Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.

Be sure to consult the FAQ section in the manual before submitting
a bug report.  In addition check if the bug is reproducable with an
up-to-date version of AUCTeX.  So please upgrade to the version
available from http://www.gnu.org/software/auctex/ if your
installation is older than the one available from the web site.

If the bug is triggered by a specific (La)TeX file, you should try
to produce a minimal sample file showing the problem and include it
in your report.

Your report will be posted for the auctex package at the GNU bug
tracker.  Visit http://debbugs.gnu.org/cgi/pkgreport.cgi?pkg=auctex
to browse existing AUCTeX bugs.
------------------------------------------------------------------------

I set in my latex main file: 

%%% TeX-command-extra-options: "-src-specials -recorder -shell-escape"

Nevertheless, when running the pdflatex compiler, 
the only option I receive is -shell-escape, the last one. 


Emacs  : GNU Emacs 24.3.1 (x86_64-suse-linux-gnu, GTK+ Version 3.16.7)
 of 2016-08-05 on lamb17
Package: 11.89.7

current state:
==============
(setq
 AUCTeX-date "2016-11-12"
 window-system 'x
 LaTeX-version "2e"
 TeX-style-path '("~/.emacs.d/auctex"
                  "/home/ernst/.emacs.d/elpa/auctex-11.89.7/style"
                  "/home/ernst/.emacs.d/auctex/auto"
                  "/home/ernst/.emacs.d/auctex/style" "auto" "style")
 TeX-auto-save t
 TeX-parse-self t
 TeX-master t
 TeX-command-list '(("TeX"
                     "%(PDF)%(tex) %(file-line-error) %(extraopts) 
%`%S%(PDFout)%(mode)%' %t"
                     TeX-run-TeX nil
                     (plain-tex-mode ams-tex-mode texinfo-mode) :help
                     "Run plain TeX")
                    ("LaTeX" "%`%l%(mode)%' %t" TeX-run-TeX nil
                     (latex-mode doctex-mode) :help "Run LaTeX")
                    ("Makeinfo" "makeinfo %(extraopts) %t" TeX-run-compile nil
                     (texinfo-mode) :help "Run Makeinfo with Info output")
                    ("Makeinfo HTML" "makeinfo %(extraopts) --html %t"
                     TeX-run-compile nil (texinfo-mode) :help
                     "Run Makeinfo with HTML output")
                    ("AmSTeX" "amstex %(PDFout) %(extraopts) %`%S%(mode)%' %t"
                     TeX-run-TeX nil (ams-tex-mode) :help "Run AMSTeX")
                    ("ConTeXt"
                     "%(cntxcom) --once --texutil %(extraopts) %(execopts)%t"
                     TeX-run-TeX nil (context-mode) :help "Run ConTeXt once")
                    ("ConTeXt Full" "%(cntxcom) %(extraopts) %(execopts)%t"
                     TeX-run-TeX nil (context-mode) :help
                     "Run ConTeXt until completion")
                    ("BibTeX" "bibtex %s" TeX-run-BibTeX nil t :help
                     "Run BibTeX")
                    ("Biber" "biber %s" TeX-run-Biber nil t :help "Run Biber")
                    ("View" "%V" TeX-run-discard-or-function t t :help
                     "Run Viewer")
                    ("Print" "%p" TeX-run-command t t :help "Print the file")
                    ("Queue" "%q" TeX-run-background nil t :help
                     "View the printer queue" :visible TeX-queue-command)
                    ("File" "%(o?)dvips %d -o %f " TeX-run-dvips t t :help
                     "Generate PostScript file")
                    ("Dvips" "%(o?)dvips %d -o %f " TeX-run-dvips nil t :help
                     "Convert DVI file to PostScript")
                    ("Dvipdfmx" "dvipdfmx %d" TeX-run-dvipdfmx nil t :help
                     "Convert DVI file to PDF with dvipdfmx")
                    ("Ps2pdf" "ps2pdf %f" TeX-run-ps2pdf nil t :help
                     "Convert PostScript file to PDF")
                    ("Index" "makeindex %s" TeX-run-index nil t :help
                     "Run makeindex to create index file")
                    ("Xindy" "texindy %s" TeX-run-command nil t :help
                     "Run xindy to create index file")
                    ("Makeglossaries" "makeglossaries %s" TeX-run-glossary nil
                     t :help "Run makeglossaries to create glossary file")
                    ("Check" "lacheck %s" TeX-run-compile nil (latex-mode)
                     :help "Check LaTeX file for correctness")
                    ("ChkTeX" "chktex -v6 %s" TeX-run-compile nil (latex-mode)
                     :help "Check LaTeX file for common mistakes")
                    ("Spell" "(TeX-ispell-document \"\")" TeX-run-function nil
                     t :help "Spell-check the document")
                    ("Clean" "TeX-clean" TeX-run-function nil t :help
                     "Delete generated intermediate files")
                    ("Clean All" "(TeX-clean t)" TeX-run-function nil t :help
                     "Delete generated intermediate and output files")
                    ("Other" "" TeX-run-command t t :help
                     "Run an arbitrary command")
                    )
 )



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