Use

my $command = q`a<-read.table("/usr/local/projects/file")`;
print "Running [$command]\n";
$R->send($command);
[download]

and

my $file="/usr/local/projects/file";
my $command = q`a<-read.table($file)`;
print "Running [$command]\n";
$R->send($command);
[download]

to see what happens and what the first cause is. Then look at perlop, especially at the "Quotes and Quote-like operators" to see what causes this behaviour of Perl and what to change.