Installation-Troubleshooting - Revision history

WikiSysop: Fix incorrect display of accented characters & umlauts

2023-11-07T13:02:53Z

Fix incorrect display of accented characters & umlauts

← Older revision		Revision as of 15:02, 7 November 2023
Line 167:		Line 167:
	In case of a latin1-based refbase installation, the contents of the <code>charset</code> attribute should read "ISO-8859-1".		In case of a latin1-based refbase installation, the contents of the <code>charset</code> attribute should read "ISO-8859-1".

	In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ~~·ÈÌ‡ËÏ~~ or ~~ÂÊ¯ˆ‰¸~~ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.		In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as áéíàèì or åæøöäü etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

	So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.		So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

WikiSysop: Fixed some typos

2023-11-05T22:27:31Z

Fixed some typos

← Older revision		Revision as of 00:27, 6 November 2023
Line 125:		Line 125:
	=== Undefined iconv() despite --with-iconv ===		=== Undefined iconv() despite --with-iconv ===

	This problem was ~~experience~~ on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:		This problem was experienced on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:

	<pre>		<pre>
Line 159:		Line 159:
	In the above command, replace <code>''DATABASE_NAME''</code> with the actual name of your refbase MySQL database.		In the above command, replace <code>''DATABASE_NAME''</code> with the actual name of your refbase MySQL database.

	If you've ~~choosen~~ "utf8" upon installation, then you have to make sure that variable <code>$contentTypeCharset</code> in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".		If you've chosen "utf8" upon installation, then you have to make sure that variable <code>$contentTypeCharset</code> in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

	If you've set variable <code>$contentTypeCharset</code> to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:		If you've set variable <code>$contentTypeCharset</code> to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

WikiSysop: Update external links

2023-11-05T22:16:46Z

Update external links

← Older revision		Revision as of 00:16, 6 November 2023
Line 49:		Line 49:
	=== Upload of files under XAMPP doesn't work ===		=== Upload of files under XAMPP doesn't work ===

	In some versions of [~~http~~://~~xampp~~.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:		In some versions of [https://www.apachefriends.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

	upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"		upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"
Line 59:		Line 59:
	=== Renaming of uploaded files does not work under XAMPP ===		=== Renaming of uploaded files does not work under XAMPP ===

	In some versions of [~~http~~://~~xampp~~.org/ XAMPP] the needed PHP function <code>iconv</code> is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for <code>iconv</code> and enable the function by deleting the heading comment sign (').		In some versions of [https://www.apachefriends.org/ XAMPP] the needed PHP function <code>iconv</code> is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for <code>iconv</code> and enable the function by deleting the heading comment sign (').

	=== Export of records results in a blank page ===		=== Export of records results in a blank page ===

WikiSysop: Hide section edit links

2023-11-05T22:10:04Z

Hide section edit links

← Older revision		Revision as of 00:10, 6 November 2023
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	[[Category:Installation]]		[[Category:Installation]]
	[[Category:Troubleshooting]]		[[Category:Troubleshooting]]
			__NOEDITSECTION__

WikiSysop: Update link to Community_portal page

2023-11-05T22:09:07Z

Update link to Community_portal page

WikiSysop: Original page content from 31-Oct-2008

2023-11-05T22:04:16Z

Original page content from 31-Oct-2008

New page

This document presents solutions & tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_Portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_Portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that <code>safe_mode</code> is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
error_reporting = E_ALL
display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue.
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the <code>phpinfo()</code> function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables <code>post_max_size</code> and <code>upload_max_filesize</code> in your active ''php.ini'' file. The values given for <code>post_max_size</code> and <code>upload_max_filesize</code> must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [http://xampp.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [http://xampp.org/ XAMPP] the needed PHP function <code>iconv</code> is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for <code>iconv</code> and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table. The <code>depends_path</code> for the <code>bibutils</code> record should '''not''' be <code>NULL</code> as seen below:

<pre>
mysql> SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
| 1 | refbase | true | NULL |
| 2 | bibutils | true | NULL |
+------------+------------------+-----------------+--------------+
</pre>

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if <code>safe_mode</code> is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in <code>safe_mode_exec_dir</code>
* the PHP temp/session directory must be accessible & writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable <code>$sessionTempDir</code> in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
.../refbase-0.9.0/includes/include.inc.php on line 3631

Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
.../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

$dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

$dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_Portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_Portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experience on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:

<pre>
if (!function_exists('iconv') && function_exists('libiconv')) {
function iconv($input_encoding, $output_encoding, $string) {
return libiconv($input_encoding, $output_encoding, $string);
}
}
</pre>

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace <code>''DATABASE_NAME''</code> with the actual name of your refbase MySQL database.

If you've choosen "utf8" upon installation, then you have to make sure that variable <code>$contentTypeCharset</code> in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable <code>$contentTypeCharset</code> to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

<meta http-equiv="content-type" content="text/html; charset=UTF-8">

In case of a latin1-based refbase installation, the contents of the <code>charset</code> attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ·ÈÌ‡ËÏ or ÂÊ¯ˆ‰¸ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View > Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_Portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]

← Older revision		Revision as of 00:09, 6 November 2023
Line 3:		Line 3:
	Other issues are discussed on the generic [[Troubleshooting]] page.		Other issues are discussed on the generic [[Troubleshooting]] page.

	If you experience any problems while installing refbase, please read this chapter before [[refbase:~~Community_Portal~~\|contacting us]].		If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal\|contacting us]].

	== Preparations before contacting us ==		== Preparations before contacting us ==
Line 9:		Line 9:
	In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.		In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

	'''Important''': Please check following settings and REPORT THEM when [[refbase:~~Community_Portal~~\|contacting us]]. This information will help us a lot to figure out what might be wrong:		'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal\|contacting us]]. This information will help us a lot to figure out what might be wrong:

	* Which version of refbase do you use?		* Which version of refbase do you use?
Line 119:		Line 119:
	then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records\|import]] page for more information and links to example records for all supported formats.		then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records\|import]] page for more information and links to example records for all supported formats.

	If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users\|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:~~Community_Portal~~\|send us]] your problematic records so that we can look into the problem.		If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users\|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal\|send us]] your problematic records so that we can look into the problem.

	If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:~~Community_Portal~~\|let us know]] and we'll try to help.		If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal\|let us know]] and we'll try to help.

	=== Undefined iconv() despite --with-iconv ===		=== Undefined iconv() despite --with-iconv ===
Line 181:		Line 181:
	Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.		Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

	If you still can't get rid of your encoding issues, please [[refbase:~~Community_Portal~~\|let us know]] and we'll see what we can do.		If you still can't get rid of your encoding issues, please [[refbase:Community_portal\|let us know]] and we'll see what we can do.

	[[Category:Installation]]		[[Category:Installation]]
	[[Category:Troubleshooting]]		[[Category:Troubleshooting]]