refdb-users — List for RefDB users

[Refdb-users] was database too old or corrupt error on debian ever solved

[Daniel O'D. <dan...@ul...>]

Hi,

I'm making one of my periodic attempts to get refdb set up under Ubuntu
(this time in dapper using mysql5). I've got the database too old or
corrupt error again.

As this ever been solved? This installation was on a clean system.

-d
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] First Start of refdbc

[Rich S. <rsh...@ap...>]

On Sat, 27 May 2006, Markus Hoenicka wrote:

> I don't know whether you followed the handbook far enough to create
> reference databases. This is something that new users stumble over every
> now and then. In brief,

Markus,

   Er, ... no. I didn't read that far. So, I will back up and do it again; the
right way this time.

> Hope this helps

   Sure does!

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.             |  The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)  |          Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] First Start of refdbc

[Markus H. <mar...@mh...>]

Rich Shepard writes:
 > On Fri, 26 May 2006, Rich Shepard wrote:
 > 
 > >  What is not a RefDB database? How do I fix the problem?
 > 
 >    I seem to have a problem. When I run the 'listdb' command it returns
 > nothing. Wthin postgres, a list of available databases shows refdb, but it's
 > the only one encoded UTF8.
 > 
 >    1.) How can I change the database encoding? Since there's no data in it I
 > can drop and recreate it. Is that the best way?
 > 
 >    2.) Is the above related to why I see no available database when I invoke
 > the refdb client and run the listdb command?
 > 

I don't know whether you followed the handbook far enough to create
reference databases. This is something that new users stumble over
every now and then. In brief,

1) your installation needs one main database, usually called "refdb"
   (unless you configure it differently). This database should use the
   UTF-8 encoding because it contains a list of journal name words
   some of which use non-ASCII characters. Bibliography styles also go
   into this database

2) your installation needs at least one reference database. These
   databases receive your bibliographic data. You'd use whichever
   encoding matches your bibliographic data best, but for
   international data UTF-8 is never wrong. You use the
   refdba:createdb command to create reference databases. The -E
   switch selects the character encoding. Once the database is
   created, you have to add yourself as a user with the refdba:adduser
   command. Only then you'll be able to access the database with your
   database user account. You should also be able to see this database
   with the refdbc:listdb command.

Hope this helps
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] First Start of refdbc

[Rich S. <rsh...@ap...>]

On Fri, 26 May 2006, Rich Shepard wrote:

>  What is not a RefDB database? How do I fix the problem?

   I seem to have a problem. When I run the 'listdb' command it returns
nothing. Wthin postgres, a list of available databases shows refdb, but it's
the only one encoded UTF8.

   1.) How can I change the database encoding? Since there's no data in it I
can drop and recreate it. Is that the best way?

   2.) Is the above related to why I see no available database when I invoke
the refdb client and run the listdb command?

Rich

-- 
Richard B. Shepard, Ph.D.             |  The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)  |          Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] First Start of refdbc

[Rich S. <rsh...@ap...>]

   Following the tutorial, I invoked the refdbc client. This is what happened:

[rshepard@salmo ~]$ refdbc
Please enter your password: 
not a RefDB database
refdbc:

   What is not a RefDB database? How do I fix the problem?

Rich

-- 
Richard B. Shepard, Ph.D.             |  The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)  |          Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Procite Translation

[Rich S. <rsh...@ap...>]

   I was given a Procite database in its native format. The source did not
know how to export it in RIS format. Is there a way to import these data into
RefDB? If not, does anyone know of someone using Procite who would be willing
to translate it for me? The .zip file is 4.3M large.

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.             |  The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)  |          Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Re: Build Problem: 0.9.7-pre2

[Rich S. <rsh...@ap...>]

On Sat, 13 May 2006, Markus Hoenicka wrote:

> If I ever mentioned pre7, that's bogus. pre6 is the latest, and it sure has
> lots of fixes compared to pre2. I'd recommend to use pre6.

Markus,

   I probably mis-remembered the number. pre6 is installed and I'm reading the
Handbook. But, today is a beautiful day and I'm getting all the yard work
done that I've put off for months. Later I'll do more reading.

Many thanks,

Rich

-- 
Richard B. Shepard, Ph.D.             |  Quantifying subjectivity for the
Applied Ecosystem Services, Inc.(TM)  |  benefit of business and society.
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Re: Build Problem: 0.9.7-pre2

[Markus H. <mar...@mh...>]

Rich Shepard writes:
 >    Can't see the change from here -- even after reloading the page. It still
 > shows pre2.
 > 
 > > You'll always get the latest version if you follow the link to the latest
 > > prerelease on the download page.
 > 

I didn't expect that a technical problem would keep me from uploading
the page when I sent the mail. But Murphy's law worked well and made
scp fail. I wanted to try later but forgot about it. Thanks for
reminding me. I've just fixed the page.

 >    That turns out to be pre6, not pre7. Should I build and install it?
 > 

If I ever mentioned pre7, that's bogus. pre6 is the latest, and it
sure has lots of fixes compared to pre2. I'd recommend to use pre6.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] Re: Build Problem: 0.9.7-pre2

[Rich S. <rsh...@ap...>]

On Sat, 13 May 2006, Markus Hoenicka wrote:

> My bad. The link on the front page should point to the latest prerelease,
> not to pre2. I've fixed that.

Markus,

   Can't see the change from here -- even after reloading the page. It still
shows pre2.

> You'll always get the latest version if you follow the link to the latest
> prerelease on the download page.

   That turns out to be pre6, not pre7. Should I build and install it?

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.             |  Quantifying subjectivity for the
Applied Ecosystem Services, Inc.(TM)  |  benefit of business and society.
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Re: Build Problem: 0.9.7-pre2

[Rich S. <rsh...@ap...>]

On Sat, 13 May 2006, Markus Hoenicka wrote:

Hi Markus,

> As long as you can make do without the docs installed, that is. I'll keep
> on investigating this build-docs-where-it-shouldn't kind of bug.

   Well, I downloaded the pdf versions (handbook, tutorial, emacs mode) and
printed them out. It's not often that I consult built-in help; I prefer the
printed docs or the man pages.

Thank you,

Rich

-- 
Richard B. Shepard, Ph.D.             |  Quantifying subjectivity for the
Applied Ecosystem Services, Inc.(TM)  |  benefit of business and society.
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Re: Build Problem: 0.9.7-pre2

[Markus H. <mar...@mh...>]

Hi Rich,

Rich Shepard writes:
 >    I downloaded, built, and installed 0.9.6, then read that there was a
 > problem with that (and the -pre1, too), so I followed the suggestion on the
 > main page of the Web site and grabbed the -pre2 tarball. Didn't see anything
 > about a newer version.
 > 

My bad. The link on the front page should point to the latest
prerelease, not to pre2. I've fixed that. You'll always get the latest
version if you follow the link to the latest prerelease on the
download page.

 >    Mailmain still hasn't sent the subscription confirmation. Must have taken
 > off early this Friday.
 > 

Too bad. Let me know if this problem persists, then I'll subscribe you
manually.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] Re: Build Problem: 0.9.7-pre2

[Markus H. <mar...@mh...>]

Hi Rich,

Rich Shepard writes:
 >    Building with --disable-docs fixed the problem. I work with LaTeX/LyX and
 > not with DocBook or SGML so this should not be a problem for my needs.
 > 

As long as you can make do without the docs installed, that is. I'll
keep on investigating this build-docs-where-it-shouldn't kind of bug.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] Re: Build Problem: 0.9.7-pre2

[Rich S. <rsh...@ap...>]

On Fri, 12 May 2006, Markus Hoenicka wrote:

> Now to the problem that you see. As far as I can tell this is a segfault in
> xsltproc. Could you check whether there are any bug reports in Slackware
> about xsltproc?

Markus,

   My Google search found nothing that appeared relevant. Locally,
/usr/bin/xsltproc is present.

   Building with --disable-docs fixed the problem. I work with LaTeX/LyX and
not with DocBook or SGML so this should not be a problem for my needs.

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.             |  Quantifying subjectivity for the
Applied Ecosystem Services, Inc.(TM)  |  benefit of business and society.
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Re: Build Problem: 0.9.7-pre2

[Rich S. <rsh...@ap...>]

On Fri, 12 May 2006, Markus Hoenicka wrote:

> Two things :
>
> - is there any specific reason why you are using 0.9.7-pre2? The
>  latest version is 0.9.7-pre6. This is not going to fix the problem
>  that you see, but I'm just wondering.

Markus,

   I downloaded, built, and installed 0.9.6, then read that there was a
problem with that (and the -pre1, too), so I followed the suggestion on the
main page of the Web site and grabbed the -pre2 tarball. Didn't see anything
about a newer version.

> Now to the problem that you see. As far as I can tell this is a segfault in
> xsltproc. Could you check whether there are any bug reports in Slackware
> about xsltproc?

   OK. I'll check.

> As a short-term fix, run configure with the --disable-docs switch to bypass
> ./the transformation of the docs.

   Will do.

   Mailmain still hasn't sent the subscription confirmation. Must have taken
off early this Friday.

Many thanks,

Rich

-- 
Richard B. Shepard, Ph.D.             |  Quantifying subjectivity for the
Applied Ecosystem Services, Inc.(TM)  |  benefit of business and society.
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Build Problem: 0.9.7-pre2

[Markus H. <mar...@mh...>]

Hi,

Rich Shepard writes:
 > xsltproc -o refdb-manual.fo --nonet --xinclude ../doc/include/manual-fo.xsl
 > refdb-manual.xml
 > *** glibc detected *** double free or corruption (!prev): 0x0826c570 ***
 > make[1]: *** [refdb-manual.pdf] Aborted
 > make[1]: Leaving directory /usr/local/refdb-0.9.7-pre2/doc'
 > make: *** [all-recursive] Error 1
 > 
 
Two things :

- is there any specific reason why you are using 0.9.7-pre2? The
  latest version is 0.9.7-pre6. This is not going to fix the problem
  that you see, but I'm just wondering.

- I'm still waiting for enlightenment why the docs are rebuilt on all
  systems but mine. The ingenious idea was to ship RefDB with the
  prebuilt docs so you don't have to install all the dependencies
  required to rebuild the docs. Although all files appear to be
  present, this idea seems to fail completely. Does anyone have an
  idea why this happens?

Now to the problem that you see. As far as I can tell this is a
segfault in xsltproc. Could you check whether there are any bug
reports in Slackware about xsltproc? As a short-term fix, run
./configure with the --disable-docs switch to bypass the
transformation of the docs.


>    I've requested subscription to the mail list and sent the confirmation, but
 > haven't yet seen the final acceptance by mailman.
 > 

If there is a problem with mailman, I won't be able to fix it. I'd
have to file a support request with SourceForge. However, as a list
admin I can subscribe you manually if you want me to.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Re: Any hint of 0.9.7 final ?

[<ste...@jo...>]

Markus Hoenicka a =E9crit :
> St=E9phane T=E9letch=E9a <ste...@jo...> was heard to say:
>=20
>=20
>>I've used this one to get a building rpm (by disabling the doc=3D20
>>generation which seems to still fail, some more dependancies are needed=
=3D20
>>for them).
>=20
>=20
> This is still a mystery to me. Everything that might ever be built in t=
he doc
> subdir is shipped with the archive. Therefore a simple "make" should no=
t
> attempt to rebuild the doc subdir. Is this caused by your RPM build fra=
mework,
> or does this happen always on your box?

Oh, sorry, i should have responded on this specifically. I presume it is=20
coming from the rpm environnment where i build. I'm not completely=20
familiar with it for the moment.

One goal for instance for this quite exhaustive building process is to=20
provide documentation, info pages, man pages, and other stuff that i=20
don't for now understand extensively.

>=20
>>I don't know if it is better to get both lists involved or keep the=3D2=
0
>>track on ly on the devel, i'll see from your answers (on the devel list=
).
>>
>=20
>=20
> As a rule of thumb, if other users might help to fix a problem, or if y=
ou find a
> problem which might be important to them, please send it to refdb-users=
. If it's
> just about packaging issues, dependencies, build failures and such, the
> refdb-devel list seems more appropriate.

Nice, i'll continue then on appropriate list when i'll be more advanced.

> regards,
> Markus

Best wishes,

St=E9phane


--=20
St=E9phane T=E9letch=E9a, PhD.                  http://www.steletch.org
Unit=E9 Math=E9matique Informatique et G=E9nome http://migale.jouy.inra.f=
r/mig
INRA, Domaine de Vilvert                  T=E9l : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

Re: [Refdb-users] Re: Any hint of 0.9.7 final ?

[Markus H. <mar...@mh...>]

St=E9phane T=E9letch=E9a <ste...@jo...> was heard to say:

> I've used this one to get a building rpm (by disabling the doc=3D20
> generation which seems to still fail, some more dependancies are needed=
=3D20
> for them).

This is still a mystery to me. Everything that might ever be built in the=
 doc
subdir is shipped with the archive. Therefore a simple "make" should not
attempt to rebuild the doc subdir. Is this caused by your RPM build frame=
work,
or does this happen always on your box?

> I don't know if it is better to get both lists involved or keep the=3D2=
0
> track on ly on the devel, i'll see from your answers (on the devel list=
).
>

As a rule of thumb, if other users might help to fix a problem, or if you=
 find a
problem which might be important to them, please send it to refdb-users. =
If it's
just about packaging issues, dependencies, build failures and such, the
refdb-devel list seems more appropriate.

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] Re: Any hint of 0.9.7 final ?

[<ste...@jo...>]

Markus Hoenicka a =E9crit :
> [I've cc'ed the list as other users may face the same problems or even
> know solutions. Please keep this discussion on the list]
>=20


> I've uploaded a new prerelease (0.9.7-pre6) based on these
> changes. Please give it a try and let me know.
>=20
> http://refdb.sourceforge.net/pre/refdb-latest.tar.gz

I've used this one to get a building rpm (by disabling the doc=20
generation which seems to still fail, some more dependancies are needed=20
for them).

I'm now working on enabling the various databases connectors (mysql,=20
pgsql, ...) and last i'll check everything works by importing/exporting=20
some stuff (in the end, this is what i need ;-).

I'll try to give as much input as possible on the list. I think it is=20
better to discuss this on the refdb-devel list (to which i've subscribed=20
to).

I don't know if it is better to get both lists involved or keep the=20
track on ly on the devel, i'll see from your answers (on the devel list).

St=E9phane

--=20
St=E9phane T=E9letch=E9a, PhD.                  http://www.steletch.org
Unit=E9 Math=E9matique Informatique et G=E9nome http://migale.jouy.inra.f=
r/mig
INRA, Domaine de Vilvert                  T=E9l : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

[Refdb-users] Re: Any hint of 0.9.7 final ?

[Markus H. <mar...@mh...>]

me typing too fast...

Markus Hoenicka writes:
 > These missing programs contribute to the build failure. More below.

These missing programs may contribute to a build failure. More below.
 > 
 > I see this warning on several problems without adverse effect. It
 > seems to be safe to ignore this.
 > 

I see this warning on several operating systems without adverse
effect.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] Re: Any hint of 0.9.7 final ?

[Markus H. <mar...@mh...>]

[I've cc'ed the list as other users may face the same problems or even
know solutions. Please keep this discussion on the list]

Hi,

St=E9phane T=E9letch=E9a writes:
 > + libtoolize --copy --force
 > Remember to add `AC=5FPROG=5FLIBTOOL' to `configure.in'.
 > You should update your `aclocal.m4' by running aclocal.

Is that something that the RPM build system forces you to do=3F RefDB
does not use libtool. RefDB's own autogen.sh script does not call
libtoolize. If you must do this anyway, it is safe to ignore the error
message.

 > checking for dtdparse... no
 > checking for dtdformat... no
 > checking for sgrep... no
 > checking for tidy... /usr/bin/tidy
 > checking for batik-rasterizer... no

These missing programs contribute to the build failure. More below.

 > checking for shared library run path origin... /bin/sh: ./conf/confi=
g.rpath: No such file or directory
 > done

I see this warning on several problems without adverse effect. It
seems to be safe to ignore this.

 > checking for http://www.tei-c.org/Stylesheets/p4/fo/tei.xsl... no
 > checking for XML file http://www.tei-c.org/Stylesheets/p4/fo/tei.xsl=
... checking for No entry for SYSTEM http://www.tei-c.org/Stylesheets/p=
4/fo/tei.xsl No entry for URI http://www.tei-c.org/Stylesheets/p4/fo/te=
i.xsl... no
 > XML file not found

This is strange if you know that the file is installed. Most likely
the TEI stylesheets are not correctly listed in the XML catalog, or
there is only an entry in one of the SGML catalogs. If this is true,
you should file a bug report for the TEI stylesheet package. As a
short-term fix, you could try to pass the location of the stylesheets
to the configure file by means of the --with-tei-xsl option.

 > refdbda.c: In function 'daemon=5Fstarted=5Fby=5Finetd':
 > refdbda.c:2494: warning: pointer targets in passing argument 5 of 'g=
etsockopt' differ in signedness

I think I've fixed this by adding a proper test to configure.in

 > refdbdbib.c: In function 'getbib':
 > refdbdbib.c:905: warning: passing argument 2 of 'iconv' from incompa=
tible pointer type
 > refdbdbib.c:1004: warning: passing argument 2 of 'iconv' from incomp=
atible pointer type

There seems to be no portable solution to this problem. Some systems
use char**, others use const char**, and no matter what you use in
your code, it'll generate a warning in half of the systems.

 > refdbc.c: In function 'addref':
 > refdbc.c:2890: warning: call to =5F=5Fbuiltin=5F=5F=5Fstrncpy=5Fchk =
will always overflow destination buffer
 > refdbc.c: In function 'com=5Fgetref':
 > refdbc.c:1820: warning: call to =5F=5Fbuiltin=5F=5F=5Fstrncpy=5Fchk =
will always overflow destination buffer
 > refdbc.c: In function 'addnote':
 > refdbc.c:3587: warning: call to =5F=5Fbuiltin=5F=5F=5Fstrncpy=5Fchk =
will always overflow destination buffer
 > refdbc.c: In function 'com=5Fgetnote':
 > refdbc.c:4538: warning: call to =5F=5Fbuiltin=5F=5F=5Fstrncpy=5Fchk =
will always overflow destination buffer
 > refdbc.c: In function 'addlink':
 > refdbc.c:5076: warning: call to =5F=5Fbuiltin=5F=5F=5Fstrncpy=5Fchk =
will always overflow destination buffer
 > refdbc.c: In function 'com=5Fupdatejo':
 > refdbc.c:5399: warning: call to =5F=5Fbuiltin=5F=5F=5Fstrncpy=5Fchk =
will always overflow destination buffer

I've fixed the incorrect string sizes.

 > nmed2ris.c: In function 'main':
 > nmed2ris.c:182: warning: incompatible implicit declaration of built-=
in function 'exit'

nmed2ris has essentially been replaced by the med2ris Perl
script years ago. I've removed it instead of attempting to fix it.

 > bib2ris.c: In function 'log=5Fprint':
 > bib2ris.c:1887: warning: incompatible implicit declaration of built-=
in function 'strftime'
 > bib2ris.c:1887: warning: passing argument 4 of 'strftime' makes poin=
ter from integer without a cast

I can't figure out what's wrong with this one. All you need to declare
strftime properly is to include <time.h> which I did. It doesn't help
here. Other files use the same strftime call, include <time.h>, and do
not generate this warning (e.g. refdbdref.c). I'm stymied.

 > ../scripts/statgen.pl docbook > refdb-manual-statustable.xml
 > make[1]: *** No rule to make target `include/doc-html.dsl', needed b=
y `refdb-manual/ch01.html'.  Stop.

I've changed the doc build system from SGML to XML after 0.9.6, so I'm
not surprised to see a few glitches. This one seems to be caused by an
incorrect dependency (dsl files are used no more). I've fixed this.

In any case, make should not attempt to build the docs as they are
shipped pre-built in the tar.gz archives. You should only need to
rebuild them after running maintainer-clean. If you do that, or if the
RPM build process mandates that, you'll need the additional tools that
I mentioned above when looking at your configure output.


I've uploaded a new prerelease (0.9.7-pre6) based on these
changes. Please give it a try and let me know.

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

regards
Markus
--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] ANN: RefDB-perlmod-0.4.1 released

[Markus H. <mar...@mh...>]

Hi all,

I've uploaded a new release of the Perl modules used by RefDB. The
only difference to 0.4 is a bugfix in the test script which avoids
erroneous error messages in three out of ten tests if the box does not
use the default locale. There were no changes to the modules
themselves. There is no reason to upgrade except for package builders.

http://sourceforge.net/project/showfiles.php?group_id=26091

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Problem for building refDB rpm ...

[Markus H. <mar...@mh...>]

St=E9phane T=E9letch=E9a <ste...@jo...> was heard to say:

> Sorry, all of them return nothing, the comparison is ok, sorting proble=
m ?
>

Just for the record: The test script uses the system command "sort" which=
 is
locale-dependent. Therefore St=E9phane got errors on his French box where=
as all
went fine for me (and for everyone else, as no one has complained yet :-)=
. I'll
fix the test script asap to work around this problem.

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Problem for building refDB rpm ...

[<ste...@jo...>]

Markus Hoenicka a =E9crit :
> Hi,
>=20
> St=E9phane T=E9letch=E9a <ste...@jo...> was heard to say:
>=20
>=20
>>Here is the testdata archive
>=20
>=20
> Thanks for the data. diff tells me that your output files are identical=
 to mine,
> so the RefDB modules apparently work ok. The only thing that fails is a=
pparently
> the command that compares the output file to the "known goods".
>=20
> Could you please run the following commands in your terminal:
>=20
> sort < testdata/testdata.out1 | cmp -s - testdata/testdata_pm.good.sort=
ed
>=20
> sort < testdata/testdata.out2 | cmp -s - testdata/testdata.good.sorted
>=20
> sort < testdata/testdata.out3 | cmp -s - testdata/testdata.good.sorted
>=20
> Maybe we'll get a little extra information about why this doesn't work.
>=20
> regards,
> Markus
>=20

Sorry, all of them return nothing, the comparison is ok, sorting problem =
?

St=E9phane

--=20
St=E9phane T=E9letch=E9a, PhD.                  http://www.steletch.org
Unit=E9 Math=E9matique Informatique et G=E9nome http://migale.jouy.inra.f=
r/mig
INRA, Domaine de Vilvert                  T=E9l : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

Re: [Refdb-users] Problem for building refDB rpm ...

[Markus H. <mar...@mh...>]

Hi,

St=E9phane T=E9letch=E9a <ste...@jo...> was heard to say:

> Here is the testdata archive

Thanks for the data. diff tells me that your output files are identical t=
o mine,
so the RefDB modules apparently work ok. The only thing that fails is app=
arently
the command that compares the output file to the "known goods".

Could you please run the following commands in your terminal:

sort < testdata/testdata.out1 | cmp -s - testdata/testdata_pm.good.sorted

sort < testdata/testdata.out2 | cmp -s - testdata/testdata.good.sorted

sort < testdata/testdata.out3 | cmp -s - testdata/testdata.good.sorted

Maybe we'll get a little extra information about why this doesn't work.

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Problem for building refDB rpm ...

[Markus H. <mar...@mh...>]

St=E9phane T=E9letch=E9a <ste...@jo...> was heard to say:

> [stephane@bioinfo RefDB-perlmod-0.4]$ make test
> PERL_DL_NONLAZY=3D3D1 /usr/bin/perl5.8.8 "-Iblib/lib" "-Iblib/arch" tes=
t.pl
> 1..10: ok
> 2..10: not ok
> 3..10: not ok
> 4..10: not ok
> 5..10: ok
> 6..10: ok
> 7..10: ok
> 8..10: ok
> 9..10: ok
> 10..10: ok
> That is ... waitaminute ... 7 out of 10
>
> I'm not very confident about a test stating 3 tests over 10 are not OK=3D=
20
> and i'm not also a perl hacker.
>

Tests 2 through 4 use testdata/testdata.in as input. There is apparently
something going wrong with these tests on your platform. I just downloade=
d and
checked the archive on a Windows/Cygwin box where it succeeds in 10 out o=
f 10
tests. Therefore I don't think the whole thing is broke. It rather seems =
to be
a platform or a Perl version issue (I run 5.8.7).

I've sent you a patched test.pl script by private mail. Please replace th=
e
packaged version with this one and re-run "make test". Instead of deletin=
g the
intermediate result files, it will just rename them for later analysis. W=
hen
done, please send me the testdata/ subdirectory as a tar.gz file so I can=
 have
a look at the output.

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de