The Programmable Pull-Up Resistor (option name "Weak Pull-Up Resistor" in Quartus II) cannot be set on dedicated clock input pins (CLK[0..15]). The Programmable Pull-Up Resistor only supports user I/O pins.
 
Please refer to the Programmable Pull-Up Resistor (Pull-Up Resistor for Stratix IV only) in the Device Handbook for each device at the URL link below.
　
・ Stratix IV devices
      https://www.altera.com/en_US/pdfs/literature/hb/stratix-iv/stx4_siv51006.pdf
 
・ Stratix III devices
      https://www.altera.com/en_US/pdfs/literature/hb/stx3/stx3_siii51007.pdf
 
・ Stratix II devices
      https://www.altera.com/en_US/pdfs/literature/hb/stx2/stx2_sii51002.pdf
 
・ Stratix devices
      https://www.altera.com/en_US/pdfs/literature/hb/stx/ch_2_vol_1.pdf
 
・ Cyclone III device
      https://www.altera.com/en_US/pdfs/literature/hb/cyc3/cyc3_ciii51007.pdf
 
・Cyclone II device
      https://www.altera.com/en_US/pdfs/literature/hb/cyc2/cyc2_cii51002.pdf
 
・ Cyclone device
      https://www.altera.com/en_US/pdfs/literature/hb/cyc/cyc_c51002.pdf