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From: <mar...@mh...> - 2012-09-11 21:04:27
|
Tim Arnold writes: > Hi Markus, > Here are some notes: > Using refdbxp 0.9.9-1 built from svn revision 531 ma...@mh... > > (1) invalid xml generated > This citation: > <citation role="REFDB">bart_m66</citation> > > After the command > refdbxp -t db50x < test1.xml > test1_full.xml > becomes (note the non-terminated xref) > <citation role="REFDB"><xref linkend="IDbart_m66-X"></citation> > This is an odd inconsistency. As refdbxp need not be aware of the DocBook or TEI version you're using, you can only choose between DocBook SGML, DocBook XML, and TEI XML. The first one is the default if no type or an incorrect type is specified. Try "-t db31x" instead and you should get valid XML. See the man page for further details. The default stems from the days of yore when XML was all fresh and new and no one used it because the tools weren't as good as they are now. XML should probably be the default these days, but I'm always careful not to break old behaviour. > > (2) documentation typo > Page 102 (section 10.3.1.2.3, step 1) the xinclude path is incorrect: > /usr/local/share/xsl should be > /usr/local/share/refdb/xsl > Thanks for catching this. I've fixed this in svn. > (3) 'chapter' as root element not supported. Which error do you get? Actually, chapter is indeed a valid root element as of DocBook V5, see http://docbook.org/tdg5/en/html/ch02.html#roots If that doesn't work with RefDB, I'd call it a bug. > Okay,this works! If you have book or article as the root element, and > citations following this pattern: > <citation role="REFDB"><xref linkend="IDkuma_v92-X" /></citation> > > My root element was 'chapter'. That is legal DocBook though, as far as I know. > > Only one problem I have now: > how to work with chapter as the root element. > > I create books, but each chapter has its own bibliography. Do you > think that is possible? > I haven't tried that. It should work though as long as the bibliographies don't "overlap", i.e. if a single reference is not listed in two or more bibliographies. In that case you'd have duplicate xml:id attributes which are not allowed in XML. Also, processing wouldn't work with the stock RefDB scripts, so you'd have to write some of your own. regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: <mar...@mh...> - 2012-09-10 19:10:18
|
Tim Arnold writes: > failed to access style data Hi Tim, this usually means that you did not add that particular style to the database. The style data have to be available to the application server refdbd rather than to any of the clients. You'll have to run a command along the lines of: refdba -C addstyle APA.xml although this should have been taken care of during the initial setup of RefDB with refdb-init. You can list the available styles with the command: refdbc -C liststyle regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: <mar...@mh...> - 2012-09-08 14:14:59
|
mar...@mh... writes: > I'll follow up on this on the list, but could you please send me your > input file test.xml and test.id.xml (if that gets proper created by > runbib) for further analysis off-list? Thanks for providing the input data and the additional debug information. I think the problem here is that you do not use the proper citation syntax for raw bibliographies. The citation syntax that you used is the short notation which would require a preprocessing with refdbxp before you run runbib, using a cooked bibliography. If you want to process the raw bibliography with the stock DocBook stylesheets, you'd have to use the standard DocBook citation syntax, like this: <citation role="REFDB"><xref linkend="kuma_v92"/></citation> This syntax, and some hints on further processing these documents, is explained in some more detail in the manual (chapter 10, section "create bibliographies", http://refdb.sourceforge.net/manual/ch10s03.html). best regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: <mar...@mh...> - 2012-09-08 08:07:22
|
Tim Arnold writes: > In my docbook test.xml file I have a couple of citations like this: > <citation role="REFDB">kuma_v92</citation>. Hi, I'll follow up on this on the list, but could you please send me your input file test.xml and test.id.xml (if that gets proper created by runbib) for further analysis off-list? regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: Tim A. <jti...@gm...> - 2012-09-07 14:54:42
|
hi, I must be doing something wrong since I can't get to the first step of creating a DocBook5.0 raw bibliography. I converted my bibtex database to ris format and I can use refdba, so my installation is okay I think. In my docbook test.xml file I have a couple of citations like this: <citation role="REFDB">kuma_v92</citation>. runbib -d mybib -r -t db50x test.xml I get Variable $SGML_CATALOG_FILES not set Parse error at line 4 column 2: syntax error The terminal where the refdbd instance is running (refdbd -s -e 0 -l 7) says this when I exec the runbib in another terminal: --------------------- sqlite3 /usr/local/var/lib/refdb/db mybib SELECT meta_app,meta_type,meta_dbversion FROM t_meta WHERE meta_type='risx' connected to database server using database: mybib no character encoding conversion required output encoding is: UTF-8 XML parse error child exited with code 1 server waiting n_max_fd=4 --------------------- So I try the step-by-step way: xsltproc --xinclude /usr/local/share/refdb/xsl/citationsraw.xsl test.xml > test.id.xml This produces a text version of the test.xml file, except it still has citations tags but no attributes on the tags. So xmllint doesn't like it: xmllint --noout --nonet --dtdvalid file:///usr/local/share/refdb/dtd/citationlistx.dtd test.id.xml test.id.xml:4: parser error : Start tag expected, '<' not found Does any of that ring a bell? Have I missed a step somewhere? thanks, --Tim p.s., in refdbc i can successfully get a reference from the database: getref -d mybib :CK:=kuma_v92 |
From: Markus H. <mar...@mh...> - 2012-06-06 09:35:49
|
Hi, as far as I can see this problem is caused by a change between PHP 5.3 and 5.4 regarding the mechanism how variables are passed by reference. I do not have a PHP interface up and running at this time, so the following is untested. Could you please check whether the following change in /usr/local/share/refdb/www/index.phpfixes the problem? The line in question is 1786 in my sources, although you mention 1531 instead. - if (!yaz_ccl_parse($id[$i], $term, &$cclresult)) { + if (!yaz_ccl_parse($id[$i], $term, $cclresult)) { (note the missing ampersand). According to what I read about this issue on the web, PHP should be able to figure out by itself how to pass the variable appropriately, and the syntax using the ampersand has been removed in PHP 5.4. regards, Markus "O. Hartmann" <oha...@ze...> was heard to say: > A couple of days ago all of our FreeBSD boxes where forced to update > their ports recompiling all PNG dependencies. > > After those updates, on ALL of our boxes providing the RefDB > webinterface, this webinterface, PHP5, has been gone. > > I put one of the servers via php.ini into "development" mode reporting > errors, since the servers in questions do show a white page with nothing > otherwise. > > I get this: > > Fatal error: Call-time pass-by-reference has been removed in > /usr/local/share/refdb/www/index.php on line 1531 > > The line in question seems to refer to YAZ: > > if (!yaz_ccl_parse($id[$i], $term, &$cclresult)) { > ... } > > I tried to recompile refdb via > portmaster -f refdb > > as well as PHP > > portmaster -f php5-5 > > but there is no solution doing it that way. > > Since RefDB worked fine before, I guess this is a unconvenience brought > in by the port's updating orgy. > > Regards > Oliver -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: O. H. <oha...@ze...> - 2012-06-06 07:39:13
|
A couple of days ago all of our FreeBSD boxes where forced to update their ports recompiling all PNG dependencies. After those updates, on ALL of our boxes providing the RefDB webinterface, this webinterface, PHP5, has been gone. I put one of the servers via php.ini into "development" mode reporting errors, since the servers in questions do show a white page with nothing otherwise. I get this: Fatal error: Call-time pass-by-reference has been removed in /usr/local/share/refdb/www/index.php on line 1531 The line in question seems to refer to YAZ: if (!yaz_ccl_parse($id[$i], $term, &$cclresult)) { ... } I tried to recompile refdb via portmaster -f refdb as well as PHP portmaster -f php5-5 but there is no solution doing it that way. Since RefDB worked fine before, I guess this is a unconvenience brought in by the port's updating orgy. Regards Oliver |
From: Stephan G. <st...@ga...> - 2012-02-03 06:20:54
|
Hello! > thanks for your analysis which is pretty much correct. I've checked in > a fix (svn revision 755). This version returns your test dataset as > DocBook 5.0 including the edition information. > Thanks a lot. Now it works perfectly for me. Regards, Stephan |
From: <mar...@mh...> - 2012-02-01 00:08:58
|
Hi, Stephan Gatzka writes: > So for me it seems that the RIS VL tag will be found in "refdb_edition" > and not in "refdb_volume". > thanks for your analysis which is pretty much correct. I've checked in a fix (svn revision 755). This version returns your test dataset as DocBook 5.0 including the edition information. best regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: Stephan G. <st...@ga...> - 2012-01-31 20:29:25
|
Hi! > Unless your mail agent unvoluntarily edited your input file, the "ER" > tag lacks a trailing space. The RIS spec is pretty clear about the > fact that each tag ends with two spaces, a dash, and another > space. The parser does not recognize "ER -" as a tag and reads it as > another line of the preceding M3 field. This does not quite explain why > the "ER -" string is duplicated though, but you should try again > using a correctly terminated RIS entry, i.e. "ER - ". Thanks for your hint with the trailing space, but again, I'm not really a RIS specialist... > I see that the edition information is missing from the DocBook > output. I'll look into this as soon as time permits. I just ran the code through the debugger. In backend-db31.c:879 is the call to get_refdb_volume which itself calls result = dbi_result_get_string(dbires, "refdb_volume"); This call always returns NULL. In comparison, in backend-risx.c:864 is also the call to get_refdb_volume. But if this call fails, it calls get_refdb_edition in the else clause. This call succeeds. So for me it seems that the RIS VL tag will be found in "refdb_edition" and not in "refdb_volume". Hope this helps. Regards, Stephan |
From: <mar...@mh...> - 2012-01-31 00:17:10
|
Hi, Stephan Gatzka writes: > M3 - DOI:10.1007/3-540-27522-3 > ER - Unless your mail agent unvoluntarily edited your input file, the "ER" tag lacks a trailing space. The RIS spec is pretty clear about the fact that each tag ends with two spaces, a dash, and another space. The parser does not recognize "ER -" as a tag and reads it as another line of the preceding M3 field. This does not quite explain why the "ER -" string is duplicated though, but you should try again using a correctly terminated RIS entry, i.e. "ER - ". > What I'm missing is the edition tag and I also have these ER - intermixed. > I see that the edition information is missing from the DocBook output. I'll look into this as soon as time permits. best regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: Stephan G. <st...@ga...> - 2012-01-28 20:53:44
|
Hello! I've found some time to compile the svn version (754) and now I got the DOI correctly, Thanks a lot. Nevertheless, I experienced some other problems. That's the RIS entry I imported into an empty database: TY - BOOK ID - SCHOLZ_SOFTWARE_ENGINEERING_EMBEDDED BT - Softwareentwicklung eingebetteter Systeme AU - Scholz,Peter PY - 2005/// VL - 2 CY - Berlin, Heidelberg PB - Springer Verlag SN - 3-540-23405-5 M3 - DOI:10.1007/3-540-27522-3 ER - When I use refdbc: getref :ID:=1 -t ris -s ALL TY - BOOK ID - SCHOLZ_SOFTWARE_ENGINEERING_EMBEDDED AU - Scholz,Peter RP - NOT IN FILE BT - Softwareentwicklung eingebetteter Systeme CY - Berlin, Heidelberg PB - Springer Verlag M3 - DOI:10.1007/3-540-27522-3 ER - ER - PY - 2005/// SN - 3-540-23405-5 VL - 2 ER - 999:1 retrieved:0 failed Now I see these weird ER tags, I expected them only at the adn of the wohle entry. Maybe that's also the reason why the docbook output also looks somehow strange: refdbc: getref :ID:=1 -t db50x -s ALL <?xml version="1.0" encoding="UTF-8"?> <bibliography xmlns="http://docbook.org/ns/docbook"> <title>Bibliography</title> <biblioentry xml:id="SCHOLZ_SOFTWARE_ENGINEERING_EMBEDDED"> <abbrev>SCHOLZ_SOFTWARE_ENGINEERING_EMBEDDED</abbrev> <biblioset relation="monogr"> <authorgroup> <author role="author"> <personname> <firstname>Peter</firstname> <surname>Scholz</surname> </personname> </author> </authorgroup> <biblioset relation="booktitle"> <title>Softwareentwicklung eingebetteter Systeme</title> </biblioset> <publisher> <publishername>Springer Verlag</publishername> <address>Berlin, Heidelberg</address> </publisher> <pubdate>2005</pubdate> </biblioset> <biblioid class="isbn">3-540-23405-5</biblioid> <biblioid class="doi">DOI:10.1007/3-540-27522-3 ER - ER -</biblioid> </biblioentry> </bibliography> 999:1 retrieved:0 failed What I'm missing is the edition tag and I also have these ER - intermixed. Is there something I did wrong? Regards, Stephan Gatzka |
From: Stephan G. <st...@ga...> - 2012-01-27 06:18:14
|
> I'd recommend to use the current svn revision if you're able to > build RefDB from the sources. I've been using this version in a > production environment for months without running into any > problems. That's no problem for me. I will try it out this evening. Many thanks! Regards, Stephan |
From: <mar...@mh...> - 2012-01-26 23:08:41
|
Hi, Stephan Gatzka writes: > Is it possible or planned to include a > <biblioid class="doi">xxxx</biblioid> > when exporting to docbook5? I've imported RIS data sets including DO tags. > This has been implemented in the svn version a while ago. > The second question is which RIS tag is the correct one for the > "edition" of a book and is this tag already exported to an <edition> tag > in docbook? > The RIS spec suggest "VL" for this purpose. I've noticed that this field was exported incorrectly in the docbook output (it was exported to volumenum regardless of the reference type). I've checked in a fix. Editions of books and related types should now be exported correctly as of svn revision 754. I'd recommend to use the current svn revision if you're able to build RefDB from the sources. I've been using this version in a production environment for months without running into any problems. regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: Stephan G. <st...@ga...> - 2012-01-23 21:48:58
|
Hi! I'm a somehow newbie to refdb, but I got it running and I'm impressed by the capabilities. I'm using the latest official version 0.9.9-1 Currently I've two questions I didn't found answers yet. Is it possible or planned to include a <biblioid class="doi">xxxx</biblioid> when exporting to docbook5? I've imported RIS data sets including DO tags. The second question is which RIS tag is the correct one for the "edition" of a book and is this tag already exported to an <edition> tag in docbook? Kind regards, Stephan |
From: <mar...@mh...> - 2011-07-17 16:51:45
|
Frank M Salter writes: > Refdb complains about the version number of the latest version of > PostgreSQL 9.0.4 and does not continue. > > Is there real incompatibility? > Hi Frank, I've set up PostgreSQL 9.03 on my FreeBSD 8.1 box. I've edited pg_hba.conf to use password authentication for everything. I've then set up a RefDB database according to http://refdb.sourceforge.net/manual/ch04s08.html#sect2-manual-setup I've used manual setup as I've already installed RefDB with MySQL as a backend. Next I've added myself as a user. The only problem that I encountered is that I cannot connect to PostgreSQL unless I provide a password with the refdba adduser command, but this is expected. After adding the user properly, I was able to use RefDB without any problems. Now if that procedure does not work on your box, we'll have to figure out other potential problems. I've checked the PostgreSQL release notes. There should not be any changes from 9.03 to 9.04 that pertain to access problems. To get an idea of what else may be the culprit, could you please provide some more system information. Please run the following command: refdb-bug This will create the file refdb-bug.txt in your current working directory. Please append that file to your response. I'd also like to know which versions of libdbi and libdbi-drivers you are using. If you built libdbi-drivers from the sources, then please run make check from the top-level directory of the libdbi-drivers sources and follow the instructions (if any) to run a test on pgsql. best regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: <mar...@mh...> - 2011-07-15 21:13:38
|
Hi Frank, Frank M Salter writes: > main database version is not supported this in fact indicates that the libdbi driver somehow doesn't manage to talk to the PostgreSQL engine properly. > At some point: I was using a number of terminal screens and did not > see the exact moment > when the following (transcribed by me) appeared: > ======================================================= > *** glibc detected *** refdb *** munmap_chunk(): invalid pointer > 0xb75f48e0 *** > ======= Backtrace: ======= > /lib/libc.so.6(+0x6f68a)[0xb76f068a] > /usr/local/lib/libdbi.so.1(dbi_result_free + 0x14c)[0xb782827c] > refdbd[0x804d9a5] > /lib/libc.so.6(__libc_start_main+0xe6)[0xb7697db6] > refdbd[0x804aa21] This looks like a crash in libdbi. This may be caused by some incompatibility between the driver and the engine, or it's just a plain libdbi bug. However, I've never had any such crashes with any of the drivers that I've used, so I still suspect the pgsql driver does not work well with the latest PostgreSQL releases. > Thank you for your prompt reply. If you need any more information, > please let me know. Is there a chance to retrieve the PostgreSQL error logs? On my system, PostgreSQL logs errors to syslog by default, so it might be sufficient to grep /var/log/messages for "postgres" or "postmaster". I'll try to find some time to get 9.03 running on my development box this weekend. I'll then run the libdbi test suite to see if the driver is the culprit. regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: <mar...@mh...> - 2011-07-13 19:43:35
|
Frank M Salter writes: > Refdb complains about the version number of the latest version of > PostgreSQL 9.0.4 and does not continue. > > Is there real incompatibility? > > Is there a workaround to allow access? > > If not, what is the latest version of PostgreSQL with which RefDB will > work successfully? > Hi Frank, it would be very helpful to actually see the error messages. In fact, I suspect the problem is more likely related to the libdbi driver rather than to RefDB itself. In any case, please use the refdbd -l (and maybe -e and -L) command line switches or the corresponding variables in /usr/local/etc/refdb/refdbdrc (don't forget to restart or reload the server in that case) to switch on debug level logging. You'll find the documentation right here: http://refdb.sourceforge.net/manual/re02.html Now run any refdbc or refdba command which demonstrates the problem, and send the refdbd log to the list. You should also try to locate the PostgreSQL log output. I can't recall where it goes to by default, but have a look at /var/log/messages for a start. As of the PostgreSQL versions compatible with RefDB (or libdbi, FWIW), I can't give a definitive answer. I used to run some 8.x versions successfully. I've upgraded my development box lately, it now has PostgreSQL 9.03 installed. However, I never got round to test libdbi or RefDB with that version. I'm heavily using a MySQL setup for some production work that will take another few weeks. This means that I have barely any time left to fiddle. regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: Frank M S. <fms...@bl...> - 2011-07-12 15:35:21
|
Refdb complains about the version number of the latest version of PostgreSQL 9.0.4 and does not continue. Is there real incompatibility? Is there a workaround to allow access? If not, what is the latest version of PostgreSQL with which RefDB will work successfully? Regards Frank Salter |
From: Torsten B. <br...@ph...> - 2011-06-19 09:10:21
|
Hallöchen! Markus Hoenicka writes: > [...] > > [...] So you should think of the listuser output as "users that > have entries" rather than as "users that have access". After some further testing, I now see what you mean, so ignore my previous posting. And adding an existing user with the same password seems to be idempotent. Howerver, password changes don't happen, at least not in Postgres. Tschö, Torsten. -- Torsten Bronger Jabber ID: tor...@ja... or http://bronger-jmp.appspot.com |
From: Torsten B. <br...@ph...> - 2011-06-19 08:29:50
|
Hallöchen! Markus Hoenicka writes: > [...] > > which PosgreSQL server version do you use? 8.4.8 > [...] > > Right after adding a user, it does not show up in the listuser > output because of the way RefDB checks for the presence of a > user. It does not query the database engine's access control > because some engines do not have such a thing. Instead, RefDB > checks whether or not the requested user has entries in the > reference database. So you should think of the listuser output as > "users that have entries" rather than as "users that have access". My Web frontend creates RefDB users for every user which is added to the Web frontend. My idea was to check with "listuser" whether a user is already in the references DB. If this doesn't work, is it okay to add a user (possibly) multiple times? Besides this, if I use "adduser", the new user appears amongst the "login roles" of PostgreSQL, but not in the t_user table. This is not correct, is it? Tschö, Torsten. -- Torsten Bronger Jabber ID: tor...@ja... or http://bronger-jmp.appspot.com |
From: Markus H. <mar...@mh...> - 2011-06-18 23:05:12
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Quoting Torsten Bronger <br...@ph...>: > Hallöchen! > > I use RefDB SVN-747 with PostgreSQL. With refdba, I experience the > following: > Hi, which PosgreSQL server version do you use? I did not have time to catch up with the latest PostgreSQL releases. My first guess is that there are some subtle changes in the database engine's access control which RefDB does not handle gracefully. The 238 status message in this context simply confirms that the ALTER GROUP ADD USER SQL query ran successfully. Right after adding a user, it does not show up in the listuser output because of the way RefDB checks for the presence of a user. It does not query the database engine's access control because some engines do not have such a thing. Instead, RefDB checks whether or not the requested user has entries in the reference database. So you should think of the listuser output as "users that have entries" rather than as "users that have access". regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |
From: Torsten B. <br...@ph...> - 2011-06-18 19:08:02
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Hallöchen! I use RefDB SVN-747 with PostgreSQL. With refdba, I experience the following: bronger@wilson:~$ refdba -u chantal Please enter your password: refdba: listuser -d biblio main database version is not supported refdba: listuser -d biblio chantal drefdbuser1 refdb 999:3 refdba: adduser -d biblio toll 238:toll:biblio 999:1 added:0 failed refdba: listuser -d biblio chantal drefdbuser1 refdb 999:3 (The first "main database version is not supported" is stange because a second try works. But this is not the main reason for my posting.) My problem is that I cannot see the user "toll" after having added him. The user "chantal" is allowed to add new users. And what does "238 - revoke user permissions successful" mean in this context? The log says: ... 7:pid=5754:Sat Jun 18 19:05:12 2011:SELECT meta_app,meta_type,meta_dbversion FROM t_meta WHERE meta_type='risx' 7:pid=5754:Sat Jun 18 19:05:12 2011:connected to database server using database: 7:pid=5754:Sat Jun 18 19:05:12 2011:biblio 7:pid=5754:Sat Jun 18 19:05:12 2011:SELECT usename FROM pg_user WHERE usename='toll' 7:pid=5754:Sat Jun 18 19:05:12 2011:ALTER GROUP refdbuser ADD USER toll 7:pid=5754:Sat Jun 18 19:05:12 2011:ALTER GROUP bibliouser ADD USER toll 6:pid=5754:Sat Jun 18 19:05:12 2011:238:toll:biblio 7:pid=5754:Sat Jun 18 19:05:12 2011:command processing done, finish dialog now 6:pid=5754:Sat Jun 18 19:05:12 2011:child finished client on fd 6 Any ideas? Tschö, Torsten. -- Torsten Bronger Jabber ID: tor...@ja... or http://bronger-jmp.appspot.com |
From: Torsten B. <br...@ph...> - 2011-06-18 00:01:57
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Hallöchen! I just updated the Ubuntu packages to * Refdb SVN-747 * Ubuntu 11.04 Installation is as easy as sudo apt-get install python-software-properties sudo add-apt-repository ppa:bronger/ppa sudo apt-get update sudo apt-get install refdb Sometimes, the very first starting of the server fails. However, a re-start fixes this. The package depends on sqlite3 and uses it as default. Tschö, Torsten. -- Torsten Bronger Jabber ID: tor...@ja... or http://bronger-jmp.appspot.com |
From: Markus H. <mar...@mh...> - 2010-06-14 19:18:18
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O. Hartmann writes: > Sorry for the noise. > The update-orgy on FreeBSD due to a gettext-update left several boxes > with partially hidden problems. After a forced reinstallation of PHP5 > and all additional PHP-ports everything runs again like expected. I > never figured out what caused the problem. Nevermind. Glad to hear it works again. regards, Markus -- Markus Hoenicka http://www.mhoenicka.de AQ score 38 |