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

[Andreas Matern]

I can confirm that we have the same problem with irix.... just in case 
it matters...  I never bothered to play with it, using bioperl on the 
linux farm is just fine by me...

-Andreas

Heikki Lehvaslaiho wrote:

> 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.
>>
>>_______________________________________________
>>Bioperl-guts-l mailing list
>>Bioperl-guts-l@bioperl.org
>>http://bioperl.org/mailman/listinfo/bioperl-guts-l
>>
> 


-- 
--------------
Andreas Matern
Bioinformatician
Bioinformatics - Research and Development
Lion Bioscience Research Inc.
141 Portland Street, 10th floor
Cambridge, MA 02139  USA
Phone: 617-245-5483
Fax: 617-245-5499
amatern@lbri.lionbioscience.com
www.lionbioscience.com