'values' not found

[clb21565]

Dear all,

Trying to run OPERA-MS on a pretty big dataset, and am getting the following error:
Problem while running this R command:
length(values)

Error:
object 'values' not found
Execution halted

---

I noticed that this might be something you've looked at :) :

#Resolve weird problem of undefined value NEED TO INVESTIGATE WHY THIS APPENS
my $nb_window = @{$window_distrib} + 0;
my @temp = ();my $val;
for(my $i = 0; $i < $nb_window; $i++){
$val = $window_distrib->[$i];
if(defined $val){
    push(@temp, $val);
}
else{
    print STDERR " *** WARNING undefined value in window_distrib " . $i . "\n";
}
}


#$R->set( 'values', $window_distrib);
$R->set( 'values', \@temp);
$R->set( 'span', 11);

$a = $R->run(
## adpated from EDDA
#q `print(sessionInfo())`,	
q `length(values)`,
q `dens <- density(values)`,
q `series <-dens$y`,
q `z <- embed(series, span)`,
q `s <- span%/%2`,
q `ind <- apply(z, 1, which.max)`,
q `v <- ind == (1 + s)`,
q `result <- c(rep(FALSE, s), v)`,
q `result <- result[1:(length(result) - s)]`,
q `print(dens$x[result])`,
);

from cluster_strain.pl

Would you have a suggestion on resolving this?

[jsgounot]

Hi, thanks for reporting this. I'm working on it and will come back as soon I find a fix !

[clb21565]

Hi there! Any update on this?

[jsgounot]

Hi. Sadly I was not able to spend enough time on this and I don't have a fix atm. This error seems weird though, since we clearly define what inside values with the set function. One possibility would be that \@temp is empty. Is it possible on your side to print what's inside the \@temp variable before the error and report it in this thread? OPERA-MS keeps in memory the last successful step so you should not have to rerun the whole analysis.