[Bioperl-l] can people with HP/Irix/Alpha confirm these reported problems with bioperl-1.0 ?

chris dagdigian dag@sonsorol.org
Fri, 22 Mar 2002 16:19:23 -0500


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This is a troubling bug report. Can others confirm? I've had zero 
trouble with OpenBSD and Linux but don't have easy access to Irix, HPUX 
or Alpha systems. We may have gotten bitten by the huge size of our 
distribution.

Actually, HP just donated a Itanium box to us so I'll have HPUX to work 
on in a few days.

-Chris

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Date: Fri, 22 Mar 2002 13:31:25 -0500

JitterBug notification

new message incoming/1133

Message summary for PR#1133
	From: batalov@gnf.org
	Subject: bioperl-1.0 doesn't build
	Date: Fri, 22 Mar 2002 13:31:24 -0500
	0 replies 	0 followups

====> ORIGINAL MESSAGE FOLLOWS <====

>From batalov@gnf.org Fri Mar 22 13:31:24 2002
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Date: Fri, 22 Mar 2002 13:31:24 -0500
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From: batalov@gnf.org
To: bioperl-bugs@bioperl.org
Subject: bioperl-1.0 doesn't build

Full_Name: Serge Batalov
Module: bioperl
Version: 1.0
PerlVer: 5.6.1
OS: IRIX,HP,DEC/Compaq-Alpha
Submission from: pat.gnf.org (63.196.132.64)


#> perl -MCPAN -e shell
#>     ...install Bundle::...
#> install B/BI/BIRNEY/bioperl-1.0.tar.gz
fails in 'make' with 'Arg list too long' message

What happens is that a list of things to MakeMake is too long for the
command line (in "# --- MakeMaker pm_to_blib section")

For the reference, command-line length limit is not 
a shell limit; it is built in kernel/libc.
It has to do with the execvp()
limit ARG_MAX, which is 4096 characters in POSIX,
but most systems have it inflated, to different extents.

Test it with
--------arg_max.c--------
#include <unistd.h>
main() {
  printf("ARG_MAX = %ld\n  This is the maximum length of the arguments to the
exec() family of functions\n",
         sysconf(_SC_ARG_MAX));
  exit(0); 
}
--------

Linux is the second most generous (most systems tested show 64K).
It is topped only by SUN (tried 5.8), where it is 128K.
IRIX and DEC/Alpha have 20K limit.
HP -- just 8K.

It would be prudent to stick to the POSIX limit, and
split the pm_to_blib into pieces.


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