[R-sig-Geo] [Gstat-info] Re: Problem installing gstat into R

Roger Bivand Roger.Bivand at nhh.no
Thu Dec 13 22:39:54 CET 2007


On Thu, 13 Dec 2007, Edzer Pebesma wrote:

> I guess then that is the issue: cygwin is not well supported, or causing 
> trouble, for reasons beyond my comprehension. Why not use the standard 
> windows distribution?

It looks like a cygwin/WIN32 crash - the lines given try to call R 
functions only (I think) available in the Win32 build:

# ifdef WIN32
 	R_FlushConsole();
 	R_ProcessEvents();
# endif

and

#ifdef USING_R
# ifdef WIN32
 		R_ProcessEvents(); /* avoid terminal freeze in R/Win */
# endif
 		R_CheckUserInterrupt();
#endif

respectively. Could you try commenting out those blocks in gstat/src/s.c - 
a nasty fix, but may get you something you can use but cannot interupt?

Building R on cygwin is such a rough ride that I guess you didn't have a 
feasible alternative, but as Edzer says, it puts you very much on your 
own.

Roger

PS:

in gstat/src:

$ grep WIN32 *.[ch]
defaults.h:#ifndef WIN32
defs.h:#ifdef SPLUS6WIN32
defs.h:#  ifndef WIN32
defs.h:#   define WIN32
defs.h:# elif defined (WIN32) /* NT/98/9x/? */
plot.c:#ifdef WIN32
plot.c:#ifdef WIN32
s.c:# ifdef WIN32
s.c:# ifdef WIN32
s.c:#ifndef WIN32


> --
> Edzer
>
> Edward Tomlinson schrieb:
>>  Hi Edzer and Roger,
>>
>>  The R ./configure was taken from the Installation and Administration
>>  manual for installing R on Cygwin.
>>
>>  i have tried R CMD INSTALL ./gstat_0.9-42.tar.gz with the same result as
>>  install.packages.
>>
>>  Results from session info.
>> >  sessionInfo()
>>  R version 2.6.1 (2007-11-26)
>>  i686-pc-cygwin
>>
>>  locale:
>>  C
>>
>>  attached base packages:
>>  [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>  loaded via a namespace (and not attached):
>>  [1] rcompgen_0.1-17
>> >
>> 
>>
>>  rgdal loads okay (have not tested for working)
>> >  library(rgdal)
>>  Loading required package: sp
>>  Geospatial Data Abstraction Library extensions to R successfully loaded
>> >
>>
>>  Thank you for helping me with the problem.
>>
>>  CHeers,
>>  Ed
>>
>>  On 12/12/2007, *Roger Bivand* <Roger.Bivand at nhh.no
>>  <mailto:Roger.Bivand at nhh.no>> wrote:
>>
>>      On Wed, 12 Dec 2007, Edzer Pebesma wrote:
>> 
>> >  Edward,
>> > 
>> >  My experiences here are limited; what I always do to install a
>>      source
>> >  package is something like:
>> > 
>> >  R CMD INSTALL -l /home/edzer/S/library R/gstat_0.9-42.tar.gz
>> > 
>> >  Could you please verify whether that works?
>>
>>      From the output below, I think that we know too little about the
>>      system to
>>      call. What does sessionInfo() say inside R? Secondly, why is your
>>      ./configure the way it is? Did you make install R itself - it looks as
>>      though the R shared objects are not being found. If gstat doesn't
>>      install,
>>      I'm surprised that rgdal did.
>>
>>      Roger
>> 
>> >  --
>> >  Edzer
>> > 
>> >  Edward Tomlinson wrote:
>> > >  Hi List,
>> > > 
>> > >  I am not entirely sure where i should be asking this question
>>      so i will
>> > >  start here.
>> > > 
>> > >  I am trying to install the gstat package into R so it can be
>>      used by a
>> > >  component of GRASS.
>> > > 
>> > >  However i cannot get gstat installed. I have already installed
>>      spgrass6
>> > >  package and its dependencies, however gstat will not install.
>>      Details below.
>> > > 
>> > >  Any ideas would be appreciated.
>> > > 
>> > >  Further info...
>> > > 
>> > >  I downloaded and installed from source. Original files came
>>      from CRAN
>> > >  website.
>> > > 
>> > >  I followed instructions from Install and Admin manual. It
>>      suggested to build
>> > >  in the following way...
>> > > 
>> > >  ./configure --disable-nls --disable-mbcs --enable-R-shlib
>> > >  make
>> > > 
>> > >  Everything worked fine. I have been able to install other
>>      packages for R
>> > >  such as maptools, spgrass6 and its dependencies.
>> > > 
>> > >  Thanks,
>> > >  Ed
>> > > 
>> > >  R version 2.6.1 (2007-11-26)
>> > >  Copyright (C) 2007 The R Foundation for Statistical Computing
>> > >  ISBN 3-900051-07-0
>> > > 
>> > > 
>> > > >  install.packages("gstat")
>> > > > 
>> > >  ...
>> > >  Content type 'application/x-tar' length 895559 bytes (874 Kb)
>> > >  opened URL
>> > >  ==================================================
>> > >  downloaded 874 Kb
>> > > 
>> > >  /usr/local/lib/R/library
>> > >  * Installing *source* package 'gstat' ...
>> > >  ....
>> > >  gcc -std=gnu99 -shared -L/usr/local/lib -o gstat.dll block.o
>>      chfactor.o
>> > >  copy.o d
>> > >  ata.o direct.o err.o fit.o getest.o gls.o glvars.o hsehldr.o
>>      init.o ivecop.olex
>> > >  .o lm.o lufactor.o machine.o mapio.o matop.o matrixio.o
>>      meminfo.o memory.omemst
>> > >  at.o msim.o norm.o nsearch.o otherio.o parse.o plot.o polygon.o
>>      pqueue.opredict
>> > >  .o pxop.o qrfactor.o random.o read.o reml.o report.o s.o
>>      select.o sem.o
>> > >  sim.o so
>> > >  lve.o sparse.o sparseio.o spbkp.o spchfctr.o splufctr.o sprow.o
>>      spswap.o
>> > >  stat.o
>> > >  submat.o userio.o utils.o vario.o vario_fn.o vario_io.o vecop.o
>>      version.owritec
>> > >  md.o xvalid.o   -L/usr/local/lib/R/lib -lR
>> > >  s.o: In function `gstat_predict':
>> > >  /tmp/R.INSTALL.uA1352/gstat/src/s.c:495: undefined reference to
>> > >  `_R_ProcessEvent
>> > >  s'
>> > >  /tmp/R.INSTALL.uA1352/gstat/src/s.c:517: undefined reference to
>> > >  `_R_ProcessEvent
>> > >  s'
>> > >  Info: resolving _R_NaReal by linking to __imp__R_NaReal
>>      (auto-import)
>> > >  Info: resolving _R_DimSymbol by linking to __imp__R_DimSymbol
>>      (auto-import)
>> > >  collect2: ld returned 1 exit status
>> > >  make: *** [gstat.dll ] Error 1
>> > >  chmod: cannot access `/usr/local/lib/R/library/gstat/libs/*':
>>      No such file
>> > >  or di
>> > >  rectory
>> > >  ERROR: compilation failed for package 'gstat'
>> > >  ** Removing '/usr/local/lib/R/library/gstat'
>> > > 
>> > > 
>> > >  Warning message:
>> > >  In install.packages("gstat") :
>> > >    installation of package 'gstat' had non-zero exit status
>> > > 
>> > > 
>> > >       [[alternative HTML version deleted]]
>> > > 
>> > >  _______________________________________________
>> > >  R-sig-Geo mailing list
>> > >  R-sig-Geo at stat.math.ethz.ch <mailto:R-sig-Geo at stat.math.ethz.ch>
>> > >  https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>> > > 
>> > 
>> >  _______________________________________________
>> >  R-sig-Geo mailing list
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>> >  https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>      <https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
>> > 
>>
>>      --
>>      Roger Bivand
>>      Economic Geography Section, Department of Economics, Norwegian
>>      School of
>>      Economics and Business Administration, Helleveien 30, N-5045 Bergen,
>>      Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
>>      e-mail: Roger.Bivand at nhh.no <mailto:Roger.Bivand at nhh.no>
>> 
>>
>>  ------------------------------------------------------------------------
>>
>>  _______________________________________________
>>  Gstat-info mailing list
>>  Gstat-info at geo.uu.nl
>>  http://mailman.geo.uu.nl/mailman/listinfo/gstat-info
>> 
>
>
>

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no




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