I've installed hdf5 [library & includes] here locally, last week. [see ?hdf5save in R] There is a remaining compilation / linking problem for me: The hdf5 library uses "compress2" a routine defined in Gnu's zlib, but not available in the zlib that comes with X11R6.3 (which we have installed). Now unfortunately, the final link statement for R (0.65) [for me, with hdf5 enabled] is gcc -o ../../bin/R.X11 arithmetic.o ....[omitted] version.o \ ../unix/libunix.a ../appl/libappl.a ../nmath/libmath.a -lSM -lICE -L/usr/local/X11R6.3/lib -R/usr/local/X11R6.3/lib -lX11 -lsocket -lnsl -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC4.2/lib -L/usr/ccs/lib -L/usr/lib /opt/SUNWspro/SC4.2/lib/libM77.a -lF77 -lsunmath -lm -lcx -lreadline -lhdf5 -lz -ldl -ltermcap -lm Undefined first referenced symbol in file compress2 /usr/local/lib/libhdf5.a(H5Z.o) ld: fatal: Symbol referencing errors. No output written to ../../bin/R.X11 ------------- Which happens because there was an -L/usr/local/X11R6.3/lib before the "-lhdf5 -lz". In the local LD_LIBRARY_PATH, /usr/local/lib (which has the proper libz.a *with* compress2) comes before the X11/lib (which has the wrong libz.a). Of course, I can manually put -L/usr/local/lib BEFORE the -L/usr/local/X11R6.3/lib, but I wonder what would be recommended, "officially". Putting " -lhdf5 -lz " BEFORE "-L/usr/local/X11R6.3/lib" simply fails as well [undefined symbol "compress2"]. Having two different "libz.a" in LD_LIBRARY_PATH doesn't make sense anyway. Would any of you know if I can safely get rid of X11's one now that I have GNU's ? Martin Maechler <maechler@stat.math.ethz.ch> http://stat.ethz.ch/~maechler/ Seminar fuer Statistik, ETH-Zentrum SOL G1 Sonneggstr.33 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-3408 fax: ...-1086 <>< -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- 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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
>>>>> Martin Maechler writes:> I've installed hdf5 [library & includes] here locally, last week. > [see ?hdf5save in R]> There is a remaining compilation / linking problem for me:> The hdf5 library uses "compress2" a routine defined in Gnu's zlib, > but not available in the zlib that comes with X11R6.3 (which we have installed).> Now unfortunately, > the final link statement for R (0.65) [for me, with hdf5 enabled] is> gcc -o ../../bin/R.X11 arithmetic.o ....[omitted] version.o \ > ../unix/libunix.a ../appl/libappl.a ../nmath/libmath.a -lSM -lICE -L/usr/local/X11R6.3/lib -R/usr/local/X11R6.3/lib -lX11 -lsocket -lnsl -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC4.2/lib -L/usr/ccs/lib -L/usr/lib /opt/SUNWspro/SC4.2/lib/libM77.a -lF77 -lsunmath -lm -lcx -lreadline -lhdf5 -lz -ldl -ltermcap -lm> Undefined first referenced > symbol in file > compress2 /usr/local/lib/libhdf5.a(H5Z.o) > ld: fatal: Symbol referencing errors. No output written to ../../bin/R.X11> ------------- > Which happens because there was an -L/usr/local/X11R6.3/lib > before the "-lhdf5 -lz". > In the local LD_LIBRARY_PATH, > /usr/local/lib (which has the proper libz.a *with* compress2) > comes before the X11/lib (which has the wrong libz.a).> Of course, I can manually > put -L/usr/local/lib BEFORE the -L/usr/local/X11R6.3/lib, > but I wonder what would be recommended, "officially".> Putting " -lhdf5 -lz " BEFORE "-L/usr/local/X11R6.3/lib" > simply fails as well [undefined symbol "compress2"].> Having two different "libz.a" in LD_LIBRARY_PATH doesn't make sense > anyway. Would any of you know if I can safely get rid of X11's one > now that I have GNU's ?We currently have ALL_LIBS = $(RLIBS) $(ALL_X_LIBS) $(FLIBS) $(R_XTRA_LIBS) $(LIBS) I assume that the order is mostly for historic reasons. You could try putting ALL_X_LIBS last and see what happens ...e.g., ALL_LIBS = $(RLIBS) $(R_XTRA_LIBS) $(FLIBS) $(LIBS) $(ALL_X_LIBS) -k -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- 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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._