[maker-devel] Issue with maker

[Carson Holt]

Try updating BioPerl. This is caused by an attempt to improve certain indexing performance in BioPerl by using C code that compiles on the fly during runtime. It’s semi-unstable and really needs to be removed from BioPerl especially since a simple perl translation operator (tr///d) already fixed the need for the performance change anyways.

Caused by lines 249-273 in this BioPerl code —> https://github.com/bioperl/bioperl-live/blob/master/lib/Bio/DB/IndexedBase.pm <https://github.com/bioperl/bioperl-live/blob/master/lib/Bio/DB/IndexedBase.pm>

Alternatively edit the file in BioPerl and comment out lines 249-273 yourself with ‘#’ signs (also get the trailing bracket on line 280).

—Carson


> On Oct 25, 2018, at 3:22 PM, Pallavi Gupta <pallavi.gupta at slu.edu> wrote:
> 
> Hi Team MAKER,
> 
> I am using maker for my research for genome annotation process. But when I run maker I am getting a weird error. I tried finding a work around on the internet by scrolling through various bioinformatics forum but I was unsuccessful. I will really appreciate if you can help me in this regard. I have attached my nohup.out log. Please let me know if you need anything else.
> 
> Thanks,
> Pallavi Gupta
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