [,dirname]] [-arch_only arch] [-o output] [-install_name name] [-
>> compatibility_version #] [-current_version #] [-seg1addr 0x#] [-
>> segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-seg_addr_table
>> <filename>] [-seg_addr_table_filename <file_system_path>] [-all_load]
>> [-noall_load]
>> make[3]: *** [libR.dylib] Error 1
>> make[2]: *** [R] Error 2
>> make[1]: *** [R] Error 1
>> make: *** [R] Error 1
>>
>> This was ok  as of my last build which was:
>>
>>> version
>>                 _
>> platform       powerpc-apple-darwin8.7.0
>> arch           powerpc
>> os             darwin8.7.0
>> system         powerpc, darwin8.7.0
>> status         Under development (unstable)
>> major          2
>> minor          4.0
>> year           2006
>> month          07
>> day            28
>> svn rev        38710
>> language       R
>> version.string R version 2.4.0 Under development (unstable)
>> (2006-07-28 r38710)
>>
>> url:    www.econ.uiuc.edu/~roger                Roger Koenker
>> email   [hidden email]                       Department of  
>> Economics
>> vox:    217-333-4558                            University of  
>> Illinois
>> fax:    217-244-6678                            Champaign, IL 61820
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>

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Re: configure on mac

RKoenker
My prior message now seems a bit premature.  R seemed fine and, for
example, installed my package SparseM without complaint, but  now
trying to install  quantreg or Matrix, I'm getting:

gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -L/
usr/local/lib -o quantreg.so akj.o boot.o bound.o boundc.o chlfct.o  
cholesky.o dsel05.o extract.o kuantile.o mcmb.o penalty.o qrcens.o  
rls.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o sparskit2.o srqfn.o  
srqfnc.o srtpai.o xlapack.o -L/Library/Frameworks/R.framework/
Resources/lib -lRblas -L/usr/local/lib/gcc/powerpc-apple-
darwin8/4.0.0 -L/usr/local/lib/gcc -lgfortran -lgcc_s -lSystemStubs -
lmx -lSystem -F/Library/Frameworks/R.framework/.. -framework R
ld: multiple definitions of symbol __gfortran_filename
/Library/Frameworks/R.framework/Resources/lib/libRblas.dylib(single  
module) definition of __gfortran_filename
/usr/local/lib/libgfortran.a(error.o) definition of  
__gfortran_filename in section (__DATA,__data)
ld: multiple definitions of symbol __gfortran_line
/Library/Frameworks/R.framework/Resources/lib/libRblas.dylib(single  
module) definition of __gfortran_line
.
.
.
/usr/bin/libtool: internal link edit command failed
make: *** [quantreg.so] Error 1
ERROR: compilation failed for package 'quantreg'

Any further suggestions would be very welcome.

Roger

url:    www.econ.uiuc.edu/~roger            Roger Koenker
email    [hidden email]            Department of Economics
vox:     217-333-4558                University of Illinois
fax:       217-244-6678                Champaign, IL 61820


On Aug 14, 2006, at 8:15 AM, roger koenker wrote:

> Yes,  upgrading to Xcode 2.4  worked perfectly.  Thanks to all.
>
> url:    www.econ.uiuc.edu/~roger            Roger Koenker
> email    [hidden email]            Department of Economics
> vox:     217-333-4558                University of Illinois
> fax:       217-244-6678                Champaign, IL 61820
>
>
> On Aug 14, 2006, at 8:07 AM, stefano iacus wrote:
>
>> Hi Roger,
>> due to latest change in the build scripts, you need to get the  
>> latest apple dev tools to correctly build r-devel. In particular,  
>> libtool needs to be updated. This is contained in the latest apple  
>> dev (XCode 2.3 as other mentioned) on apple developer web site.
>> stefano
>>
>> On 12/ago/06, at 18:56, roger koenker wrote:
>>
>>> I'm having trouble making yesterday's R-devel on my macs.
>>>
>>> ./configure seems fine, but eventually in make I get:
>>>
>>> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined
>>> dynamic_lookup -single_module -multiply_defined suppress -L/sw/
>>> lib -L/
>>> usr/local/lib -install_name libR.dylib -compatibility_version  
>>> 2.4.0  -
>>> current_version 2.4.0  -headerpad_max_install_names -o libR.dylib
>>> Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o
>>> RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o
>>> builtin.o character.o coerce.o colors.o complex.o connections.o
>>> context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o
>>> dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o
>>> eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o
>>> identical.o internet.o iosupport.o lapack.o list.o localecharset.o
>>> logic.o main.o mapply.o match.o memory.o model.o names.o objects.o
>>> optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o
>>> plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o
>>> qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o
>>> scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o
>>> startup.o subassign.o subscript.o subset.o summary.o sysutils.o
>>> unique.o util.o version.o vfonts.o xxxpr.o   `ls ../appl/*.o ../
>>> nmath/
>>> *.o ../unix/*.o  2>/dev/null|grep -v /ext-` -framework vecLib -
>>> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem  ../extra/zlib/
>>> libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  -lintl -
>>> liconv -Wl,-framework -Wl,CoreFoundation -lreadline  -lm -liconv
>>> /usr/bin/libtool: unknown option character `m' in: -
>>> macosx_version_min
>>> Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile
>>> [,dirname]] [-arch_only arch] [-sacLT]
>>> Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile
>>> [,dirname]] [-arch_only arch] [-o output] [-install_name name] [-
>>> compatibility_version #] [-current_version #] [-seg1addr 0x#] [-
>>> segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-
>>> seg_addr_table
>>> <filename>] [-seg_addr_table_filename <file_system_path>] [-
>>> all_load]
>>> [-noall_load]
>>> make[3]: *** [libR.dylib] Error 1
>>> make[2]: *** [R] Error 2
>>> make[1]: *** [R] Error 1
>>> make: *** [R] Error 1
>>>
>>> This was ok  as of my last build which was:
>>>
>>>> version
>>>                 _
>>> platform       powerpc-apple-darwin8.7.0
>>> arch           powerpc
>>> os             darwin8.7.0
>>> system         powerpc, darwin8.7.0
>>> status         Under development (unstable)
>>> major          2
>>> minor          4.0
>>> year           2006
>>> month          07
>>> day            28
>>> svn rev        38710
>>> language       R
>>> version.string R version 2.4.0 Under development (unstable)
>>> (2006-07-28 r38710)
>>>
>>> url:    www.econ.uiuc.edu/~roger                Roger Koenker
>>> email   [hidden email]                       Department of  
>>> Economics
>>> vox:    217-333-4558                            University of  
>>> Illinois
>>> fax:    217-244-6678                            Champaign, IL 61820
>>>
>>> ______________________________________________
>>> [hidden email] mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>

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Re: configure on mac

stefano iacus
It seems that there are symbols defined in more than one header. This  
causes problems on mac. You should define the symbol in one header  
and declare elsewhere as extern. You can find examples in main.c (if  
I remember well).
I'm not sure this is the problems, but it looks like
stefano

On 14/ago/06, at 18:36, roger koenker wrote:

> My prior message now seems a bit premature.  R seemed fine and, for
> example, installed my package SparseM without complaint, but  now
> trying to install  quantreg or Matrix, I'm getting:
>
> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
> dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -
> L/usr/local/lib -o quantreg.so akj.o boot.o bound.o boundc.o  
> chlfct.o cholesky.o dsel05.o extract.o kuantile.o mcmb.o penalty.o  
> qrcens.o rls.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o sparskit2.o  
> srqfn.o srqfnc.o srtpai.o xlapack.o -L/Library/Frameworks/
> R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/powerpc-
> apple-darwin8/4.0.0 -L/usr/local/lib/gcc -lgfortran -lgcc_s -
> lSystemStubs -lmx -lSystem -F/Library/Frameworks/R.framework/.. -
> framework R
> ld: multiple definitions of symbol __gfortran_filename
> /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib(single  
> module) definition of __gfortran_filename
> /usr/local/lib/libgfortran.a(error.o) definition of  
> __gfortran_filename in section (__DATA,__data)
> ld: multiple definitions of symbol __gfortran_line
> /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib(single  
> module) definition of __gfortran_line
> .
> .
> .
> /usr/bin/libtool: internal link edit command failed
> make: *** [quantreg.so] Error 1
> ERROR: compilation failed for package 'quantreg'
>
> Any further suggestions would be very welcome.
>
> Roger
>
> url:    www.econ.uiuc.edu/~roger            Roger Koenker
> email    [hidden email]            Department of Economics
> vox:     217-333-4558                University of Illinois
> fax:       217-244-6678                Champaign, IL 61820
>
>
> On Aug 14, 2006, at 8:15 AM, roger koenker wrote:
>
>> Yes,  upgrading to Xcode 2.4  worked perfectly.  Thanks to all.
>>
>> url:    www.econ.uiuc.edu/~roger            Roger Koenker
>> email    [hidden email]            Department of Economics
>> vox:     217-333-4558                University of Illinois
>> fax:       217-244-6678                Champaign, IL 61820
>>
>>
>> On Aug 14, 2006, at 8:07 AM, stefano iacus wrote:
>>
>>> Hi Roger,
>>> due to latest change in the build scripts, you need to get the  
>>> latest apple dev tools to correctly build r-devel. In particular,  
>>> libtool needs to be updated. This is contained in the latest  
>>> apple dev (XCode 2.3 as other mentioned) on apple developer web  
>>> site.
>>> stefano
>>>
>>> On 12/ago/06, at 18:56, roger koenker wrote:
>>>
>>>> I'm having trouble making yesterday's R-devel on my macs.
>>>>
>>>> ./configure seems fine, but eventually in make I get:
>>>>
>>>> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined
>>>> dynamic_lookup -single_module -multiply_defined suppress -L/sw/
>>>> lib -L/
>>>> usr/local/lib -install_name libR.dylib -compatibility_version  
>>>> 2.4.0  -
>>>> current_version 2.4.0  -headerpad_max_install_names -o libR.dylib
>>>> Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o
>>>> RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o
>>>> builtin.o character.o coerce.o colors.o complex.o connections.o
>>>> context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o
>>>> dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o
>>>> eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o
>>>> identical.o internet.o iosupport.o lapack.o list.o localecharset.o
>>>> logic.o main.o mapply.o match.o memory.o model.o names.o objects.o
>>>> optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o
>>>> plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o
>>>> qsort.o random.o regex.o registration.o relop.o rlocale.o  
>>>> saveload.o
>>>> scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o
>>>> startup.o subassign.o subscript.o subset.o summary.o sysutils.o
>>>> unique.o util.o version.o vfonts.o xxxpr.o   `ls ../appl/*.o ../
>>>> nmath/
>>>> *.o ../unix/*.o  2>/dev/null|grep -v /ext-` -framework vecLib -
>>>> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem  ../extra/zlib/
>>>> libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  -lintl -
>>>> liconv -Wl,-framework -Wl,CoreFoundation -lreadline  -lm -liconv
>>>> /usr/bin/libtool: unknown option character `m' in: -
>>>> macosx_version_min
>>>> Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile
>>>> [,dirname]] [-arch_only arch] [-sacLT]
>>>> Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile
>>>> [,dirname]] [-arch_only arch] [-o output] [-install_name name] [-
>>>> compatibility_version #] [-current_version #] [-seg1addr 0x#] [-
>>>> segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-
>>>> seg_addr_table
>>>> <filename>] [-seg_addr_table_filename <file_system_path>] [-
>>>> all_load]
>>>> [-noall_load]
>>>> make[3]: *** [libR.dylib] Error 1
>>>> make[2]: *** [R] Error 2
>>>> make[1]: *** [R] Error 1
>>>> make: *** [R] Error 1
>>>>
>>>> This was ok  as of my last build which was:
>>>>
>>>>> version
>>>>                 _
>>>> platform       powerpc-apple-darwin8.7.0
>>>> arch           powerpc
>>>> os             darwin8.7.0
>>>> system         powerpc, darwin8.7.0
>>>> status         Under development (unstable)
>>>> major          2
>>>> minor          4.0
>>>> year           2006
>>>> month          07
>>>> day            28
>>>> svn rev        38710
>>>> language       R
>>>> version.string R version 2.4.0 Under development (unstable)
>>>> (2006-07-28 r38710)
>>>>
>>>> url:    www.econ.uiuc.edu/~roger                Roger Koenker
>>>> email   [hidden email]                       Department of  
>>>> Economics
>>>> vox:    217-333-4558                            University of  
>>>> Illinois
>>>> fax:    217-244-6678                            Champaign, IL 61820
>>>>
>>>> ______________________________________________
>>>> [hidden email] mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>
>

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Re: configure on mac

Prof Brian Ripley
On Tue, 15 Aug 2006, stefano iacus wrote:

> It seems that there are symbols defined in more than one header. This  
> causes problems on mac. You should define the symbol in one header  
> and declare elsewhere as extern. You can find examples in main.c (if  
> I remember well).
> I'm not sure this is the problems, but it looks like

One of the reasons given by Simon for this change was that was no longer
a problem: see the last sentence of

    o   MacOS X 10.3 and higher now use two-level namespaces, single
        module in a shared library and allow undefined symbols to be
        resolved at run-time. This implies that common symbols are now
        allowed in package libraries.

What apparently is a problem is having the same entry point in multiple
dynamic libraries (we have had to deal with LSAME, NEWS item two up).  I
think this means that having arranged specially to satisfy symbols on
MacOS, we now need to change it, so in src/extra/blas/Makefile.in

Rblas_la_LIBADD = @RBLAS_LDFLAGS@ @DYLIB_UNDEFINED_ALLOWED_FALSE@ $(FLIBS)

'@DYLIB_UNDEFINED_ALLOWED_FALSE@' needs to be '#'.

and we may then need to link against $(FLIBS) elsewhere.

We need Simon's input: to the rest of us the ever-increasing number of
ways that MacOS needs special pampering is a mystery.

> stefano
>
> On 14/ago/06, at 18:36, roger koenker wrote:
>
> > My prior message now seems a bit premature.  R seemed fine and, for
> > example, installed my package SparseM without complaint, but  now
> > trying to install  quantreg or Matrix, I'm getting:
> >
> > gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
> > dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -
> > L/usr/local/lib -o quantreg.so akj.o boot.o bound.o boundc.o  
> > chlfct.o cholesky.o dsel05.o extract.o kuantile.o mcmb.o penalty.o  
> > qrcens.o rls.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o sparskit2.o  
> > srqfn.o srqfnc.o srtpai.o xlapack.o -L/Library/Frameworks/
> > R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/powerpc-
> > apple-darwin8/4.0.0 -L/usr/local/lib/gcc -lgfortran -lgcc_s -
> > lSystemStubs -lmx -lSystem -F/Library/Frameworks/R.framework/.. -
> > framework R
> > ld: multiple definitions of symbol __gfortran_filename
> > /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib(single  
> > module) definition of __gfortran_filename
> > /usr/local/lib/libgfortran.a(error.o) definition of  
> > __gfortran_filename in section (__DATA,__data)
> > ld: multiple definitions of symbol __gfortran_line
> > /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib(single  
> > module) definition of __gfortran_line
> > .
> > .
> > .
> > /usr/bin/libtool: internal link edit command failed
> > make: *** [quantreg.so] Error 1
> > ERROR: compilation failed for package 'quantreg'
> >
> > Any further suggestions would be very welcome.
> >
> > Roger
> >
> > url:    www.econ.uiuc.edu/~roger            Roger Koenker
> > email    [hidden email]            Department of Economics
> > vox:     217-333-4558                University of Illinois
> > fax:       217-244-6678                Champaign, IL 61820
> >
> >
> > On Aug 14, 2006, at 8:15 AM, roger koenker wrote:
> >
> >> Yes,  upgrading to Xcode 2.4  worked perfectly.  Thanks to all.
> >>
> >> url:    www.econ.uiuc.edu/~roger            Roger Koenker
> >> email    [hidden email]            Department of Economics
> >> vox:     217-333-4558                University of Illinois
> >> fax:       217-244-6678                Champaign, IL 61820
> >>
> >>
> >> On Aug 14, 2006, at 8:07 AM, stefano iacus wrote:
> >>
> >>> Hi Roger,
> >>> due to latest change in the build scripts, you need to get the  
> >>> latest apple dev tools to correctly build r-devel. In particular,  
> >>> libtool needs to be updated. This is contained in the latest  
> >>> apple dev (XCode 2.3 as other mentioned) on apple developer web  
> >>> site.
> >>> stefano
> >>>
> >>> On 12/ago/06, at 18:56, roger koenker wrote:
> >>>
> >>>> I'm having trouble making yesterday's R-devel on my macs.
> >>>>
> >>>> ./configure seems fine, but eventually in make I get:
> >>>>
> >>>> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined
> >>>> dynamic_lookup -single_module -multiply_defined suppress -L/sw/
> >>>> lib -L/
> >>>> usr/local/lib -install_name libR.dylib -compatibility_version  
> >>>> 2.4.0  -
> >>>> current_version 2.4.0  -headerpad_max_install_names -o libR.dylib
> >>>> Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o
> >>>> RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o
> >>>> builtin.o character.o coerce.o colors.o complex.o connections.o
> >>>> context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o
> >>>> dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o
> >>>> eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o
> >>>> identical.o internet.o iosupport.o lapack.o list.o localecharset.o
> >>>> logic.o main.o mapply.o match.o memory.o model.o names.o objects.o
> >>>> optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o
> >>>> plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o
> >>>> qsort.o random.o regex.o registration.o relop.o rlocale.o  
> >>>> saveload.o
> >>>> scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o
> >>>> startup.o subassign.o subscript.o subset.o summary.o sysutils.o
> >>>> unique.o util.o version.o vfonts.o xxxpr.o   `ls ../appl/*.o ../
> >>>> nmath/
> >>>> *.o ../unix/*.o  2>/dev/null|grep -v /ext-` -framework vecLib -
> >>>> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem  ../extra/zlib/
> >>>> libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  -lintl -
> >>>> liconv -Wl,-framework -Wl,CoreFoundation -lreadline  -lm -liconv
> >>>> /usr/bin/libtool: unknown option character `m' in: -
> >>>> macosx_version_min
> >>>> Usage: /usr/bin/libtool -static [-] file [...] [-filelist listfile
> >>>> [,dirname]] [-arch_only arch] [-sacLT]
> >>>> Usage: /usr/bin/libtool -dynamic [-] file [...] [-filelist listfile
> >>>> [,dirname]] [-arch_only arch] [-o output] [-install_name name] [-
> >>>> compatibility_version #] [-current_version #] [-seg1addr 0x#] [-
> >>>> segs_read_only_addr 0x#] [-segs_read_write_addr 0x#] [-
> >>>> seg_addr_table
> >>>> <filename>] [-seg_addr_table_filename <file_system_path>] [-
> >>>> all_load]
> >>>> [-noall_load]
> >>>> make[3]: *** [libR.dylib] Error 1
> >>>> make[2]: *** [R] Error 2
> >>>> make[1]: *** [R] Error 1
> >>>> make: *** [R] Error 1
> >>>>
> >>>> This was ok  as of my last build which was:
> >>>>
> >>>>> version
> >>>>                 _
> >>>> platform       powerpc-apple-darwin8.7.0
> >>>> arch           powerpc
> >>>> os             darwin8.7.0
> >>>> system         powerpc, darwin8.7.0
> >>>> status         Under development (unstable)
> >>>> major          2
> >>>> minor          4.0
> >>>> year           2006
> >>>> month          07
> >>>> day            28
> >>>> svn rev        38710
> >>>> language       R
> >>>> version.string R version 2.4.0 Under development (unstable)
> >>>> (2006-07-28 r38710)
> >>>>
> >>>> url:    www.econ.uiuc.edu/~roger                Roger Koenker
> >>>> email   [hidden email]                       Department of  
> >>>> Economics
> >>>> vox:    217-333-4558                            University of  
> >>>> Illinois
> >>>> fax:    217-244-6678                            Champaign, IL 61820
> >>>>
> >>>> ______________________________________________
> >>>> [hidden email] mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>>
> >
> >
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: configure on mac

RKoenker
Apologies for my ignorance about these matters.

I think that the multiply defined symbols were probably my fault.  After
removing some lapack routines and using a
modified version of Makevars  suggested by Martin Maechler

## we use the BLAS and now also the LAPACK library:
PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

The multiple definitions problems don't appear, but instead I get  --  
trying to INSTALL
quantreg  --  the same problem with undefined _xerbla_ appears when I  
try to install
Matrix.  A variety of other source packages install without complaint.

gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
dynamic_lookup -single_module
-multiply_defined suppress -L/sw/lib -L/usr/local/lib -o quantreg.so  
akj.o boot.o chlfct.o
cholesky.o dsel05.o extract.o kuantile.o mcmb.o penalty.o qrcens.o  
rls.o rq1.o rqbr.o rqf
n.o rqfnb.o rqfnc.o sparskit2.o srqfn.o srqfnc.o srtpai.o -L/Library/
Frameworks/R.framewor
k/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/
lib -lRblas -L/usr/l
ocal/lib/gcc/powerpc-apple-darwin8/4.0.0 -L/usr/local/lib/gcc -
lgfortran -lgcc_s -lSystemS
tubs -lmx -lSystem -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.0.0 -
L/usr/local/lib/gcc -
lgfortran -lgcc_s -lSystemStubs -lmx -lSystem -F/Library/Frameworks/
R.framework/.. -framew
ork R
ld: warning can't open dynamic library: libR.dylib referenced from: /
Library/Frameworks/R.
framework/Resources/lib/libRlapack.dylib (checking for undefined  
symbols may be affected)
(No such file or directory, errno = 2)
ld: Undefined symbols:
_xerbla_ referenced from libRlapack expected to be defined in libR.dylib
/usr/bin/libtool: internal link edit command failed

_xerbla_  is in

yzzy: otool -Tv libR.dylib | grep xerbla
single module    _xerbla_

which doesn't appear to be part of the ld above.... should it be?  
Can this be arranged
by modifying Makevars?


url:    www.econ.uiuc.edu/~roger            Roger Koenker
email    [hidden email]            Department of Economics
vox:     217-333-4558                University of Illinois
fax:       217-244-6678                Champaign, IL 61820

On Aug 15, 2006, at 1:08 AM, Prof Brian Ripley wrote:

> On Tue, 15 Aug 2006, stefano iacus wrote:
>
>> It seems that there are symbols defined in more than one header. This
>> causes problems on mac. You should define the symbol in one header
>> and declare elsewhere as extern. You can find examples in main.c (if
>> I remember well).
>> I'm not sure this is the problems, but it looks like
>
> One of the reasons given by Simon for this change was that was no  
> longer
> a problem: see the last sentence of
>
>     o   MacOS X 10.3 and higher now use two-level namespaces, single
>         module in a shared library and allow undefined symbols to be
>         resolved at run-time. This implies that common symbols are now
>         allowed in package libraries.
>
> What apparently is a problem is having the same entry point in  
> multiple
> dynamic libraries (we have had to deal with LSAME, NEWS item two  
> up).  I
> think this means that having arranged specially to satisfy symbols on
> MacOS, we now need to change it, so in src/extra/blas/Makefile.in
>
> Rblas_la_LIBADD = @RBLAS_LDFLAGS@ @DYLIB_UNDEFINED_ALLOWED_FALSE@ $
> (FLIBS)
>
> '@DYLIB_UNDEFINED_ALLOWED_FALSE@' needs to be '#'.
>
> and we may then need to link against $(FLIBS) elsewhere.
>
> We need Simon's input: to the rest of us the ever-increasing number of
> ways that MacOS needs special pampering is a mystery.
>
>> stefano
>>

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Re: configure on mac

Prof Brian Ripley
On Tue, 15 Aug 2006, roger koenker wrote:

> Apologies for my ignorance about these matters.

All of us except Simon are in the same boat, it seems.  It might be
helpful to know for his benefit what CPU this is and how you configured R.

This seems to a manifestation of an apparent MacOS bug Simon told me
about.  xerbla_ is in libR.dylib, which loads Matrix.so and that is linked
against libRblas.dylib and libRlapack.dylib, both of are looking for
xerbla_.  On any other OS (except perhaps AIX), the runtime linker would
resolve this, but apparently not on the MacOS two-level linking scheme he
is currently using.

> I think that the multiply defined symbols were probably my fault.  After
> removing some lapack routines and using a
> modified version of Makevars  suggested by Martin Maechler
>
> ## we use the BLAS and now also the LAPACK library:
> PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
>
> The multiple definitions problems don't appear, but instead I get  --  
> trying to INSTALL
> quantreg  --  the same problem with undefined _xerbla_ appears when I  
> try to install
> Matrix.  A variety of other source packages install without complaint.
>
> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
> dynamic_lookup -single_module
> -multiply_defined suppress -L/sw/lib -L/usr/local/lib -o quantreg.so  
> akj.o boot.o chlfct.o
> cholesky.o dsel05.o extract.o kuantile.o mcmb.o penalty.o qrcens.o  
> rls.o rq1.o rqbr.o rqf
> n.o rqfnb.o rqfnc.o sparskit2.o srqfn.o srqfnc.o srtpai.o -L/Library/
> Frameworks/R.framewor
> k/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/
> lib -lRblas -L/usr/l
> ocal/lib/gcc/powerpc-apple-darwin8/4.0.0 -L/usr/local/lib/gcc -
> lgfortran -lgcc_s -lSystemS
> tubs -lmx -lSystem -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.0.0 -
> L/usr/local/lib/gcc -
> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem -F/Library/Frameworks/
> R.framework/.. -framew
> ork R
> ld: warning can't open dynamic library: libR.dylib referenced from: /
> Library/Frameworks/R.
> framework/Resources/lib/libRlapack.dylib (checking for undefined  
> symbols may be affected)
> (No such file or directory, errno = 2)
> ld: Undefined symbols:
> _xerbla_ referenced from libRlapack expected to be defined in libR.dylib
> /usr/bin/libtool: internal link edit command failed
>
> _xerbla_  is in
>
> yzzy: otool -Tv libR.dylib | grep xerbla
> single module    _xerbla_
>
> which doesn't appear to be part of the ld above.... should it be?  
> Can this be arranged
> by modifying Makevars?
>
>
> url:    www.econ.uiuc.edu/~roger            Roger Koenker
> email    [hidden email]            Department of Economics
> vox:     217-333-4558                University of Illinois
> fax:       217-244-6678                Champaign, IL 61820
>
> On Aug 15, 2006, at 1:08 AM, Prof Brian Ripley wrote:
>
> > On Tue, 15 Aug 2006, stefano iacus wrote:
> >
> >> It seems that there are symbols defined in more than one header. This
> >> causes problems on mac. You should define the symbol in one header
> >> and declare elsewhere as extern. You can find examples in main.c (if
> >> I remember well).
> >> I'm not sure this is the problems, but it looks like
> >
> > One of the reasons given by Simon for this change was that was no  
> > longer
> > a problem: see the last sentence of
> >
> >     o   MacOS X 10.3 and higher now use two-level namespaces, single
> >         module in a shared library and allow undefined symbols to be
> >         resolved at run-time. This implies that common symbols are now
> >         allowed in package libraries.
> >
> > What apparently is a problem is having the same entry point in  
> > multiple
> > dynamic libraries (we have had to deal with LSAME, NEWS item two  
> > up).  I
> > think this means that having arranged specially to satisfy symbols on
> > MacOS, we now need to change it, so in src/extra/blas/Makefile.in
> >
> > Rblas_la_LIBADD = @RBLAS_LDFLAGS@ @DYLIB_UNDEFINED_ALLOWED_FALSE@ $
> > (FLIBS)
> >
> > '@DYLIB_UNDEFINED_ALLOWED_FALSE@' needs to be '#'.
> >
> > and we may then need to link against $(FLIBS) elsewhere.
> >
> > We need Simon's input: to the rest of us the ever-increasing number of
> > ways that MacOS needs special pampering is a mystery.
> >
> >> stefano
> >>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: configure on mac

Simon Urbanek
In reply to this post by RKoenker
On Aug 15, 2006, at 3:21 PM, roger koenker wrote:

Sorry this, is my fault:

> gcc -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined  
> dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -
> L/usr/local/lib -o quantreg.so akj.o boot.o chlfct.o cholesky.o  
> dsel05.o extract.o kuantile.o mcmb.o penalty.o qrcens.o rls.o rq1.o  
> rqbr.o rqfn.o rqfnb.o rqfnc.o sparskit2.o srqfn.o srqfnc.o srtpai.o  
> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/
> Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/
> lib/gcc/powerpc-apple-darwin8/4.0.0 -L/usr/local/lib/gcc -  
> lgfortran -lgcc_s -lSystemStubs -lmx -lSystem -L/usr/local/lib/gcc/
> powerpc-apple-darwin8/4.0.0 - L/usr/local/lib/gcc -lgfortran -
> lgcc_s -lSystemStubs -lmx -lSystem -F/Library/Frameworks/  
> R.framework/.. -framework R
> ld: warning can't open dynamic library: libR.dylib referenced  
> from: / Library/Frameworks/R.framework/Resources/lib/
> libRlapack.dylib (checking for undefined symbols may be affected)

^^ the actual error is here - it cannot find libR

> (No such file or directory, errno = 2)
> ld: Undefined symbols:
> _xerbla_ referenced from libRlapack expected to be defined in  
> libR.dylib

This is just a consequence of the above, _xerbla_ is not found as it  
is defined libR which couldn't be loaded. The reason is that the  
framework install didn't set the correct path in libRlapack. It is  
now fixed in the current R-devel.

The current R-devel now also checks the Xcode capabilities and will  
fall-back to flat namespaces if the linker is too old (the other  
error reported here). I tested some combinations of BLAS and tools,  
but not all of them, so please drop me a line if you find a setup  
that doesn't work.

Thanks,
Simon

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Re: configure on mac

RKoenker

On Aug 16, 2006, at 4:25 PM, Simon Urbanek wrote:

> On Aug 15, 2006, at 3:21 PM, roger koenker wrote:
>
> Sorry this, is my fault:
>
>>
>> ld: warning can't open dynamic library: libR.dylib referenced  
>> from: / Library/Frameworks/R.framework/Resources/lib/
>> libRlapack.dylib (checking for undefined symbols may be affected)
>
> ^^ the actual error is here - it cannot find libR
>
>> (No such file or directory, errno = 2)
>> ld: Undefined symbols:
>> _xerbla_ referenced from libRlapack expected to be defined in  
>> libR.dylib
>
> This is just a consequence of the above, _xerbla_ is not found as  
> it is defined libR which couldn't be loaded. The reason is that the  
> framework install didn't set the correct path in libRlapack. It is  
> now fixed in the current R-devel.
>
> The current R-devel now also checks the Xcode capabilities and will  
> fall-back to flat namespaces if the linker is too old (the other  
> error reported here). I tested some combinations of BLAS and tools,  
> but not all of them, so please drop me a line if you find a setup  
> that doesn't work.

Yes, R-devel_2006-08-16 now installs both packages I was having  
trouble with without any difficulties.
Thanks again!

Roger

>

url:    www.econ.uiuc.edu/~roger            Roger Koenker
email    [hidden email]            Department of Economics
vox:     217-333-4558                University of Illinois
fax:       217-244-6678                Champaign, IL 61820

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