Fwd: makeconf issue on R-devel 2006-03-12 r37524

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Fwd: makeconf issue on R-devel 2006-03-12 r37524

RKoenker
I sent the message below to r-sig-mac yesterday, but having no reply
I decided to explore a bit myself and found that editing:

/Library/Frameworks/R.framework/Versions/2.3/Resources/share/make/
shlib.mk

yzzy: diff shlib.mk shlib.mk~
3c3
< include $(R_HOME)/etc/Makeconf
---
 > include $(R_HOME)/etc${R_ARCH}/Makeconf

restored the functionality of R CMD INSTALL.

Is this a known issue?


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


Begin forwarded message:

> From: roger koenker <[hidden email]>
> Date: March 13, 2006 4:46:30 PM CST
> To: [hidden email]
> Subject: makeconf issue on R-devel 2006-03-12 r37524
>
> I've just installed R-devel   Version 2.3.0 Under development  
> (unstable) (2006-03-12 r37524)
> on a G5 and things went smoothly despite my gfortran configuration,  
> (that is ./configure, make,
> make install was fine), but now trying to install  a source package  
> I get:
>
> yzzy: R CMD check kuantile
> * checking for working latex ... OK
> * using log directory '/Users/roger/Projects/kuantile/kuantile.Rcheck'
> * using Version 2.3.0 Under development (unstable) (2006-03-12 r37524)
> * checking for file 'kuantile/DESCRIPTION' ... OK
> * this is package 'kuantile' version '1.00'
> * checking package dependencies ... OK
> * checking if this is a source package ... WARNING
> Subdirectory 'kuantile/src' contains object files.
> * checking whether package 'kuantile' can be installed ... ERROR
> Installation failed.
> See '/Users/roger/Projects/kuantile/kuantile.Rcheck/00install.out'  
> for details.
>
> yzzy: more /Users/roger/Projects/kuantile/kuantile.Rcheck/
> 00install.out
> * Installing *source* package 'kuantile' ...
> ** libs
> ** arch - Frameworks
> /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: /
> Library/Frameworks/R.fra
> mework/Resources/etc/Frameworks/Makeconf: No such file or directory
> make: *** No rule to make target `/Library/Frameworks/R.framework/
> Resources/etc/Frameworks
> /Makeconf'.  Stop.
> chmod: /Users/roger/Projects/kuantile/kuantile.Rcheck/kuantile/libs/
> Frameworks/*: No such
> file or directory
> gfortran   -fPIC -fno-common  -g -O2 -c dsel05.f -o dsel05.o
> gfortran   -fPIC -fno-common  -g -O2 -c kuantile.f -o kuantile.o
> gcc -flat_namespace -bundle -undefined suppress -L/sw/lib -L/usr/
> local/lib -o kuantile.so
> dsel05.o kuantile.o  -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/.. -fram
> ework R
> ERROR: compilation failed for package 'kuantile'
> ** Removing '/Users/roger/Projects/kuantile/kuantile.Rcheck/kuantile'
>
> isn't there something fishy with the specification of the Makeconf  
> file in ..../etc/Frameworks???
>
> 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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Re: Fwd: makeconf issue on R-devel 2006-03-12 r37524

Brian Ripley
On Tue, 14 Mar 2006, roger koenker wrote:

> I sent the message below to r-sig-mac yesterday, but having no reply
> I decided to explore a bit myself and found that editing:
>
> /Library/Frameworks/R.framework/Versions/2.3/Resources/share/make/
> shlib.mk
>
> yzzy: diff shlib.mk shlib.mk~
> 3c3
> < include $(R_HOME)/etc/Makeconf
> ---
> > include $(R_HOME)/etc${R_ARCH}/Makeconf
>
> restored the functionality of R CMD INSTALL.
>
> Is this a known issue?

No, and the change will break things which currently work correctly.

Looks like this is something specific to how Macs install under the
bin/exec directory.  It likely stems from the following line in INSTALL.

      archs=`(cd ${R_HOME}/bin/exec; ls)`

which on other systems will only contain directories for sub-architectures
or the R or Rgnome executables, since it says

>> ** arch - Frameworks


>
> 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
>
>
> Begin forwarded message:
>
>> From: roger koenker <[hidden email]>
>> Date: March 13, 2006 4:46:30 PM CST
>> To: [hidden email]
>> Subject: makeconf issue on R-devel 2006-03-12 r37524
>>
>> I've just installed R-devel   Version 2.3.0 Under development
>> (unstable) (2006-03-12 r37524)
>> on a G5 and things went smoothly despite my gfortran configuration,
>> (that is ./configure, make,
>> make install was fine), but now trying to install  a source package
>> I get:
>>
>> yzzy: R CMD check kuantile
>> * checking for working latex ... OK
>> * using log directory '/Users/roger/Projects/kuantile/kuantile.Rcheck'
>> * using Version 2.3.0 Under development (unstable) (2006-03-12 r37524)
>> * checking for file 'kuantile/DESCRIPTION' ... OK
>> * this is package 'kuantile' version '1.00'
>> * checking package dependencies ... OK
>> * checking if this is a source package ... WARNING
>> Subdirectory 'kuantile/src' contains object files.
>> * checking whether package 'kuantile' can be installed ... ERROR
>> Installation failed.
>> See '/Users/roger/Projects/kuantile/kuantile.Rcheck/00install.out'
>> for details.
>>
>> yzzy: more /Users/roger/Projects/kuantile/kuantile.Rcheck/
>> 00install.out
>> * Installing *source* package 'kuantile' ...
>> ** libs
>> ** arch - Frameworks
>> /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: /
>> Library/Frameworks/R.fra
>> mework/Resources/etc/Frameworks/Makeconf: No such file or directory
>> make: *** No rule to make target `/Library/Frameworks/R.framework/
>> Resources/etc/Frameworks
>> /Makeconf'.  Stop.
>> chmod: /Users/roger/Projects/kuantile/kuantile.Rcheck/kuantile/libs/
>> Frameworks/*: No such
>> file or directory
>> gfortran   -fPIC -fno-common  -g -O2 -c dsel05.f -o dsel05.o
>> gfortran   -fPIC -fno-common  -g -O2 -c kuantile.f -o kuantile.o
>> gcc -flat_namespace -bundle -undefined suppress -L/sw/lib -L/usr/
>> local/lib -o kuantile.so
>> dsel05.o kuantile.o  -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/.. -fram
>> ework R
>> ERROR: compilation failed for package 'kuantile'
>> ** Removing '/Users/roger/Projects/kuantile/kuantile.Rcheck/kuantile'
>>
>> isn't there something fishy with the specification of the Makeconf
>> file in ..../etc/Frameworks???
>>
>> 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
>>
>>
>
> ______________________________________________
> [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: Fwd: makeconf issue on R-devel 2006-03-12 r37524

Roger Koenker-2
For what it is worth, I've just installed R-alpha Version 2.3.0 alpha  
(2006-04-07 r37668)
on my G5 and encountered the same problem reported below.  The same  
treatment
got  things going again.  If this reflects some idiosyncrasy in my  
setup,  my apologies....


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 Mar 14, 2006, at 1:31 PM, Prof Brian Ripley wrote:

> On Tue, 14 Mar 2006, roger koenker wrote:
>
>> I sent the message below to r-sig-mac yesterday, but having no reply
>> I decided to explore a bit myself and found that editing:
>>
>> /Library/Frameworks/R.framework/Versions/2.3/Resources/share/make/
>> shlib.mk
>>
>> yzzy: diff shlib.mk shlib.mk~
>> 3c3
>> < include $(R_HOME)/etc/Makeconf
>> ---
>> > include $(R_HOME)/etc${R_ARCH}/Makeconf
>>
>> restored the functionality of R CMD INSTALL.
>>
>> Is this a known issue?
>
> No, and the change will break things which currently work correctly.
>
> Looks like this is something specific to how Macs install under the  
> bin/exec directory.  It likely stems from the following line in  
> INSTALL.
>
>      archs=`(cd ${R_HOME}/bin/exec; ls)`
>
> which on other systems will only contain directories for sub-
> architectures or the R or Rgnome executables, since it says
>
>>> ** arch - Frameworks
>
>
>>
>> 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
>>
>>
>> Begin forwarded message:
>>
>>> From: roger koenker <[hidden email]>
>>> Date: March 13, 2006 4:46:30 PM CST
>>> To: [hidden email]
>>> Subject: makeconf issue on R-devel 2006-03-12 r37524
>>>
>>> I've just installed R-devel   Version 2.3.0 Under development
>>> (unstable) (2006-03-12 r37524)
>>> on a G5 and things went smoothly despite my gfortran configuration,
>>> (that is ./configure, make,
>>> make install was fine), but now trying to install  a source package
>>> I get:
>>>
>>> yzzy: R CMD check kuantile
>>> * checking for working latex ... OK
>>> * using log directory '/Users/roger/Projects/kuantile/
>>> kuantile.Rcheck'
>>> * using Version 2.3.0 Under development (unstable) (2006-03-12  
>>> r37524)
>>> * checking for file 'kuantile/DESCRIPTION' ... OK
>>> * this is package 'kuantile' version '1.00'
>>> * checking package dependencies ... OK
>>> * checking if this is a source package ... WARNING
>>> Subdirectory 'kuantile/src' contains object files.
>>> * checking whether package 'kuantile' can be installed ... ERROR
>>> Installation failed.
>>> See '/Users/roger/Projects/kuantile/kuantile.Rcheck/00install.out'
>>> for details.
>>>
>>> yzzy: more /Users/roger/Projects/kuantile/kuantile.Rcheck/
>>> 00install.out
>>> * Installing *source* package 'kuantile' ...
>>> ** libs
>>> ** arch - Frameworks
>>> /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: /
>>> Library/Frameworks/R.fra
>>> mework/Resources/etc/Frameworks/Makeconf: No such file or directory
>>> make: *** No rule to make target `/Library/Frameworks/R.framework/
>>> Resources/etc/Frameworks
>>> /Makeconf'.  Stop.
>>> chmod: /Users/roger/Projects/kuantile/kuantile.Rcheck/kuantile/libs/
>>> Frameworks/*: No such
>>> file or directory
>>> gfortran   -fPIC -fno-common  -g -O2 -c dsel05.f -o dsel05.o
>>> gfortran   -fPIC -fno-common  -g -O2 -c kuantile.f -o kuantile.o
>>> gcc -flat_namespace -bundle -undefined suppress -L/sw/lib -L/usr/
>>> local/lib -o kuantile.so
>>> dsel05.o kuantile.o  -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/.. -fram
>>> ework R
>>> ERROR: compilation failed for package 'kuantile'
>>> ** Removing '/Users/roger/Projects/kuantile/kuantile.Rcheck/
>>> kuantile'
>>>
>>> isn't there something fishy with the specification of the Makeconf
>>> file in ..../etc/Frameworks???
>>>
>>> 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
>>>
>>>
>>
>> ______________________________________________
>> [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: Fwd: makeconf issue on R-devel 2006-03-12 r37524

Brian Ripley
On Sat, 8 Apr 2006, roger koenker wrote:

> For what it is worth, I've just installed R-alpha Version 2.3.0 alpha
> (2006-04-07 r37668)
> on my G5 and encountered the same problem reported below.  The same
> treatment
> got  things going again.  If this reflects some idiosyncrasy in my
> setup,  my apologies....

Well, no one else is reporting it, and that includes the daily checks run
by Simon on MacOS X so it is not that no one has tested R-devel for the
last few weeks (and Simon was involved with the design of this change).

It looks as if 'make install-R-framework' puts a link in bin/exec, which
is not supposed to be used for other than front-ends.  I think you need to
take this up with the MacOS X maintainers, since the problem is in their
code, not in general R, and no one else can address it.  If the link is
really necessary, it is INSTALL.in that needs a patch.


> 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 Mar 14, 2006, at 1:31 PM, Prof Brian Ripley wrote:
>
>> On Tue, 14 Mar 2006, roger koenker wrote:
>>
>>> I sent the message below to r-sig-mac yesterday, but having no reply
>>> I decided to explore a bit myself and found that editing:
>>>
>>> /Library/Frameworks/R.framework/Versions/2.3/Resources/share/make/
>>> shlib.mk
>>>
>>> yzzy: diff shlib.mk shlib.mk~
>>> 3c3
>>> < include $(R_HOME)/etc/Makeconf
>>> ---
>>>> include $(R_HOME)/etc${R_ARCH}/Makeconf
>>>
>>> restored the functionality of R CMD INSTALL.
>>>
>>> Is this a known issue?
>>
>> No, and the change will break things which currently work correctly.
>>
>> Looks like this is something specific to how Macs install under the
>> bin/exec directory.  It likely stems from the following line in
>> INSTALL.
>>
>>      archs=`(cd ${R_HOME}/bin/exec; ls)`
>>
>> which on other systems will only contain directories for sub-
>> architectures or the R or Rgnome executables, since it says
>>
>>>> ** arch - Frameworks
>>
>>
>>>
>>> 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
>>>
>>>
>>> Begin forwarded message:
>>>
>>>> From: roger koenker <[hidden email]>
>>>> Date: March 13, 2006 4:46:30 PM CST
>>>> To: [hidden email]
>>>> Subject: makeconf issue on R-devel 2006-03-12 r37524
>>>>
>>>> I've just installed R-devel   Version 2.3.0 Under development
>>>> (unstable) (2006-03-12 r37524)
>>>> on a G5 and things went smoothly despite my gfortran configuration,
>>>> (that is ./configure, make,
>>>> make install was fine), but now trying to install  a source package
>>>> I get:
>>>>
>>>> yzzy: R CMD check kuantile
>>>> * checking for working latex ... OK
>>>> * using log directory '/Users/roger/Projects/kuantile/
>>>> kuantile.Rcheck'
>>>> * using Version 2.3.0 Under development (unstable) (2006-03-12
>>>> r37524)
>>>> * checking for file 'kuantile/DESCRIPTION' ... OK
>>>> * this is package 'kuantile' version '1.00'
>>>> * checking package dependencies ... OK
>>>> * checking if this is a source package ... WARNING
>>>> Subdirectory 'kuantile/src' contains object files.
>>>> * checking whether package 'kuantile' can be installed ... ERROR
>>>> Installation failed.
>>>> See '/Users/roger/Projects/kuantile/kuantile.Rcheck/00install.out'
>>>> for details.
>>>>
>>>> yzzy: more /Users/roger/Projects/kuantile/kuantile.Rcheck/
>>>> 00install.out
>>>> * Installing *source* package 'kuantile' ...
>>>> ** libs
>>>> ** arch - Frameworks
>>>> /Library/Frameworks/R.framework/Resources/share/make/shlib.mk:3: /
>>>> Library/Frameworks/R.fra
>>>> mework/Resources/etc/Frameworks/Makeconf: No such file or directory
>>>> make: *** No rule to make target `/Library/Frameworks/R.framework/
>>>> Resources/etc/Frameworks
>>>> /Makeconf'.  Stop.
>>>> chmod: /Users/roger/Projects/kuantile/kuantile.Rcheck/kuantile/libs/
>>>> Frameworks/*: No such
>>>> file or directory
>>>> gfortran   -fPIC -fno-common  -g -O2 -c dsel05.f -o dsel05.o
>>>> gfortran   -fPIC -fno-common  -g -O2 -c kuantile.f -o kuantile.o
>>>> gcc -flat_namespace -bundle -undefined suppress -L/sw/lib -L/usr/
>>>> local/lib -o kuantile.so
>>>> dsel05.o kuantile.o  -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/.. -fram
>>>> ework R
>>>> ERROR: compilation failed for package 'kuantile'
>>>> ** Removing '/Users/roger/Projects/kuantile/kuantile.Rcheck/
>>>> kuantile'
>>>>
>>>> isn't there something fishy with the specification of the Makeconf
>>>> file in ..../etc/Frameworks???
>>>>
>>>> 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
>>>>
>>>>
>>>
>>> ______________________________________________
>>> [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
>
> ______________________________________________
> [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: Fwd: makeconf issue on R-devel 2006-03-12 r37524

Simon Urbanek

On Apr 8, 2006, at 2:27 PM, Prof Brian Ripley wrote:

> On Sat, 8 Apr 2006, roger koenker wrote:
>
>> For what it is worth, I've just installed R-alpha Version 2.3.0 alpha
>> (2006-04-07 r37668)
>> on my G5 and encountered the same problem reported below.  The same
>> treatment
>> got  things going again.  If this reflects some idiosyncrasy in my
>> setup,  my apologies....
>
> Well, no one else is reporting it, and that includes the daily  
> checks run
> by Simon on MacOS X so it is not that no one has tested R-devel for  
> the
> last few weeks (and Simon was involved with the design of this  
> change).
>
> It looks as if 'make install-R-framework' puts a link in bin/exec,  
> which is not supposed to be used for other than front-ends.

This is a relic from the time when the Mac GUI was also started via  
exec/R and the Frameworks subdirectory relative to the binary is  
where dependent frameworks went. It is now obsolete, and can be  
removed. I'm cleaning up the framework install code and tonight's  
nightly build should be ok.

Thanks for spotting this. My package builds used R 2.2 so they didn't  
catch this and make install didn't either. I'll now switch both  
machines to 2.3 so hopefully we'll catch things like that now.

Cheers,
Simon

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