Re: [Rpy] compiling rpy2 on windows R-2.8.1

[James Yoo]

Hmmm, I'm trying to use mingw to compile rpy2.   I've setup my paths to only
include R, Rtools, mingw... but for some dang reason, setup.py keeps finding
msvc instead... what am I missing here?

On Sat, Jan 3, 2009 at 2:22 AM, Laurent Gautier  wrote:

> James Yoo wrote:
>
>>
>> line 112 (or thereabouts) in setup.py:
>> include_dirs = [x.lstrip('-I') for x in include_dirs]
>>
>> lstrip tends to be too greedy and turns "-II:\path\to\include" into
>> ":\path\to\include"...
>>
>
>
> I see. I misused 'lstrip' (thinking that the characters '-I' passed where
> considered as a string, while they are considered as any possible
> characters).
> This means that the bug is more serious: any path/to/include with any
> of the characters '-' or 'I' will cause problem.
>
> The fix you propose does not solve the problem in all cases (think of
> someone having a path like /path/to/My-Includes/).
>
> I'd propose the following instead:
>
>for i, d in enumerate(include_dirs):
>if d.startswith('-I'):
>   include_dirs[i] = d[2:]
>
> Regarding the other errors you encounter, I am afraid that you are on your
> own: all compilations for win32 I know of used mingw instead of msvc.
>
>
> L.
>
>
>
>
>
>> On Fri, Jan 2, 2009 at 2:18 PM, Laurent Gautier > lgaut...@gmail.com>> wrote:
>>
>>James Yoo wrote:
>>
>>
>>Sorry for the redundant post, but I felt that I should change
>>the subject header.
>>On Fri, Jan 2, 2009 at 11:31 AM, James Yoo > >
>>>> wrote:
>>
>>   Hi,
>>
>>   Running into a couple problems compiling rpy2 on windows.
>>   I have R_HOME defined and R in the system path.
>>   first off in setup.py, def getRinterface_ext:
>>
>>   include_dirs = [x.lstrip('-I','') for x in include_dirs]
>>
>>
>>The line above does not seem to be found in setup.py
>>(as the signature for the method str.lstrip() differs)
>>
>>
>>
>>
>>
>>   is bad if your drive letter happens to be 'I', I've replaced
>> this
>>   with x.replace('-I','') in my version.
>>
>>
>>1- To my knowledge, str.strip() and str.replace() do different things.
>>2- An oversight of Win32 subtleties cannot be excluded, but telling
>>here what happens exactly what happens drive I:\ could be helpful.
>>
>>   ... moving on...
>>
>>   During setup.py install, rinterface is running into multiple
>>problems:
>>
>>   w:\rpy2-2.0.0\rpy\rinterface\rinterface.h(19)
>>   : warning C4114: same type qualifier used more than once
>>   w:\rpy2-2.0.0\rpy\rinterface\rinterface.h(20)
>>   : warning C4114: same type qualifier used more than once
>>   rpy\rinterface\array.c(110) : error C2275: 'PyArrayInterface' :
>>   illegal use of t
>>   his type as an expression
>>   rpy\rinterface\array.c(27) : see declaration of
>>   'PyArrayInterface'
>>   rpy\rinterface\array.c(110) : error C2065: 'inter' : undeclared
>>   identifier
>>   rpy\rinterface\array.c(111) : error C2143: syntax error :
>> missing
>>   ';' before 'ty
>>   pe'
>>   rpy\rinterface\array.c(112) : error C2065: 'typekind' :
>>undeclared
>>   identifier
>>   rpy\rinterface\array.c(116) : warning C4047: '=' : 'int'
>>differs in
>>   levels of in
>>   direction from 'PyArrayInterface *'
>>   rpy\rinterface\array.c(120) : error C2143: syntax error :
>> missing
>>   ';' before 'ty
>>   pe'
>>   rpy\rinterface\array.c(121) : error C2143: syntax error :
>> missing
>>   ';' before 'ty
>>   pe'
>>   rpy\rinterface\array.c(122) : error C2223: left of
>>'->version' must
>>   point to str
>>   uct/union
>>   rpy\rinterface\array.c(123) : error C2223: left of '->nd'
>>must point
>>   to struct/u
>>   nion
>>   rpy\rinterface\array.c(123) : error C2065: 'nd' : undeclared
>>identifier
>>   rpy\rinterface\array.c(124) : error C2223: left of
>>'->typekind' must
>>   point to st
>>   ruct/union
>>   rpy\rinterface\array.c(125) : error C2223: left of
>>'->itemsize' must
>>   point to st
>>   ruct/union
>>   rpy\rinterface\array.c(126) : error C2223: left of '->flags'
>> must
>>   point to struc
>>   t/union
>>   rpy\rinterface\array.c(127) : error C2223: left of '->shape'
>> must
>>   point to struc
>>   t/union
>>   rpy\rinterface\array.c(128) : error C2223: left of '->shape'
>> must
>>   point to struc
>>   t/union
>>   rpy\rinterface\array.c(128) : warning C4047: 'function' :
>>   'Py_intptr_t *' differ
>>   s in levels of indirection from 'int'

Re: [Rpy] compiling rpy2 on windows R-2.8.1

[James Yoo]

okay, I'm making some progress... finally figured out how to make sure
mingw32 is used as the compiler du jour:

python setup.py build --compiler=mingw32

running build
running build_py
running build_ext
building 'rpy2.rinterface.rinterface' extension
\tools\Rtools\MinGW\bin\gcc.exe -mno-cygwin -
mdll -O -Wall -DWin32=1 -DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1
-II:/R/R-2.8.1/include -Irpy\rinterface
-Ii:\Python2.5\include -I\43\Python2.5\PC -c
rpy\rinterface\array.c -o build\temp.win32-2.5\Release\rpy\rinterface
\array.o
\tools\Rtools\MinGW\bin\gcc.exe -mno-cygwin -mdll -O -Wall
-DWin32=1 -DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1
-II:/R/R-2.8.1/include -Irpy\rinterface
-I\Python2.5\include -I\43\Pytho
n2.5\PC -c rpy\rinterface\r_utils.c -o
build\temp.win32-2.5\Release\rpy\rinterface\r_utils.o
\tools\Rtools\MinGW\bin\gcc.exe -mno-cygwin -mdll -O -Wall
-DWin32=1 -DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1
-II:/R/R-2.8.1/include -Irpy\rinterface
-Ii:\Python2.5\include -I\43\Pytho
n2.5\PC -c rpy\rinterface\rinterface.c -o
build\temp.win32-2.5\Release\rpy\rinterface\rinterface.o
rpy\rinterface\rinterface.c: In function
'EmbeddedR_init':rpy\rinterface\rinterface.c:368: error: 'R_SignalHandlers'
undeclared (first use in this function)
rpy\rinterface\rinterface.c:368: error: (Each undeclared identifier is
reportedonly once
rpy\rinterface\rinterface.c:368: error: for each function it appears in.)
rpy\rinterface\rinterface.c:372: error: 'R_Interactive' undeclared (first
use in this function)
rpy\rinterface\rinterface.c: In function
'EmbeddedR_exception_from_errmessage':
rpy\rinterface\rinterface.c:473: warning: initialization discards qualifiers
from pointer target type
error: command 'gcc' failed with exit status 1


On Mon, Jan 12, 2009 at 11:49 AM, James Yoo  wrote:

> Hmmm, I'm trying to use mingw to compile rpy2.   I've setup my paths to
> only include R, Rtools, mingw... but for some dang reason, setup.py keeps
> finding msvc instead... what am I missing here?
>
>
> On Sat, Jan 3, 2009 at 2:22 AM, Laurent Gautier wrote:
>
>> James Yoo wrote:
>>
>>>
>>> line 112 (or thereabouts) in setup.py:
>>> include_dirs = [x.lstrip('-I') for x in include_dirs]
>>>
>>> lstrip tends to be too greedy and turns "-II:\path\to\include" into
>>> ":\path\to\include"...
>>>
>>
>>
>> I see. I misused 'lstrip' (thinking that the characters '-I' passed where
>> considered as a string, while they are considered as any possible
>> characters).
>> This means that the bug is more serious: any path/to/include with any
>> of the characters '-' or 'I' will cause problem.
>>
>> The fix you propose does not solve the problem in all cases (think of
>> someone having a path like /path/to/My-Includes/).
>>
>> I'd propose the following instead:
>>
>>for i, d in enumerate(include_dirs):
>>if d.startswith('-I'):
>>   include_dirs[i] = d[2:]
>>
>> Regarding the other errors you encounter, I am afraid that you are on your
>> own: all compilations for win32 I know of used mingw instead of msvc.
>>
>>
>> L.
>>
>>
>>
>>
>>
>>> On Fri, Jan 2, 2009 at 2:18 PM, Laurent Gautier >> lgaut...@gmail.com>> wrote:
>>>
>>>James Yoo wrote:
>>>
>>>
>>>Sorry for the redundant post, but I felt that I should change
>>>the subject header.
>>>On Fri, Jan 2, 2009 at 11:31 AM, James Yoo >> >>
>>>>> wrote:
>>>
>>>   Hi,
>>>
>>>   Running into a couple problems compiling rpy2 on windows.
>>>   I have R_HOME defined and R in the system path.
>>>   first off in setup.py, def getRinterface_ext:
>>>
>>>   include_dirs = [x.lstrip('-I','') for x in include_dirs]
>>>
>>>
>>>The line above does not seem to be found in setup.py
>>>(as the signature for the method str.lstrip() differs)
>>>
>>>
>>>
>>>
>>>
>>>   is bad if your drive letter happens to be 'I', I've replaced
>>> this
>>>   with x.replace('-I','') in my version.
>>>
>>>
>>>1- To my knowledge, str.strip() and str.replace() do different things.
>>>2- An oversight of Win32 subtleties cannot be excluded, but telling
>>>here what happens exactly what happens drive I:\ could be helpful.
>>>
>>>   ... moving on...
>>>
>>>   During setup.py install, rinterface is running into multiple
>>>problems:
>>>
>>>   w:\rpy2-2.0.0\rpy\rinterface\rinterface.h(19)
>>>   : warning C4114: same type qualifier used more than once
>>>   w:\rpy2-2.0.0\rpy\rinterface\rinterface.h(20)
>>>   : warning C4114: same type qualifier used more than once
>>>   rpy\rinterface\array.c(110) : error C2275: 'PyArrayInterface' :
>>>   illegal use of t
>>>   his type as an expression
>>>   rpy\rinterface\array.c(27) : see declaration of
>>>   'PyArrayInterface'
>>>   rpy\rinterface\array.c(110) : error C2065: 'inter' : undeclared
>>>  

Re: [Rpy] compiling rpy2 on windows R-2.8.1

[Peter]

On Mon, Jan 12, 2009 at 5:49 PM, James Yoo  wrote:
> Hmmm, I'm trying to use mingw to compile rpy2.   I've setup my paths to only
> include R, Rtools, mingw... but for some dang reason, setup.py keeps finding
> msvc instead... what am I missing here?

I think setup.py will default to the MS compiler, try:

python setup.py build --compiler=mingw32

Or, create/edit the file distutils.cfg to make mingw32 the default
compiler for distutils.

Peter

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[Rpy] playwith

[Jan Wijffels]

Hi,

I was wondering how something like

library(playwith)
playwith(plot(1:10))

could be achieved with RPy2?


thanks,
Jan


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[Rpy] Rpy and concurrency

[laurent oget]

Does Rpy2 use any systemwide locking to ensure that only one instance is
running at a given time or is this only a process-wide logging to make sure
only one thread within one process is using R?

Thanks,

Laurent
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Re: [Rpy] Rpy and concurrency

[Laurent Gautier]

   Two things.

   rpy2.rinterface if making sure that R gets initialized only once 
(otherwise everything breaks), which translates at the level of 
rpy2.robjects as a singleton pattern (r singleton of class R).

   For evaluating R code, the locking is somehow ensured by Python's 
GIL. All accesses to R are at the C level, and currently none of this 
code is releasing the GIL. There a locking mechanism already present in 
the C code, but it does not have much influence in the 2.0.x serie (work 
on that is under progress, but that's for 2.1.x). When done, long 
evaluations of R code will not hold the GIL, and that locking mechanism 
will be making sure only one thread is doing R things.



L.


laurent oget wrote:
> Does Rpy2 use any systemwide locking to ensure that only one instance is 
> running at a given time or is this only a process-wide logging to make 
> sure only one thread within one process is using R?
> 
> Thanks,
> 
> Laurent
> 
> 
> 
> 
> --
> This SF.net email is sponsored by:
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> 
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Re: [Rpy] Rpy and concurrency

[laurent oget]

But in any case no global between process locking through a file lock or
something of that sort, right?

L


2009/1/12 Laurent Gautier 

>  Two things.
>
>  rpy2.rinterface if making sure that R gets initialized only once
> (otherwise everything breaks), which translates at the level of
> rpy2.robjects as a singleton pattern (r singleton of class R).
>
>  For evaluating R code, the locking is somehow ensured by Python's GIL. All
> accesses to R are at the C level, and currently none of this code is
> releasing the GIL. There a locking mechanism already present in the C code,
> but it does not have much influence in the 2.0.x serie (work on that is
> under progress, but that's for 2.1.x). When done, long evaluations of R code
> will not hold the GIL, and that locking mechanism will be making sure only
> one thread is doing R things.
>
>
>
> L.
>
>
> laurent oget wrote:
>
>> Does Rpy2 use any systemwide locking to ensure that only one instance is
>> running at a given time or is this only a process-wide logging to make sure
>> only one thread within one process is using R?
>>
>> Thanks,
>>
>> Laurent
>>
>>
>> 
>>
>>
>> --
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>>
>> 
>>
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>>
>
>
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Re: [Rpy] playwith

[Laurent Gautier]

Currently, I think that your only hope is that the package "playwith" is 
working when called from rpy2.

I have something like that on my TODO list, but I am not sure on when, 
and if I can find the time to do it.


L.



Jan Wijffels wrote:
> Hi,
> 
> I was wondering how something like
> 
> library(playwith)
> playwith(plot(1:10))
> 
> could be achieved with RPy2?
> 
> 
> thanks,
> Jan
> 
> 
> 
> Windows Live™ Hotmail®: Chat. Store. Share. Do more with mail. See how 
> it works. 
> 
> 
> 
> 
> 
> --
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Re: [Rpy] Rpy and concurrency

[Laurent Gautier]

No need. Because of the GIL, a C call has to return before any thread 
can proceed (or so I think - I have tried or investigated this in 
details at the moment).

laurent oget wrote:
> But in any case no global between process locking through a file lock or 
> something of that sort, right?
> 
> L
> 
> 
> 2009/1/12 Laurent Gautier mailto:lgaut...@gmail.com>>
> 
>  Two things.
> 
>  rpy2.rinterface if making sure that R gets initialized only once
> (otherwise everything breaks), which translates at the level of
> rpy2.robjects as a singleton pattern (r singleton of class R).
> 
>  For evaluating R code, the locking is somehow ensured by Python's
> GIL. All accesses to R are at the C level, and currently none of
> this code is releasing the GIL. There a locking mechanism already
> present in the C code, but it does not have much influence in the
> 2.0.x serie (work on that is under progress, but that's for 2.1.x).
> When done, long evaluations of R code will not hold the GIL, and
> that locking mechanism will be making sure only one thread is doing
> R things.
> 
> 
> 
> L.
> 
> 
> laurent oget wrote:
> 
> Does Rpy2 use any systemwide locking to ensure that only one
> instance is running at a given time or is this only a
> process-wide logging to make sure only one thread within one
> process is using R?
> 
> Thanks,
> 
> Laurent
> 
> 
> 
> 
> 
> 
> --
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> 
> 
> 
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> 
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> 
> 
> 


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Re: [Rpy] Rpy and concurrency

[Laurent Gautier]

Laurent Gautier wrote:
> No need. Because of the GIL, a C call has to return before any thread 
> can proceed (or so I think - I have tried or investigated this in 
> details at the moment).

edit: I have *not* tried.

> laurent oget wrote:
>> But in any case no global between process locking through a file lock 
>> or something of that sort, right?
>>
>> L
>>
>>
>> 2009/1/12 Laurent Gautier > >
>>
>>  Two things.
>>
>>  rpy2.rinterface if making sure that R gets initialized only once
>> (otherwise everything breaks), which translates at the level of
>> rpy2.robjects as a singleton pattern (r singleton of class R).
>>
>>  For evaluating R code, the locking is somehow ensured by Python's
>> GIL. All accesses to R are at the C level, and currently none of
>> this code is releasing the GIL. There a locking mechanism already
>> present in the C code, but it does not have much influence in the
>> 2.0.x serie (work on that is under progress, but that's for 2.1.x).
>> When done, long evaluations of R code will not hold the GIL, and
>> that locking mechanism will be making sure only one thread is doing
>> R things.
>>
>>
>>
>> L.
>>
>>
>> laurent oget wrote:
>>
>> Does Rpy2 use any systemwide locking to ensure that only one
>> instance is running at a given time or is this only a
>> process-wide logging to make sure only one thread within one
>> process is using R?
>>
>> Thanks,
>>
>> Laurent
>>
>>
>> 
>> 
>>
>> 
>> --
>>  
>>
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>>
>>
> 


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Re: [Rpy] compiling rpy2 on windows R-2.8.1

[Laurent Gautier]

Odd.
The error message suggests missing definitions found in R headers.


L.



James Yoo wrote:
> okay, I'm making some progress... finally figured out how to make sure 
> mingw32 is used as the compiler du jour:
> 
> python setup.py build --compiler=mingw32
> 
> running build
> running build_py
> running build_ext
> building 'rpy2.rinterface.rinterface' extension
> \tools\Rtools\MinGW\bin\gcc.exe -mno-cygwin -
> mdll -O -Wall -DWin32=1 -DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1 
> -II:/R/R-2.8.1/include -Irpy\rinterface 
> -Ii:\Python2.5\include -I\43\Python2.5\PC -c 
> rpy\rinterface\array.c -o build\temp.win32-2.5\Release\rpy\rinterface
> \array.o
> \tools\Rtools\MinGW\bin\gcc.exe -mno-cygwin -mdll -O -Wall 
> -DWin32=1 -DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1 
> -II:/R/R-2.8.1/include -Irpy\rinterface 
> -I\Python2.5\include -I\43\Pytho
> n2.5\PC -c rpy\rinterface\r_utils.c -o 
> build\temp.win32-2.5\Release\rpy\rinterface\r_utils.o
> \tools\Rtools\MinGW\bin\gcc.exe -mno-cygwin -mdll -O -Wall 
> -DWin32=1 -DCSTACK_DEFNS=1 -DRIF_HAS_RSIGHAND=1 
> -II:/R/R-2.8.1/include -Irpy\rinterface 
> -Ii:\Python2.5\include -I\43\Pytho
> n2.5\PC -c rpy\rinterface\rinterface.c -o 
> build\temp.win32-2.5\Release\rpy\rinterface\rinterface.o
> rpy\rinterface\rinterface.c: In function 
> 'EmbeddedR_init':rpy\rinterface\rinterface.c:368: error: 
> 'R_SignalHandlers' undeclared (first use in this function)
> rpy\rinterface\rinterface.c:368: error: (Each undeclared identifier is 
> reportedonly once
> rpy\rinterface\rinterface.c:368: error: for each function it appears in.)
> rpy\rinterface\rinterface.c:372: error: 'R_Interactive' undeclared 
> (first use in this function)
> rpy\rinterface\rinterface.c: In function 
> 'EmbeddedR_exception_from_errmessage':
> rpy\rinterface\rinterface.c:473: warning: initialization discards 
> qualifiers from pointer target type
> error: command 'gcc' failed with exit status 1
> 
> 
> On Mon, Jan 12, 2009 at 11:49 AM, James Yoo  > wrote:
> 
> Hmmm, I'm trying to use mingw to compile rpy2.   I've setup my paths
> to only include R, Rtools, mingw... but for some dang reason,
> setup.py keeps finding msvc instead... what am I missing here?
> 
> 
> On Sat, Jan 3, 2009 at 2:22 AM, Laurent Gautier  > wrote:
> 
> James Yoo wrote:
> 
> 
> line 112 (or thereabouts) in setup.py:  
> include_dirs = [x.lstrip('-I') for x in include_dirs]
> 
> lstrip tends to be too greedy and turns
> "-II:\path\to\include" into ":\path\to\include"...
> 
> 
> 
> I see. I misused 'lstrip' (thinking that the characters '-I'
> passed where considered as a string, while they are considered
> as any possible
> characters).
> This means that the bug is more serious: any path/to/include
> with any
> of the characters '-' or 'I' will cause problem.
> 
> The fix you propose does not solve the problem in all cases
> (think of someone having a path like /path/to/My-Includes/).
> 
> I'd propose the following instead:
> 
>for i, d in enumerate(include_dirs):
>if d.startswith('-I'):
>   include_dirs[i] = d[2:]
> 
> Regarding the other errors you encounter, I am afraid that you
> are on your own: all compilations for win32 I know of used mingw
> instead of msvc.
> 
> 
> L.
> 
> 
> 
> 
> 
> On Fri, Jan 2, 2009 at 2:18 PM, Laurent Gautier
> mailto:lgaut...@gmail.com>
> >> wrote:
> 
>James Yoo wrote:
> 
> 
>Sorry for the redundant post, but I felt that I
> should change
>the subject header.
>On Fri, Jan 2, 2009 at 11:31 AM, James Yoo
> mailto:james@gmail.com>
> >  
> 
>  
>   Hi,
> 
>   Running into a couple problems compiling rpy2 on
> windows.
>   I have R_HOME defined and R in the system path.
>   first off in setup.py, def getRinterface_ext:
> 
>   include_dirs = [x.lstrip('-I','') for x in
> include_dirs]
> 
> 
>The line above does not seem to be found in setup.py
>(as the signature for the method str.lstrip() differs)
> 
> 
>  
> 
> 
>   is bad if your drive letter happens to be 'I',
> I've replaced this
>   with x.replace('-I','') in my version.
> 
> 
>1- To my knowledge, s