refdb-users — List for RefDB users

Re: [Refdb-users] php webinterface: php8: Uncaught TypeError:

[FreeBSD U. <fr...@wa...>]

On Sun, 13 Feb 2022 18:04:54 +0100
Markus Hoenicka <mar...@mh...> wrote:

> Hi,
> 
> I'm not running the PHP interface myself, so I'm sorry that it took a 
> while to respond. I've set up my FreeBSD box with Apache 2.4, PHP 8.0 
> and the required PHP extensions (session, dom, xml, xsl). PHP does not 
> complain about a TypeError when starting the web interface. Retrieving 
> an existing test dataset works as well. So I cannot reproduce the 
> problem here. How exactly did you trigger the problem?
> 
> regards,
> Markus
> 
> Am 2022-01-30 16:26, schrieb FreeBSD User:
> > Hello folks,
> > 
> > despite the fact that refDB is pretty inactive, it is still in use on
> > several private
> > projects and internal installations. The base OS is always FreeBSD
> > (I'm officially the
> > FreeBSD mainatiner so far).
> > 
> > Sources: most recent copy of the subversion repo provided by source 
> > forge.
> > 
> > Since FreeBSD ports now switched from php 7.4 to 8.0 as the default,
> > the php-driven
> > webinterface is broken and it seems this error is very common in the
> > group of those
> > switching from php 7.4 to 8.0. The error is triggered by
> > 
> > phpweb/idex.php.in
> > 
> > The apache's log reports:
> > 
> > [..]
> >  PHP Fatal error:  Uncaught TypeError: Cannot access offset of type
> > string on string in
> >  /usr/local/share/refdb/www/index.php:900\nStack trace:\n#0 {main}\n  
> > thrown in
> >  /usr/local/share/refdb/www/index.php on line 900, referer:
> >  https://my-host.local/refdb/index.php?thisPage=Search%20indices
> > 
> > $defaultValue seems to be treated as STRING but should be ARRAY
> > 
> > How can this be solved?
> > 
> > Kind regards,
> > 
> > Oliver
> > 
> > 
> > _______________________________________________
> > Refdb-users mailing list
> > Ref...@li...
> > https://lists.sourceforge.net/lists/listinfo/refdb-users  
> 

Hello list,

in the meanwhile other issues with our setup and the migration of PHP from 7.4 towards
8.0 occured. I guess the issue could be triggered due to a rogue php port, officially
php80 incorporates now a bunch of modules formerly realized as separate ports/modules.
I'll check and I'll report back as soon as possible.

Kind regards,

oh

Re: [Refdb-users] Release announcement: refdb-1.0.3

[FreeBSD U. <fr...@wa...>]

On Sun, 13 Feb 2022 23:56:34 +0100
Markus Hoenicka <mar...@mh...> wrote:

> Hi all,
> 
> upon popular demand a new version of RefDB has been released into the 
> wild:
> 
> https://sourceforge.net/projects/refdb/files/refdb-src/refdb-src-1.0.3/
> 
> This version collects a couple of changes and fixes that have been 
> committed to the Subversion repository over the years. The documentation 
> and some styles have been updated, new styles were added, and refdbd now 
> supports a config file option to set the SQL mode of MySQL and MariaDB 
> database servers on a per-session base. NB this feature requires an 
> updated version of the corresponding libdbi driver which is available 
> from git only at present.
> 
> Feedback and questions are welcome.
> 
> regards,
> Markus
> 

Hello,

that is great news! Thank you very much.

Kind regards,

O. Hartmann

[Refdb-users] Release announcement: refdb-1.0.3

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

Hi all,

upon popular demand a new version of RefDB has been released into the 
wild:

https://sourceforge.net/projects/refdb/files/refdb-src/refdb-src-1.0.3/

This version collects a couple of changes and fixes that have been 
committed to the Subversion repository over the years. The documentation 
and some styles have been updated, new styles were added, and refdbd now 
supports a config file option to set the SQL mode of MySQL and MariaDB 
database servers on a per-session base. NB this feature requires an 
updated version of the corresponding libdbi driver which is available 
from git only at present.

Feedback and questions are welcome.

regards,
Markus

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38

Re: [Refdb-users] [REQUEST] new refdb tarball derived from trunk

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

Hi Oliver,

I'm done adding my latest local changes, updated the documentation and 
implemented a new option to obviate the need to reconfigure an entire 
database server just to allow RefDB to run some legacy SQL. Please find 
the new tarball right here:

https://sourceforge.net/projects/refdb/files/refdb-src/refdb-src-1.0.3/

Let me know if this new release should not work as expected.

regards,
Markus


Am 2022-01-30 16:47, schrieb FreeBSD User:
> The most recent refDB tarball is revision 1.0.2.
> 
> Most recent LLVM/clang compiler default to gnu99, so there is an
> linker error triggered
> sourcing to src/readln.h (ld: error: duplicate symbol:
> thecommandlist), this problem has
> been solved in the main tree 4 months ago with commit 816.
> 
> There are a couple of fixes in the trunk I'd like to see in a tarball,
> including the
> above compiler issue.
> As mainatiner of the FreeBSD port, the port is now marked unusable due
> to the linker
> error. For my private purposes, I solved the discrepancy via a large,
> 5 Mbytes large diff
> between trunk and 1.0.2, but it is considered inappropriate to
> maintain such a large diff
> file in the ports tree of FreeBSD ports.
> 
> It would be very nice to have the recent trunk as a downloadable 
> tarball.
> 
> Kind regards,
> 
> Oliver
> 
> 
> _______________________________________________
> Refdb-users mailing list
> Ref...@li...
> https://lists.sourceforge.net/lists/listinfo/refdb-users

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38

Re: [Refdb-users] php webinterface: php8: Uncaught TypeError:

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

Hi,

I'm not running the PHP interface myself, so I'm sorry that it took a 
while to respond. I've set up my FreeBSD box with Apache 2.4, PHP 8.0 
and the required PHP extensions (session, dom, xml, xsl). PHP does not 
complain about a TypeError when starting the web interface. Retrieving 
an existing test dataset works as well. So I cannot reproduce the 
problem here. How exactly did you trigger the problem?

regards,
Markus

Am 2022-01-30 16:26, schrieb FreeBSD User:
> Hello folks,
> 
> despite the fact that refDB is pretty inactive, it is still in use on
> several private
> projects and internal installations. The base OS is always FreeBSD
> (I'm officially the
> FreeBSD mainatiner so far).
> 
> Sources: most recent copy of the subversion repo provided by source 
> forge.
> 
> Since FreeBSD ports now switched from php 7.4 to 8.0 as the default,
> the php-driven
> webinterface is broken and it seems this error is very common in the
> group of those
> switching from php 7.4 to 8.0. The error is triggered by
> 
> phpweb/idex.php.in
> 
> The apache's log reports:
> 
> [..]
>  PHP Fatal error:  Uncaught TypeError: Cannot access offset of type
> string on string in
>  /usr/local/share/refdb/www/index.php:900\nStack trace:\n#0 {main}\n  
> thrown in
>  /usr/local/share/refdb/www/index.php on line 900, referer:
>  https://my-host.local/refdb/index.php?thisPage=Search%20indices
> 
> $defaultValue seems to be treated as STRING but should be ARRAY
> 
> How can this be solved?
> 
> Kind regards,
> 
> Oliver
> 
> 
> _______________________________________________
> Refdb-users mailing list
> Ref...@li...
> https://lists.sourceforge.net/lists/listinfo/refdb-users

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38

Re: [Refdb-users] [REQUEST] new refdb tarball derived from trunk

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

Hi Oliver,

just a quick response, although I don't have a new tarball yet. The 
project isn't dead as such. It still serves my purposes here at work, so 
there is no real need to change things from my end. I still try to fix 
incompatibilities that arise every now and then. I use the refdb-pubmed 
tool a lot which required a few fixes, and a few glitches had to be 
fixed in libdbi or its drivers. I have a few local changes on 
Windows+Cygwin that are not committed yet, and moving to a new desktop 
at work a few months ago left me unable to commit to the Subversion 
repository. This seems to be a local permission issue which I may not be 
able to resolve (I'm in a healthcare environment, I'm not allowed to 
fiddle with permissions). I'll move the local changes to my FreeBSD box 
at home to get them submitted eventually. I did a major FreeBSD version 
upgrade lately, so RefDB may need to be recompiled for any testing. The 
new tarball may take a few days so please don't hang on the edge of your 
seat. The good thing is that the present code here at work has been 
tested for quite a while.

regards,
Markus

Am 2022-01-30 16:47, schrieb FreeBSD User:
> The most recent refDB tarball is revision 1.0.2.
> 
> Most recent LLVM/clang compiler default to gnu99, so there is an
> linker error triggered
> sourcing to src/readln.h (ld: error: duplicate symbol:
> thecommandlist), this problem has
> been solved in the main tree 4 months ago with commit 816.
> 
> There are a couple of fixes in the trunk I'd like to see in a tarball,
> including the
> above compiler issue.
> As mainatiner of the FreeBSD port, the port is now marked unusable due
> to the linker
> error. For my private purposes, I solved the discrepancy via a large,
> 5 Mbytes large diff
> between trunk and 1.0.2, but it is considered inappropriate to
> maintain such a large diff
> file in the ports tree of FreeBSD ports.
> 
> It would be very nice to have the recent trunk as a downloadable 
> tarball.
> 
> Kind regards,
> 
> Oliver
> 
> 
> _______________________________________________
> Refdb-users mailing list
> Ref...@li...
> https://lists.sourceforge.net/lists/listinfo/refdb-users

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38

[Refdb-users] [REQUEST] new refdb tarball derived from trunk

[FreeBSD U. <fr...@wa...>]

The most recent refDB tarball is revision 1.0.2.

Most recent LLVM/clang compiler default to gnu99, so there is an linker error triggered
sourcing to src/readln.h (ld: error: duplicate symbol: thecommandlist), this problem has
been solved in the main tree 4 months ago with commit 816.

There are a couple of fixes in the trunk I'd like to see in a tarball, including the
above compiler issue.
As mainatiner of the FreeBSD port, the port is now marked unusable due to the linker
error. For my private purposes, I solved the discrepancy via a large, 5 Mbytes large diff
between trunk and 1.0.2, but it is considered inappropriate to maintain such a large diff
file in the ports tree of FreeBSD ports.

It would be very nice to have the recent trunk as a downloadable tarball.

Kind regards,

Oliver

[Refdb-users] php webinterface: php8: Uncaught TypeError:

[FreeBSD U. <fr...@wa...>]

Hello folks,

despite the fact that refDB is pretty inactive, it is still in use on several private
projects and internal installations. The base OS is always FreeBSD (I'm officially the
FreeBSD mainatiner so far).

Sources: most recent copy of the subversion repo provided by source forge.

Since FreeBSD ports now switched from php 7.4 to 8.0 as the default, the php-driven
webinterface is broken and it seems this error is very common in the group of those
switching from php 7.4 to 8.0. The error is triggered by

phpweb/idex.php.in

The apache's log reports:

[..]
 PHP Fatal error:  Uncaught TypeError: Cannot access offset of type string on string in
 /usr/local/share/refdb/www/index.php:900\nStack trace:\n#0 {main}\n  thrown in
 /usr/local/share/refdb/www/index.php on line 900, referer:
 https://my-host.local/refdb/index.php?thisPage=Search%20indices

$defaultValue seems to be treated as STRING but should be ARRAY

How can this be solved?

Kind regards,

Oliver

Re: [Refdb-users] refdb-init help

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

On 2019-03-21 11:20, Michael Strack was heard to say:
> Trying to wrap up installation with the refdb-init script on and off
> over the past couple of weeks, getting the following errors:
> 
> #+BEGIN_QUOTE
> Saved existing refdbd configuration file as
> /usr/local/etc/refdb/refdbdrc.201903191931.16
> scripts/refdb-init: line 410: refdbdrc.example: No such file or 
> directory
> /usr/local/bin/refdbd: option requires an argument -- 'w'
> unknown option w: use refdbd -h to display usage
> 
> Check for PostgreSQL authentication problems
> 
> refdbd-init.sh failed.
> refdb-init is finished.
> #+END_QUOTE
> 
> Environment:
> 
> - SVN version of refdb
> - Debian
> - Using PostgreSQL as back-end
> 
> First, the missing file.  This may be because of the following code in
> refdb-init (around line 410, as it said):
> 
> #+BEGIN_SRC
> if [ "${engine_name}" = "mysql" ]; then
>     sed "s%<refdblib>%/usr/local/share/refdb%" <
> /usr/local/etc/refdb/refdbdrc.mysql.example | \
> 	sed "s/\tlocalhost/\t${refdbdrc_hostname}/" | \
> 	sed "s/\t3306/\t${refdbdrc_port}/">/usr/local/etc/refdb/refdbdrc \
> 	|| endScript "Could not create refdbd config file" "failed"
> elif [ "${engine_name}" = "pgsql" ]; then
>     sed "s%<refdblib>%/usr/local/share/refdb%" < refdbdrc.example | \
> 	sed "s/\tlocalhost/\t${refdbdrc_hostname}/" | \
> 	sed "s/\t5432/\t${refdbdrc_port}/" >/usr/local/etc/refdb/refdbdrc \
> 	|| endScript "Could not create refdbd config file" "failed"
> #+END_SRC
> 
> You can see that in the mysql case, the database-specific file
> 'refdbdrc.mysql.example' is used, while in the PostgreSQL case, the
> non-existent generic file 'refdbdrc.example' is referenced.  Perhaps
> this should instead refer to 'refdbdrc.pgsql.example', which /does/
> exist?
> 
> As for PostgreSQL authentication issues, the relevant call to refdbd
> in refdb-init seems to be:
> 
> #+BEGIN_SRC
> if [ "${engine_name}" = "pgsql" ]; then
>     su $postgres_name -c "$MYREFDBD -a -e 0 -l 6 -u $dbadmin_name -w
> $dbadmin_password"	|| endScript "Check for PostgreSQL authentication
> problems" "failed"
> #+END_SRC
> 
> Have tested general functioning of PostgreSQL from shell and it seems
> to work fine.  The default PostgreSQL installation on Debian has a
> single database admin and super user account, 'postgres', which is
> locked.  No password, can only be access by su/sudo.  I figured since
> I run refdb-init as root, this would be handled.  So I just pass this
> username and a blank password to refdb-init.  But maybe I am required
> to set a password for the admin account?
> 
> I've tried passing a blank (i.e. hitting RETURN), empty quotes (''),
> an asterisk (*), a quoted asterisk ('*').  Sometimes this prompts for
> password, sometimes it gives me "cannot open PID file"...
> 

Hi,

I think your analysis regarding the .example file is correct. This is a 
leftover of an older version which customized a single template instead 
of using one template per database engine. I've checked in the fixed 
version of refdb-init.in. Remember that you have to re-run configure in 
order to create a fixed refdb-init.

I can't tell off the top of my head if refdb-init can handle database 
logins without a password. Even if superuser access is restricted to a 
dedicated account, I think it is still recommended to set a superuser 
database password before doing anything interesting with the database. I 
can't guarantee this will fix your initialization problem, but it seems 
to be the proper way for security reasons anyway. If nothing else helps, 
please follow the steps of the handbook for manual initialization.

best regards,
Markus

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38

[Refdb-users] refdb-init help

[Michael S. <mi...@st...>]

Trying to wrap up installation with the refdb-init script on and off
over the past couple of weeks, getting the following errors:

#+BEGIN_QUOTE
Saved existing refdbd configuration file as
/usr/local/etc/refdb/refdbdrc.201903191931.16
scripts/refdb-init: line 410: refdbdrc.example: No such file or directory
/usr/local/bin/refdbd: option requires an argument -- 'w'
unknown option w: use refdbd -h to display usage

Check for PostgreSQL authentication problems

refdbd-init.sh failed.
refdb-init is finished.
#+END_QUOTE

Environment:

- SVN version of refdb
- Debian
- Using PostgreSQL as back-end

First, the missing file.  This may be because of the following code in
refdb-init (around line 410, as it said):

#+BEGIN_SRC 
if [ "${engine_name}" = "mysql" ]; then
    sed "s%<refdblib>%/usr/local/share/refdb%" < /usr/local/etc/refdb/refdbdrc.mysql.example | \
	sed "s/\tlocalhost/\t${refdbdrc_hostname}/" | \
	sed "s/\t3306/\t${refdbdrc_port}/">/usr/local/etc/refdb/refdbdrc \
	|| endScript "Could not create refdbd config file" "failed"
elif [ "${engine_name}" = "pgsql" ]; then
    sed "s%<refdblib>%/usr/local/share/refdb%" < refdbdrc.example | \
	sed "s/\tlocalhost/\t${refdbdrc_hostname}/" | \
	sed "s/\t5432/\t${refdbdrc_port}/" >/usr/local/etc/refdb/refdbdrc \
	|| endScript "Could not create refdbd config file" "failed"
#+END_SRC

You can see that in the mysql case, the database-specific file
'refdbdrc.mysql.example' is used, while in the PostgreSQL case, the
non-existent generic file 'refdbdrc.example' is referenced.  Perhaps
this should instead refer to 'refdbdrc.pgsql.example', which /does/
exist?

As for PostgreSQL authentication issues, the relevant call to refdbd
in refdb-init seems to be:

#+BEGIN_SRC 
if [ "${engine_name}" = "pgsql" ]; then
    su $postgres_name -c "$MYREFDBD -a -e 0 -l 6 -u $dbadmin_name -w $dbadmin_password"	|| endScript "Check for PostgreSQL authentication problems" "failed"
#+END_SRC

Have tested general functioning of PostgreSQL from shell and it seems
to work fine.  The default PostgreSQL installation on Debian has a
single database admin and super user account, 'postgres', which is
locked.  No password, can only be access by su/sudo.  I figured since
I run refdb-init as root, this would be handled.  So I just pass this
username and a blank password to refdb-init.  But maybe I am required
to set a password for the admin account?

I've tried passing a blank (i.e. hitting RETURN), empty quotes (''),
an asterisk (*), a quoted asterisk ('*').  Sometimes this prompts for
password, sometimes it gives me "cannot open PID file"...

Re: [Refdb-users] Help with RefDB build errors

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

Zitat von Michael Strack <mi...@st...>:

> I'm keeping a log of all the build/install/configure steps so I can
> (hopefully) be useful to any other Debian users who try to build from
> source.
>
> Is the existing Debian package currently unmaintained? I'm not
> suggesting I have the skills to perform that role, just seeking to
> confirm.

The Debian package that used to be available from the RefDB website is  
no longer maintained. There is a set of packages in Debian Oldstable.  
I don't know if the maintainer of these packages has any plans to  
support other releases.

Best regards,
Markus

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38

Re: [Refdb-users] Help with RefDB build errors

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

Hi,

I'm glad it worked out. Building the docs is a bit of a hassle as they 
have a boatload of dependencies. This is why the official source 
tarballs contain prebuilt docs.

best regards,
Markus

On 2019-03-07 11:42, Michael Strack was heard to say:
> Oops. Of course, I spent hours on this the other day, and then solved 
> it
> immediately after sending this email.
> 
> I was missing the docbook-xsl package. Then I got more errors and
> installed the fop package. Then more and installed sgrep.
> 
> Then I ran make and sudo make install which appear to have
> completed without errors.
> 
> Sorry for the false alarm.
> 
> On Thursday, March 7, 2019 at 6:16 PM, Michael Strack
> <mi...@st...> wrote:
>> Hello refdb-users, prospective new user here.
>> 
>> Got a little stuck installing. I'm afraid I don't have a lot of
>> experience building software from source (unless you count R
>> packages). Would appreciate if anyone has time to take a look at the
>> log and tell me what I'm missing.
>> 
>> I'll put the complete list of dependencies I installed down the
>> end. It's a bit long.
>> 
>> On Debian Stretch (with Gnome), performed the following steps:
>> 
>> - Cloned refdb-code with SVN
>> - cd refdb/trunk
>> - Run autogen.sh, followed by configure
>> - Divine missing dependencies from error messages and either install
>>   these from the Debian repositories or (in the case of the Perl
>>   modules) build them from source from the various directories under
>>   perlmod/trunk
>> - Also installed yaz because it's recommended
>> - Run make, install more dependencies
>> - Stuck on following error:
>> 
>> #+BEGIN_QUOTE
>> Making all in doc
>> make[1]: Entering directory
>> '/home/mixtrak/repos/refdb-code/refdb/trunk/doc'
>> make[1]: Circular citationlistx/elements.html <-
>> citationlistx/elements.html dependency dropped.
>> make[1]: Circular citestylex/elements.html <- citestylex/elements.html
>> dependency dropped.
>> Creating PDF manual...
>> hyphenation temporarily unavailable
>> xsltproc -o refdb-manual.fo --stringparam hyphenate 0 --nonet 
>> --xinclude
>> ../doc/include/manual-fo.xsl ../doc/refdb-manual.xml
>> I/O error : Attempt to load network entity
>> http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
>> warning: failed to load external entity
>> "http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl"
>> compilation error: file ../doc/include/manual-fo.xsl line 12 element
>> import
>> xsl:import : unable to load
>> http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
>> Makefile:993: recipe for target 'refdb-manual.pdf' failed
>> make[1]: *** [refdb-manual.pdf] Error 5
>> make[1]: Leaving directory
>> '/home/mixtrak/repos/refdb-code/refdb/trunk/doc'
>> Makefile:402: recipe for target 'all-recursive' failed
>> make: *** [all-recursive] Error 1
>> #+END_QUOTE
>> 
>> * Installed dependencies
>> 
>> Here's my records of what I was missing:
>> 
>> - autoconf
>> - gettext
>> - libdbi-dev and dependencies including libdbi1
>>   - Discretionary: libdbi-doc, libdbd-pgsql
>> - libsgml-dtdparse-perl
>> - xsltproc
>> - Perl module build dependencies
>>   - libxml-writer-perl
>>   - libcql-parser-perl
>>   - libmarc-charset-perl
>>   - libmarc-record-perl
>>   - libhttp-server-simple-perl
>>   - Already had libtext-iconv-perl, libxml-parser-perl, libfcgi-perl
>> 
>> Just for laffs tried to solve the problem by installing dsssl engine &
>> style sheets. I already had the openjade package installed, and tried
>> to add docbook-dsssl (and docbook-dsssl-doc), but no luck, natch.
> 
> 
> _______________________________________________
> Refdb-users mailing list
> Ref...@li...
> https://lists.sourceforge.net/lists/listinfo/refdb-users

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38

Re: [Refdb-users] Help with RefDB build errors

[Michael S. <mi...@st...>]

Oops. Of course, I spent hours on this the other day, and then solved it 
immediately after sending this email.

I was missing the docbook-xsl package. Then I got more errors and 
installed the fop package. Then more and installed sgrep.

Then I ran make and sudo make install which appear to have 
completed without errors.

Sorry for the false alarm.

On Thursday, March 7, 2019 at 6:16 PM, Michael Strack <mi...@st...> wrote:
> Hello refdb-users, prospective new user here.
> 
> Got a little stuck installing. I'm afraid I don't have a lot of
> experience building software from source (unless you count R
> packages). Would appreciate if anyone has time to take a look at the
> log and tell me what I'm missing.
> 
> I'll put the complete list of dependencies I installed down the
> end. It's a bit long.
> 
> On Debian Stretch (with Gnome), performed the following steps:
> 
> - Cloned refdb-code with SVN
> - cd refdb/trunk
> - Run autogen.sh, followed by configure
> - Divine missing dependencies from error messages and either install
>   these from the Debian repositories or (in the case of the Perl
>   modules) build them from source from the various directories under
>   perlmod/trunk
> - Also installed yaz because it's recommended
> - Run make, install more dependencies
> - Stuck on following error:
> 
> #+BEGIN_QUOTE
> Making all in doc
> make[1]: Entering directory
> '/home/mixtrak/repos/refdb-code/refdb/trunk/doc'
> make[1]: Circular citationlistx/elements.html <-
> citationlistx/elements.html dependency dropped.
> make[1]: Circular citestylex/elements.html <- citestylex/elements.html
> dependency dropped.
> Creating PDF manual...
> hyphenation temporarily unavailable
> xsltproc -o refdb-manual.fo --stringparam hyphenate 0 --nonet --xinclude
> ../doc/include/manual-fo.xsl ../doc/refdb-manual.xml
> I/O error : Attempt to load network entity
> http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
> warning: failed to load external entity
> "http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl"
> compilation error: file ../doc/include/manual-fo.xsl line 12 element
> import
> xsl:import : unable to load
> http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
> Makefile:993: recipe for target 'refdb-manual.pdf' failed
> make[1]: *** [refdb-manual.pdf] Error 5
> make[1]: Leaving directory
> '/home/mixtrak/repos/refdb-code/refdb/trunk/doc'
> Makefile:402: recipe for target 'all-recursive' failed
> make: *** [all-recursive] Error 1
> #+END_QUOTE
> 
> * Installed dependencies
> 
> Here's my records of what I was missing:
> 
> - autoconf
> - gettext
> - libdbi-dev and dependencies including libdbi1
>   - Discretionary: libdbi-doc, libdbd-pgsql
> - libsgml-dtdparse-perl
> - xsltproc
> - Perl module build dependencies
>   - libxml-writer-perl
>   - libcql-parser-perl
>   - libmarc-charset-perl
>   - libmarc-record-perl
>   - libhttp-server-simple-perl
>   - Already had libtext-iconv-perl, libxml-parser-perl, libfcgi-perl
> 
> Just for laffs tried to solve the problem by installing dsssl engine &
> style sheets. I already had the openjade package installed, and tried
> to add docbook-dsssl (and docbook-dsssl-doc), but no luck, natch.

[Refdb-users] Help with RefDB build errors

[Michael S. <mi...@st...>]

Hello refdb-users, prospective new user here.

Got a little stuck installing. I'm afraid I don't have a lot of
experience building software from source (unless you count R
packages). Would appreciate if anyone has time to take a look at the
log and tell me what I'm missing.

I'll put the complete list of dependencies I installed down the
end. It's a bit long.

On Debian Stretch (with Gnome), performed the following steps:

- Cloned refdb-code with SVN
- cd refdb/trunk
- Run autogen.sh, followed by configure
- Divine missing dependencies from error messages and either install
  these from the Debian repositories or (in the case of the Perl
  modules) build them from source from the various directories under
  perlmod/trunk
- Also installed yaz because it's recommended
- Run make, install more dependencies
- Stuck on following error:

#+BEGIN_QUOTE
Making all in doc
make[1]: Entering directory '/home/mixtrak/repos/refdb-code/refdb/trunk/doc'
make[1]: Circular citationlistx/elements.html <- citationlistx/elements.html dependency dropped.
make[1]: Circular citestylex/elements.html <- citestylex/elements.html dependency dropped.
Creating PDF manual...
hyphenation temporarily unavailable
xsltproc -o refdb-manual.fo --stringparam hyphenate 0 --nonet --xinclude ../doc/include/manual-fo.xsl ../doc/refdb-manual.xml
I/O error : Attempt to load network entity http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
warning: failed to load external entity "http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl"
compilation error: file ../doc/include/manual-fo.xsl line 12 element import
xsl:import : unable to load http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
Makefile:993: recipe for target 'refdb-manual.pdf' failed
make[1]: *** [refdb-manual.pdf] Error 5
make[1]: Leaving directory '/home/mixtrak/repos/refdb-code/refdb/trunk/doc'
Makefile:402: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1
#+END_QUOTE

* Installed dependencies

Here's my records of what I was missing:

- autoconf
- gettext
- libdbi-dev and dependencies including libdbi1
  - Discretionary: libdbi-doc, libdbd-pgsql
- libsgml-dtdparse-perl
- xsltproc
- Perl module build dependencies
  - libxml-writer-perl
  - libcql-parser-perl
  - libmarc-charset-perl
  - libmarc-record-perl
  - libhttp-server-simple-perl
  - Already had libtext-iconv-perl, libxml-parser-perl, libfcgi-perl

Just for laffs tried to solve the problem by installing dsssl engine &
style sheets. I already had the openjade package installed, and tried
to add docbook-dsssl (and docbook-dsssl-doc), but no luck, natch.

[Refdb-users] phpweb: Problems with correct handling of $formfields[] array

[O. H. <oha...@ze...>]

Running refdb from SVN (Rev 813 at the moment) with some necessary FreeBSD patches, we
had to move to PHP 7.1 recently. Since then, the phpweb Interface acts weird and very
unconvenient in some places when inserting data or when using "Edit this entry" on an
already existing entry.

When selecting  Reference type to be "Report" or "Web page" (we use those a lot, I can
not tell whether there are other types with the same issues), the "title" is empty/gone
whenever we choose "Edit this entry". The same is for "Local URL". These problems are
since back pre 1.0 of refdb.

With the recent svn version and PHP 7.1, now the fields "Publication Year (most recent)"
and "Publication Year(earlier or additional)" do have some serious issues. Additionaly to
the above mentioned problems when Editing an existing refdb entry, PY and Y2 become
truncated. Somehow the year is truncated to one digit (for 2018, it remains 2) and the
month and day as well as the optional "Other:" field have some strange settings, even
when nothing inserted.

Kind regards,

oh 

[Refdb-users] Problem to configure refdb php interface...

[anonyme <sit...@fr...>]

Hi,

I'm using linux debian jessie, apache2, mysql, php 5.

My refdb server is installed with a first user and one reference 
database (with Mysql driver).

But I've got a problem with php interface configuration because 
localhost/refdb/ is a white page...

I follow this short tutorial about php install 
<http://refdb.sourceforge.net/manual/ch04s11.html> :

[http://refdb.sourceforge.net/manual/ch04s11.html]

I added into apache default server the alias /refdb/ to 
/usr/share/refdb/www/ directory. Apache restart loading refdb module 
without any error.But http://localhost/refdb/ is a withe page ! I can't 
see any error into apache2/error.log file, exept "[:error] [pid 4946] 
[client 127.0.0.1:51702] PHP Fatal error: Call-time pass-by-reference 
has been removed$" but I doesn't know if it's relative to refdb php 
scrip... may be it's the clok time of my test...

Thank you for your help !

Patrick

Re: [Refdb-users] Problem to create first refdb user database with mysql

[anonyme <sit...@fr...>]

Thank you very much, now it's Ok, my server is running ! The problem was 
the driver path was wrong. In fact I had to install mysql driver to find 
the correct driver file under /usr/lib/i386-linux-gnu/dbd and now it's 
fine.

I've got an other problem with php interface configuration because 
localhost/refdb/ is a white page... But I create a new message to ask help.

Thank you again !
Patrick

Le 05/08/2016 à 15:19, Markus Hoenicka a écrit :
> Hi,
>
> At 2016-08-05 13:46, anonyme was heard to say:
>
>> Hi,
>>
>> I installed by hands my refdb server onto debian Jessie, and the 
>> service start without problem. I'm using mysql backend database.
>>
>> But below is the bug when attempting to create first refdb user 
>> database ... I can't understand because all packages have been 
>> installed with debian package manager, so they coul'nt be wrong 
>> version... May be a problem with libraries dependecies to refresh but 
>> I forgot the command to use... At the end I added my refdbdrc file.
>>
>> Thank yoiu for your help !
>> Patrick
>>
>> ROOT@GELINUX:/USR/SBIN# REFDBD -A -U ROOT -W #######
>> libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicule.so
>> libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libtxc_dxtn.so
>> libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnspr4.so
>
> These error messages indicate that libdbi fails to load the given 
> shared libs as drivers. This is because it somehow looks into the 
> wrong directory. /usr/lib/i386-linux-gnu/ seems to be the directory 
> which holds most shared libs on your system. Usually the libdbi 
> drivers are installed in a subdirectory of such a directory. By 
> default, the drivers are installed in /usr/local/lib/dbd/. I'm not too 
> familiar with Debian, but dpkg, apt or synapse, whichever you use, 
> should have methods to display where files were installed.
>
> [...]
>>
>> refdbdrc file :
>> # Specify the directory that contains the libdbi drivers. This is only
>> # necessary if you use precompiled libdbi binaries in locations the
>> # binaries were not built for
>> #dbi_driverdir /usr/local/lib/dbd
>> dbi_driverdir /usr/lib/i386-linux-gnu
>
> This entry may be the culprit because it points to a directory 
> containing general-purpose shared libs, not to the libdbi driver 
> subdir. Usually it is not necessary to set this at all, the libdbi 
> package(s) should take care of everything. Try removing this line to 
> see if libdbi manages to load the mysql driver.
>
> Also, I assume you are aware that the libdbi package contains only the 
> database abstraction framework. Drivers for particular database 
> engines need to be installed separately.
>
> best regards,
> Markus
>

Re: [Refdb-users] Problem to create first refdb user database with mysql

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

Hi,

At 2016-08-05 13:46, anonyme was heard to say:

> Hi,
> 
> I installed by hands my refdb server onto debian Jessie, and the 
> service start without problem. I'm using mysql backend database.
> 
> But below is the bug when attempting to create first refdb user 
> database ... I can't understand because all packages have been 
> installed with debian package manager, so they coul'nt be wrong 
> version... May be a problem with libraries dependecies to refresh but I 
> forgot the command to use... At the end I added my refdbdrc file.
> 
> Thank yoiu for your help !
> Patrick
> 
> ROOT@GELINUX:/USR/SBIN# REFDBD -A -U ROOT -W #######
> libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicule.so
> libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libtxc_dxtn.so
> libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnspr4.so

These error messages indicate that libdbi fails to load the given shared 
libs as drivers. This is because it somehow looks into the wrong 
directory. /usr/lib/i386-linux-gnu/ seems to be the directory which 
holds most shared libs on your system. Usually the libdbi drivers are 
installed in a subdirectory of such a directory. By default, the drivers 
are installed in /usr/local/lib/dbd/. I'm not too familiar with Debian, 
but dpkg, apt or synapse, whichever you use, should have methods to 
display where files were installed.

[...]
> 
> refdbdrc file :
> # Specify the directory that contains the libdbi drivers. This is only
> # necessary if you use precompiled libdbi binaries in locations the
> # binaries were not built for
> #dbi_driverdir /usr/local/lib/dbd
> dbi_driverdir /usr/lib/i386-linux-gnu

This entry may be the culprit because it points to a directory 
containing general-purpose shared libs, not to the libdbi driver subdir. 
Usually it is not necessary to set this at all, the libdbi package(s) 
should take care of everything. Try removing this line to see if libdbi 
manages to load the mysql driver.

Also, I assume you are aware that the libdbi package contains only the 
database abstraction framework. Drivers for particular database engines 
need to be installed separately.

best regards,
Markus

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38



Links:
------
[1] https://lists.sourceforge.net/lists/listinfo/refdb-users
[2] http://refdb.sourceforge.net

[Refdb-users] Problem to create first refdb user database with mysql

[anonyme <sit...@fr...>]

Hi,

I installed by hands my refdb server onto debian Jessie, and the service 
start without problem. I'm using mysql backend database.

But below is the bug when attempting to create first refdb user database 
... I can't understand because all packages have been installed with 
debian package manager, so they coul'nt be wrong version... May be a 
problem with libraries dependecies to refresh but I forgot the command 
to use...  At the end I added my refdbdrc file.

Thank yoiu for your help !
Patrick

*root@gelinux:/usr/sbin# refdbd -a -u root -w #######*
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicule.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libtxc_dxtn.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnspr4.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgio-2.0.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_aui-3.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgmp.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXcomposite.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-present.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxshmfence.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/liba52-0.7.4.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_mpi_python-py34.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgnutls-openssl.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_iostreams.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicuio.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libX11.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_wave.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnss_hesiod.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgtk-x11-2.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXft.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/pkcs11-spy.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libanl.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libguilereadline-v-18.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpng.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libdrm_intel.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnuma.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-render.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgthread-2.0.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/onepin-opensc-pkcs11.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnettle.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnss_compat.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libglib-2.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libdb-5.3.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libz.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXxf86vm.so
/usr/lib/i386-linux-gnu/libthread_db.so: undefined symbol: ps_pdwrite
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libthread_db.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_prg_exec_monitor.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-sync.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnss_nisplus.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_math_tr1.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libexpat.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnsl.so
/usr/lib/i386-linux-gnu/libboost_python-py27.so: undefined symbol: 
PyExc_ImportError
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_python-py27.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-dri2.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libtasn1.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgmpxx.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpango-1.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libp11-kit.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXdamage.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicuuc.so
/usr/lib/i386-linux-gnu/libfl.so: invalid ELF header
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libfl.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_serialization.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXrender.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnss3.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libhwloc.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-xfixes.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_baseu_net-3.0.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicudata.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpng12.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_signals.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxerces-c-3.1.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_thread.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_program_options.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libspice-server.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libdrm_nouveau.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXinerama.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnss_nis.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libGL.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libdrm.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libdl.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_media-3.0.so
/usr/lib/i386-linux-gnu/libboost_python.so: undefined symbol: 
PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_python.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnssutil3.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgnutlsxx.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpangoft2-1.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libelf-0.159.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_atomic.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libexpatw.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_graph_parallel.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpangocairo-1.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/librt.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpangoxft-1.0.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libharfbuzz.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libssl.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libwx_gtk2u_qa-3.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_timer.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_adv-3.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_system.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgmodule-2.0.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libspice-client-gtk-2.0.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgdk-x11-2.0.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXi.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXext.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_regex.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libharfbuzz-icu.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libresolv.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libICE.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_math_tr1l.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libcairo-gobject.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libdrm_radeon.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libplds4.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_math_c99l.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libm.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libBrokenLocale.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_log.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_python-py34.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libcrypt.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libwrap.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libcrypto.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libatk-1.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicui18n.so
/usr/lib/i386-linux-gnu/libfl_pic.so: undefined symbol: yylex
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libfl_pic.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_log_setup.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicutu.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_propgrid-3.0.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpcre.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-glx.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpcrecpp.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxml2.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_stc-3.0.so
/usr/lib/i386-linux-gnu/libpthread.so: invalid ELF header
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpthread.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libfreetype.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libspice-controller.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpcreposix.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libwx_baseu-3.0.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_wserialization.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libfontconfig.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_html-3.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-dri3.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_random.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libSM.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_chrono.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libtcl8.6.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-randr.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXrandr.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_unit_test_framework.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libgdk_pixbuf_xlib-2.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libsmime3.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnss_files.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-shm.so
/usr/lib/i386-linux-gnu/libboost_python-py27.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_mpi_python.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgobject-2.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libX11-xcb.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgnutls.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_date_time.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libicutest.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libiculx.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libharfbuzz-gobject.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_richtext-3.0.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_xrc-3.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libGLU.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libhogweed.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXau.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_math_tr1f.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libcidn.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/opensc-pkcs11.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_locale.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libexslt.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXcursor.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXfixes.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_ribbon-3.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_math_c99f.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libgdk_pixbuf-2.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpython2.7.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libXdmcp.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_graph.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libltdl.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libtk8.6.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libspice-client-glib-2.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxcb-shape.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_baseu_xml-3.0.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libcairo.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libwx_gtk2u_gl-3.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_context.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libssl3.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libwx_gtk2u_core-3.0.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libplc4.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_filesystem.so
/usr/lib/i386-linux-gnu/libc.so: invalid ELF header
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libc.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libutil.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libnss_dns.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libijs-0.35.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_math_c99.so
/usr/lib/i386-linux-gnu/libboost_python-py27.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libboost_mpi_python-py27.so
/usr/lib/i386-linux-gnu/libboost_python-py34.so.1.55.0: undefined 
symbol: PyExc_ImportError
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libpixman-1.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libboost_mpi.so
libdbi: Failed to load driver: 
/usr/lib/i386-linux-gnu/libcairo-script-interpreter.so
libdbi: Failed to load driver: /usr/lib/i386-linux-gnu/libxslt.so

refdbdrc file :
# this is an example configuration file for refdbd, the application server
# of RefDB, preconfigured for use with MySQL as a database engine
# to use this file as a configuration file for refdbd, create a copy
# named refdbdrc in the same directory, or create a symlink with that
# name pointing to this file
#
# RefDB is a reference database and bibliography tool, see
# http://refdb.sourceforge.net for further information

# Syntax rules of this file:
# 1. Each line contains a pair of variable name and variable value,
#    separated by whitespace.
# 2. The hash (#) denotes the start of a comment, the rest of the line
#    will be ignored
# 3. The line ending must be Unix-style (LF) regardless of the operating
#    system

# The full path of a directory for shareable application files
refdblib /usr/share/refdb

# The name of the main database. The main database contains citation
# and bibliography styles, as well as the journal word list. There is
# no need to change this name unless you are forced to use a database
# with a given name, e.g. on rented webspace
main_db    refdb

# Either the IP address or the hostname of the computer that runs the
# database server. Use "localhost" if refdbd and the database server
# run on the same computer. This variable is ignored by embedded
# database engines
serverip    localhost

# The port on which the database server listens. Default values are
# 3306 (MySQL) and 5432 (PostgreSQL). This variable is ignored by
# embedded database engines
dbsport        3306

# The database server we want to connect to. Currently mysql,
# pgsql, sqlite, and sqlite3 are supported
dbserver    mysql

# The directory where embedded database servers keep their files
# and where the database version file is created
*dbpath        /srv/mysql*

# The port on which refdbd listens for client connections
port    9734

# The time in seconds which has to elapse before a stalled connection
# to the client is taken down
#timeout    180

# The full path of a custom log file. This will be used if logdest is
# set accordingly
logfile /var/log/refdbd.log

# The destination of the log information. Uncomment *one* of the
# following definitions. "file" uses the file specified with the
# logfile variable
#logdest stderr
#logdest syslog
logdest file

# The priority up to which messages are logged. Uncomment *one* of the
# following definitions. "emerg" will result in the fewest, "debug" in
# the most log messages
#loglevel emerg
#loglevel alert
#loglevel crit
#loglevel err
#loglevel warning
#loglevel notice
loglevel info
#loglevel debug

# The full path of the file where the refdbd stores the current process
# ID of the parent process
pidfile        /run/refdbd.pid

# Allow (t) or deny (f) remote administration of refdbd through refdba
remoteadmin f

# Allow (t) or deny (f) remote access
remoteconnect f

# Keep (t) or delete(f) periodical names and synonyms when deleting
# references
keep_pnames t

# Perform an automatic keyword scan after references are added or
# updated if set to 't'. Set this to 'f' to skip the automatic keyword
# scan.
keyword_scan t

# Specify the directory that contains the libdbi drivers. This is only
# necessary if you use precompiled libdbi binaries in locations the
# binaries were not built for
#dbi_driverdir /usr/local/lib/dbd
*dbi_driverdir /usr/lib/i386-linux-gnu*

# Specify the default encoding that newly created databases use. This
# feature is currently only supported by PostgreSQL and MySQL 4.x./5.x
# Possible values are UTF-8, ISO-8859-1, ASCII, and a variety of others
# see the libdbi documentation for the values supported by your database
# engine
db_encoding    UTF-8

# Specify the default encoding of imported RIS data.
in_encoding    UTF-8

# Set this to t if you want refdbd to uppercase citation keys when
# adding datasets. This is convenient to make sure your datasets work
# properly with SGML documents
#upper_citekey    t

# extended notes which do not carry a share attribute can be handled
# either as public or as private by default. In the first case,
# every RefDB user will be able to read them. In the latter case, only
# the note owner will be able to read his notes. In both cases the
# share attribute of an extended note, if set, will override the default
#share_default public

# end of refdbdrc

Re: [Refdb-users] Deprecated function PHP 5.4+: session_register

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

At 2015-08-31 03:33, MK was heard to say:
> Hi,
> I'm using PHP 5.6 and received some errors regarding a deprecated
> function (session_register). I was able to fix these by adding some
> code to index.php. (Code from php.net):
> http://www.php.net/manual/en/function.session-register.php
> 
> 
> index.php:
> ----
> $_SESSION["refdbc"]="/usr/local/bin/refdbc";
> $_SESSION["refdba"]="/usr/local/bin/refdba";
> $_SESSION["path"]="/usr/local/bin";
> $refdbc=$_SESSION["refdbc"];
> $refdba=$_SESSION["refdba"];
> 
> // Fix for removed Session functions
> function fix_session_register(){
>     function session_register(){
>         $args = func_get_args();
>         foreach ($args as $key){
>             $_SESSION[$key]=$GLOBALS[$key];
>         }
>     }
>     function session_is_registered($key){
>         return isset($_SESSION[$key]);
>     }
>     function session_unregister($key){
>         unset($_SESSION[$key]);
>     }
> }
> if (!function_exists('session_register')) fix_session_register();
> ----
> 

Hi,

thanks for this and the previous reports. Apparently there were a couple 
of backwards-incompatible changes in PHP 5.6 which broke a few things in 
the web frontend. I do not use the frontend myself, but I appreciate 
your attempts at fixing the problems. I'll add your fixes to the svn 
code as soon as time permits.

best regards,
Markus

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38

[Refdb-users] Deprecated function PHP 5.4+: session_register

[MK <per...@gm...>]

Hi,
I'm using PHP 5.6 and received some errors regarding a deprecated
function (session_register). I was able to fix these by adding some
code to index.php. (Code from php.net):
http://www.php.net/manual/en/function.session-register.php


index.php:
----
$_SESSION["refdbc"]="/usr/local/bin/refdbc";
$_SESSION["refdba"]="/usr/local/bin/refdba";
$_SESSION["path"]="/usr/local/bin";
$refdbc=$_SESSION["refdbc"];
$refdba=$_SESSION["refdba"];

// Fix for removed Session functions
function fix_session_register(){
    function session_register(){
        $args = func_get_args();
        foreach ($args as $key){
            $_SESSION[$key]=$GLOBALS[$key];
        }
    }
    function session_is_registered($key){
        return isset($_SESSION[$key]);
    }
    function session_unregister($key){
        unset($_SESSION[$key]);
    }
}
if (!function_exists('session_register')) fix_session_register();
----

Regards,
MK

Re: [Refdb-users] Results found (counted), but not displayed, in PHP-interface with sqlite3

[MK <per...@gm...>]

Hi again,
I found the problem in the log files.

----
Fatal error:  Class 'XSLTProcessor' not found in
/usr/local/share/refdb/www/includes/functions.inc.php on line 146"
while reading response header from upstream
----

The fix was rather simple, at least on my Debian system:
apt-get install php5-xsl

The results are *displayed* correctly now.

Regards,
MK

[Refdb-users] Fatal error: Call-time pass-by-reference

[MK <per...@gm...>]

Hi,
when trying out PHP-interface i received a fatal error. I could fix it
by using the instructions listed here:
http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2013-June/256993.html

+- if (!yaz_ccl_parse($id[$i], $term, &$cclresult)) {
++ if (!yaz_ccl_parse($id[$i], $term, $cclresult)) {

Regards,
MK

[Refdb-users] Results found (counted), but not displayed, in PHP-interface with sqlite3

[MK <per...@gm...>]

Hi,
I'm trying out the PHP interface for refdb, using sqlite3 as my
database. I am able to add new references to the database by uploading
.ris files. The searching of references, however, is only partially
working. If I do a "simple field-based search" I am greeted with
results of the following kind:

----
Your search for :AX:~Marder% generated 1 result.
----

But no actual result is displayed on the page. (There is nothing in
the HTML code.)

If I search for indices, I am greeted with the following:
----
Your index search for retina in keyword generated 1 entries.

Sorry, there were no results.
----

It seems like the "first part" of the search works -- as something is
found, and counted but that something breaks in section that follows.

Any clues on what's going on?

Regards,
MK

Re: [Refdb-users] docbook5, getting started

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

Tim Arnold <jti...@gm...> was heard to say:

> As for the problem with the chapter vs book root element:
> When I have a source xml file (test1_full.xml) with chapter as the
> root and citations like this:
> <citation role="REFDB"><xref linkend="IDbart_m66-X"/></citation>.
>
> runbib gives me an error:
> -----------------------------------
> runbib -d saslatexbib -S Chicago -t db50x test1_full.xml
> Variable $SGML_CATALOG_FILES not set
> Please enter your password:
> Parse error at line 1:
> no element found
> error
> -----------------------------------
>

I see. This is caused by a limitation of  
/usr/local/share/refdb/xsl/citations.xsl. This stylesheet is used to  
extract the citations from the source document and write them into the  
foo.id.xml file. For reasons that I don't quite understand right now,  
the script limits itself to processing book and article elements. As a  
short term fix you could simply extend the regexp in line 39 like this  
(untested!):

         <xsl:template match="article|d:article|chapter|d:chapter">

I'll try to figure out if there was some obscure reason for this  
limitation. If not I'll adapt the stylesheet to the current DocBook V5  
top-level elements.

regards,
Markus

-- 
Markus Hoenicka
http://www.mhoenicka.de
AQ score 38