Hello,
Gretl should open a window indicating the number of missing observations.
It should ask: "Continue (yes/no)?"
So the user can decide what he wants to do.
With greetings 
Jürgen Malitte
-----Original-Nachricht-----
 Betreff: Re: [Gretl-users] Principal component analysis: Missing
 values encountered
 Datum: Thu, 03 Nov 2016 22:33:13 +0100
 Von: Allin Cottrell <cottrell(a)wfu.edu>
 An: Gretl list <gretl-users(a)lists.wfu.edu> 
 On Thu, 3 Nov 2016, Allin Cottrell wrote:
 
 > On Thu, 3 Nov 2016, Jaromir Baxa wrote:
 >
 >> Dear all,
 >> few days ago I've updated my gretl installation from 1.9.91 to
 2016b and >> re-run one of my examples that I use in class and I've
 found that the >> principal components analysis behaves quite
 different now (perhaps a bug): >> After performing pca on the same
 dataset as before, gretl returns "Missing >> values encountered", both
 via GUI and via console and PC's are not >> calculated.
 
 Second response: OK, I can confirm that the "pca" command used to skip
 rows in the dataset on which there were missing values (in gretl
 version 1.9.*), but in current gretl missing values provoke an error.
 
 This isn't a bug, as such, but it may not be a well considered
 change in behavior. I think the motivation for the change may have
 been related to the fact that under the old behaviour there was no
 indication of the number of missing observations that were dropped.
 But of course that could be fixed by printing a count of
 observations actually used (or dropped), rather than rejecting a
 sample containing missing observations.
 
 Thoughts from other users on this?
 
 Allin Cottrell
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