headers
David Nebauer | 1 Oct 2006 13:37
Picon

ANN: Updated debian packages available

Updated debian packages for svn (revision 189) and pre-release 
(0.9.8-pre4) are now available.

Both sets of packages use the refdbd server in maintenance mode to 
upgrade the main database.  As this feature is still experimental users 
are advised to back up their data before upgrading.

Regards,
David.

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys -- and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
Permalink | Reply | 0 comments |
headers
Markus Hoenicka | 10 Oct 2006 23:49
Picon

ANN: refdb-0.9.8-dupcheck-pre1 available for testing

Hi,

here's the first prerelease from the dupcheck branch of refdb, built
from repository revision 191:

http://refdb.sourceforge.net/pre/refdb-0.9.8-dupcheck-pre1.tar.gz

This prerelease is identical with 0.9.8-pre4, except for the new
checkref command which I'll explain shortly. I'd appreciate bug
reports and success stories with the dupcheck branch, as I'd like to
merge this code back to the trunk as soon as it turns out to be
functional and stable.

You don't need to install this prerelease in order to test it if you
have 0.9.8-pre4 installed. The new prerelease works with the same
databases and does not alter them when running checkref. All you need
to do is to download the tarball, configure and build it as usual, and
then run the server (./refdbd -s <other options>) and the client
(./refdbc <options>) from the src directory. Again, "make install"
should not be required, and I wouldn't recommend it at this time. If
you find some time, please export your references from your existing
database and add them to a new database using the new prerelease, then
query, update, and delete to your heart's content to check that
everything is working ok.

Now what is that new refdbc: checkref command? It is a simple way to
check your reference data for duplicates and faulty data before adding
them to your database permanently. The data will be added to temporary
tables in your database, using the same functions as when adding data
permanently. If your input data are somehow screwed up, you'll notice
(Continue reading)

Permalink | Reply | 0 comments |
headers
Markus Hoenicka | 11 Oct 2006 22:48
Picon

ANN: refdb-0.9.8-pre5 available for download, fixing possible segfault

Hi all,

get the latest prerelease of RefDB as usual:

http://refdb.sourceforge.net/pre/refdb-latest.tar.gz

This is a bugfix release for pre4. No new features, but a few memory
problems detected by valgrind were fixed. I recommend upgrading to
pre5 due to a possible segfault that affects 0.9.8-pre2 through
pre4. The symptoms and implications are described below.

regards,
Markus

Bug Alert
=========

Adding references with refdbc:addref may crash refdbd. The crash may
lead to the last reference before the crash being added incompletely,
thus causing a possible loss of data.

Symptoms:

You'll see the message "could not read to refdbd", usually after a few
references were added successfully. In addition, you should find a
refdbd dump file (refdbd.core on Unix-like systems,
refdbd.exe.stackdump on Windows) somewhere on your system.

Affected systems:
(Continue reading)

Permalink | Reply | 1 comment |
headers
Markus Hoenicka | 11 Oct 2006 23:00
Picon

ANN: refdb-0.9.8-pre5 available for download, fixing possible segfault

Markus Hoenicka writes:
 > You'll see the message "could not read to refdbd", usually after a few

Oh dear... s/read/write/

Markus

--

-- 
Markus Hoenicka
markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
Permalink | Reply | 0 comments |
headers
Jeremy Malcolm | 12 Oct 2006 10:57
Picon
Favicon

Usual trouble - runbib says "error"

runbib is aborting for me again with the unhelpful message "error", and 
I've gone through all the usual reasons why this always happens (eg. 
obviously missing fields in references I've added recently, stray colons 
in citation keys) to no avail.  When I run refdbd in debugging mode the 
last lines it shows as runbib spits out its error are:

SELECT

thesis.t_author.author_name,thesis.t_author.author_lastname,thesis.t_author.author_firstname,thesis.t_author.author_middlename,thesis.t_author.author_suffix,thesis.t_xauthor.xauthor_role 
FROM thesis.t_author, thesis.t_xauthor WHERE 
thesis.t_author.author_id=thesis.t_xauthor.author_id AND 
thesis.t_xauthor.xauthor_type='primary' AND 
thesis.t_xauthor.refdb_id=416 ORDER BY t_xauthor.xauthor_position
child finished client on fd 5
child exited with code 1
server waiting n_max_fd=4

That same SELECT query appears a few times further up, in fact it almost 
seems to be stuck in a loop.  Its results are:

+-------------+-----------------+------------------+
| author_name | author_lastname | author_firstname |
+-------------+-----------------+------------------+
| ACA         | ACA             | NULL             |
+-------------+-----------------+------------------+ ...

-------------------+---------------+--------------+
  author_middlename | author_suffix | xauthor_role |
-------------------+---------------+--------------+
  NULL              | NULL          |              |
(Continue reading)

Permalink | Reply | 4 comments |
headers
Markus Hoenicka | 12 Oct 2006 11:34
Picon

Re: Usual trouble - runbib says "error"

Hi Jeremy,

I'm really sorry to hear that this is "usual trouble" on your end. It shouldn't
be, and I'll try my best to fix this.

Jeremy Malcolm <Jeremy <at> Malcolm.id.au> was heard to say:

> runbib is aborting for me again with the unhelpful message "error", and
> I've gone through all the usual reasons why this always happens (eg.
> obviously missing fields in references I've added recently, stray colons
> in citation keys) to no avail.

You may have tried this already, but does the bug depend on a particular
citation? Does runbib finish ok if you remove one or some of the citations you
added most recently?

> When I run refdbd in debugging mode the
> last lines it shows as runbib spits out its error are:
>
> SELECT
>
thesis.t_author.author_name,thesis.t_author.author_lastname,thesis.t_author.author_firstname,thesis.t_author.author_middlename,thesis.t_author.author_suffix,thesis.t_xauthor.xauthor_role
> FROM thesis.t_author, thesis.t_xauthor WHERE
> thesis.t_author.author_id=thesis.t_xauthor.author_id AND
> thesis.t_xauthor.xauthor_type='primary' AND
> thesis.t_xauthor.refdb_id=416 ORDER BY t_xauthor.xauthor_position
> child finished client on fd 5
> child exited with code 1
> server waiting n_max_fd=4
>
(Continue reading)

Permalink | Reply | 0 comments |
headers
Markus Hoenicka | 12 Oct 2006 13:30
Picon

Re: Usual trouble - runbib says "error"

Jeremy Malcolm <Jeremy <at> Malcolm.id.au> was heard to say:

> > thanks for the test data. I forgot to ask one question: which style are you
> > using? If it is not one of those shipped with RefDB, could you please send
> me
> > that too?
>
> Sure here it is.

Thanks again. A quick test on my Windows/Cygwin box here at work shows that I
can reproduce *a* problem. We'll have to see whether it is the same problem
that you see, because my error message is different ("character set conversion
failed"). I'll try to reproduce this on my development box and will get back as
soon as I know more.

regards,
Markus

--

-- 
Markus Hoenicka
markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
(Continue reading)

Permalink | Reply | 0 comments |
headers
David Nebauer | 12 Oct 2006 19:50
Picon

ANN: Updated refdb debian packages

RefDB debian repositories have been updated:
    svn     = revision 193
    release = 0.9.8-pre5

Regards,
David.

-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
Permalink | Reply | 4 comments |
headers
Markus Hoenicka | 12 Oct 2006 21:27
Picon

Usual trouble - runbib says "error"

Hi Jeremy,

I've tried to reproduce this problem on my development platform, but I
didn't quite "succeed".

I noticed that your data apparently use an uncommon encoding. When I
tried to add them as they are, assuming they're ISO-8859-1 encoded, I
received 10 errors from refdbd. All of the failed references contained
umlauts or the "ae" ligature. I started over, this time converting the
encoding manually:

iconv -f iso-8859-1 -t utf-8 < Thesis.ris | refdbc -d malcolm -C addref -E UTF-8 -o addresult.txt
22850 byte written to addresult.txt
999:576 added:1 skipped:0 failed

This obviously gave better results. One reference was skipped because
it has a duplicate citation key
(UNITED-NATIONS2003CREATION-OF-A-G). As per the publication date these
seem to be different references so you may want to fix this.

I then tried to create the bibliography like this:

refdbib -d malcolm -S Murdoch.Law. -t db31x Thesis.id.xml > Thesis.bib.xml
999:565 retrieved:0 failed:0 not found

That is, no problem on FreeBSD. I'll try to run the same test on
Cygwin tomorrow, maybe the manual character conversion prevents the
libiconv error that I ran into. I also ran the same test using
valgrind. This tool did not report any invalid write attempts,
although approx. 2MB of memory get lost during the test (most of this
(Continue reading)

Permalink | Reply | 2 comments |
headers
Jeremy Malcolm | 13 Oct 2006 04:41
Picon
Favicon

Re: Usual trouble - runbib says "error"

Markus Hoenicka wrote:
> What database engine do you use btw? I'm running PostgreSQL on FreeBSD
> and MySQL on Cygwin.

MySQL on Darwin.

> Unfortunately this doesn't get you any closer to a working
> bibliography. It may be a platform issue but I wouldn't bet. In order
> to further identify what is going wrong, you should try the following:
> 
> - remove the citations you last added and see when runbib starts to
>   work again. Can you attribute the failure to a single citation?

I deleted the last month worth of references, because I know with 
certainty that it was working a month ago.  It didn't help, both times 
the client stopping following this line after a long pause:

/sw/bin/openjade:Thesis.sgml:3867:38:X: reference to non-existent ID 
"IDCOOTER1994STRUCTURAL-ADJU-X"

(This in itself doesn't indicate a problem, because I get "reference to 
non-existent ID" for *all* my references and it usually doesn't matter - 
except that in this case it is followed by "error".)

> - can you clean up the reference data by converting them to utf-8
>   manually as shown above? You'd best use a test database that uses
>   the UTF-8 encoding anyway. Does that affect the outcome in any way?

No, same result (though I hadn't been getting the errors you got when 
using ISO-8859-1 anyway).
(Continue reading)

Permalink | Reply | 1 comment |

Gmane