[Bioperl-l] Installing Bio-perl on dreamhost via CPAN

Mark A. Jensen maj at fortinbras.us
Fri Nov 20 23:33:02 EST 2009


Maybe 'nightmarehost' is more appropriate. I've had no problems on AWS,
but this may not exactly what you need. MAJ
----- Original Message ----- 
From: "Chu, Roy" <roychu at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Friday, November 20, 2009 3:23 PM
Subject: Re: [Bioperl-l] Installing Bio-perl on dreamhost via CPAN


"sounds very much like you process was killed for prolonged execution
time, or memory usage. We have a daemon in place that monitors for
processes that take up too much of a shared web server's resources, and
this may have kicked in (and often does when trying to install packages
on a shared server)."

This was the explanation they had.  Regarding asking their admins to
install, it seems is a "they'll try to get to it but don't hold your
breath situation."

Hmmm, I tried some other attempts, installing 1.4.0 posed no problems.
 I'm not a perl guru, so I tried to increase the build cache size from
the default, 10 MB, hoping that that may be the problem--can't imagine
how though, since I can't imagine how big the whole package version
can differ by (though honestly, I haven't checked).
Whenever I try to install 1.6.1, it runs into a problem I guess after
the 'make' step and lists the
modules--BioPerl-1.6.0/t/Variation/SeqDiff.t
BioPerl-1.6.0/t/Variation/SNP.t
BioPerl-1.6.0/t/Variation/Variation_IO.t
--and typically gets killed here '> Killed'

Next, I tried 1.6.0, then I get this:
"(I think you ran Build.PL directly, so will use CPAN to install
prerequisites on demand)
CPAN: Storable loaded ok (v2.12)
Going to read '/home/$username/.cpan/Metadata'
Killed" (everything prior works and it seems to get further along than
when I try to install 1.6.1)

Any insight into why this may be happening would be appreciated.
Something EQUALLY appreciated would be a recommendation of a decent
enough hosting service where someone has had success installing
Bio-Perl.  I'd try to set up my Mac web sharing feature and then try
to setup the stuff locally, but I haven't yet been able to
successfully get the port forwarding feature working properly on the
apple airport extreme--perplexing.  Next, I might just try to install
via the Build.pl script.

Hmm, checking the wiki, it seems I'll still be able to run remote
blast and use the basic seq modules, although some discrepancies and
idiosyncrasies may be expected?  Any head-ups about any false
assumptions by me would be greatly appreciated.

Thanks in advance,
Roy

On Fri, Nov 20, 2009 at 5:00 AM, Chris Fields <cjfields at illinois.edu> wrote:
>
> On Nov 20, 2009, at 4:44 AM, Charles Plessy wrote:
>
>> Le Fri, Nov 20, 2009 at 02:21:54AM -0800, Chu, Roy a écrit :
>>>
>>> Does anyone use dreamhost as a web hosting service? I'm just curious
>>> if anyone has had any luck installing the module as their daemon seems
>>> to kill my process whenever I try to install it. Dreamhost tech
>>> support attributes it to either exceeding the allocated memory cache
>>> or exceeding the processing time. I tried to nice the process, but
>>> that didn't help for me. Any luck or experience in resolving this
>>> would be much appreciated. I suppose my next attempt would be to try
>>> installing it directly and hope I don't need root...
>>
>> Dear Roy,
>>
>> DreamHost uses Debian, so you can suggest them to install the Debian package.
>> If you are in contact with the tech service, do not hesitate to tell them to
>> contact me if they are interested by a backport of the 1.6.0 package. For
>> version 1.6.1, it may be more difficult as it depends on perl 5.10.1.
>
> Any reason why this is so? We specify compatibility back to 5.6.1.
>
> Alex mentioned the reliance on the specific Extutils::Manifest version. The 
> version requested has an important bug fix, is present on CPAN, and is 
> backwards-compatible to 5.6.1. It should be fairly easy to request that as a 
> separate package.
>
> A strict requirement for perl 5.10.1 doesn't make sense in that light, unless 
> said perl maintainer can enlighten us as to why this is an issue? This one may 
> require a ranty blog post.
>
>> PS: if you propse to install BioPerl as a feature in the Dreamhost panel, I
>> will vote for it :)
>>
>> Have a nice day,
>>
>> --
>> Charles Plessy
>> Debian Med packaging team,
>> http://www.debian.org/devel/debian-med
>> Tsurumi, Kanagawa, Japan
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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