Undefined symbol "Rf_pythag" while loading spatstat
On 19.03.2011 15:52 (UTC+1), Prof Brian Ripley wrote:
On Sat, 19 Mar 2011, Rainer Hurling wrote:
Today I installed the newest R develepment branch R version 2.14.0 Under development (unstable) (2011-03-18 r54866) on FreeBSD 9.0-CURRENT (amd64). All seems fine so far.
But that is very raw: testing on 2.13.0 alpha would be more useful at this point.
Yes, it is raw. But I need it for some reason. Testing of 2.13.0 alpha (r54865) on FreeBSD 9.0-CURRENT (amd64) shows no problems so far. For testing purposes, I customized the port math/R from b.f. and built from that port, so R installed correct on FreeBSD with gcc45 and gfortran45. As to be expected, I had no problems with R packages using pythag on 2.13.0 alpha. All needed packages could beinstalled. Also, some of my more complicated R scripts (with database access, spatial computings and pdf production) work fine.
After that I updated my R packages with option 'checkBuilt=TRUE'. There are four packages (spatstat, pscl, adehabitatLT, adehabitatHR) which gives an error like this: Error in dyn.load(file, DLLpath = DLLpath, ...) : kann shared object '/usr/local/lib/R/library/spatstat/libs/spatstat.so' nicht laden: /usr/local/lib/R/library/spatstat/libs/spatstat.so: Undefined symbol "Rf_pythag" Fehler: loading failed Ausf?hrung angehalten Fehler: loading failed Searching around I found a hint in http://developer.r-project.org/R_svnlog_2011 about upcoming changes with 'Rf_pythag': ------------------------------------------------------------------------ r54767 | ripley | 2011-03-13 07:30:32 -0400 (Sun, 13 Mar 2011) | 1 line Changed paths: M /trunk/doc/NEWS.Rd M /trunk/src/include/Rmath.h0.in M /trunk/src/nmath/imax2.c keep Rf_pythag for a little longer ------------------------------------------------------------------------ R News of newest devel has three entries about the change: CHANGES IN R VERSION 2.14.0: DEPRECATED AND DEFUNCT: o The entry point pythag formerly in Rmath.h is defunct: use instead the C99 function hypot. CHANGES IN R VERSION 2.13.0: C-LEVEL FACILITIES: o pythag duplicated the C99 function hypot. It is no longer provided, but is used a substitute for hypot in the very unlikely event that the latter is not available. DEPRECATED & DEFUNCT: o The entry point pythag in Rmath.h is deprecated in favour of the C99 function hypot. A wrapper for hypot is provided for R 2.13.x only. Because of that informations I attempted to change 'pythag' against 'hypot' in spatstat/src/lookup.c and it works. Is this the only required adaption which has to be done on the four named packages?
For adehabitatLT, adehabitatHR, simply update. For pscl, spatstat, change pythag to hypot -- the maintainers have been asked for updates.
Ok, as I suspected. You had been aware of these packages before ;-)
You can see CRAN R-devel test results on the CRAN check page. There are a number of other failures due to deprecated -> defunct changes (we make them very early in the development cycle).
I know of this page. It is very useful for identifying problems with packages, especially on Windows, Linux, OSX and Solaris. Understandably it does not support my 'rare' platform FreeBSD directly ;-) Thanks for anwsering and clearing up my request, Rainer Hurling