[MOBY-dev] Perl BioMoby install
José María Fernández González
jmfernandez at cnio.es
Tue May 13 09:51:09 UTC 2008
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;
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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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
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