Re: [Samtools-help] picard tool emits stack guard warning

[Nils H. <nh...@br...>]

Hey Lionel,

this can be ignored or you can you can download the latest release (1.121)
that should remove the warning (see the following commit
https://github.com/samtools/htsjdk/commit/f19cec4a2e12dab19dab7df22fd909ddadba7123).
Thanks for reporting this issue,

Nils

On Tue, Sep 9, 2014 at 1:03 PM, Lionel Brooks <lbr...@gm...>
wrote:

> Hello kind people,
>
> Please forgive me if this question has been addressed previously. I am
> trying to resolve the following warning:
>
> Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library
> /home/user01/Packages/picard/picard-tools-1.119/libIntelDeflater.so which
> might have disabled stack guard. The VM will try to fix the stack guard now.
> It's highly recommended that you fix the library with 'execstack -c
> <libfile>', or link it with '-z noexecstack'.
>
> The warning was emitted when I ran the picard tool called
> AddOrReplaceReadGroups. I am using 64-bit Linux with the following java
> version:
>
> java version "1.7.0_67"
> Java(TM) SE Runtime Environment (build 1.7.0_67-b01)
> Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
>
> The job seemed to run to completion but I am concerned about the warning.
> Should I ignore it? Can you suggest a fix?
>
> Thank you for your time,
> Lee
>
>
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