Bioperl-guts: distribution issues

[Steve Chervitz]

Ewan and Chris:

I tested the installation and everything went well, but a few issues
came up: 

1) We are requiring 5.004 but can probably get away with 5.003. I know 
   all of my modules are 5.003-safe. I changed the Makefile.PL and the
   modules Bio::Seq.pm & Bio::Parse to require 5.003 instead of 5.004 and 
   all the make tests worked. 

   Unless we are doing 5.004-specific things like $object->isa() and
   $object->can(), I say don't require 5.004. We can always require
   5.004 and higher with later distributions. This way, we can cover a
   wider perl install base.

   You might argue that 5.004 has been out for a long time (nearly 2
   years, I think), who will be using anything earlier? 
   This is true, I know some respected institutions that have 
   yet to upgrade from 5.003. The excuse: "we need to test all of our 
   production scripts first", which gets put off since everything 
   is working and there are enough new things to do.

   This is a major issue that we should discuss especially now that
   5.005 is out with even more features. 

2) I ran into some permission trouble when installing using the 
   perl Makefile.PL PREFIX=/mypath command. I also needed a
   INSTALLSITELIB=/mypath/lib.

3) I reorganized the README a bit and explained about INSTALLSITELIB. I
   also updated bioperl.pod to include the perl version requirement as
   a TODO item. Also added some entries to PLATFORMS (with note about
   Compile/SW trouble, see below).

4) Ewan, I ran into some errors with the Compile/SW installation. 
   Reports are included below. Likely something trivial.

5) I created a new version of the distribution on bio.perl.org at 
   ~sac/bioperl-0.04.tar.gz
   Ewan, make sure I assembled it properly (it should be fine
   if "make dist" is sufficient). 
   I have not checked in the new modules or other altered files
   into cvs.

Not yet ready for prime-time, but almost there.

-SteveC

======================================================================
Error reports for building Compile/SW:

On a dec:

> gcc -v
Reading specs from /tools/gnu/lib/gcc-lib/alpha-dec-osf3.2/2.7.2/specs
gcc version 2.7.2

>cd Compile/SW
>perl Makefile.PL 
>make
mkdir ./blib
mkdir ./blib/lib
mkdir ./blib/arch
mkdir ./blib/arch/auto
mkdir ./blib/arch/auto/bp_sw
mkdir ./blib/lib/auto
mkdir ./blib/lib/auto/bp_sw
cp bp_sw.pm ./blib/lib/bp_sw.pm
AutoSplitting bp_sw (./blib/lib/auto/bp_sw)
DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC;  cd libs && make libsw.a -e
gcc -c -O -c aln.c
In file included from /usr/include/sys/timers.h:46,
                 from /tools/gnu/lib/gcc-lib/alpha-dec-osf3.2/2.7.2/include/time.h:167,
                 from wisetime.h:7,
                 from wisebase.h:44,
                 from aln.h:6,
                 from aln.c:4:
/usr/include/sys/sysmisc.h:100: parse error before `pthread_attr_t'
/usr/include/sys/sysmisc.h:100: warning: no semicolon at end of struct or union
/usr/include/sys/sysmisc.h:100: warning: no semicolon at end of struct or union
/usr/include/sys/sysmisc.h:102: warning: data definition has no type or storage class
/usr/include/sys/sysmisc.h:103: parse error before `}'
/usr/include/sys/sysmisc.h:103: warning: data definition has no type or storage class
In file included from /tools/gnu/lib/gcc-lib/alpha-dec-osf3.2/2.7.2/include/time.h:167,
                 from wisetime.h:7,
                 from wisebase.h:44,
                 from aln.h:6,
                 from aln.c:4:
/usr/include/sys/timers.h:98: warning: redefinition of `clockid_t'
/tools/gnu/lib/gcc-lib/alpha-dec-osf3.2/2.7.2/include/time.h:96: warning: `clockid_t' previously declared here
*** Exit 1
Stop.
*** Exit 1
Stop.

===========================
on solaris:

> gcc -v
Reading specs from /tools/gnu/lib/gcc-lib/sparc-sun-solaris2.6/2.7.2/specs
gcc version 2.7.2

>cd Compile/SW
>perl Makefile.PL 
> make
cp bp_sw.pm ./blib/lib/bp_sw.pm
AutoSplitting bp_sw (./blib/lib/auto/bp_sw)
make: Warning: Infinite loop: Target `libs/libsw.a' depends on itself
DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \
cd libs && make libsw.a -e
cc -c -O  -c  aln.c
/usr/ucb/cc:  language optional software package not installed
*** Error code 1
make: Fatal error: Command failed for target `aln.o'
Current working directory /amd/fafner/home/fafner3/sac/bioperl/bioperl-0.04/Compile/SW/libs
*** Error code 1
make: Fatal error: Command failed for target `libs/libsw.a'

My attempt to forcing gcc 
> perl Makefile.PL CC=gcc
was ignored since I got the same "cc -c -O  -c  aln.c" command.

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