configure / linking problem when using hdf5

Martin Maechler
1999-08-16T07:05:15Z

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			<><
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