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Jeremy Malcolm | 7 Dec 2005 04:35
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0.9.6 compilation error on Darwin

Has anyone else seen this?

if gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" 
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"refdb\" 
-DVERSION=\"0.9.6\" -D_GNU_SOURCE=1 -DREADLINE42=1 -DHAVE_ICONV=1 
-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 
-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_FCNTL_H=1 
-DHAVE_LIMITS_H=1 -DHAVE_SYS_FILE_H=1 -DHAVE_SYS_TIME_H=1 
-DHAVE_SYS_IOCTL_H=1 -DHAVE_SYSLOG_H=1 -DHAVE_UNISTD_H=1 
-DTIME_WITH_SYS_TIME=1 -DRETSIGTYPE=void -DHAVE_STRFTIME=1 
-DHAVE_MKFIFO=1 -DHAVE_GETHOSTNAME=1 -DHAVE_SELECT=1 -DHAVE_SOCKET=1 
-DHAVE_STRCSPN=1 -DHAVE_STRSTR=1 -DHAVE_STRTOLL=1 -DHAVE_ATOLL=1  -I. 
-I.  -DSYSCONFDIR=\"/usr/local/etc/refdb\" -DULLSPEC=\"%llu\" 
-I/sw/include -MT refdbdref.o -MD -MP -MF ".deps/refdbdref.Tpo" -c -o 
refdbdref.o refdbdref.c; \
then mv -f ".deps/refdbdref.Tpo" ".deps/refdbdref.Po"; else rm -f 
".deps/refdbdref.Tpo"; exit 1; fi
refdbdref.c: In function `is_journal':
refdbdref.c:2363: error: `DBI_ROW_ERROR' undeclared (first use in this 
function)
refdbdref.c:2363: error: (Each undeclared identifier is reported only once
refdbdref.c:2363: error: for each function it appears in.)
make[2]: *** [refdbdref.o] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

TIA

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Markus Hoenicka | 7 Dec 2005 09:18
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Re: 0.9.6 compilation error on Darwin

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

> Has anyone else seen this?
>
[...]
> refdbdref.c: In function `is_journal':
> refdbdref.c:2363: error: `DBI_ROW_ERROR' undeclared (first use in this
> function)

Sure enough yes. The reason is most likely that you don't have libdbi-0.8.1 but
an older version installed. Please upgrade and see whether this fixes the
problem.

regards,
Markus

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Markus Hoenicka | 7 Dec 2005 11:01
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Re: 0.9.6 compilation error on Darwin

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

> I upgraded libdbi OK (no change to the above error though), but when I
> tried to upgrade libdbi-drivers, I got:
>
[...]
> dbd_mysql.c:164: warning: previous implicit declaration of
> `dbd_get_encoding'

This and the other errors point to a problem with a leftover dbi header which is
in your path before the correct 0.8.1 header. Please scan your drive for all
instances of dbi.h, dbi-dev.h, and dbd.h, and make sure you leave only the
latest on your drive.

You may also verify the CVS revision which is close to the end of the initial
comment block in each header. You should see the following revisions:

dbd.h: 1.29
dbi-dev.h: 1.39
dbi.h: 1.60

hope this helps
Markus

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Jeremy Malcolm | 8 Dec 2005 05:37
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Re: Re: help wanted for refdb-mode

Jeremy Malcolm wrote:
> Markus Hoenicka wrote:
> 
 >>> PS. Any joy with that Murdoch-style.xml file I sent a while ago?
 >>
>> Do you have a chance to test 0.9.6? If I recall correctly the problems
>> should be fixed here.
>>  
>>
> Thanks, will try it as soon as my iBook comes back from repair.

No, no change; I still get:

<bibliomset role="intext" id="IDAREND1999LEGAL-RULES-AND-X"><bibliomset 
relation
="author"></bibliomset></bibliomset>(<pubdate 
role="primary">1999</pubdate>)</bibliomset>

(ie. with an extra </bibliomset> in the middle, but with no title) from 
this:

<CITSTYLE INTEXTSEQUENCE="ASIS">
   <CITSEPARATOR>; </CITSEPARATOR>
   <INTEXTDEF>
     <AUTHORLIST>
       <ABBREVIATEFIRST DISPLAYAUTHOR="1" MAXAUTHOR="2">et 
al</ABBREVIATEFIRST>
       <ABBREVIATESUBSEQ DISPLAYAUTHOR="1" MAXAUTHOR="2">et 
al</ABBREVIATESUBSEQ>
       <AEMPTY>Anonymous</AEMPTY>
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Jeremy Malcolm | 8 Dec 2005 06:01
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Re: Re: help wanted for refdb-mode

Jeremy Malcolm wrote:
>> Thanks, will try it as soon as my iBook comes back from repair.
> 
> 
> No, no change; I still get:

Sorry, there is a change, but still the same error; please ignore the 
last message until I have investigated further.

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Markus Hoenicka | 8 Dec 2005 13:52
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Re: Re: help wanted for refdb-mode

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

> Sorry, there is a change, but still the same error; please ignore the
> last message until I have investigated further.
>

Ok, I'll wait. Rest assured that I want to fix these problems, as they're most
likely caused by thoughtless programming.

regards,
Markus

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Jeremy Malcolm | 12 Dec 2005 04:44
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Re: Re: help wanted for refdb-mode

Markus Hoenicka wrote:
> Good. I've analyzed the situation and saw a couple of problems that I
> need to fix. The most stupid error is that the field sizes of the
> *nameorder fields are not sufficiently long in MySQL (other engines
> use TEXT with unlimited length, so it's not a problem). I've attached
> a fixed refdb.dump.mysql41.in. Let me know if you have an older MySQL
> version.
> 
> All other problems are related to the style itself. I've appended a
> style that works on my system. While your style was incorrect, this
> was not your fault. Either refdbd did not use the proper defaults if
> particular elements or attributes were not used, or the DTD did not
> enforce the presence of attributes and elements that are
> mandatory. I'll fix these bugs in the next prerelease.
> 
> The output is still not quite correct as far as I can see. There are
> some spaces and other separators missing, but these are probably real
> style issues.

Except for one thing, which is that the title is still being omitted 
from the in-text references.  Footnote-endnote styles of citation are 
not really supported by RefDB it seems.  I may be able to work around 
this issue for now by seeking special dispensation to use the Chicago 
referencing style instead of the Murdoch Law style.

> I've also noticed that the author names in your RIS file are quite
> odd. Did you enter them this way or was there a problem during
> import/export? You have lots of entries like "Last, FirstMiddle" instead
> of "Last, First Middle".
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Markus Hoenicka | 18 Dec 2005 21:57
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FYI - xnote

Hi,

Damien Jade Duff writes:
 > Changing the below line in noteshandler.c seemed to fix it but I'm not 
 > going to bet my life it's actually fixed everything as all I did was 
 > search for "key".
 > //djd20051218   else if (!strcmp(ptr_attr[i], "key")) {
 >          else if(!strcmp(ptr_attr[i],"citekey")){
 > 

Thanks for this lucid and precise dissection of my dumbness :-) In
fact, the first (unreleased) version of the DTD used the attribute
name "key" but I later dropped it in favour of "citekey", hence the
leftover reference to "key" in noteshandler.c. Your fix seems
absolutely correct to me. I'll apply it and check it in.

regards,
Markus

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Damien Jade Duff | 18 Dec 2005 17:14
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FYI - xnote

Gidday

I'm having one minor issue with RefDB's handling of xnote documents for 
extended notes. I'm using the 0.9.6 release of RefDB. I cannot find any 
reference to this problem on the lists so I thought I should bring it to 
the attention of the brainy developer(s).

I suspect this one is very straightforward.

Now the xnote element in 
http://refdb.sourceforge.net/dtd/xnote/xnote.dtd has two attributes that 
might readily be called kinds of ID fields:

"id" and "citekey"

The former is numeric, sequential, internal to RefDB and usually 
irrelevant to me as a user except when deleting references.

The later is the unique key I can use to extract the extended note from 
RefDB, such as "MYNOTE20051218150255"

When I extract information from RefDB, RefDB behaves as expected from 
the dtd, but when I add to the DB, RefDB seems to be looking for an 
attribute called:

"key" (as opposed to "citekey")

Eg. If I try to add the following (XNOTESET XML follows)...

<xnoteset>
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Markus Hoenicka | 22 Dec 2005 00:30
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ANN: refdb-elisp-1.1 released

Hi,

I've uploaded a new version of the refdb-elisp package which contains:

refdb-mode: a minor mode which implements a GUI-based RefDB frontend
            in Emacs

ris-mode: a major mode for editing RIS datasets

The most important change is a far better support for NTEmacs on
Windows, including a manual section which describes the (somewhat
arcane) setup on this platform. The changes are listed below.

The package is available on the RefDB download page at SF:

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

I've also posted my NTEmacs porting experience to my blog:

http://www.mhoenicka.de/system-cgi/blog/

regards
Markus

- manual is now chunked with CSS styling

- configure now tries to find appropriate file viewers and
  preconfigures refdb-mode-config.el accordingly

- improved minibuffer completion
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Gmane