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Gregory R. Warnes

2001-Jul-23 22:25 UTC

[Rd] Installing RSPython with R 1.3.0

To get RSPython installed on my debian test box, I had to make a couple
of changes not listed in
ftp://www.omegahat.org/pub/Omega/RSPython/FAQ.html 

1) I had to change $R_HOME/src/modules/X11 :

$(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES)
        $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
$(R_X11_la_LIBADD) $(LIBS) 

to

$(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES)
        $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
$(R_X11_la_LIBADD) $(LIBS) -L$(R_HOME)/bin -lR

2) I had the same link problem with ctest, so I changed

PKG_LIBS =  -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm

to

PKG_LIBS =  -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm
-L$(R_HOME)/bin -lR


3)  Will all libraries that get loaded into R inside of python require
this?


If I try to load other 'recommended' packages that include C code I get
dyn.load erros, EG:
>>> RS.call("library","splines")Error in dyn.load(x, as.logical(local), as.logical(now)) :
        unable to load shared library
"/usr/local/lib/R/library/splines/libs/splines.so":
  /usr/local/lib/R/library/splines/libs/splines.so: undefined symbol:
R_NaN
Error in function (package, help, lib.loc = .lib.loc, character.only FALSE,  :
        .First.lib failed
In the local error handler
In the local error handler
Error in if (!is.numeric(name) || name != (pos <- as.integer(name))) { :
        missing value where logical needed
In the local error handler
In the local error handler
Error in pos.to.env(pos) : invalid argument
In the local error handler
In the local error handler
Error in objects(lib.pos) : invalid envir= argument
In the local error handler
['RSPython', 'ctest', 'base']

-Greg
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A.J. Rossini

2001-Jul-23 22:38 UTC

head link

[Rd] Re: [Omega-remote] Installing RSPython with R 1.3.0

I'm not seeing this:

121$ python
Python 1.5.2 (#0, Apr 10 2001, 10:03:44)  [GCC 2.95.3 20010219
(prerelease)] on linux2
Copyright 1991-1995 Stichting Mathematisch Centrum,
Amsterdam>>> import RS
Initialized R-Python interface package.>>> RS.call("library","splines")['splines', 'RSPython', 'ctest',
'base']>>> 

for example.  

I made a slightly different set of changes (I didn't make the ones you
suggested, Greg).

I'd be happy to email a copy of the new version
(RSPython_0.3-1ajr.tar.gz, use as RSPython_0.3-1.tar.gz) which has
configure patched to find the Debian default locations of things; it
would be interesting to see if it works for you (it did for me on 2
Sid/unstable boxes).

best,
-tony


>>>>> "GRW" == Gregory R Warnes <greg@warnes.net>
writes:
    GRW> To get RSPython installed on my debian test box, I had to
    GRW> make a couple of changes not listed in
    GRW> ftp://www.omegahat.org/pub/Omega/RSPython/FAQ.html

    GRW> 1) I had to change $R_HOME/src/modules/X11 :

    GRW> $(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES)
    GRW> $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
    GRW> $(R_X11_la_LIBADD) $(LIBS)

    GRW> to

    GRW> $(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES)
    GRW> $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
    GRW> $(R_X11_la_LIBADD) $(LIBS) -L$(R_HOME)/bin -lR

    GRW> 2) I had the same link problem with ctest, so I changed

    GRW> PKG_LIBS = -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm

    GRW> to

    GRW> PKG_LIBS = -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm
    GRW> -L$(R_HOME)/bin -lR


    GRW> 3) Will all libraries that get loaded into R inside of python
    GRW> require this?


    GRW> If I try to load other 'recommended' packages that include C
    GRW> code I get dyn.load erros, EG:

    >>>> RS.call("library","splines")
    GRW> Error in dyn.load(x, as.logical(local), as.logical(now)) :
    GRW> unable to load shared library
    GRW> "/usr/local/lib/R/library/splines/libs/splines.so":
    GRW> /usr/local/lib/R/library/splines/libs/splines.so: undefined
    GRW> symbol: R_NaN Error in function (package, help, lib.loc     GRW>
.lib.loc, character.only = FALSE, : .First.lib failed In the
    GRW> local error handler In the local error handler Error in if
    GRW> (!is.numeric(name) || name != (pos <- as.integer(name))) { :
    GRW> missing value where logical needed In the local error handler
    GRW> In the local error handler Error in pos.to.env(pos) : invalid
    GRW> argument In the local error handler In the local error
    GRW> handler Error in objects(lib.pos) : invalid envir= argument
    GRW> In the local error handler ['RSPython', 'ctest',
'base']

    GRW> -Greg _______________________________________________
    GRW> Omega-remote mailing list - Omega-remote@www.omegahat.org
    GRW> http://www.omegahat.org/mailman/listinfo/omega-remote




-- 
A.J. Rossini				Rsrch. Asst. Prof. of Biostatistics
U. of Washington Biostatistics		rossini@u.washington.edu	
FHCRC/SCHARP/HIV Vaccine Trials Net	rossini@scharp.org
-------- (wednesday/friday is unknown) --------
FHCRC: M-Tu : 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email
UW:    Th   : 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX

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Duncan Temple Lang

2001-Jul-23 23:36 UTC

head link

[Rd] Re: [Omega-remote] Installing RSPython with R 1.3.0

Hi Greg.

  What you are seeing is probably a result of using R embedded within another
application/system (Python in this case) but having R originally compiled
without support for R as a shared library. If you were to build R in the default
manner, i.e.
    configure
    make
and then re-configure to build as a shared library
    configure --enable-R-shlib
    make
the shared objects that make up the modules and package libraries
will not be rebuilt. Perhaps they should, but that is not currently
what happens.

 If you were to start afresh (e.g. make distclean) 
and then configure with shared library support
(
    configure --enable-R-shlib
    make
)
all should be well and all the .so's that R attempts to load will
also be linked against libR.so and so the symbols within R on which
they depend will be located.

  Hope this is the correct diagnosis of the problem.

     D.

Gregory R. Warnes wrote:> 
> To get RSPython installed on my debian test box, I had to make a couple
> of changes not listed in
> ftp://www.omegahat.org/pub/Omega/RSPython/FAQ.html 
> 
> 1) I had to change $R_HOME/src/modules/X11 :
> 
> $(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES)
>         $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
> $(R_X11_la_LIBADD) $(LIBS) 
> 
> to
> 
> $(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES)
>         $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
> $(R_X11_la_LIBADD) $(LIBS) -L$(R_HOME)/bin -lR
> 
> 2) I had the same link problem with ctest, so I changed
> 
> PKG_LIBS =  -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm
> 
> to
> 
> PKG_LIBS =  -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm
> -L$(R_HOME)/bin -lR
> 
> 
> 3)  Will all libraries that get loaded into R inside of python require
> this?
> 
> 
> If I try to load other 'recommended' packages that include C code I
get
> dyn.load erros, EG:
> 
> >>> RS.call("library","splines")
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>         unable to load shared library
> "/usr/local/lib/R/library/splines/libs/splines.so":
>   /usr/local/lib/R/library/splines/libs/splines.so: undefined symbol:
> R_NaN
> Error in function (package, help, lib.loc = .lib.loc, character.only >
FALSE,  :
>         .First.lib failed
> In the local error handler
> In the local error handler
> Error in if (!is.numeric(name) || name != (pos <- as.integer(name))) { :
>         missing value where logical needed
> In the local error handler
> In the local error handler
> Error in pos.to.env(pos) : invalid argument
> In the local error handler
> In the local error handler
> Error in objects(lib.pos) : invalid envir= argument
> In the local error handler
> ['RSPython', 'ctest', 'base']
> 
> -Greg
> _______________________________________________
> Omega-remote mailing list  -  Omega-remote@www.omegahat.org
> http://www.omegahat.org/mailman/listinfo/omega-remote-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-devel 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-devel-request@stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._

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