NA in PCA

So there is no na.action argument for the form you used, and your
'na.omit' matches 'retx'.  Try

prcomp(~ ., data=ot, na.action=na.omit, scale=TRUE)

or

prcomp(na.omit(ot), scale=TRUE)

prcomp(~V1+V2, data=d, center = TRUE, scale = TRUE, na.action = na.omit)

prcomp(na.omit(d), center = TRUE, scale = TRUE)

prcomp(na.omit(log.ir), center = TRUE, scale = TRUE)
Error in prcomp.default(na.omit(log.ir), center = TRUE, scale = TRUE) : 
  cannot rescale a constant/zero column to unit variance

Your problem is not PCA problem but a wider missing values trearment problem. If you're not familiar with it, please read a bit on it. 
You have many opportunities:
(1) delete cases listwise or 
(2) pairwise, or 
(3) replace missings by mean or median. Or 
(4) replace by random chosen of valid values (hot-deck approach). Or impute missings by 
(5) mutual regression (with or without noise addition) approach or by a better, 
(6) EM approach. 

REF:

https://stats.stackexchange.com/questions/35561/imputation-of-missing-values-for-pca

https://stackoverflow.com/questions/12078291/r-function-prcomp-fails-with-nas-values-even-though-nas-are-allowed

http://menugget.blogspot.de/2011/11/empirical-orthogonal-function-eof.html

http://menugget.blogspot.de/2014/09/pca-eof-for-data-with-missing-values.html

 https://stat.ethz.ch/pipermail/r-help/2008-January/150896.html

https://rdrr.io/r/stats/prcomp.html