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NeoOffice :: View topic - Loss of superscripts in documents formatted with EndNote!
Loss of superscripts in documents formatted with EndNote!
 
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DavidS
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Joined: Jun 04, 2007
Posts: 14
Location: Reno, NV, USA

PostPosted: Thu Dec 29, 2011 2:25 pm    Post subject: Loss of superscripts in documents formatted with EndNote! Reply with quote

HI-

I use NeoOffice for scientific papers and grants, where references are formatted with EndNote. I am using EndNote X3. When I use a journal format which has superscripted references, the superscripts are 95+% there the first time the formatted document is opened with NeoOffice. However, on closing the document, most of the superscripts revert to ordinary text. The more often the document is opened and closed, the more they revert to ordinary text.
Curiously, if the document is saved as a doc file the first time it is opened, the superscripts are stable. I just tried opening and closing a document ten times, which was saved with identical file name to the odt version. The doc version preserves the superscripts forever. Of course, it has its own problems, like not supporting Unicode, and spacing weirdness.
I do most of my work on a DP G5 running OS 10.4.11, and NeoOffice V. 3.1.2, patch 9. However, I have also tried this on a MacBook Air, running OS 10.6.7 with NeoOffice V. 3.2.1, patch 2. Same identical problem exists there.

David S.

PS- Am attaching a file which has been just formatted with EndNote, and not yet opened at all with NeoOffice, so you can see what I report.
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pluby
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Joined: Jun 16, 2003
Posts: 11932

PostPosted: Thu Dec 29, 2011 3:56 pm    Post subject: Reply with quote

Edit by pluby: please ignore this post as I was able to reproduce the problem in my next post.

I am unable to reproduce what you describe on my Mac OS X 10.6.8 machine with NeoOffice 3.2.1 Patch 2 but maybe I am missing some steps or I am looking at only the "good" references? If so, please let me know what steps I may have skipped. I only opened and closed your .odt file several times but did not make any changes to the file and all of the footnote references show as superscript.

One thing I did notice is that the entire document is set to use the Palatino font. That font is not bundled with Mac OS X and is, instead, only bundled with Microsoft Office so I do not have that font on my most of my machines. This makes me wonder if you have the Palatino font on your machine.

To determine if you have the Palatino font on your machine an you open the /Applications/Font Book application and search for the Palatino font in the list. If that font is listed, can you select that font, select the Edit :: Disable "Palatino" Family menu, and then restart NeoOffice. Does the problem remain after disabling the Palatino font?

Patrick


Last edited by pluby on Thu Dec 29, 2011 4:50 pm; edited 1 time in total
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pluby
The Architect
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Joined: Jun 16, 2003
Posts: 11932

PostPosted: Thu Dec 29, 2011 4:46 pm    Post subject: Reply with quote

Please ignore my last post as I am able to reproduce this on my Mac OS X 10.5 machine using NeoOffice 3.2.1 Patch 2. Specifically, every other time I open your .odt file, footnote reference "31" after the "antihypertensive drug" text is not displayed in superscript.

The bad news is that this appears to be a bug in NeoOffice's underlying OpenOffice.org code as I can reproduce this same problem in both OpenOffice.org 3.3 and LibreOffice 3.3.2.

From my quick look inside the .odt file, my theory is that NeoOffice's underlying OpenOffice.org is skipping over the style setting for some of the footnote references. I based my theory on the fact the I can see that the "31" footnote reference has a superscript style applied to it within your .odt file. However, after opening the file and the bug appears, I resave the file and the new .odt is nearly identical except that particular style is no longer applied to that footnote reference.

Unfortunately, we have not modified any of the underlying OpenOffice.org .odt file parsing code so this will likely require at least a few days of work to search for where in the OpenOffice.org code the .odt file parsing is failing but once I have more new - most likely sometime next week - I will post what I have found.

Patrick
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DavidS
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Joined: Jun 04, 2007
Posts: 14
Location: Reno, NV, USA

PostPosted: Thu Dec 29, 2011 4:54 pm    Post subject: Reply with quote

Hi Patrick-
Thanks for your prompt reply. Yes, I use Palatino font. One reason is that it is available both on PCs and Macs, and NIH has decreed that they will accept only TWO fonts for proposals: Arial, a sans serif font which I find hard to read, and Palatino, a serif font, which looks much nicer.
So I changed everything to Times New Roman, which I believe is DEFINITELY a Mac supported font, and more economical of space than either of the two fonts NIH accepts. File looked OK first time I opened it, but not second time! I am attaching the file which was opened TWICE only on my computer (note that TNR in file name is font acronym).

David S.
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pluby
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Posts: 11932

PostPosted: Thu Dec 29, 2011 4:57 pm    Post subject: Reply with quote

DavidS,

It looks like we were posting our last posts at the same time so take a look at my second post as I can now reproduce the problem and I have a theory of what is happening in NeoOffice's underlying OpenOffice.org code.

Patrick
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pluby
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PostPosted: Mon Jan 02, 2012 2:33 pm    Post subject: Reply with quote

FYI. While I do not have a fix for this OpenOffice.org bug yet, after quite a bit of iterative debugging work I have narrowed down the area of the OpenOffice.org code in which this bug is occurring.

My debugging work has been to verify what the state of the superscript text blocks at each stage of the loading and display of the .odt file. So far, I have worked through the loading code and at the end of that step, the superscrip text blocks all have the superscript text formatting correctly set.

The next step is to move into the code that displays the loaded data. I will post again when I have more news to report.

Patrick
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pluby
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PostPosted: Tue Jan 03, 2012 10:38 pm    Post subject: Reply with quote

I think that I finally found the OpenOffice.org code that was causing this bug and I think that I have fixed it in the following test patch.

Can you install the test patch and tell us if the bug is fixed for you and if you notice any new unintended formatting errors? Please note that I was only able to fix this bug in NeoOffice 3.2.1 so you will only be able to install the test patch on Mac OS X 10.5 Leopard or higher:

Intel:
http://joe.neooffice.org/test/NeoOffice-3.2.1-Patch-2-Test-5-Intel.dmg

Patrick
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DavidS
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PostPosted: Thu Jan 05, 2012 2:35 pm    Post subject: Reply with quote

Hi Patrick-
Yes, that is terrific- you have fixed it with that patch. I opened and closed the file 5 times, and not a single superscript disappeared. It would be ever so nice if you could also patch version 3.1.2, as I have to borrow another computer to use with NeoOffice, and also transfer my library over each time. I paid to join the forum just to see if I could get this bug fixed, and am so grateful. I will continue to support you in the same way in the future if you patch the 3.1.2 version.

David
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pluby
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PostPosted: Thu Jan 05, 2012 6:12 pm    Post subject: Reply with quote

To be honest, we stopped doing any on NeoOffice 3.1.2 almost a year ago as supporting Mac OS X 10.4 and 10.7 at the same time was just too much for us to handle. Not only does NeoOffice 3.1.2 have large amounts of different code because Mac OS X 10.4 is missing many of the newer functions that Apple added in Mac OS X 10.5, but our PowerPC hardware was starting to get very old and flaky so obtaining used replacement PowerPC hardware and set it up to build NeoOffice 3.1.2 would require not only money, but significant amounts of time that we just don't have.

A more pressing problem for us is ensuring that we have hardware that supports Mac OS X 10.5 as Apple has not sold hardware that even supports that version and our existing Mac OS X 10.5 machines are getting old.

I know that this is not the news you wanted to hear, but supporting NeoOffice more than 3 versions of Mac OS X is too much for us to do with our limited development labor and the older the version.

Patrick
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DavidS
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Location: Reno, NV, USA

PostPosted: Thu Jan 05, 2012 6:27 pm    Post subject: Reply with quote

That's OK Patrick, I understand. At least the DP G5s I have at home and at work were made in US, and are built well. I hear a lot about the new made in China Macs frying VERY quickly by comparison.
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pluby
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PostPosted: Thu Jan 05, 2012 7:08 pm    Post subject: Reply with quote

I will release NeoOffice 3.2.1 Patch 3 next Monday with the fix for the bug that you found. If you find any problems with the test patch before then, please let us know and we will investigate whatever new problems you find.

Speaking of hardware issues... Eerily, my Mac Mini's disk started making clicking noises today so it looks like I might want to preemptive replace my Mac Mini's disk. Sad Fortunately, since Ed and I expect disk and other machine failures, we try to maintain a redundant backup build machines and web servers.

For example, since our NeoOffice 3.2.1 builds must be built on Mac OS X 10.5 (compiling must be done on the lowest supported Mac OS X version), I have an early Intel laptop that I clone my entire Mac OS X 10.5 volume to so that if my old Mac Mini fails, I can immediately switch over to the laptop and not have to miss a beat while the primary machine is in the shop.

Whenever I get a machine back from repair, I then clone from the laptop or from a backup on a secondary external drive since I assume that the some of the bits on the old disk won't be recoverable.

Patrick
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pluby
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PostPosted: Mon Jan 09, 2012 7:41 pm    Post subject: Reply with quote

FYI. I have included the fix for this bug in NeoOffice 3.2.1 Patch 3. You can download the patch from the NeoOffice 3.2.1 patch download page.

Patrick
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