Problem updating from ojs 2.4.8-4 to ojs 3.1.2

Hi, I want to upgrade my ojs 2.4.8-4 to 3.1.2 but failed.
i’m using php version 7.0.33 for this upgrade, but previously for running ojs 2.4.8-4 the php version is 5.6.40.
the CLI always ended in

[code]…
[data: dbscripts/xml/upgrade/3.0.0_scheduledTasks.xml]

[code: Installer Installer::localizeCustomBlockSettings]

[code: Installer Installer::convertEditorDecisionNotes]

[code: Installer Installer::convertQueries]

[code: Installer Installer::migrateFiles]

[code: Installer Installer::convertSupplementaryFiles]


C:\wamp64\www\ojs-3.1.2>

with php error log like this

[11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbObject has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 106 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbTable has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 205 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbIndex has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 613 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbData has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 774 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbQuerySet has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 959 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; adoSchema has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 1217 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; ADODB_Cache_File has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb.inc.php on line 263 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; ADOConnection has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb.inc.php on line 359 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; ADORecordSet has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb.inc.php on line 2921 [11-Mar-2019 04:45:58 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; ADORecordSet_array has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb.inc.php on line 3939 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbObject has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 106 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbTable has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 205 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbIndex has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 613 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbData has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 774 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; dbQuerySet has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 959 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; adoSchema has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 1217 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; ADODB_Cache_File has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb.inc.php on line 263 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; ADOConnection has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb.inc.php on line 359 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; ADORecordSet has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb.inc.php on line 2921 [11-Mar-2019 04:47:42 UTC] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; ADORecordSet_array has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb.inc.php on line 3939 [11-Mar-2019 11:47:45 Asia/Jakarta] PHP Deprecated: Methods with the same name as their class will not be constructors in a future version of PHP; CounterReport has a deprecated constructor in C:\wamp64\www\ojs-3.1.2\plugins\reports\counter\classes\CounterReport.inc.php on line 33 [11-Mar-2019 11:47:50 Asia/Jakarta] PHP Notice: Only variables should be assigned by reference in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\db\DBDataXMLParser.inc.php on line 122 [11-Mar-2019 11:47:50 Asia/Jakarta] PHP Notice: Only variables should be assigned by reference in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\db\DBDataXMLParser.inc.php on line 122 [11-Mar-2019 11:49:54 Asia/Jakarta] PHP Notice: Only variables should be passed by reference in C:\wamp64\www\ojs-3.1.2\lib\pkp\lib\adodb\adodb-xmlschema.inc.php on line 267 [11-Mar-2019 11:50:22 Asia/Jakarta] PHP Warning: Invalid argument supplied for foreach() in C:\wamp64\www\ojs-3.1.2\classes\install\Upgrade.inc.php on line 2081 [11-Mar-2019 11:50:22 Asia/Jakarta] PHP Warning: Invalid argument supplied for foreach() in C:\wamp64\www\ojs-3.1.2\classes\install\Upgrade.inc.php on line 2240 [11-Mar-2019 11:50:28 Asia/Jakarta] PHP Warning: Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\submission\SubmissionKeywordEntryDAO.inc.php on line 20 [11-Mar-2019 11:50:28 Asia/Jakarta] PHP Warning: Declaration of SubmissionLanguageEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\submission\SubmissionLanguageEntryDAO.inc.php on line 46 [11-Mar-2019 11:50:28 Asia/Jakarta] PHP Warning: Declaration of SubmissionAgencyEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\submission\SubmissionAgencyEntryDAO.inc.php on line 44 [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "149-513-1-CE.pdf" in "files/journals/1//articles/149/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "150-515-1-SM.pdf" in "files/journals/1//articles/150/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "150-516-1-RV.pdf" in "files/journals/1//articles/150/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "150-517-1-CE.pdf" in "files/journals/1//articles/150/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "151-519-1-SM.pdf" in "files/journals/1//articles/151/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "151-520-1-RV.pdf" in "files/journals/1//articles/151/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "151-521-1-CE.pdf" in "files/journals/1//articles/151/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "152-523-1-SM.pdf" in "files/journals/1//articles/152/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "152-524-1-RV.pdf" in "files/journals/1//articles/152/". Skipping this file. [11-Mar-2019 11:51:21 Asia/Jakarta] WARNING: Unable to find a match for "152-525-1-CE.pdf" in "files/journals/1//articles/152/". Skipping this file. [11-Mar-2019 11:51:26 Asia/Jakarta] WARNING: Unable to find a match for "377-1052-2-SM.phtml" in "files/journals/1//articles/377/". Skipping this file. [11-Mar-2019 11:51:26 Asia/Jakarta] WARNING: Unable to find a match for "426-1103-1-SM.phtml" in "files/journals/1//articles/426/". Skipping this file. [11-Mar-2019 11:51:26 Asia/Jakarta] WARNING: Unable to find a match for "428-1104-1-SM.phtml" in "files/journals/1//articles/428/". Skipping this file. [11-Mar-2019 11:51:26 Asia/Jakarta] WARNING: Unable to find a match for "428-1105-1-RV.phtml" in "files/journals/1//articles/428/". Skipping this file. [11-Mar-2019 11:51:29 Asia/Jakarta] WARNING: Unable to find a match for "675-1580-4-SM.aspx" in "files/journals/1//articles/675/". Skipping this file. [11-Mar-2019 11:51:33 Asia/Jakarta] PHP Warning: copy(files/journals/1//articles/142/attachment/142-1-491-1-13-20111230.doc): failed to open stream: No such file or directory in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\file\FileManager.inc.php on line 162 [11-Mar-2019 11:51:33 Asia/Jakarta] PHP Warning: assert(): assert(is_readable($targetFilePath)) failed in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\submission\SubmissionFileDAODelegate.inc.php on line 123 [11-Mar-2019 11:51:40 Asia/Jakarta] PHP Warning: assert(): assert(is_readable($sourceFile)) failed in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\submission\SubmissionFileDAODelegate.inc.php on line 112 [11-Mar-2019 11:51:40 Asia/Jakarta] PHP Warning: copy(files/journals/1//articles/142/submission/proof/142-4-491-1-10-20111230.doc): failed to open stream: No such file or directory in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\file\FileManager.inc.php on line 162 [11-Mar-2019 11:51:40 Asia/Jakarta] PHP Fatal error: Uncaught Error: Call to a member function getFileId() on null in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\file\SubmissionFileManager.inc.php:184 Stack trace: #0 C:\wamp64\www\ojs-3.1.2\classes\install\Upgrade.inc.php(1476): SubmissionFileManager->copyFileToFileStage('491', 1, 4, NULL, true) #1 C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\install\Installer.inc.php(421): Upgrade->provideSupplementaryFilesForReview(Object(Upgrade), Array) #2 C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\install\Installer.inc.php(265): Installer->executeAction(Array) #3 C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\install\Installer.inc.php(186): Installer->executeInstaller() #4 C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\cliTool\UpgradeTool.inc.php(88): Installer->execute() #5 C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\cliTool\UpgradeTool.inc.php(64): UpgradeTool->upgrade() #6 C:\wamp64\www\ojs-3.1.2\tools\upgrade.php(34): UpgradeTool->execute() #7 {main} thrown in C:\wamp64\www\ojs-3.1.2\lib\pkp\classes\file\SubmissionFileManager.inc.php on line 184

what would be the problem for this error?
thank you for any of your help/suggestion.

regards,
Ario.

I was trying to upgrade an OJS 2.4.8.3 to OJS 3.1.2-1, but it didn’t work out. I was using Debian 9.1, Apache 2.4.25, PHP 7.0.33 and MariaDB 10.1.26. Here is the error report:

root@server:/opt/rev# php tools/upgrade.php upgrade

PHP Warning: filemtime(): stat failed for registry/locales.xml in /opt/rev/lib/pkp/classes/i18n/PKPLocale.inc.php on line 691

[pre-install]

[load: upgrade.xml]

[version: 3.1.2.1]

[code: Installer Installer::checkPhpVersion]

[code: Installer Installer::syncSeriesAssocType]

[data: dbscripts/xml/upgrade/2.4.0_preupdate_usageStatistics.xml (skipped)]

[data: dbscripts/xml/upgrade/2.4.0_preupdate_usageStatistics2.xml (skipped)]

[code: Installer Installer::removeReviewEntries]

WARNING: Unable to find a match for “26-89-1-RV.doc” in “/opt/rev-f1l3z/journals/1//articles/26/”. Skipping this file.

WARNING: Unable to find a match for “126-540-1-RV.doc” in “/opt/rev-f1l3z/journals/3//articles/126/”. Skipping this file.

WARNING: Unable to find a match for “138-598-1-RV.docx” in “/opt/rev-f1l3z/journals/3//articles/138/”. Skipping this file.

WARNING: Unable to find a match for “140-602-1-RV.docx” in “/opt/rev-f1l3z/journals/3//articles/140/”. Skipping this file.

WARNING: Unable to find a match for “993-4992-1-RV.doc” in “/opt/rev-f1l3z/journals/3//articles/993/”. Skipping this file.

WARNING: Unable to find a match for “995-5005-1-RV.doc” in “/opt/rev-f1l3z/journals/3//articles/995/”. Skipping this file.

WARNING: Unable to find a match for “1000-5015-1-RV.docx” in “/opt/rev-f1l3z/journals/1//articles/1000/”. Skipping this file.

[data: dbscripts/xml/upgrade/3.0.0_preupdate.xml]

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

[data: dbscripts/xml/upgrade/3.0.0_adaptTimedViews.xml (skipped)]

[data: dbscripts/xml/upgrade/3.0.0_adaptReferrals.xml]

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

[data: dbscripts/xml/upgrade/3.0.0_adaptBooksForReview.xml]

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

[data: dbscripts/xml/upgrade/remove_timed_views_bots.xml (skipped)]

[data: dbscripts/xml/upgrade/3.0.0_preupdate_commentsToEditor.xml]

[data: dbscripts/xml/upgrade/3.1.0_preupdate_review_assignments.xml]

[data: dbscripts/xml/upgrade/3.1.0_preupdate_notes.xml]

[data: dbscripts/xml/upgrade/3.1.0_preupdate_payments.xml]

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

[data: dbscripts/xml/upgrade/3.1.1_preupdate_citations.xml]

PHP Notice: Only variables should be assigned by reference in /opt/rev/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122

[data: dbscripts/xml/upgrade/3.1.2_preupdate_user_author_names.xml]

[schema: lib/pkp/xml/schema/common.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/log.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/announcements.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/scheduledTasks.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/temporaryFiles.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/metadata.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/reviewForms.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/controlledVocab.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/submissions.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/submissionFiles.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/categories.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/notes.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/genres.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/tombstone.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/rolesAndUserGroups.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/metrics.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/views.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/libraryFiles.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: lib/pkp/xml/schema/navigationMenus.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[schema: dbscripts/xml/ojs_schema.xml]

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be passed by reference in /opt/rev/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

[data: dbscripts/xml/indexes.xml]

[code: Installer Installer::installDefaultNavigationMenus]

PHP Warning: fopen(registry/navigationMenus.xml): failed to open stream: No existe el fichero o el directorio in /opt/rev/lib/pkp/classes/file/FileWrapper.inc.php on line 70

PHP Warning: fopen(registry/navigationMenus.xml): failed to open stream: No existe el fichero o el directorio in /opt/rev/lib/pkp/classes/file/FileWrapper.inc.php on line 70

PHP Warning: fopen(registry/navigationMenus.xml): failed to open stream: No existe el fichero o el directorio in /opt/rev/lib/pkp/classes/file/FileWrapper.inc.php on line 70

[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]

[code: Installer Installer::migrateSRLocale]

[code: Installer Installer::migrateUserAndAuthorNames]

[code: Installer Installer::concatenateIntoAbout]

[code: Installer Installer::concatenateIntoMasthead]

[code: Installer Installer::migrateCounterPluginUsageStatistics (skipped)]

[code: Installer Installer::migrateTimedViewsUsageStatistics (skipped)]

[code: Installer Installer::migrateDefaultUsageStatistics (skipped)]

[data: dbscripts/xml/upgrade/2.4.0_postUsageStatsMigration.xml (skipped)]

[data: dbscripts/xml/upgrade/2.4.0_postUsageStatsMigration2.xml (skipped)]

[data: dbscripts/xml/upgrade/2.4.0_postCounterMigration.xml (skipped)]

[data: dbscripts/xml/upgrade/2.4.0_postTimedViewsMigration.xml (skipped)]

[data: dbscripts/xml/upgrade/3.0.0_change_assoc_type.xml]

[data: dbscripts/xml/upgrade/3.0.0_change_assoc_type_metrics.xml]

[data: dbscripts/xml/upgrade/3.0.0_settings.xml]

[code: Installer Installer::installDefaultGenres]

PHP Warning: fopen(registry/genres.xml): failed to open stream: No existe el fichero o el directorio in /opt/rev/lib/pkp/classes/file/FileWrapper.inc.php on line 70

PHP Warning: fopen(registry/genres.xml): failed to open stream: No existe el fichero o el directorio in /opt/rev/lib/pkp/classes/file/FileWrapper.inc.php on line 70

[code: Installer Installer::migrateArticleMetadata]

PHP Warning: Declaration of SubmissionDisciplineEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /opt/rev/lib/pkp/classes/submission/SubmissionDisciplineEntryDAO.inc.php on line 20

PHP Warning: Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /opt/rev/lib/pkp/classes/submission/SubmissionKeywordEntryDAO.inc.php on line 45

PHP Warning: Declaration of SubmissionAgencyEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /opt/rev/lib/pkp/classes/submission/SubmissionAgencyEntryDAO.inc.php on line 44

PHP Warning: Declaration of SubmissionLanguageEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /opt/rev/lib/pkp/classes/submission/SubmissionLanguageEntryDAO.inc.php on line 46

[data: dbscripts/xml/upgrade/3.0.0_update.xml]

[code: Installer Installer::clearDataCache]

[code: Installer Installer::migrateUserRoles]

PHP Warning: fopen(registry/userGroups.xml): failed to open stream: No existe el fichero o el directorio in /opt/rev/lib/pkp/classes/file/FileWrapper.inc.php on line 70

PHP Fatal error: Uncaught Error: Call to a member function getId() on boolean in /opt/rev/classes/install/Upgrade.inc.php:311

Stack trace:#0 /opt/rev/lib/pkp/classes/install/Installer.inc.php(421): Upgrade->migrateUserRoles(Object(Upgrade), Array)

#1 /opt/rev/lib/pkp/classes/install/Installer.inc.php(265): Installer->executeAction(Array)

#2 /opt/rev/lib/pkp/classes/install/Installer.inc.php(186): Installer->executeInstaller()

#3 /opt/rev/lib/pkp/classes/cliTool/UpgradeTool.inc.php(88): Installer->execute()

#4 /opt/rev/lib/pkp/classes/cliTool/UpgradeTool.inc.php(64): UpgradeTool->upgrade()

#5 /opt/rev/tools/upgrade.php(34): UpgradeTool->execute()

#6 {main}

thrown in /opt/rev/classes/install/Upgrade.inc.php on line 311


However, on the same test server a few months ago, I updated OJS 3.1.2, the previous version successfully.

Hi @yassiel,

The file registry/userGroups.xml appears to be missing; make sure you unpacked all the contents of the OJS .tar.gz file.

Regards,
Alec Smecher
Public Knowledge Project Team

1 Like

Hi @asmecher,

It was successfully updated to version 3.1.2.1, but the report shows some php notices and warnings, such as the following:

WARNING: Unable to find a match for “26-89-1-RV.doc” in “/opt/r3v1staz-f1l3z/jou rnals/1//articles/26/”. Skipping this file.
WARNING: Unable to find a match for “126-540-1-RV.doc” in “/opt/r3v1staz-f1l3z/j ournals/3//articles/126/”. Skipping this file.
WARNING: Unable to find a match for “138-598-1-RV.docx” in “/opt/r3v1staz-f1l3z/ journals/3//articles/138/”. Skipping this file.
WARNING: Unable to find a match for “140-602-1-RV.docx” in “/opt/r3v1staz-f1l3z/ journals/3//articles/140/”. Skipping this file.

PHP Notice: Only variables should be assigned by reference in /opt/r3v1staz/lib /pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /opt/r3v1staz/lib /pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /opt/r3v1staz/lib /pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /opt/r3v1staz/lib /pkp/classes/db/DBDataXMLParser.inc.php on line 122

PHP Warning: Declaration of SubmissionDisciplineEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /opt/r3v1staz/lib/pkp/classes/submission/SubmissionDisciplineEntryDAO.inc.php on line 20
PHP Warning: Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /opt/r3v1staz/lib/pkp/classes/submission/SubmissionKeywordEntryDAO.inc.php on line 45
PHP Warning: Declaration of SubmissionAgencyEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /opt/r3v1staz/lib/pkp/classes/submission/SubmissionAgencyEntryDAO.inc.php on line 44
PHP Warning: Declaration of SubmissionLanguageEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /opt/r3v1staz/lib/pkp/classes/submission/SubmissionLanguageEntryDAO.inc.php on line 46

PHP Warning: copy(/opt/r3v1staz-f1l3z/journals/1//articles/443/attachment/443-1-1867-5-13-20160921.phtml): failed to open stream: No existe el fichero o el directorio in /opt/r3v1staz/lib/pkp/classes/file/FileManager.inc.php on line 162

PHP Notice: Only variables should be passed by reference in /opt/r3v1staz/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
PHP Notice: Only variables should be passed by reference in /opt/r3v1staz/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267
PHP Notice: Only variables should be passed by reference in /opt/r3v1staz/lib/pkp/lib/adodb/adodb-xmlschema.inc.php on line 267

PHP Notice: Only variables should be assigned by reference in /opt/r3v1staz/lib/pkp/classes/cliTool/UpgradeTool.inc.php on line 97
Successfully upgraded to version 3.1.2.1

Thank you!

Hi @yassiel,

The warnings can all be ignored, though I’d suggest reviewing the submissions associated with the missing file warnings to make sure all important files are accessible.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher!

What the report means is that there is inconsistency between some article files and their respective records in the database?

Actually, I did not install the site from the beginning and I cannot know how some articles were lost. It could have been some penetration attack that altered the database?

I remember that in a copy to the PC, the antivirus deleted some malicious files like .phtml, for example.

Regards,
Yassiel
UNISS

Hi @yassiel,

I don’t think it’s likely that an attack altered the database. It’s OK for malicious .phtml files to be uploaded into OJS as long as your files_dir (in config.inc.php) is not directly web-accessible. I see that at least one of the missing files was a .phtml – likely this was found and removed by your anti-virus, which is fine.

Some of the other warnings look like Word documents, e.g.:

WARNING: Unable to find a match for "26-89-1-RV.doc" in "/opt/r3v1staz-f1l3z/jou rnals/1//articles/26/". Skipping this file.

You’ll need to look at submission ID 26 to judge whether or not that’s important.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher,

Now everything works almost fine, but when I access I can’t see the content of the links, because they show me something like this:

{“status”:true,“content”:"<a href="#" class=“requestHelpPanel pkp_help_link pkp_help_tab” data-topic=“settings.md#website”>\n\t<span class=“fa fa-info-circle pkpIcon–inline” aria-hidden=“true”></span>\n\t\t\tAyuda\n\t</a>\n\n\n<script type=“text/javascript”>\n\t$(function() {\n\t\t// Attach the form handler.\n\t\t$(’#navigationMenuSettingsForm’).pkpHandler(’$.pkp.controllers.form.AjaxFormHandler’);\n\t});\n</script>\n\n<form id=“navigationMenuSettingsForm” class=“pkp_form” method=“post” action=\

In addition, the website displays messages as if it were still ‘Loading’.

imagen

Hi @yassiel,

Check both your PHP error log & browser console. Make sure you hard-reload the page first.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher,
I activated all debug options, and this was the result:

Notice : Deprecated call without request object. in /lib/pkp/classes/template/PKPTemplateManager.inc.php on line 872

Notice : Deprecated call without request object. in /lib/pkp/classes/template/PKPTemplateManager.inc.php on line 872

Notice : Deprecated call without request object. in /lib/pkp/classes/template/PKPTemplateManager.inc.php on line 872

Notice : Deprecated call without request object. in /lib/pkp/classes/template/PKPTemplateManager.inc.php on line 872

Notice : Deprecated call without request object. in /lib/pkp/classes/template/PKPTemplateManager.inc.php on line 872

Regards,
Yassiel
UNISS

Hi @yassiel,

Those are only notices; notices and warnings shouldn’t cause your system to misbehave and can be ignored. Check the log for something containing the word “Error”.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher,

I placed the config.inc.php file and directories (public, uploaded files directory and cache), and restored the migrated database on the test server where it had worked long ago but in 3.1.2. Now it seems that the site works fine, but the server information shows version 5 for PHP, not version 7 that is required, and 3.1.2.1 for OJS.

Captura

Best regards

Hi @asmecher,

Now some links do not work, HTTP ERROR 500:

http://x.x.x.x/index.php/yyyyy/submissions
http://x.x.x.x/index.php/yyyyy/issue/archive

Regards

Hi @asmecher,

Problem solved: the operating system also had PHP 5.6 working, by default. What I don’t understand is why it allowed me to update.

Did the previous notifications and warnings belong to PHP 5.6? Why did the process end successfully? Do I have to update again?

Greetings and thanks for your help.

Hi @yassiel,

It sounds like you’re back up and running; you shouldn’t need to do anything more than switch your PHP over to 7.x as you’ve done.

Regards,
Alec Smecher
Public Knowledge Project Team