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I use IEEEtran bare_jrnl.tex and my .tex file builds on my machine without any problem. I use subfig package. (subfigure doesn't work)

When I try to submit my manuscript IEEE page says subfig is missing.enter image description here

I tried to change my .tex file and disable subfig package. However, I couldn't. I use subfloat several times. And since subfloat works on my machine perfectly, I don't want to change my .tex file.

So, what is the best solution to submit my paper?

PS: I downloaded the style file from: http://drucmwebproxy.ieee.org/documents/IEEEtran.zip and using bare_jrnl.tex.

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IEEE doesn't require a TeX file, you need to upload the PDF file and if any the multimedia attachments etc. You should not upload the source files unless you are done with the reviews and sending it to the publication office which is done via Author Gateway portal of IEEE. – percusse Nov 15 '12 at 20:27
You sure? We are trying to submit it to IEEE Cybernetics Part C. The reason I ask you sure is, in the submission panel, you are able to give your .tex file and the system is able to build it. (If your .tex file doesn't give any error like mine.) So, if they don't want my .tex file, why do they have a .tex enabled system like that? – Sait Nov 16 '12 at 15:51
I have never sent my TeX file to any journal unless it's accepted. I don't know about Cybernetics but I've been involved with IEEE TRO, IEEE TAC, IEEE CST and have never been asked for the source file(one article is going to appear this December). It's sent directly to the reviewers anyhow. I can also ask the same, why do they have a template if they are going to build it for you? It might be a new thing but again IEEE introducing these nonsense instead of fixing their workflow... I digress. – percusse Nov 16 '12 at 16:34

This is off-topic for TeX-SX but IEEE article submission is always weird and unpredictable. Contrary to my comments above, now I've realized that Cybernetics C is using ScholarOne instead of PaperPlaza which is again ... great.

And additionally there is a change notice in the login page

NOTICE: Starting in January 1, 2013 the IEEE Transactions on Systems, Man, and Cybernetics Part C: Applications & Reviews is renamed to IEEE Transactions on Human-Machine Systems. The IEEE Transactions on Systems, Man, and Cybernetics Part C do not consider any new papers, authors are requested to submit manuscripts to the new SMC Transactions. For details see http://www.ieeesmc.org/publications/Scope_of_the_SMC_Transactions.htm.

In any case, since IEEE adopts blind review method (as opposed to double blind) there is no need for anonymizing the article. Thus, journal submissions are done via PDF files and reviewers see the PDF output. In fact you don't even use one column double spacing version since the system checks for the 17 page limit directly (you pay 175 USD per extra page over 12, for the page nobody prints!).

After the review process, the submission is forwarded to the publisher and then your TeX nightmare begins. The current situation with most journals is that you provide the TeX file the images (if any) and other related material as a .zip file and the publication office compiles it for you. Then you receive an email to proof-read the uncorrected proof and (I'm not joking) you annotate the resulting PDF or submit a separate document about the changes. Then the publication office sends you the result once again as many times as necessary.

Citing IEEE.org header;

The world's largest professional association for advancement of technology.

and this is how they handle the publications.

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