Error upgrading from 2.4.8 to 3.1.1: "Invalid file!"


#1

Hello

Trying to upgrade from OJS 2.4.8-3 to OJS 3.1.1-2 I receive this error
that blocks the upgrade process:

[code: Installer Installer::provideSupplementaryFilesForReview]

Invalid file!

ojs2: Invalid file!

My situation is:

  • upgrading from OJS 2.4.8-3 to OJS 3.1.1-2
  • PHP version : 7.1.6
  • MySQL version 5.5.45
  • upgrade done via command line (tools/upgrade.php upgrade)
    Ai also have to report that the database had a latin1 charset and I have migrated it tu utf8

Here is the whole upgrade log :

PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0
[pre-install]
[load: upgrade.xml]
[version: 3.1.1.2]

[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]
[data: dbscripts/xml/upgrade/3.0.0_preupdate.xml]
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/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 /var/www/vhosts/actaitalica-ojs-new.archicoop.it/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 /var/www/vhosts/actaitalica-ojs-new.archicoop.it/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 /var/www/vhosts/actaitalica-ojs-new.archicoop.it/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 /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
[schema: lib/pkp/xml/schema/common.xml]
[schema: lib/pkp/xml/schema/log.xml]
[schema: lib/pkp/xml/schema/announcements.xml]
[schema: lib/pkp/xml/schema/scheduledTasks.xml]
[schema: lib/pkp/xml/schema/temporaryFiles.xml]
[schema: lib/pkp/xml/schema/metadata.xml]
[schema: lib/pkp/xml/schema/reviews.xml]
[schema: lib/pkp/xml/schema/reviewForms.xml]
[schema: lib/pkp/xml/schema/controlledVocab.xml]
[schema: lib/pkp/xml/schema/submissions.xml]
[schema: lib/pkp/xml/schema/submissionFiles.xml]
[schema: lib/pkp/xml/schema/notes.xml]
[schema: lib/pkp/xml/schema/views.xml]
[schema: lib/pkp/xml/schema/genres.xml]
[schema: lib/pkp/xml/schema/tombstone.xml]
[schema: lib/pkp/xml/schema/rolesAndUserGroups.xml]
[schema: lib/pkp/xml/schema/metrics.xml]
[schema: lib/pkp/xml/schema/views.xml]
[schema: lib/pkp/xml/schema/libraryFiles.xml]
[schema: lib/pkp/xml/schema/navigationMenus.xml]
[schema: dbscripts/xml/ojs_schema.xml]
[data: dbscripts/xml/indexes.xml]

[code: Installer Installer::installDefaultNavigationMenus]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::migrateSRLocale]

[code: Installer Installer::concatenateIntoAbout]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::concatenateIntoMasthead]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[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]

[code: Installer Installer::migrateArticleMetadata]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Warning: Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/submission/SubmissionKeywordEntryDAO.inc.php on line 20
PHP Warning: Declaration of SubmissionLanguageEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/submission/SubmissionLanguageEntryDAO.inc.php on line 0
PHP Warning: Declaration of SubmissionAgencyEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/submission/SubmissionAgencyEntryDAO.inc.php on line 0
[data: dbscripts/xml/upgrade/3.0.0_update.xml]

[code: Installer Installer::clearDataCache]

[code: Installer Installer::migrateUserRoles]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::fixReviewForms]

[code: Installer Installer::htmlifyEmailTemplates]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
[note: docs/release-notes/README-BEACON]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

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

[code: Installer Installer::localizeCustomBlockSettings]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::convertEditorDecisionNotes]

[code: Installer Installer::convertQueries]
PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/classes/article/SubmissionFileDAO.inc.php on line 23

[code: Installer Installer::migrateFiles]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
WARNING: Unable to find a match for “8-16-1-SP.pdf” in “/var/www/vhosts/files/journals/1//articles/8/”. Skipping this file.
WARNING: Unable to find a match for “10-13-1-SM.rtf” in “/var/www/vhosts/files/journals/1//articles/10/”. Skipping this file.

[code: Installer Installer::convertSupplementaryFiles]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Warning: copy(/var/www/vhosts/files/journals/1//articles/8/attachment/8-1-16-1-13-20120126.pdf): failed to open stream: No such file or directory in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/file/FileManager.inc.php on line 159

[code: Installer Installer::provideSupplementaryFilesForReview]

Invalid file!

ojs2: Invalid file!

Then I’ve applied this patch (https://github.com/pkp/ojs/pull/2009/files 1)

but this do not resolve my problem.

Here is the whole upgrade log after the patch:

PHP Warning: Declaration of PKPUsageEventPlugin::getEnabled() should be compatible with LazyLoadPlugin::getEnabled($contextId = NULL) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/plugins/generic/usageEvent/PKPUsageEventPlugin.inc.php on line 0
[pre-install]
[load: upgrade.xml]
[version: 3.1.1.2]

[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]
[data: dbscripts/xml/upgrade/3.0.0_preupdate.xml]
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
PHP Notice: Only variables should be assigned by reference in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/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 /var/www/vhosts/actaitalica-ojs-new.archicoop.it/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 /var/www/vhosts/actaitalica-ojs-new.archicoop.it/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 /var/www/vhosts/actaitalica-ojs-new.archicoop.it/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 /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DBDataXMLParser.inc.php on line 122
[schema: lib/pkp/xml/schema/common.xml]
[schema: lib/pkp/xml/schema/log.xml]
[schema: lib/pkp/xml/schema/announcements.xml]
[schema: lib/pkp/xml/schema/scheduledTasks.xml]
[schema: lib/pkp/xml/schema/temporaryFiles.xml]
[schema: lib/pkp/xml/schema/metadata.xml]
[schema: lib/pkp/xml/schema/reviews.xml]
[schema: lib/pkp/xml/schema/reviewForms.xml]
[schema: lib/pkp/xml/schema/controlledVocab.xml]
[schema: lib/pkp/xml/schema/submissions.xml]
[schema: lib/pkp/xml/schema/submissionFiles.xml]
[schema: lib/pkp/xml/schema/notes.xml]
[schema: lib/pkp/xml/schema/views.xml]
[schema: lib/pkp/xml/schema/genres.xml]
[schema: lib/pkp/xml/schema/tombstone.xml]
[schema: lib/pkp/xml/schema/rolesAndUserGroups.xml]
[schema: lib/pkp/xml/schema/metrics.xml]
[schema: lib/pkp/xml/schema/views.xml]
[schema: lib/pkp/xml/schema/libraryFiles.xml]
[schema: lib/pkp/xml/schema/navigationMenus.xml]
[schema: dbscripts/xml/ojs_schema.xml]
[data: dbscripts/xml/indexes.xml]

[code: Installer Installer::installDefaultNavigationMenus]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::migrateStaticPagesToNavigationMenuItems]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::migrateSRLocale]

[code: Installer Installer::concatenateIntoAbout]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::concatenateIntoMasthead]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[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]

[code: Installer Installer::migrateArticleMetadata]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Warning: Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/submission/SubmissionKeywordEntryDAO.inc.php on line 20
PHP Warning: Declaration of SubmissionLanguageEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/submission/SubmissionLanguageEntryDAO.inc.php on line 0
PHP Warning: Declaration of SubmissionAgencyEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/submission/SubmissionAgencyEntryDAO.inc.php on line 0
[data: dbscripts/xml/upgrade/3.0.0_update.xml]

[code: Installer Installer::clearDataCache]

[code: Installer Installer::migrateUserRoles]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::fixReviewForms]

[code: Installer Installer::htmlifyEmailTemplates]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
[note: docs/release-notes/README-BEACON]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

[code: Installer Installer::installEmailTemplate]

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

[code: Installer Installer::localizeCustomBlockSettings]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352

[code: Installer Installer::convertEditorDecisionNotes]

[code: Installer Installer::convertQueries]
PHP Warning: Declaration of SubmissionFileDAO::fromRow($row) should be compatible with PKPSubmissionFileDAO::fromRow($row, $fileImplementation) in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/classes/article/SubmissionFileDAO.inc.php on line 23

[code: Installer Installer::migrateFiles]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
WARNING: Unable to find a match for “8-16-1-SP.pdf” in “/var/www/vhosts/files/journals/1//articles/8/”. Skipping this file.
WARNING: Unable to find a match for “10-13-1-SM.rtf” in “/var/www/vhosts/files/journals/1//articles/10/”. Skipping this file.

[code: Installer Installer::convertSupplementaryFiles]
PHP Notice: unserialize(): Error at offset 127 of 756 bytes in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/db/DAO.inc.php on line 352
PHP Warning: copy(/var/www/vhosts/files/journals/1//articles/8/attachment/8-1-16-1-13-20120126.pdf): failed to open stream: No such file or directory in /var/www/vhosts/actaitalica-ojs-new.archicoop.it/lib/pkp/classes/file/FileManager.inc.php on line 159

[code: Installer Installer::provideSupplementaryFilesForReview]

Invalid file!

ojs2: Invalid file!

A did a last attempt, removing the unmatched files listed in the log:

WARNING: Unable to find a match for “8-16-1-SP.pdf” in “/var/www/vhosts/files/journals/1//articles/8/”. Skipping this file.
WARNING: Unable to find a match for “10-13-1-SM.rtf” in “/var/www/vhosts/files/journals/1//articles/10/”. Skipping this file.

Still the rpblem is not solved and the final error is

[code: Installer Installer::provideSupplementaryFilesForReview]

Invalid file!

ojs2: Invalid file!

Thanks in advance for your help


Cannot upgrade OJS 2.4.8 to 3.1.1-2
#2

It looks like you have already seen the thread here:


Pointing to https://github.com/pkp/ojs/pull/2009/files

I also found this error to arise when a supplementary file entry exists in OJS but there is no corresponding submission file. Specifically:

SELECT a.context_id, sf.* FROM article_supplementary_files sf, submissions a WHERE a.submission_id = sf.article_id AND sf.file_id <> 0 AND sf.show_reviewers = 1 AND sf.remote_url IS NULL and sf.file_id not in (select f.file_id from submission_files f);

This presents in the user interface as a supplementary file with no file information:

I’m testing a patch adding the and sf.file_id in (select f.file_id from submission_files f) to: