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+cmake_minimum_required(VERSION 2.8)
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+
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+project(thesis NONE)
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+
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+include(/usr/share/cmake-2.8/Modules/UseLATEX.cmake)
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+
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+# Set R executable
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+set(R_COMPILE "/usr/bin/Rscript")
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+# Set the location of data files
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+##set(DATA_DIR data)
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+# Set the location of the directory for image files
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+set(IMAGE_DIR graphicsauto)
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+
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+# Get a list of R files
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+file(GLOB_RECURSE R_FILES "R/*.R")
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+
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+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/R DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${IMAGE_DIR})
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+
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+foreach(file ${R_FILES})
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+ message("processing ${file}")
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+ get_filename_component(basename "${file}" NAME_WE)
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+
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+ # Command to run R
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+ if(R_COMPILE)
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+ message("Adding ........... ${CMAKE_CURRENT_BINARY_DIR}/R/${basename}.R")
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+
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+ add_custom_command(
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+ OUTPUT
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+ ${CMAKE_CURRENT_BINARY_DIR}/${IMAGE_DIR}/${basename}.eps
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+ DEPENDS
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+ ${CMAKE_CURRENT_BINARY_DIR}/R/${basename}.R
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+ # ${CMAKE_CURRENT_BINARY_DIR}/${IMAGE_DIR}/${DATA_DIR}
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+ COMMAND
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+ ${R_COMPILE}
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+ ARGS
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+ ${CMAKE_CURRENT_BINARY_DIR}/R/${basename}.R
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+ ${CMAKE_CURRENT_BINARY_DIR}/${IMAGE_DIR}/${basename}.eps
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+ )
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+ message("Running ${R_COMPILE} ${CMAKE_CURRENT_BINARY_DIR}/R/${basename}.R ${CMAKE_CURRENT_BINARY_DIR}/${IMAGE_DIR}/${basename}.eps")
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+
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+ endif(R_COMPILE)
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+
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+ # Make a list of all R files (for ADD_LATEX_DOCUMENT depend)
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+ set(ALL_R_FILES ${ALL_R_FILES}
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+ ${CMAKE_CURRENT_BINARY_DIR}/${IMAGE_DIR}/${basename}.eps
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+ )
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+endforeach(file)
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+
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+# ------- export mainThesis.org -----------------------
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+latex_get_output_path(OUTPUT_DIR)
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+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/mainThesis.org DESTINATION ${OUTPUT_DIR}/ )
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+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/thesis.el DESTINATION ${OUTPUT_DIR}/ )
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+
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+add_custom_target( orgfile ALL
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+ DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/mainThesis.org )
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+
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+add_custom_target( elfile ALL
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+ DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/thesis.el )
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+
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+add_custom_command(
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+ OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/mainThesis.tex
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+ COMMAND emacs -Q --batch --eval \"(progn
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+ (add-to-list 'load-path
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+ (expand-file-name \\"~/.emacs.d/plugins/org-mode/lisp/\\"))
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+ (add-to-list 'load-path
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+ (expand-file-name \\"~/.emacs.d/plugins/org-mode/contrib/lisp/\\" t))
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+ (require 'org)
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+ (require 'ox)
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+ (require 'org-exp)
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+ (require 'org-inlinetask)
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+ (require 'ob-plantuml)
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+ (setq org-plantuml-jar-path \\"/home/myles/Downloads/plantuml.jar\\")
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+ (org-babel-do-load-languages
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+ 'org-babel-load-languages
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+ '((emacs-lisp . t)
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+ (sh . t)
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+ (plantuml . t)))
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+ (setq org-confirm-babel-evaluate nil)
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+ (setq org-latex-listings 'minted)
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+ (setq org-latex-with-hyperref nil)
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+ (add-to-list 'org-latex-packages-alist '(\\"\\" \\"minted\\"))
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+
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+ (add-to-list 'org-latex-classes
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+ '(\\"mynewthesis\\" \\"\\\\\\documentclass[11pt]{mythesis}\\"
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+ (\\"\\\\\\chapter{%s}\\" . \\"\\\\\\chapter*{%s}\\")
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+ (\\"\\\\\\section{%s}\\" . \\"\\\\\\section*{%s}\\")
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+ (\\"\\\\\\subsection{%s}\\" . \\"\\\\\\subsection*{%s}\\")
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+ (\\"\\\\\\subsubsection{%s}\\" . \\"\\\\\\subsubsection*{%s}\\")
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+ (\\"\\\\\\paragraph{%s}\\" . \\"\\\\\\paragraph*{%s}\\")))
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+ (setq org-export-with-todo-keywords nil)
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+ (load-library \\"/home/myles/lib/lisp/my-export.el\\")
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+ (add-to-list 'org-export-before-parsing-hook 'my-export-delete-headlines-tagged-noheading)
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+ (add-to-list 'org-export-filter-link-functions 'my-autoref-filter-link-func)
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+ (load-file \\"thesis.el\\")
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+ (find-file \\"${CMAKE_CURRENT_BINARY_DIR}/mainThesis.org\\")
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+ (org-latex-export-to-latex))\"
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+ DEPENDS orgfile elfile
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+ COMMENT "Exporting orgmode file to LaTeX using emacs")
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+
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+add_custom_target( mainfile ALL
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+ DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/mainThesis.tex )
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+# ------ end mainThesis.org ---------------------------
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+
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+# add_custom_command(
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+# OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/master.tex
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+# COMMAND echo "\\\\input{mainThesis.tex}" > ${CMAKE_CURRENT_BINARY_DIR}/master.tex
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+# DEPENDS orgfile
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+# COMMENT "Writing file master.tex")
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+
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+# add_custom_target( masterfile ALL
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+# DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/master.tex )
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+
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+add_latex_document(master.tex
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+ BIBFILES texlib/mybiblatex.bib
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+ INPUTS biber.conf
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+ phd_papers.bib
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+ tex/title.tex
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+ tex/titleBasic.tex
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+ tex/abstract.tex
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+ tex/sharedMemory_sec.tex
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+ texlib/mystyle.sty
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+ tex/linked_nodes_test.tex
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+ IMAGE_DIRS ${IMAGE_DIR} ../graphics/thirdParty ../graphics/VE
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+ DEPENDS ${ALL_R_FILES}
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+ DEFAULT_PDF
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+ USE_NOMENCL)
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