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From: <mro...@cs...> - 2006-10-27 23:22:45
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Mark, Thanks for you answer. I downloaded Error.pm version 0.17006, and I looked into every GUS folder to see if there is another file called Error.pm to replace it, but could not find any. The file called PluginError.pm which seems to be the one with errors is located at: /home/acrl-storage-1/gusdb-dev/GUS/gus_home/lib/perl/GUS/PluginMgr Do I need to replace PluginError.pm with Error.pm version 0.17006, rename it Error.pm to PluginError.pm, or added in the same directory? Thanks again Michael > I'm coming in late to this thread but it looks like you need to > install the Error module from CPAN. > > http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm > > I had to install version 0.17006, the latest 0.17008 version didn't > compile for me out of the box. > > -M > On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote: > >> Steve, >> >> I am sorry to be a pain, but I was wondering if you have received >> any news >> from John concerning the PluginError.pm >> >> Thank you >> >> >> Michael >> >> >> >>> john- >>> >>> this GUS user, michael, has downloaded and installed the latest GUS. >>> >>> your new PluginError.pm is giving him problems. see below. >>> >>> steve >>> >>> mro...@cs... wrote: >>> >>>> Steve, >>>> >>>> Thanks for the phone orientation offer, tomorrow will be great, I >>>> am on >>>> my >>>> way to a 3 hour class. >>>> >>>> In the meantime I run: >>>> >>>> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >>>> gus_home/lib/perl/GUS/Supported/Plugin 9% >>>> ga GUS::Supported::Plugin::InsertSequenceFeatures >>>> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >>>> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >>>> --fileFormat genbank >>>> --extDbName "Pseudomonas_aeruginosa" >>>> --extDbRlsVer "1000" >>>> --soCvsVersion "1.1.4" >>>> --commit >>>> >>>> >>>> and got: >>>> >>>> Base class package "Error" is empty. >>>> (Perhaps you need to 'use' the module which defines that package % |
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From: <mro...@cs...> - 2006-10-28 00:46:38
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Mark Yes I downloaded the tar file, I am going to read the installation instructions and let you know how it went Thanks again Michael > See "HOW TO INSTALL IT" in the README that comes in the Error tar > file (that's the actual letter case used; I'm not shouting at you). > > Did you download the tar file or just the Error.pm file? Get the tar > file. > > By default it installs into your system-wide Perl library (so you'll > likely need root privileges). Technically you could install it in > your gus_home, but don't do that. > > GUS' PluginError.pm uses Error.pm. One is not a replacement for the > other. > > Good luck, > -Mark > > On Oct 27, 2006, at 7:22 PM, mro...@cs... wrote: > >> Mark, >> >> Thanks for you answer. >> >> I downloaded Error.pm version 0.17006, and I looked into every GUS >> folder >> to see if there is another file called Error.pm to replace it, but >> could >> not find any. >> >> The file called PluginError.pm which seems to be the one with >> errors is >> located at: >> /home/acrl-storage-1/gusdb-dev/GUS/gus_home/lib/perl/GUS/PluginMgr >> >> Do I need to replace PluginError.pm with Error.pm version 0.17006, >> rename >> it Error.pm to PluginError.pm, or added in the same directory? >> >> Thanks again >> >> Michael >> >> >>> I'm coming in late to this thread but it looks like you need to >>> install the Error module from CPAN. >>> >>> http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm >>> >>> I had to install version 0.17006, the latest 0.17008 version didn't >>> compile for me out of the box. >>> >>> -M >>> On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote: >>> >>>> Steve, >>>> >>>> I am sorry to be a pain, but I was wondering if you have received >>>> any news >>>> from John concerning the PluginError.pm >>>> >>>> Thank you >>>> >>>> >>>> Michael >>>> >>>> >>>> >>>>> john- >>>>> >>>>> this GUS user, michael, has downloaded and installed the latest >>>>> GUS. >>>>> >>>>> your new PluginError.pm is giving him problems. see below. >>>>> >>>>> steve >>>>> >>>>> mrobi002@cs.f |
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From: <mro...@cs...> - 2006-10-31 21:13:47
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John,
Help please....
This is a brand new GUS 3.5 from SVN install.
After installation i have only done:
+meta to ga and +create to all plugins.
At postgres:
insert into core.databaseversion (
database_version_id,
version,
modification_date,
user_read,
user_write,
group_read,
group_write,
other_read,
other_write,
row_user_id,
row_group_id,
row_project_id,
row_alg_invocation_id
) values (
nextval('core.databaseversion_sq'),
3.5,
now(),
1, 0, 1, 0, 1, 0,
1, 1, 1, 1
);
We had the IT department install "Error.pm version 0.17006" today, and
then I run
ga GUS::Supported::Plugin::InsertSequenceFeatures --help
Getting the same errors as before:
Base class package "Error" is empty.
(Perhaps you need to 'use' the module which defines that package first=
.)
at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/lib/perl/GUS/PluginMgr
/PluginError.pm line 3
BEGIN failed--compilation aborted at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 3.
Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29.
BEGIN failed--compilation aborted at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29.
Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27.
BEGIN failed--compilation aborted at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27.
Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/bin/ga line 7.
BEGIN failed--compilation aborted at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/bin/ga line 7.
Could you please tell what I am doing wrong
Thank you
Michael
> Hi Michael - Sorry to just be responding...Mark is right that
> PluginError.pm is a subclass of Error.pm. Were you successful with
> the installation?
>
> I will add this to the documentation of required packages.
>
> thanks
> john
>
>
> At 07:46 PM 10/27/2006, you wrote:
>>Mark
>>
>>Yes I downloaded the tar file, I am going to read the installation
>>instructions and let you know how it went
>>
>>Thanks again
>>
>>Michael
>>
>>
>>
>> > See "HOW TO INSTALL IT" in the README that comes in the Error tar
>> > file (that's the actual letter case used; I'm not shouting at you).
>> >
>> > Did you download the tar file or just the Error.pm file? Get the tar
>> > file.
>> >
>> > By default it installs into your system-wide Perl library (so you'll
>> > likely need root privileges). Technically you could install it in
>> > your gus_home, but don't do tha
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From: Mark S. H. <mh...@ug...> - 2006-10-31 22:26:54
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On Oct 31, 2006, at 4:13 PM, mro...@cs... wrote: > We had the IT department install "Error.pm version 0.17006" today, and > then I run > > ga GUS::Supported::Plugin::InsertSequenceFeatures --help > > Getting the same errors as before: > > Base class package "Error" is empty. Michael, Run this test: perl -e 'use Error'; It should give no output. If it complains that it "Can't locate Error.pm in @INC ......." show this test and error message to your IT department. They should be able to help your perl find the Error.pm they installed. It's not a GUS issue. Good luck, Mark |
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From: Mark S. H. <mh...@ug...> - 2006-11-01 19:59:08
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On Oct 31, 2006, at 5:35 PM, mro...@cs... wrote: > Mark, > > I did: > > mrobi002@acrl-linux-1:~ 116% cd $HOME > mrobi002@acrl-linux-1:~ 117% perl -e 'use Error'; > mrobi002@acrl-linux-1:~ 118% > > > It gave not output, so does this means that perl found Error.pl, > correct? > That's my understanding of the world. hmmm. Now I'm at a loss to explain your 'ga' failure. Was your plugin command and the perl 'use Error' command executed in exactly the same environment? (that is, if running one immediately after the other, ga fails and 'use Error' succeeds ?) Anyone else have an idea? -Mark > Michael > >> >> On Oct 31, 2006, at 4:13 PM, mro...@cs... wrote: >>> We had the IT department install "Error.pm version 0.17006" >>> today, and >>> then I run >>> >>> ga GUS::Supported::Plugin::InsertSequenceFeatures --help >>> >>> Getting the same errors as before: >>> >>> Base class package "Error" is empty. >> >> Michael, >> >> Run this test: >> >> perl -e 'use Error'; >> >> It should give no output. If it complains that it "Can't locate >> Error.pm in @INC ......." show this test and error message to your IT >> department. They should be able to help your perl find the Error.pm >> they installed. It's not a GUS issue. >> >> Good luck, >> Mark >> > > |
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From: Mark S. H. <mh...@ug...> - 2006-10-27 23:52:58
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See "HOW TO INSTALL IT" in the README that comes in the Error tar file (that's the actual letter case used; I'm not shouting at you). Did you download the tar file or just the Error.pm file? Get the tar file. By default it installs into your system-wide Perl library (so you'll likely need root privileges). Technically you could install it in your gus_home, but don't do that. GUS' PluginError.pm uses Error.pm. One is not a replacement for the other. Good luck, -Mark On Oct 27, 2006, at 7:22 PM, mro...@cs... wrote: > Mark, > > Thanks for you answer. > > I downloaded Error.pm version 0.17006, and I looked into every GUS > folder > to see if there is another file called Error.pm to replace it, but > could > not find any. > > The file called PluginError.pm which seems to be the one with > errors is > located at: > /home/acrl-storage-1/gusdb-dev/GUS/gus_home/lib/perl/GUS/PluginMgr > > Do I need to replace PluginError.pm with Error.pm version 0.17006, > rename > it Error.pm to PluginError.pm, or added in the same directory? > > Thanks again > > Michael > > >> I'm coming in late to this thread but it looks like you need to >> install the Error module from CPAN. >> >> http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm >> >> I had to install version 0.17006, the latest 0.17008 version didn't >> compile for me out of the box. >> >> -M >> On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote: >> >>> Steve, >>> >>> I am sorry to be a pain, but I was wondering if you have received >>> any news >>> from John concerning the PluginError.pm >>> >>> Thank you >>> >>> >>> Michael >>> >>> >>> >>>> john- >>>> >>>> this GUS user, michael, has downloaded and installed the latest >>>> GUS. >>>> >>>> your new PluginError.pm is giving him problems. see below. >>>> >>>> steve >>>> >>>> mro...@cs... wrote: >>>> >>>>> Steve, >>>>> >>>>> Thanks for the phone orientation offer, tomorrow will be great, I >>>>> am on >>>>> my >>>>> way to a 3 hour class. >>>>> >>>>> In the meantime I run: >>>>> >>>>> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >>>>> gus_home/lib/perl/GUS/Supported/Plugin 9% >>>>> ga GUS::Supported::Plugin::InsertSequenceFeatures >>>>> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >>>>> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/ >>>>> NC_002516.gbk >>>>> --fileFormat genbank >>>>> --extDbName "Pseudomonas_aeruginosa" >>>>> --extDbRlsVer "1000" >>>>> --soCvsVersion "1.1.4" >>>>> --commit >>>>> >>>>> >>>>> and got: >>>>> >>>>> Base class package "Error" is empty. >>>>> (Perhaps you need to 'use' the module which defines that >>>>> package > % > |
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