Upgrade 2.4.8.2 to 3

Hi,

I am doing upgrade test for www.neuropsicolatina.org.

Current installation is 2.4.8.2.
I tried update to the latest 3.1.1-4 (and 3.0.1, just to make sure sure it is not a version issue).
With no success.

I have some warnings about missing files and a PHP Fatal error: Call to a member function getFileId().

Should I create dummy empty files to be able to upgrade?
Will this broke something?

Thank you.

Here is the log

[Fri Jan 25 10:59:10.360861 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “14-52-1-RV.doc” in “/var/www/files/journals/1//articles/14/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 10:59:10.366021 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “24-87-1-RV.doc” in “/var/www/files/journals/1//articles/24/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 10:59:10.373672 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “53-398-1-RV.doc” in “/var/www/files/journals/1//articles/53/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 10:59:10.376284 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “54-413-1-RV.doc” in “/var/www/files/journals/1//articles/54/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 10:59:34.217874 2019] [:error] [pid 17237] [client 10.140.164.171:54805] PHP Warning: Invalid argument supplied for foreach() in /var/www/neuro/classes/install/Upgrade.inc.php on line 2096, referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 10:59:34.349873 2019] [:error] [pid 17237] [client 10.140.164.171:54805] PHP Warning: Invalid argument supplied for foreach() in /var/www/neuro/classes/install/Upgrade.inc.php on line 2255, referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:28.544407 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “14-51-1-SM.doc” in “/var/www/files/journals/1//articles/14/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:28.720614 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “24-86-1-SM.doc” in “/var/www/files/journals/1//articles/24/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.029466 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “42-292-1-SM.pdf” in “/var/www/files/journals/1//articles/42/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.029610 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “42-293-2-RV.pdf” in “/var/www/files/journals/1//articles/42/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.030225 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “42-293-1-RV.pdf” in “/var/www/files/journals/1//articles/42/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.030352 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “42-294-2-LE.pdf” in “/var/www/files/journals/1//articles/42/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.030474 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “42-299-1-ED.pdf” in “/var/www/files/journals/1//articles/42/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.030596 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “42-296-3-CE.pdf” in “/var/www/files/journals/1//articles/42/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.030716 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “42-296-2-CE.pdf” in “/var/www/files/journals/1//articles/42/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.030837 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “42-296-1-CE.pdf” in “/var/www/files/journals/1//articles/42/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.140572 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “53-397-1-SM.doc” in “/var/www/files/journals/1//articles/53/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.144175 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “54-412-1-SM.doc” in “/var/www/files/journals/1//articles/54/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.161310 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “56-449-1-SM.doc” in “/var/www/files/journals/1//articles/56/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.161444 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “56-451-1-RV.doc” in “/var/www/files/journals/1//articles/56/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.161567 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “56-450-1-SP.doc” in “/var/www/files/journals/1//articles/56/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.294110 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “69-540-1-RV.doc” in “/var/www/files/journals/1//articles/69/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.482318 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “83-616-1-SM.docx” in “/var/www/files/journals/1//articles/83/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:29.482560 2019] [:error] [pid 17237] [client 10.140.164.171:54805] WARNING: Unable to find a match for “83-617-1-RV.docx” in “/var/www/files/journals/1//articles/83/”. Skipping this file., referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:32.460341 2019] [:error] [pid 17237] [client 10.140.164.171:54805] PHP Warning: copy(/var/www/files/journals/1//articles/56/attachment/56-1-450-1-13-20101230.doc): failed to open stream: No such file or directory in /var/www/neuro/lib/pkp/classes/file/FileManager.inc.php on line 159, referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:32.475386 2019] [:error] [pid 17237] [client 10.140.164.171:54805] PHP Warning: assert(): Assertion failed in /var/www/neuro/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 123, referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:37.654427 2019] [:error] [pid 17237] [client 10.140.164.171:54805] PHP Warning: copy(/var/www/files/journals/1//articles/56/submission/56-8-450-1-2-20101230.doc): failed to open stream: No such file or directory in /var/www/neuro/lib/pkp/classes/file/FileManager.inc.php on line 159, referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:37.676271 2019] [:error] [pid 17237] [client 10.140.164.171:54805] PHP Warning: assert(): Assertion failed in /var/www/neuro/lib/pkp/classes/submission/SubmissionFileDAODelegate.inc.php on line 112, referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:37.676357 2019] [:error] [pid 17237] [client 10.140.164.171:54805] PHP Warning: copy(/var/www/files/journals/1//articles/56/submission/review/56-8–1-4-20101230.doc): failed to open stream: No such file or directory in /var/www/neuro/lib/pkp/classes/file/FileManager.inc.php on line 159, referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade
[Fri Jan 25 11:00:37.689663 2019] [:error] [pid 17237] [client 10.140.164.171:54805] PHP Fatal error: Call to a member function getFileId() on null in /var/www/neuro/lib/pkp/classes/submission/PKPSubmissionFileDAO.inc.php on line 1065, referer: http://ojs3.criugm.qc.ca/index.php/index/install/upgrade