[Bioperl-l] bioperl-ext1.4 installation problem (Sean MacEachern)

[Sean.Maceachern at dpi.vic.gov.au]

Hello,

I am trying to install bioperl on a machine running fedora core 3 and I
have run across a few problems installing bioperl-ext-1.4. I have installed
all of the appropriate Inline and io_lib files however whenever I try to
execute the perl Makefile.PL command I get the following error:

[root at fred bioperl-ext-1.4] # perl Makefile.PL
Checking if your kit is complete...
Looks good
Writing Makefile for Bio::Ext::Align
Found Staden io_lib "libread" in /usr/local/lib ...
Automatically using the Read.h found in /usr/local/include/io_lib ...
Writing Makefile for Bio::SeqIO::staden::read
Writing Makefile for Bio
One or more DATA sections were not processed by Inline.


I then attempted to make the staden::read file independently, however I
came across another error which I believe may have something to do with a
line out of place in one of the io_lib *.h files but was unable to
determine which file it was (Read.h os.h etc...). I have attached some of
the error mesage below, hopefully someone will be able to help me identify
the problem.


[root at fred read] # perl Makefile.PL
Writing Makefile for Bio::SeqIO::staden::read
[root at fred read] # make
gcc -c  -I/usr/local/genomics/bioperl-ext-1.4/Bio/SeqIO/staden
-I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
-DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe
-m32 -march=i386 -mtune=pentium4   -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
-fPIC "-I/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE"   read.c
In file included from /usr/local/include/io_lib/Read.h:43,
                 from read.xs:5:
/usr/local/include/io_lib/os.h:9:1: warning: "INT_MAX" redefined
In file included from /usr/include/sys/param.h:22,
                 from
/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE/perl.h:446,
                 from read.xs:2:
/usr/lib/gcc/i386-redhat-linux/3.4.3/include/limits.h:74:1: warning: this
is the location of the previous definition
In file included from /usr/local/include/io_lib/Read.h:43,
                 from read.xs:5:
/usr/local/include/io_lib/os.h:10:1: warning: "SHRT_MAX" redefined
In file included from /usr/include/sys/param.h:22,
                 from
/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE/perl.h:446,
                 from read.xs:2:
/usr/lib/gcc/i386-redhat-linux/3.4.3/include/limits.h:60:1: warning: this
is the location of the previous definition
In file included from /usr/local/include/io_lib/Read.h:43,
                 from read.xs:5:
/usr/local/include/io_lib/os.h:24:4: #error No 2-byte integer type found.
/usr/local/include/io_lib/os.h:34:4: #error No 4-byte integer type found.
In file included from /usr/local/include/io_lib/Read.h:43,
                 from read.xs:5:
/usr/local/include/io_lib/os.h:40: error: syntax error before "int_2"
/usr/local/include/io_lib/os.h:40: warning: data definition has no type or
storage class
/usr/local/include/io_lib/os.h:41: error: syntax error before "uint_2"
/usr/local/include/io_lib/os.h:41: warning: data definition has no type or
storage class
/usr/local/include/io_lib/os.h:42: error: syntax error before "int_4"
/usr/local/include/io_lib/os.h:42: warning: data definition has no type or
storage class
/usr/local/include/io_lib/os.h:43: error: syntax error before "uint_4"
/usr/local/include/io_lib/os.h:43: warning: data definition has no type or
storage class



Regards,


Sean