Subject: configure / linking problem when using hdf5
From: Martin Maechler (firstname.lastname@example.org)
Date: Mon 16 Aug 1999 - 17:05:15 EST
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).
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
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
Martin Maechler <email@example.com> 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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