[MOBY-dev] Perl BioMoby install
Pieter Neerincx
pieter.neerincx at gmail.com
Tue May 13 10:28:32 UTC 2008
Hi José María,
On 13•May•2008, at 11:51 AM, José María Fernández González wrote:
> Hi everybody,
> although WSRF::Lite already has a $VERSION variable, it is not
> defined as a string, which is a problem for installation packages.
> It is set as:
>
> $VERSION=0.8.2.2;
Ok my bad. I thought I had installed 0.8.2.2, which I did but not in
the proper path. Mix that with an outdated WSRF::Lite 0.6 in the
correct path that reports it's version number in the wrong context and
this is what you get :(. Problem solved :)
Pi
> instead of
>
> $VERSION='0.8.2.2';
>
> José Manuel Rodríguez and I made some tries fixing that for
> Makefile.PL (see jmrc commits).
>
> The main problem is that more and more Perl packages are migrating
> from string representation to 'literal' one (IO::Prompt for
> instance, I guess).
>
> Best Regards,
> José María
>
> Pieter Neerincx wrote:
>> Hi Eddie,
>> On 12•May•2008, at 3:14 PM, Edward Kawas wrote:
>>> Hi Pieter,
>>>
>>> I have fixed the first problem that you have encountered, but I
>>> haven't
>>> gotten around to a new cpan release. I have been waiting on a few
>>> things
>>> first.
>> Thanks!
>>> The second problem with regards to versioning may also be fixed. I
>>> am not
>>> sure if the versioning for wsrf has been fixed for our makefile,
>>> but the
>>> io::prompt and LS should be.
>> Thanks again! I e-mailed the maintainer of the WSRF::Lite module
>> and requested the addition of a $VERSION variable... So that might
>> get fixed in the near future too :) We'll see...
>> Cheers,
>> Pi
>>> Thanks,
>>>
>>> Eddie
>>>
>>> -----Original Message-----
>>> From: moby-dev-bounces at lists.open-bio.org
>>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter
>>> Neerincx
>>> Sent: May-12-08 4:20 AM
>>> To: Core developer announcements
>>> Subject: [MOBY-dev] Perl BioMoby install
>>>
>>> Hi,
>>>
>>> I upgraded my Perl BioMoby install yesterday and noticed two minor
>>> problems:
>>>
>>> 1. Failed test t/MOBY:
>>>
>>> t/MOBY........................
>>> # Failed test 'use MOBY;'
>>> # in t/MOBY.t at line 9.
>>> # Tried to use 'MOBY'.
>>> # Error: Can't locate MOBY.pm in @INC (@INC contains:
>>> .....<cut>.....
>>> # BEGIN failed--compilation aborted at t/MOBY.t line 9.
>>> t/MOBY........................NOK 1/1# Looks like you failed 1
>>> test of
>>> 1.
>>> t/MOBY........................dubious
>>> Test returned status 1 (wstat 256, 0x100)
>>> DIED. FAILED test 1
>>> Failed 1/1 tests, 0.00% okay
>>>
>>>
>>> This test doesn't seem to be very useful. All it does is try a "use
>>> MOBY;", which fails as MOBY.pm doesn't exist and as far is I know
>>> shouldn't exist. Can I remove this test from the CVS tree or did I
>>> miss something and is the test correctly reporting a failure
>>> indicating a problem?
>>>
>>> 2. Perl module version number fishiness:
>>>
>>> -----------------------------------------
>>> *** Module::AutoInstall version 1.03
>>> *** Checking for Perl dependencies...
>>> [Core Features]
>>> - Test::More ...loaded. (0.62 >= 0.42)
>>> - Test::Simple ...loaded. (0.62 >= 0.44)
>>> - ExtUtils::MakeMaker ...loaded. (6.17 >= 6.11)
>>> - Carp ...loaded. (1.01)
>>> - File::Spec ...loaded. (3.19 >= 0.80)
>>> - SOAP::Lite ...loaded. (0.69 >= 0.69)
>>> - XML::LibXML ...loaded. (1.66 >= 1.62)
>>> - IO::Stringy ...loaded. (2.110 >= 2.110)
>>> - Unicode::String ...loaded. (2.09 >= 2.09)
>>> - File::ShareDir ...loaded. (0.05 >= 0.05)
>>> - Template ...loaded. (2.19)
>>> - Class::Inspector ...loaded. (1.18 >= 1.17)
>>> - RDF::Core ...loaded. (0.51 >= 0.51)
>>> - XML::XPath ...loaded. (1.13 >= 1.12)
>>> - Text::Shellwords ...loaded. (1.08 >= 1.00)
>>> - HTML::Entities ...loaded. (1.27 >= 0.01)
>>> - LS ...loaded. (1.1.7 >= 1.1.7)
>>> - DBI ...loaded. (1.410 >= 0.01)
>>> - DBD::mysql ...loaded. (2.900300 >= 0.01)
>>> - IO::Prompt ...loaded. (0.099004 >= 0.99.2)
>>> - IPC::Shareable ...loaded. (0.600 >= 0.6)
>>> - WSRF::Lite ...missing. (would need 0.008.2.2)
>>> - XML::DOM ...loaded. (1.430)
>>> - DateTime::Format::Epoch ...loaded. (0.100)
>>> - DateTime::Format::W3CDTF ...loaded. (0.040)
>>> - HTTP::Daemon ...loaded. (1.360)
>>> - HTTP::Daemon::SSL ...loaded. (1.020)
>>> - MIME::Base64 ...loaded. (3.050)
>>> - Digest::SHA1 ...loaded. (2.070)
>>> - Crypt::OpenSSL::RSA ...loaded. (0.250)
>>> - XML::CanonicalizeXML ...loaded. (0.030 >= 0.02)
>>> - Sys::Hostname::Long ...loaded. (1.400)
>>> - Crypt::OpenSSL::X509 ...loaded. (0.500)
>>> ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
>>> ==> The module(s) are mandatory! Really skip? [n] y
>>> *** Module::AutoInstall configuration finished.
>>> -----------------------------------------
>>> So far so good. It only complains about WSRF::Lite. I have version
>>> 0.8.2.2 installed, but this module doesn't report a version number
>>> and
>>> therefore the dependency check fails. But now it continues:
>>>
>>> -----------------------------------------
>>>
>>> Checking if your kit is complete...
>>>
>>> Looks good
>>>
>>> Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
>>> Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
>>> Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have
>>> unknown
>>> version.
>>>
>>>>
>>> -----------------------------------------
>>>
>>> This is weird. First it finds LS and IO::Prompt and detects the
>>> version numbers correctly, but apparently it checks them slightly
>>> differently now and fails to notice the versions I have are just
>>> fine...
>>>
>>> Cheers,
>>>
>>> Pi
>>>
>>>
>>>
>>>
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>
> --
> "There is no reason why anybody would want a computer in their home" -
> Ken Olson, founder of DEC 1977
> "640K ought to be enough for anybody" - Bill Gates, 1981
> "Nobody will ever outgrow a 20Mb hard drive." - ???
>
> "Premature optimization is the root of all evil." - Donald Knuth
>
> José María Fernández González
> Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
> e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76
> Unidad del Instituto Nacional de Bioinformática
> Biología Estructural y Biocomputación Structural Biology and
> Biocomputing
> Centro Nacional de Investigaciones Oncológicas
> C.P.: 28029 Zip Code: 28029
> C/. Melchor Fernández Almagro, 3 Madrid (Spain)
>
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