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

[Heikki Lehvaslaiho]

chris dagdigian wrote:
> 
> 
> 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.

Serge seems to know what he is talking about. In the past I've had the same
problem in IRIX but I never bothered to find out what exactly was wrong.
Thanks Serge!



Confirmed on IRIX:

cetus /tmp/bioperl-1.0> make
make: execvp: /bin/sh: Arg list too long
make: *** [pm_to_blib] Error 127
cetus /tmp/bioperl-1.0>

I got curious and ran Serges program on various platforms:

IRIX64:  ARG_MAX =   20480
SUNOS:   ARG_MAX = 1048320
OSF1:    ARG_MAX =   38912
LINUX:   ARG_MAX =  131072

I've no access to HPUX.


Looks like we have to come up with a 1.01 quite soon.

	-Heikki


> Actually, HP just donated a Itanium box to us so I'll have HPUX to work
> on in a few days.
> 
> -Chris
> 
>   ----------------------------------------------------------------------------
> 
> Subject: [Bioperl-guts-l] Notification: incoming/1133
> Date: Fri, 22 Mar 2002 13:31:25 -0500
> From: bioperl-bugs@bioperl.org
> To: bioperl-guts-l@bioperl.org
> 
> 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
> Received: from localhost (localhost [127.0.0.1])
>         by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g2MIVOkO005811
>         for <bioperl-bugs@pw600a.bioperl.org>; Fri, 22 Mar 2002 13:31:24 -0500
> Date: Fri, 22 Mar 2002 13:31:24 -0500
> Message-Id: <200203221831.g2MIVOkO005811@pw600a.bioperl.org>
> 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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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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