Try graphicsmagick-imagemagick-compat-based convert utility for svg->pdf instead of inkscape.

CMakeStuff/modules/convert_svg.bash

@@ -7,6 +7,6 @@ FILES=$@
 
 for f in $FILES
 do
-  echo " file : $f"
-  inkscape --without-gui --export-pdf="${f%.svg}.pdf" $f
+  echo "Converting svg file $f to pdf file ${f%.svg}.pdf"
+  convert $f ${f%.svg}.pdf
 done

templates/share/applications/masschroq-gui.desktop

@@ -3,7 +3,7 @@ Name=MassChroQ GUI 2.2.23
 Categories=Education;Science;Math;
 Comment=MassChroQ GUI launcher
 Exec=masschroq_gui %U
-Icon=/usr/local/share/masschroq/masschroq.svg
+Icon=/usr/share/masschroq/masschroq.svg
 Terminal=false
 Type=Application
 StartupNotify=true

templates/share/applications/masschroq-studio.desktop

@@ -3,7 +3,7 @@ Name=MassChroQ Studio 2.2.23
 Categories=Education;Science;Math;
 Comment=MassChroQ parameters editor
 Exec=masschroq_studio %U
-Icon=/usr/local/share/masschroq/masschroq.svg
+Icon=/usr/share/masschroq/masschroq.svg
 Terminal=false
 Type=Application
 StartupNotify=true