[ensembl-dev] VEP Term::ReadKey error

[Michael Yourshaw]

I have just begun to notice a non-destructive error with the Variant Effect Predictor:

Unable to get Terminal Size. The TIOCGWINSZ ioctl didn't work. The COLUMNS and LINES environment variables didn't work. The resize program didn't work. The stty program didn't work. at /home/myourshaw/apps/ActivePerl-5.18/site/lib/Term/ReadKey.pm line 426.

This originates with line 1212 in VEP 74
                ($w, $h) = GetTerminalSize();
and the actual error comes in ReadKey.pm line 339
        @results = GetTermSizeGWINSZ($file);

I don’t remember seeing this before VEP 74, but we recently updated our Perl installation from 5.16 to 5.18 and it is possible that the previous one either did not have Term::ReadKey installed or it behaved differently.

The error seems to be harmless, but it does put something in STDERR and our users like to see that be empty.

We actually run with the progress bar turned off. You might want to consider not running GetTerminalSize if it is not needed for the progress bar.

ॐ

Michael Yourshaw, PhD
UCLA Geffen School of Medicine
Department of Pediatrics
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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