OJS upgrade issues (2.4.6.0 -->3.0.2.0)

Hi @dung,

You’ll want to use the section_id corresponding to the journal section the articles should belong to. See Settings > Journal > Sections.

Regards,
Alec Smecher
Public Knowledge Project Team

on the front end @asmecher such as https://cjc-rcc.ucalgary.ca/ ?
Thanks so much!

(For this I left it for our OJS admin staff to find the section_id for us.)

Good Morning @asmecher,

Working with my OJS admin, we were able to pick out the section_id(s) for article_id(s). Thanks for your pointer. Now we are running into a minor issue that upon successful test upgrade the system sent out emails to our users to notify as below:

Just a gentle reminder of our request for your review of the submission, "Competency-based education frameworks across Canadian health professions and implications for multisource feedback," for Canadian Medical Education Journal. We were hoping to have this review by 2019-02-16. We would still be pleased to receive it as soon as you are able to prepare it.

If you do not have your username and password for the journal’s web site, you can use this link to reset your password (which will then be emailed to you along with your username). http://136.159.200.207/index.php/cmej/login/resetPassword/tgilchrist?confirm=e64e139bcd03f290fcea355e50a8a40e20272a0bf569c32497c175014ab851f7%3A1550912413

Submission URL: http://136.159.200.207/index.php/cmej/reviewer/submission?submissionId=61807

Please confirm your ability to complete this vital contribution to the work of the journal. I look forward to hearing from you.

Hi Alec, we have 2 questions to ask you

  1. Is it possible to identify all emails that were sent? Some journal managers would like to personally contact all reviewers who were erroneously contacted.

  2. How can I prevent this from sending out automated emails/notification in my next test upgrade? I have disable email service such as

; Use SMTP for sending mail instead of mail()
smtp = Off

But it still sends out email somehow. Thank you again for any help and pointers.

Dung.

Hi @dung,

Emails will be logged in your system’s mail transport agent log, but also in the database in the email_log table.

When smtp = Off, OJS uses the local MTA to send messages (via PHP’s mail() function). If you want to disable email sending entirely, you’ll need to either…

  • Configure a non-existent SMTP server
  • Configure your local MTA not to deliver email, or
  • Edit lib/pkp/classes/mail/Mail.inc.php and modify the send() function to avoid actually sending the message.

Regards,
Alec Smecher
Public Knowledge Project Team

Hello @asmecher,

Thanks so much, I am on my way again. You have a wonderful day! (cold but sunny here in Calgary:)

Best regards.

Dung.

Hi @asmecher,

The upgrade was successful with message “Successfully upgraded to version 3.1.1.4” But when I navigate to hosted journals after login as ojsadmin I got the below errors in php_errors.log within ojs application folder. Can you point me again? where or what to fix? Thanks!

Dung.

Best regards,

[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 691 of 1698 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 877 of 1336 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 1000 of 3751 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 245 of 1296 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 1390 of 1392 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 155 of 1069 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 1025 of 1532 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 285 of 1664 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 4115 of 4115 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:05 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 360 of 2476 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Warning: file_put_contents(/var/www/html/ojs-3.1.1-4/cache/fc-pluginSettings-0-defaultthemeplugin.php): failed to open stream: Permission denied in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/cache/FileCache.inc.php on line 90
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 691 of 1698 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 877 of 1336 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 1000 of 3751 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 245 of 1296 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 1390 of 1392 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 155 of 1069 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 1025 of 1532 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 285 of 1664 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 4115 of 4115 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:05 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:05 America/Edmonton] PHP Notice: unserialize(): Error at offset 360 of 2476 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:05 America/Edmonton] PHP Warning: file_put_contents(/var/www/html/ojs-3.1.1-4/cache/fc-pluginSettings-0-defaultthemeplugin.php): failed to open stream: Permission denied in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/cache/FileCache.inc.php on line 90
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 691 of 1698 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 691 of 1698 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 877 of 1336 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 877 of 1336 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1000 of 3751 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 245 of 1296 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1390 of 1392 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 155 of 1069 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1000 of 3751 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 245 of 1296 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1025 of 1532 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 285 of 1664 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1390 of 1392 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 155 of 1069 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1025 of 1532 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 4115 of 4115 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 285 of 1664 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 4115 of 4115 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 360 of 2476 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 360 of 2476 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: file_put_contents(/var/www/html/ojs-3.1.1-4/cache/fc-pluginSettings-0-defaultthemeplugin.php): failed to open stream: Permission denied in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/cache/FileCache.inc.php on line 90
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: file_put_contents(/var/www/html/ojs-3.1.1-4/cache/fc-pluginSettings-0-defaultthemeplugin.php): failed to open stream: Permission denied in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/cache/FileCache.inc.php on line 90
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 691 of 1698 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 877 of 1336 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 691 of 1698 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 877 of 1336 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1000 of 3751 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 245 of 1296 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1390 of 1392 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 155 of 1069 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1025 of 1532 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1000 of 3751 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 285 of 1664 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 245 of 1296 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1390 of 1392 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 155 of 1069 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 4115 of 4115 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1025 of 1532 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 285 of 1664 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 4115 of 4115 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:06 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 627 of 1340 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 627 of 1340 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 396 of 695 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 360 of 2476 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1467 of 3014 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 396 of 695 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 360 of 2476 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] PHP Notice: unserialize(): Error at offset 1467 of 3014 bytes in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/db/DAO.inc.php on line 352
[02-Mar-2019 17:01:06 America/Edmonton] Malformed UTF-8 characters, possibly incorrectly encoded
[02-Mar-2019 17:01:06 America/Edmonton] Malformed UTF-8 characters, possibly incorrectly encoded

Hi @dung,

There are at least 2 problems here – file permissions in cache (see the FAQ area of this forum for details), and a likely accidental change in character set configuration during the upgrade (search the forum for unserialize for other discussions of this).

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher,

Thanks for your quick response, for sure I will search and read up. I will post back the result.

Best regards,

Dung.

  1. Following instruction here

Article Not Displaying

and also issued command

chown -Rf www-data:www-data cache/

this resolved

failed to open stream: Permission denied

  1. following instruction here

Problem upgrading database 2.3.7.0 to 3.0 - #8 by pir

I had a typo utf-8 it should be utf8 as below:

database_charset = utf8

this resolved issue

“unserialize(): Error at offset”

Now, still at the same page loading … new error shows up:

[04-Mar-2019 09:17:18 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:18 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:18 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:18 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133
[04-Mar-2019 09:17:19 America/Edmonton] Malformed UTF-8 characters, possibly incorrectly encoded
[04-Mar-2019 09:17:19 America/Edmonton] Malformed UTF-8 characters, possibly incorrectly encoded

I am searching the forum, Hi Alec if you can point me again please?

Thanks @asmecher!

Dung.

Hi @dung,

Check e.g. OJS 3.1.1 upgrade problem - #37 by akyeame for more on the “Malformed UTF-8 characters” issue.

Unless you manually transcoded your database, make sure that your character set configuration in your old config.inc.php matches the ones in your new config.inc.php – even if these look slightly inconsistent, e.g. utf8 vs. utf-8.

Regards,
Alec Smecher
Public Knowledge Project Team

@asmecher, after changing from

database_charset = utf-8

to

database_charset = utf8

I wonder if I need to re-run the upgrade?

Thanks!

Dung.

Hi @dung,

Yes, I would recommend that – the upgrade script will rearrange content in your database, and it’s entirely possible that this garbled your content if your settings weren’t consistent.

Regards,
Alec Smecher
Public Knowledge Project Team

I thought so too, the upgrade uses new config settings. that will be another 10 to 12 hours for me. Thanks very much @asmecher!

Hello @asmecher,

We (without re-run the upgrade process)

cleared data caches

and

cleared template cache

under

ojsadmin site administration/administrative functions

and that resolved the error

Malformed UTF-8 characters, possibly incorrectly encoded

Now, it makes sense. That was because the configuration was incorrectly set to UTF-8 instead of UTF8, and the site loaded properly with out garbled characters or not loading at all.

I still have a minor issue, the application log php_errors.log still shows error/warning

[04-Mar-2019 14:24:23 America/Edmonton] PHP Warning: Cannot use a scalar value as an array in /var/www/html/ojs-3.1.1-4/lib/pkp/classes/core/DataObject.inc.php on line 133

But the site seems to be working properly, do you know how to get rid of this error/warning?

Many thanks!

Dung.

Hi @dung,

This thread walks through debugging that warning, which is almost certainly a data problem: Cannot use a scalar as an array - #20 by JCar

That said, it’s cosmetic, so you can continue to ignore it if it doesn’t bother you. But it will clutter your web server logs.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher,

I will try to clean them out. its worth it. We here will be happy to be on OJS3x.

Next, our ojs admins will QA the upgrade to make sure everything is good before a prod migration.

Thank you for your support!

Dung.

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Good morning @asmecher,

Your instruction in other post resolved the issue in 2 steps: Cannot use a scalar as an array - #21 by asmecher

You can safely delete all metaCitations rows from OJS 3.x – they’re a hold-over from OJS 2.x that is no longer useful. Execute:

 DELETE FROM journal_settings WHERE setting_name='metaCitations`;

Then remove all .php files from your cache/ subdirectory.

root@ojs-upgrade-2:/var/www/html/ojs-3.1.1-4/cache# rm *.php

Best regards,

Dung.

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Just want to verify with all readers that by properly setting configuration BEFORE upgrading it resolved the issue of garbled content such as:

;;;;;;;;;;;;;;;;;;;;;;;;;
; Localization Settings ;
;;;;;;;;;;;;;;;;;;;;;;;;;

[i18n]

; Default locale
locale = en_US

; Client output/input character set
client_charset = utf-8

; Database connection character set
; Must be set to “Off” if not supported by the database server
; If enabled, must be the same character set as “client_charset”
; (although the actual name may differ slightly depending on the server)
connection_charset = utf8

; Database storage character set
; Must be set to “Off” if not supported by the database server
database_charset = utf8

in response to this post and section OJS upgrade issues (2.4.6.0 -->3.0.2.0) - #32 by asmecher (solution of re-run upgrade from @asmecher is correct and needed)

Today, learnt more things/errors that can possibly happen during the upgrade that is the submission_search_object_keywords table has corrupted records that results in an error during upgrade. The fix is easy just empty/truncate the table and re-index after migration please look at this issue for example OJS 3.1.2.1 - 3.1.2.4 - Upgrade failed due to corrupt 'submission search object keywords' table

But before you run the re-indexing command “php tools/rebuildSearchIndex.php” be sure you install Pdftotext linux filter/library https://docs.bitnami.com/oci/apps/resourcespace/configuration/install-pdftotext/

  • Debian:
    sudo apt-get update && sudo apt-get install -y xpdf
  • CentOS:
    sudo yum install poppler-utils

Transferring files_dir in number 6 between servers over network, running rebuildSearchIndex.php in number 4 above and running upgrade command “php tools/upgrade.php upgrade”, these are long running process if you are working from home and your vpn times out from idling it will break the running process results in corrupted database during migration (need to re-import dbase). To solve this problem we can run processes in the background using this command for example:

[root@vmojs01 ojs]# nohup php tools/rebuildSearchIndex.php 2>&1 > output.log &
[1] 68308
[root@ivmojs01 ojs]# nohup: ignoring input and redirecting stderr to stdout

To view your output:

[root@ivmojs01 ojs]# tail -f output.log

Make sure you transferred all necessary contents from previous ojs to new upgrade ojs before running the migration script like mentioned in this good old video Upgrading to OJS 3 - YouTube especially the files_dir is very big in my case 100g worth of data files and as well public_files_dir a much smaller size.

1 Like

muy interesante este post…