Re: [Swarm-Support] R and hdf5 question on OSX

[paul box]

Thanks Marcus

The command you suggested produced the following output:

yanajipa:~/apps paulbox$ R CMD INSTALL hdf5_1.6.0.tar.gz
--configure-args="--with-hdf5=/usr/local/hdf5_1.6.1"
* Installing *source* package 'hdf5' ...
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for library containing inflate... no
checking for library containing H5open... no
configure: error: Can't find zlib
ERROR: configuration failed for package 'hdf5'


When I check for zlib on the machine, I find zlib.h in a couple of places:
yanajipa:/usr/local paulbox$ locate zlib |less
 [... some lines of output ...]
/usr/include/bzlib.h
/usr/include/zlib.h
/usr/local/include/szlib.h
/usr/share/man/man3/zlib.3
/usr/X11R6/include/X11/extensions/lbxzlib.h
  [... some more lines of output ...]

The deleted lines in the output above point to applications (like
iPodder) that have zlib.so distributed with them, and copies of zlib
in directories on a mounted volume with linux swarm builds.

When I check on the OSX and zlib websites, they say that zlib comes as
part of OSX (which makes sense).

When I try uncompressing the archive and running the ./configure
script from within the directory, specifying where zlib lives:
yanajipa:~/apps/hdf5/R-package paulbox$ ls
ChangeLog       NAMESPACE       config.log      configure.win   src
DESCRIPTION     R               configure       hdf5.pdf        win_readme.txt
INDEX           cleanup         configure.in    man
yanajipa:~/apps/hdf5/R-package paulbox$ ./configure
--with-hdf5=/usr/local/hdf5_1.6.1 --with-zlib=/usr/include
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for library containing inflate... no
checking for library containing H5open... no
configure: error: Can't find zlib

I get the same output if I try to configure with --without-zlib or
other variants of that switch.

This confuses me.  First, from my 'locate' command: is zlib.h enough
to "have zlib" on the system?  If not, where is the rest of it? 
Second, how did Bill Northcott's swarm build on OSX compile without
zlib?

Thanks for any more enlightenment.
Paul


On 11/18/05, Marcus G. Daniels <address@hidden> wrote:
> paul box wrote:
>
> >I am installing the hdf5 library for R on my OSX machine.  The
> >'configure' script searches to find if hdf5 is installed on the
> >machine, and in my case says it is not.  I have hdf5 installed in
> >/usr/local/hdf5_1.6.1, right next to /usr/local/swarm2.2.  I obviously
> >don't have that directory in my library path.
> >
> Paul, this should work:
>
> R CMD INSTALL hdf5_1.6.0.tar.gz
> --configure-args="--with-hdf5=/usr/local/hdf5_1.6.1"
> _______________________________________________
> Support mailing list
> address@hidden
> http://www.swarm.org/mailman/listinfo/support
>


--
//////////////////////////
// Paul Box
// Alice Springs, NT  Australia
//