RPMs for R; question about HDf5 compiling, gcc egcs etc

[Paul E. Johnson]

I've got the RPM/SRPM for the version of R at SFI ready to go.  You can
get them at
http://lark.cc.ukans.edu/~pauljohn/Swarm:

-rwxr-xr-x   1 pauljohn pols     2387335 Feb  8 13:54
R-devel-sfi-1999-02-07-1.i386.rpm
-rwxr-xr-x   1 pauljohn pols     1648751 Feb  8 13:54
R-devel-sfi-1999-02-07-1.src.rpm

I installed the RPM on one machine and ran the demos, so it does work,
at least on one machine.

========================================================================


Now I'm working on compiling the HDF5-1.0.1 software and it is giving me
some crap.  I'm compiling it with the configure line:

CC=egcs ./configure --prefix=/test

and that uses the RedHat 5.2 version of egcs, which is 1.0.3a.
But then it gives me this harrassment and I'm not sure how to take it. I
thought egcs was gcc 2.8.1 or better, so maybe I can ignore the compiler
warnings, but certainly not the crash. I do not want to change gcc and
egcs because the RedHat configuration (rightly or wrongly, probably the
latter) somewhat tricky. Recall they keep gcc (without the c++ or obj-C
stuff) and add egcs with a binary named "egcs" rather than gcc. If I
have to change the compiler, then I have to recompile other things, and
the Swarm RPMs won't work anymore. And the RPMs I compile for other
users won't work on their machines unless they change compilers too.

 So if anybody has an idea of a way around this problem, I would
appreciate it.

Look here:

$ make
(cd /usr_sda1/src/redhat/BUILD/hdf5-1.0.1; autoconf)
configure.in:144: warning: AC_TRY_RUN called without default to allow
cross compiling
configure.in:259: warning: AC_TRY_RUN called without default to allow
cross compiling
(cd /usr_sda1/src/redhat/BUILD/hdf5-1.0.1; ./config.status --recheck)
running /bin/sh ./configure  --prefix=/test --no-create --no-recursion
loading cache ./config.cache
checking host system type... i686-unknown-linux
checking for cached host... (cached) i686-unknown-linux
checking for host config file... config/linux
  +------------------------------------------------+
  | You have an old version of gcc. Please upgrade |
  | to 2.8.1 or better.  Continuing anyway, but    |
  | code generation may be wrong on some platforms.|
  +------------------------------------------------+
checking for gcc... (cached) egcs
make[1]: Entering directory `/usr_sda1/src/redhat/BUILD/hdf5-1.0.1'
make[2]: Entering directory `/usr_sda1/src/redhat/BUILD/hdf5-1.0.1/src'
checking whether the C compiler (egcs  -ansi ) is a cross-compiler... no
checking whether we are using GNU C... (cached) yes
checking whether egcs accepts -g... (cached) yes
checking whether make sets ${MAKE}... (cached) yes
checking for a BSD compatible install... (cached) /usr/bin/install -c
checking for ranlib... (cached) ranlib
checking for ar... (cached) ar
checking for GNU Make... yes
checking for production mode... production
checking for ceil in -lm... (cached) yes
checking for main in -lcoug... (cached) no
checking for compress2 in -lz... (cached) yes
checking how to run the C preprocessor... (cached) egcs -E
checking for ANSI C header files... (cached) yes
checking for unistd.h... (cached) yes
checking for zlib.h... (cached) yes
checking for off_t... (cached) yes
checking for size_t... (cached) yes
checking whether byte ordering is bigendian... (cached) no
checking size of short... (cached) 2
checking size of int... (cached) 4
checking size of long... (cached) 4
checking size of long long... (cached) 8
checking size of float... (cached) 4
checking size of double... (cached) 8
checking size of long double... (cached) 12
checking size of size_t... (cached) 4
checking size of off_t... (cached) 4
checking for sizeof hsize_t and hssize_t... large
checking for tm_gmtoff in struct tm... no
checking for global timezone variable... no

-----(blur of messages omitted)---------------
egcs -ansi -Wall -W -Wshadow -Wpointer-arith -Wbad-function-cast
-Wcast-qual -Wcast-align                          
-Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wmissing-declarations -Wnested-e                         
xterns -Winline -mcpu=pentiumpro -march=pentiumpro -O3
-finline-functions -malign-double -                         
fomit-frame-pointer -fschedule-insns2 -I.   -DNDEBUG -UH5_DEBUG_API -c
H5detect.c
H5detect.c: In function `print_header':
H5detect.c:879: warning: implicit declaration of function `gethostname'
egcs -ansi -Wall -W -Wshadow -Wpointer-arith -Wbad-function-cast
-Wcast-qual -Wcast-align                          
-Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes
-Wmissing-declarations -Wnested-e                         
xterns -Winline -mcpu=pentiumpro -march=pentiumpro -O3
-finline-functions -malign-double -                         
fomit-frame-pointer -fschedule-insns2 -o H5detect H5detect.o -lz -lm 
./H5detect >H5Tinit.c
Building dependencies for H5.c
Building dependencies for H5A.c
Building dependencies for H5AC.c
Building dependencies for H5B.c
Building dependencies for H5D.c
Building dependencies for H5E.c
H5E.c: in function `H5Eprint':
H5E.c:244: warning: trace info was not inserted
H5E.c: in function `H5Ewalk_cb':
H5E.c:325: warning: trace info was not inserted
---------(some messages
omitted)------------------------------------------------

egcs -ansi -Wall -W -Wshadow -Wpointer-arith -Wbad-function-cast
-Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes
-Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Winline
-mcpu=pentiumpro -march=pentiumpro -O3 -finline-functions -malign-double
-fomit-frame-pointer -fschedule-insns2 -I.   -DNDEBUG -UH5_DEBUG_API -c
H5Fstdio.c
H5Fstdio.c: In function `H5F_stdio_open':
H5Fstdio.c:128: warning: implicit declaration of function `fileno'
egcs -ansi -Wall -W -Wshadow -Wpointer-arith -Wbad-function-cast
-Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes
-Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Winline
-mcpu=pentiumpro -march=pentiumpro -O3 -finline-functions -malign-double
-fomit-frame-pointer -fschedule-insns2 -I.   -DNDEBUG -UH5_DEBUG_API -c
H5G.c
H5G.c: In function `H5G_loc':
H5G.c:1631: warning: enumeration value `H5I_REFERENCE' not handled in
switch
egcs -ansi -Wall -W -Wshadow -Wpointer-arith -Wbad-function-cast
-Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes
-Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Winline
-mcpu=pentiumpro -march=pentiumpro -O3 -finline-functions -malign-double
-fomit-frame-pointer -fschedule-insns2 -I.   -DNDEBUG -UH5_DEBUG_API -c
H5Gent.c
---------(some messages
omitted)------------------------------------------

egcs -ansi -Wall -W -Wshadow -Wpointer-arith -Wbad-function-cast
-Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes
-Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Winline
-mcpu=pentiumpro -march=pentiumpro -O3 -finline-functions -malign-double
-fomit-frame-pointer -fschedule-insns2 -I.   -DNDEBUG -UH5_DEBUG_API -c
H5Tconv.c
/usr/include/__math.h: In function `tan':
In file included from /usr/include/math.h:208,
                 from H5Tconv.c:17:
/usr/include/__math.h:127: parse error before `__attribute__'
/usr/include/__math.h:130: `__value2' undeclared (first use this
function)
/usr/include/__math.h:130: (Each undeclared identifier is reported only
once
/usr/include/__math.h:130: for each function it appears in.)
make[2]: *** [H5Tconv.o] Error 1
make[2]: Leaving directory `/usr_sda1/src/redhat/BUILD/hdf5-1.0.1/src'
make[1]: *** [lib] Error 1
make[1]: Leaving directory `/usr_sda1/src/redhat/BUILD/hdf5-1.0.1'
make: *** [all] Error 2
address@hidden hdf5-1.0.1]$ 

-- 
Paul E. Johnson                       email: address@hidden
Dept. of Political Science            http://lark.cc.ukans.edu/~pauljohn
University of Kansas                  Office: (913) 864-9086
Lawrence, Kansas 66045                FAX: (913) 864-5700

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