warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

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warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

Tony Power
Hi,

Does anybody know what could cause this error?
How to fix?

Thank you very much,
Tony

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Re: warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

Lacey-Anne Sanderson
Hi Tony,

I just need a little more information from you to figure out what's going on.

What version of tripal are you running?
When does this error appear? What are you doing at that time? What pages are you trying to load?

Also I'm assuming you're entire tripal installation is in /etc/drupal/6/sites/all/modules/tripal_stock (ie: within tripal_stock you have tripal_core, tripal_stock, tripal_feature, etc.). Is this correct?

Thanks,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-05-07, at 10:20 AM, Tony Power wrote:

Hi,

Does anybody know what could cause this error?
How to fix?

Thank you very much,
Tony

------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

Tony Power
Hi Lacey-Anne,

I am using the SVN version from last week.
This error shows up when I am accessing to a contig page. Please, see
the full error on the attached file.
Although I get those errors, the page shows up well, below the errors.

$ pwd
/etc/drupal/6/sites/all/modules

$ ls
tripal_analysis           tripal_core               tripal_organism
tripal_analysis_blast     tripal_cv                 tripal_phenotype
tripal_analysis_go        tripal_db                 tripal_project
tripal_analysis_interpro  tripal_feature            tripal_pub
tripal_analysis_kegg      tripal_gbrowse            tripal_search
tripal_analysis_unigene   tripal_genetic            tripal_search_unigene
tripal_bulk_loader        tripal_library            tripal_stock
tripal_contact            tripal_natural_diversity


Thank you very much for your time,

On Mon, May 7, 2012 at 6:12 PM, Lacey-Anne Sanderson
<[hidden email]> wrote:

> Hi Tony,
>
> I just need a little more information from you to figure out what's going
> on.
>
> What version of tripal are you running?
> When does this error appear? What are you doing at that time? What pages are
> you trying to load?
>
> Also I'm assuming you're entire tripal installation is
> in /etc/drupal/6/sites/all/modules/tripal_stock (ie: within tripal_stock you
> have tripal_core, tripal_stock, tripal_feature, etc.). Is this correct?
>
> Thanks,
> ~Lacey
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-4975
> Email: [hidden email]
> Room 3C06 Agriculture
> Department of Plant Sciences
> University of Saskatchewan
>
> On 2012-05-07, at 10:20 AM, Tony Power wrote:
>
> Hi,
>
> Does anybody know what could cause this error?
> How to fix?
>
> Thank you very much,
> Tony
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>

------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

Lacey-Anne Sanderson
Hi Tony,

We have moved to Drupal GIT for version control so the SVN version you have is quite outdated and the error that you are seeing has likely been fixed. I would recommend upgrading to either the newest development version or 6.x-0.3 through the following steps:
1. Disable all Tripal modules (you don't need to uninstall them so you won't lose any pages/etc. already loaded)
2. Delete all the tripal_* modules in /etc/drupal/6/sites/all/modules
3. Execute the following command in /etc/drupal/6/sites/all/modules
Stable Version: git clone --recursive --branch 6.x-release http://git.drupal.org/sandbox/spficklin/1337878.git tripal
Dev Version:  git clone --recursive --branch 6.x-0.4-dev http://git.drupal.org/sandbox/spficklin/1337878.git tripal
4. Then re-enable all the Tripal modules you are using
5. Run <you're site>/update.php to update the Drupal database for the new changes.

Requirements: You need to have git installed on your system.

The development version is not stable enough for a production website so I would only recommend using it if you are just exploring Tripal, setting up a new site that won't go live until sometime in the Fall (after 0.4 is released) or you are upgrading a current clone of your production site in anticipation of the new version. Otherwise, you should install the Stable version using the same instructions above or one of the Tutorials for 0.3.

Hope that helps!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-05-08, at 6:26 AM, Tony Power wrote:

Hi Lacey-Anne,

I am using the SVN version from last week.
This error shows up when I am accessing to a contig page. Please, see
the full error on the attached file.
Although I get those errors, the page shows up well, below the errors.

$ pwd
/etc/drupal/6/sites/all/modules

$ ls
tripal_analysis           tripal_core               tripal_organism
tripal_analysis_blast     tripal_cv                 tripal_phenotype
tripal_analysis_go        tripal_db                 tripal_project
tripal_analysis_interpro  tripal_feature            tripal_pub
tripal_analysis_kegg      tripal_gbrowse            tripal_search
tripal_analysis_unigene   tripal_genetic            tripal_search_unigene
tripal_bulk_loader        tripal_library            tripal_stock
tripal_contact            tripal_natural_diversity


Thank you very much for your time,

On Mon, May 7, 2012 at 6:12 PM, Lacey-Anne Sanderson
<[hidden email]> wrote:
Hi Tony,

I just need a little more information from you to figure out what's going
on.

What version of tripal are you running?
When does this error appear? What are you doing at that time? What pages are
you trying to load?

Also I'm assuming you're entire tripal installation is
in /etc/drupal/6/sites/all/modules/tripal_stock (ie: within tripal_stock you
have tripal_core, tripal_stock, tripal_feature, etc.). Is this correct?

Thanks,
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-4975
Email: [hidden email]
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan

On 2012-05-07, at 10:20 AM, Tony Power wrote:

Hi,

Does anybody know what could cause this error?
How to fix?

Thank you very much,
Tony

------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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[hidden email]
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threat landscape has changed and how IT managers can respond. Discussions
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threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
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threat landscape has changed and how IT managers can respond. Discussions
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Re: warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

Tony Power
Hi Lacey-Anne,

After following your instructions I end up with a file structure under
tripal, but I can't find the modules nor they show up in drupal.
Do I need to do anything else? By the way, the README file just says:
"This branch is just a place holder and is not used.  See an
appropriate release or development branch for current source code."

Here goes what I am doing:

/etc/drupal/6/sites/all/modules# git clone --recursive --branch
6.x-release http://git.drupal.org/sandbox/spficklin/1337878.git tripal
Cloning into 'tripal'...
remote: Counting objects: 6719, done.
remote: Compressing objects: 100% (3173/3173), done.
remote: Total 6719 (delta 4433), reused 5284 (delta 3430)
Receiving objects: 100% (6719/6719), 3.88 MiB | 687 KiB/s, done.
Resolving deltas: 100% (4433/4433), done.
/etc/drupal/6/sites/all/modules# ls
tripal
/etc/drupal/6/sites/all/modules# ls -la
total 12
drwxr-xr-x 3 root root 4096 May  8 23:59 .
drwxr-xr-x 6 root root 4096 May  4 12:31 ..
drwxr-xr-x 3 root root 4096 May  8 23:59 tripal
/etc/drupal/6/sites/all/modules# cd tripal/
/etc/drupal/6/sites/all/modules/tripal# ls
README.txt
/etc/drupal/6/sites/all/modules/tripal# ls -la
total 20
drwxr-xr-x 3 root root 4096 May  8 23:59 .
drwxr-xr-x 3 root root 4096 May  8 23:59 ..
drwxr-xr-x 8 root root 4096 May  8 23:59 .git
-rw-r--r-- 1 root root   19 May  8 23:59 .gitignore
-rw-r--r-- 1 root root  127 May  8 23:59 README.txt
root@drako:/etc/drupal/6/sites/all/modules/tripal#

Thank you for your time,

On Tue, May 8, 2012 at 5:32 PM, Lacey-Anne Sanderson
<[hidden email]> wrote:

> Hi Tony,
>
> We have moved to Drupal GIT for version control so the SVN version you have
> is quite outdated and the error that you are seeing has likely been fixed. I
> would recommend upgrading to either the newest development version or
> 6.x-0.3 through the following steps:
> 1. Disable all Tripal modules (you don't need to uninstall them so you won't
> lose any pages/etc. already loaded)
> 2. Delete all the tripal_* modules in /etc/drupal/6/sites/all/modules
> 3. Execute the following command in /etc/drupal/6/sites/all/modules
> Stable Version: git clone --recursive --branch 6.x-release
> http://git.drupal.org/sandbox/spficklin/1337878.git tripal
> Dev Version:  git clone --recursive --branch 6.x-0.4-dev
> http://git.drupal.org/sandbox/spficklin/1337878.git tripal
> 4. Then re-enable all the Tripal modules you are using
> 5. Run <you're site>/update.php to update the Drupal database for the new
> changes.
>
> Requirements: You need to have git installed on your system.
>
> The development version is not stable enough for a production website so I
> would only recommend using it if you are just exploring Tripal, setting up a
> new site that won't go live until sometime in the Fall (after 0.4 is
> released) or you are upgrading a current clone of your production site in
> anticipation of the new version. Otherwise, you should install the Stable
> version using the same instructions above or one of the Tutorials for 0.3.
>
> Hope that helps!
> ~Lacey
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-4975
> Email: [hidden email]
> Room 3C06 Agriculture
> Department of Plant Sciences
> University of Saskatchewan
>
> On 2012-05-08, at 6:26 AM, Tony Power wrote:
>
> Hi Lacey-Anne,
>
> I am using the SVN version from last week.
> This error shows up when I am accessing to a contig page. Please, see
> the full error on the attached file.
> Although I get those errors, the page shows up well, below the errors.
>
> $ pwd
> /etc/drupal/6/sites/all/modules
>
> $ ls
> tripal_analysis           tripal_core               tripal_organism
> tripal_analysis_blast     tripal_cv                 tripal_phenotype
> tripal_analysis_go        tripal_db                 tripal_project
> tripal_analysis_interpro  tripal_feature            tripal_pub
> tripal_analysis_kegg      tripal_gbrowse            tripal_search
> tripal_analysis_unigene   tripal_genetic            tripal_search_unigene
> tripal_bulk_loader        tripal_library            tripal_stock
> tripal_contact            tripal_natural_diversity
>
>
> Thank you very much for your time,
>
> On Mon, May 7, 2012 at 6:12 PM, Lacey-Anne Sanderson
> <[hidden email]> wrote:
>
> Hi Tony,
>
>
> I just need a little more information from you to figure out what's going
>
> on.
>
>
> What version of tripal are you running?
>
> When does this error appear? What are you doing at that time? What pages are
>
> you trying to load?
>
>
> Also I'm assuming you're entire tripal installation is
>
> in /etc/drupal/6/sites/all/modules/tripal_stock (ie: within tripal_stock you
>
> have tripal_core, tripal_stock, tripal_feature, etc.). Is this correct?
>
>
> Thanks,
>
> ~Lacey
>
>
> ------------------------------------------------------
>
> Lacey-Anne Sanderson
>
> Bioinformaticist
>
> Pulse Crop Breeding and Genetics
>
> Phone: (306) 966-4975
>
> Email: [hidden email]
>
> Room 3C06 Agriculture
>
> Department of Plant Sciences
>
> University of Saskatchewan
>
>
> On 2012-05-07, at 10:20 AM, Tony Power wrote:
>
>
> Hi,
>
>
> Does anybody know what could cause this error?
>
> How to fix?
>
>
> Thank you very much,
>
> Tony
>
>
> ------------------------------------------------------------------------------
>
> Live Security Virtual Conference
>
> Exclusive live event will cover all the ways today's security and
>
> threat landscape has changed and how IT managers can respond. Discussions
>
> will include endpoint security, mobile security and the latest in malware
>
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
> _______________________________________________
>
> Gmod-tripal mailing list
>
> [hidden email]
>
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
>
> <error.txt>------------------------------------------------------------------------------
>
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats.
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>

------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

Tony Power
Anybody, please?

On Wed, May 9, 2012 at 12:05 AM, Tony Power <[hidden email]> wrote:

> Hi Lacey-Anne,
>
> After following your instructions I end up with a file structure under
> tripal, but I can't find the modules nor they show up in drupal.
> Do I need to do anything else? By the way, the README file just says:
> "This branch is just a place holder and is not used.  See an
> appropriate release or development branch for current source code."
>
> Here goes what I am doing:
>
> /etc/drupal/6/sites/all/modules# git clone --recursive --branch
> 6.x-release http://git.drupal.org/sandbox/spficklin/1337878.git tripal
> Cloning into 'tripal'...
> remote: Counting objects: 6719, done.
> remote: Compressing objects: 100% (3173/3173), done.
> remote: Total 6719 (delta 4433), reused 5284 (delta 3430)
> Receiving objects: 100% (6719/6719), 3.88 MiB | 687 KiB/s, done.
> Resolving deltas: 100% (4433/4433), done.
> /etc/drupal/6/sites/all/modules# ls
> tripal
> /etc/drupal/6/sites/all/modules# ls -la
> total 12
> drwxr-xr-x 3 root root 4096 May  8 23:59 .
> drwxr-xr-x 6 root root 4096 May  4 12:31 ..
> drwxr-xr-x 3 root root 4096 May  8 23:59 tripal
> /etc/drupal/6/sites/all/modules# cd tripal/
> /etc/drupal/6/sites/all/modules/tripal# ls
> README.txt
> /etc/drupal/6/sites/all/modules/tripal# ls -la
> total 20
> drwxr-xr-x 3 root root 4096 May  8 23:59 .
> drwxr-xr-x 3 root root 4096 May  8 23:59 ..
> drwxr-xr-x 8 root root 4096 May  8 23:59 .git
> -rw-r--r-- 1 root root   19 May  8 23:59 .gitignore
> -rw-r--r-- 1 root root  127 May  8 23:59 README.txt
> root@drako:/etc/drupal/6/sites/all/modules/tripal#
>
> Thank you for your time,
>
> On Tue, May 8, 2012 at 5:32 PM, Lacey-Anne Sanderson
> <[hidden email]> wrote:
>> Hi Tony,
>>
>> We have moved to Drupal GIT for version control so the SVN version you have
>> is quite outdated and the error that you are seeing has likely been fixed. I
>> would recommend upgrading to either the newest development version or
>> 6.x-0.3 through the following steps:
>> 1. Disable all Tripal modules (you don't need to uninstall them so you won't
>> lose any pages/etc. already loaded)
>> 2. Delete all the tripal_* modules in /etc/drupal/6/sites/all/modules
>> 3. Execute the following command in /etc/drupal/6/sites/all/modules
>> Stable Version: git clone --recursive --branch 6.x-release
>> http://git.drupal.org/sandbox/spficklin/1337878.git tripal
>> Dev Version:  git clone --recursive --branch 6.x-0.4-dev
>> http://git.drupal.org/sandbox/spficklin/1337878.git tripal
>> 4. Then re-enable all the Tripal modules you are using
>> 5. Run <you're site>/update.php to update the Drupal database for the new
>> changes.
>>
>> Requirements: You need to have git installed on your system.
>>
>> The development version is not stable enough for a production website so I
>> would only recommend using it if you are just exploring Tripal, setting up a
>> new site that won't go live until sometime in the Fall (after 0.4 is
>> released) or you are upgrading a current clone of your production site in
>> anticipation of the new version. Otherwise, you should install the Stable
>> version using the same instructions above or one of the Tutorials for 0.3.
>>
>> Hope that helps!
>> ~Lacey
>>
>> ------------------------------------------------------
>> Lacey-Anne Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Phone: (306) 966-4975
>> Email: [hidden email]
>> Room 3C06 Agriculture
>> Department of Plant Sciences
>> University of Saskatchewan
>>
>> On 2012-05-08, at 6:26 AM, Tony Power wrote:
>>
>> Hi Lacey-Anne,
>>
>> I am using the SVN version from last week.
>> This error shows up when I am accessing to a contig page. Please, see
>> the full error on the attached file.
>> Although I get those errors, the page shows up well, below the errors.
>>
>> $ pwd
>> /etc/drupal/6/sites/all/modules
>>
>> $ ls
>> tripal_analysis           tripal_core               tripal_organism
>> tripal_analysis_blast     tripal_cv                 tripal_phenotype
>> tripal_analysis_go        tripal_db                 tripal_project
>> tripal_analysis_interpro  tripal_feature            tripal_pub
>> tripal_analysis_kegg      tripal_gbrowse            tripal_search
>> tripal_analysis_unigene   tripal_genetic            tripal_search_unigene
>> tripal_bulk_loader        tripal_library            tripal_stock
>> tripal_contact            tripal_natural_diversity
>>
>>
>> Thank you very much for your time,
>>
>> On Mon, May 7, 2012 at 6:12 PM, Lacey-Anne Sanderson
>> <[hidden email]> wrote:
>>
>> Hi Tony,
>>
>>
>> I just need a little more information from you to figure out what's going
>>
>> on.
>>
>>
>> What version of tripal are you running?
>>
>> When does this error appear? What are you doing at that time? What pages are
>>
>> you trying to load?
>>
>>
>> Also I'm assuming you're entire tripal installation is
>>
>> in /etc/drupal/6/sites/all/modules/tripal_stock (ie: within tripal_stock you
>>
>> have tripal_core, tripal_stock, tripal_feature, etc.). Is this correct?
>>
>>
>> Thanks,
>>
>> ~Lacey
>>
>>
>> ------------------------------------------------------
>>
>> Lacey-Anne Sanderson
>>
>> Bioinformaticist
>>
>> Pulse Crop Breeding and Genetics
>>
>> Phone: (306) 966-4975
>>
>> Email: [hidden email]
>>
>> Room 3C06 Agriculture
>>
>> Department of Plant Sciences
>>
>> University of Saskatchewan
>>
>>
>> On 2012-05-07, at 10:20 AM, Tony Power wrote:
>>
>>
>> Hi,
>>
>>
>> Does anybody know what could cause this error?
>>
>> How to fix?
>>
>>
>> Thank you very much,
>>
>> Tony
>>
>>
>> ------------------------------------------------------------------------------
>>
>> Live Security Virtual Conference
>>
>> Exclusive live event will cover all the ways today's security and
>>
>> threat landscape has changed and how IT managers can respond. Discussions
>>
>> will include endpoint security, mobile security and the latest in malware
>>
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>
>> _______________________________________________
>>
>> Gmod-tripal mailing list
>>
>> [hidden email]
>>
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>>
>> <error.txt>------------------------------------------------------------------------------
>>
>> Live Security Virtual Conference
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>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats.
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>>
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Re: warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

Stephen Ficklin-2
Hi Tony,

Sorry for the delay.  There was a mistake in the instructions below.  We
didn't actually have the stable code in GIT.  I have put it there and
you can get it this way:

git checkout 6.x-release

However, this is the same code as the 6.x-0.3.1b version which is the
last stable version we released.    If you downloaded the development
code from SVN you probably have a later version than this and so I doubt
this stable code will help you.

You are welcome to try our most recent development code. If you were
using the SVN code you were expecting some non-stable code anyway:

git checkout 6.x-0.4-dev

It should update  the code for you automatically to the most recent
development version.  Please note that all of the extension modules are
in this code so you'll be getting the blast, kegg, interpro modules.  
Those will move out eventually and may disappear if you continue to use
the development branch.  If you are using the developers code you are
welcome to subscribe to our developers mailing list to keep up with
what's going on:
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

Looking through your email below, you mention you are looking at a
contig page when you get this error. Are you using the stock module?  If
not, you can disable it and I expect the error would go away.

Stephen



On 5/10/2012 7:41 AM, Tony Power wrote:

> Anybody, please?
>
> On Wed, May 9, 2012 at 12:05 AM, Tony Power<[hidden email]>  wrote:
>> Hi Lacey-Anne,
>>
>> After following your instructions I end up with a file structure under
>> tripal, but I can't find the modules nor they show up in drupal.
>> Do I need to do anything else? By the way, the README file just says:
>> "This branch is just a place holder and is not used.  See an
>> appropriate release or development branch for current source code."
>>
>> Here goes what I am doing:
>>
>> /etc/drupal/6/sites/all/modules# git clone --recursive --branch
>> 6.x-release http://git.drupal.org/sandbox/spficklin/1337878.git tripal
>> Cloning into 'tripal'...
>> remote: Counting objects: 6719, done.
>> remote: Compressing objects: 100% (3173/3173), done.
>> remote: Total 6719 (delta 4433), reused 5284 (delta 3430)
>> Receiving objects: 100% (6719/6719), 3.88 MiB | 687 KiB/s, done.
>> Resolving deltas: 100% (4433/4433), done.
>> /etc/drupal/6/sites/all/modules# ls
>> tripal
>> /etc/drupal/6/sites/all/modules# ls -la
>> total 12
>> drwxr-xr-x 3 root root 4096 May  8 23:59 .
>> drwxr-xr-x 6 root root 4096 May  4 12:31 ..
>> drwxr-xr-x 3 root root 4096 May  8 23:59 tripal
>> /etc/drupal/6/sites/all/modules# cd tripal/
>> /etc/drupal/6/sites/all/modules/tripal# ls
>> README.txt
>> /etc/drupal/6/sites/all/modules/tripal# ls -la
>> total 20
>> drwxr-xr-x 3 root root 4096 May  8 23:59 .
>> drwxr-xr-x 3 root root 4096 May  8 23:59 ..
>> drwxr-xr-x 8 root root 4096 May  8 23:59 .git
>> -rw-r--r-- 1 root root   19 May  8 23:59 .gitignore
>> -rw-r--r-- 1 root root  127 May  8 23:59 README.txt
>> root@drako:/etc/drupal/6/sites/all/modules/tripal#
>>
>> Thank you for your time,
>>
>> On Tue, May 8, 2012 at 5:32 PM, Lacey-Anne Sanderson
>> <[hidden email]>  wrote:
>>> Hi Tony,
>>>
>>> We have moved to Drupal GIT for version control so the SVN version you have
>>> is quite outdated and the error that you are seeing has likely been fixed. I
>>> would recommend upgrading to either the newest development version or
>>> 6.x-0.3 through the following steps:
>>> 1. Disable all Tripal modules (you don't need to uninstall them so you won't
>>> lose any pages/etc. already loaded)
>>> 2. Delete all the tripal_* modules in /etc/drupal/6/sites/all/modules
>>> 3. Execute the following command in /etc/drupal/6/sites/all/modules
>>> Stable Version: git clone --recursive --branch 6.x-release
>>> http://git.drupal.org/sandbox/spficklin/1337878.git tripal
>>> Dev Version:  git clone --recursive --branch 6.x-0.4-dev
>>> http://git.drupal.org/sandbox/spficklin/1337878.git tripal
>>> 4. Then re-enable all the Tripal modules you are using
>>> 5. Run<you're site>/update.php to update the Drupal database for the new
>>> changes.
>>>
>>> Requirements: You need to have git installed on your system.
>>>
>>> The development version is not stable enough for a production website so I
>>> would only recommend using it if you are just exploring Tripal, setting up a
>>> new site that won't go live until sometime in the Fall (after 0.4 is
>>> released) or you are upgrading a current clone of your production site in
>>> anticipation of the new version. Otherwise, you should install the Stable
>>> version using the same instructions above or one of the Tutorials for 0.3.
>>>
>>> Hope that helps!
>>> ~Lacey
>>>
>>> ------------------------------------------------------
>>> Lacey-Anne Sanderson
>>> Bioinformaticist
>>> Pulse Crop Breeding and Genetics
>>> Phone: (306) 966-4975
>>> Email: [hidden email]
>>> Room 3C06 Agriculture
>>> Department of Plant Sciences
>>> University of Saskatchewan
>>>
>>> On 2012-05-08, at 6:26 AM, Tony Power wrote:
>>>
>>> Hi Lacey-Anne,
>>>
>>> I am using the SVN version from last week.
>>> This error shows up when I am accessing to a contig page. Please, see
>>> the full error on the attached file.
>>> Although I get those errors, the page shows up well, below the errors.
>>>
>>> $ pwd
>>> /etc/drupal/6/sites/all/modules
>>>
>>> $ ls
>>> tripal_analysis           tripal_core               tripal_organism
>>> tripal_analysis_blast     tripal_cv                 tripal_phenotype
>>> tripal_analysis_go        tripal_db                 tripal_project
>>> tripal_analysis_interpro  tripal_feature            tripal_pub
>>> tripal_analysis_kegg      tripal_gbrowse            tripal_search
>>> tripal_analysis_unigene   tripal_genetic            tripal_search_unigene
>>> tripal_bulk_loader        tripal_library            tripal_stock
>>> tripal_contact            tripal_natural_diversity
>>>
>>>
>>> Thank you very much for your time,
>>>
>>> On Mon, May 7, 2012 at 6:12 PM, Lacey-Anne Sanderson
>>> <[hidden email]>  wrote:
>>>
>>> Hi Tony,
>>>
>>>
>>> I just need a little more information from you to figure out what's going
>>>
>>> on.
>>>
>>>
>>> What version of tripal are you running?
>>>
>>> When does this error appear? What are you doing at that time? What pages are
>>>
>>> you trying to load?
>>>
>>>
>>> Also I'm assuming you're entire tripal installation is
>>>
>>> in /etc/drupal/6/sites/all/modules/tripal_stock (ie: within tripal_stock you
>>>
>>> have tripal_core, tripal_stock, tripal_feature, etc.). Is this correct?
>>>
>>>
>>> Thanks,
>>>
>>> ~Lacey
>>>
>>>
>>> ------------------------------------------------------
>>>
>>> Lacey-Anne Sanderson
>>>
>>> Bioinformaticist
>>>
>>> Pulse Crop Breeding and Genetics
>>>
>>> Phone: (306) 966-4975
>>>
>>> Email: [hidden email]
>>>
>>> Room 3C06 Agriculture
>>>
>>> Department of Plant Sciences
>>>
>>> University of Saskatchewan
>>>
>>>
>>> On 2012-05-07, at 10:20 AM, Tony Power wrote:
>>>
>>>
>>> Hi,
>>>
>>>
>>> Does anybody know what could cause this error?
>>>
>>> How to fix?
>>>
>>>
>>> Thank you very much,
>>>
>>> Tony
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> Live Security Virtual Conference
>>>
>>> Exclusive live event will cover all the ways today's security and
>>>
>>> threat landscape has changed and how IT managers can respond. Discussions
>>>
>>> will include endpoint security, mobile security and the latest in malware
>>>
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>
>>> _______________________________________________
>>>
>>> Gmod-tripal mailing list
>>>
>>> [hidden email]
>>>
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>>
>>>
>>> <error.txt>------------------------------------------------------------------------------
>>>
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>>> Gmod-tripal mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>>
> ------------------------------------------------------------------------------
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> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


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Re: warning: Creating default object from empty value in /etc/drupal/6/sites/all/modules/tripal_stock/tripal_core/tripal_core.api.inc on line 839.

Stephen Ficklin-2
In reply to this post by Tony Power
For the sake of everyone following this thread, after talking with Tony
offline a bit it looks as though the default setup for Debian linux is
to have E_STRICT turned on in PHP.  Unfortunately, Tripal has been
developed primarily in Ubuntu which does not have E_STRICT turned on.  
So, to resolve the problem the setting will have to be disabled in PHP.  
We will update the code so that in the next release this won't be a
problem.   The setting change can be made in the php.ini file.

Stephen


On 5/10/2012 7:41 AM, Tony Power wrote:

> Anybody, please?
>
> On Wed, May 9, 2012 at 12:05 AM, Tony Power<[hidden email]>  wrote:
>> Hi Lacey-Anne,
>>
>> After following your instructions I end up with a file structure under
>> tripal, but I can't find the modules nor they show up in drupal.
>> Do I need to do anything else? By the way, the README file just says:
>> "This branch is just a place holder and is not used.  See an
>> appropriate release or development branch for current source code."
>>
>> Here goes what I am doing:
>>
>> /etc/drupal/6/sites/all/modules# git clone --recursive --branch
>> 6.x-release http://git.drupal.org/sandbox/spficklin/1337878.git tripal
>> Cloning into 'tripal'...
>> remote: Counting objects: 6719, done.
>> remote: Compressing objects: 100% (3173/3173), done.
>> remote: Total 6719 (delta 4433), reused 5284 (delta 3430)
>> Receiving objects: 100% (6719/6719), 3.88 MiB | 687 KiB/s, done.
>> Resolving deltas: 100% (4433/4433), done.
>> /etc/drupal/6/sites/all/modules# ls
>> tripal
>> /etc/drupal/6/sites/all/modules# ls -la
>> total 12
>> drwxr-xr-x 3 root root 4096 May  8 23:59 .
>> drwxr-xr-x 6 root root 4096 May  4 12:31 ..
>> drwxr-xr-x 3 root root 4096 May  8 23:59 tripal
>> /etc/drupal/6/sites/all/modules# cd tripal/
>> /etc/drupal/6/sites/all/modules/tripal# ls
>> README.txt
>> /etc/drupal/6/sites/all/modules/tripal# ls -la
>> total 20
>> drwxr-xr-x 3 root root 4096 May  8 23:59 .
>> drwxr-xr-x 3 root root 4096 May  8 23:59 ..
>> drwxr-xr-x 8 root root 4096 May  8 23:59 .git
>> -rw-r--r-- 1 root root   19 May  8 23:59 .gitignore
>> -rw-r--r-- 1 root root  127 May  8 23:59 README.txt
>> root@drako:/etc/drupal/6/sites/all/modules/tripal#
>>
>> Thank you for your time,
>>
>> On Tue, May 8, 2012 at 5:32 PM, Lacey-Anne Sanderson
>> <[hidden email]>  wrote:
>>> Hi Tony,
>>>
>>> We have moved to Drupal GIT for version control so the SVN version you have
>>> is quite outdated and the error that you are seeing has likely been fixed. I
>>> would recommend upgrading to either the newest development version or
>>> 6.x-0.3 through the following steps:
>>> 1. Disable all Tripal modules (you don't need to uninstall them so you won't
>>> lose any pages/etc. already loaded)
>>> 2. Delete all the tripal_* modules in /etc/drupal/6/sites/all/modules
>>> 3. Execute the following command in /etc/drupal/6/sites/all/modules
>>> Stable Version: git clone --recursive --branch 6.x-release
>>> http://git.drupal.org/sandbox/spficklin/1337878.git tripal
>>> Dev Version:  git clone --recursive --branch 6.x-0.4-dev
>>> http://git.drupal.org/sandbox/spficklin/1337878.git tripal
>>> 4. Then re-enable all the Tripal modules you are using
>>> 5. Run<you're site>/update.php to update the Drupal database for the new
>>> changes.
>>>
>>> Requirements: You need to have git installed on your system.
>>>
>>> The development version is not stable enough for a production website so I
>>> would only recommend using it if you are just exploring Tripal, setting up a
>>> new site that won't go live until sometime in the Fall (after 0.4 is
>>> released) or you are upgrading a current clone of your production site in
>>> anticipation of the new version. Otherwise, you should install the Stable
>>> version using the same instructions above or one of the Tutorials for 0.3.
>>>
>>> Hope that helps!
>>> ~Lacey
>>>
>>> ------------------------------------------------------
>>> Lacey-Anne Sanderson
>>> Bioinformaticist
>>> Pulse Crop Breeding and Genetics
>>> Phone: (306) 966-4975
>>> Email: [hidden email]
>>> Room 3C06 Agriculture
>>> Department of Plant Sciences
>>> University of Saskatchewan
>>>
>>> On 2012-05-08, at 6:26 AM, Tony Power wrote:
>>>
>>> Hi Lacey-Anne,
>>>
>>> I am using the SVN version from last week.
>>> This error shows up when I am accessing to a contig page. Please, see
>>> the full error on the attached file.
>>> Although I get those errors, the page shows up well, below the errors.
>>>
>>> $ pwd
>>> /etc/drupal/6/sites/all/modules
>>>
>>> $ ls
>>> tripal_analysis           tripal_core               tripal_organism
>>> tripal_analysis_blast     tripal_cv                 tripal_phenotype
>>> tripal_analysis_go        tripal_db                 tripal_project
>>> tripal_analysis_interpro  tripal_feature            tripal_pub
>>> tripal_analysis_kegg      tripal_gbrowse            tripal_search
>>> tripal_analysis_unigene   tripal_genetic            tripal_search_unigene
>>> tripal_bulk_loader        tripal_library            tripal_stock
>>> tripal_contact            tripal_natural_diversity
>>>
>>>
>>> Thank you very much for your time,
>>>
>>> On Mon, May 7, 2012 at 6:12 PM, Lacey-Anne Sanderson
>>> <[hidden email]>  wrote:
>>>
>>> Hi Tony,
>>>
>>>
>>> I just need a little more information from you to figure out what's going
>>>
>>> on.
>>>
>>>
>>> What version of tripal are you running?
>>>
>>> When does this error appear? What are you doing at that time? What pages are
>>>
>>> you trying to load?
>>>
>>>
>>> Also I'm assuming you're entire tripal installation is
>>>
>>> in /etc/drupal/6/sites/all/modules/tripal_stock (ie: within tripal_stock you
>>>
>>> have tripal_core, tripal_stock, tripal_feature, etc.). Is this correct?
>>>
>>>
>>> Thanks,
>>>
>>> ~Lacey
>>>
>>>
>>> ------------------------------------------------------
>>>
>>> Lacey-Anne Sanderson
>>>
>>> Bioinformaticist
>>>
>>> Pulse Crop Breeding and Genetics
>>>
>>> Phone: (306) 966-4975
>>>
>>> Email: [hidden email]
>>>
>>> Room 3C06 Agriculture
>>>
>>> Department of Plant Sciences
>>>
>>> University of Saskatchewan
>>>
>>>
>>> On 2012-05-07, at 10:20 AM, Tony Power wrote:
>>>
>>>
>>> Hi,
>>>
>>>
>>> Does anybody know what could cause this error?
>>>
>>> How to fix?
>>>
>>>
>>> Thank you very much,
>>>
>>> Tony
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> Live Security Virtual Conference
>>>
>>> Exclusive live event will cover all the ways today's security and
>>>
>>> threat landscape has changed and how IT managers can respond. Discussions
>>>
>>> will include endpoint security, mobile security and the latest in malware
>>>
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>
>>> _______________________________________________
>>>
>>> Gmod-tripal mailing list
>>>
>>> [hidden email]
>>>
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>>
>>>
>>> <error.txt>------------------------------------------------------------------------------
>>>
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>>> Gmod-tripal mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>>
>>>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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