OK, its a real clumsy fudge but it seems to stop the hanging. With this modification in place, my Perl/R script misses some tests out (probably the ones it would have hung on)--but with a properly designed Perl script you can catch which ones it missed and have another go at the end.
(The script I am currently working on with this is a DBI script, uses a MySQL database ENUM column to record whether all of the required tests have been carried out).

In pipe.pm, I changed

if ( $x == 20 ) {
        my (undef , $data) = $this->read_processR ;
        if ( $data =~ /\s$n\s+\.\.\.\s+\// ) { last ;}
        $x = 0 ;
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to

if ( $x == 20 ) {
        my (undef , $data) = $this->read_processR ;
        last;
        $x = 0 ;
[download]