help me with a routine that has workouts that i can not do please

[steam308]

i just started lifting (on my second week as i write this) and i am currently using this work out routine and i like it so far(THE COMPLETE 4-WEEK BEGINNER'S WORKOUT PROGRAM by health and fitness) , i want to finish this and then move on to Jim Stoppani's 12-Week Shortcut To Size , the reason why i don't use rippetoes or the 5x5 routine is because my gym does not have a bench or squat rack yet there is a smith machine & i have been doing dumbbells to do the bench press.

the reason why i'm writing this is because i can do every work out in both routines except for barbell squats, dead lifts (no bars) bent knee hip raises, ab crunch machine and standing calf raises. i can squat but i have heard mixed views on squatting in a smith machine because its not a free weight, are there any other routines i can follow that would work ? or substitutes i can use to exchange the exercises that i can't do ?

the gym plans on getting a squat rack but it wont be here till the beginning of the new year, its a small gym