Re: configure / linking problem when using hdf5

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Subject: Re: configure / linking problem when using hdf5
From: Kurt Hornik (Kurt.Hornik@ci.tuwien.ac.at)
Date: Mon 16 Aug 1999 - 17:19:59 EST


Message-ID: <14263.48031.406276.341146@fangorn.ci.tuwien.ac.at>

>>>>> 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
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