Install/compile fails about gramtools HOT 14 CLOSED

and yes, I did run this first

scl enable devtoolset-1.1 bash

from gramtools.

These are all SDSL errors!

from gramtools.

Is totally weird. Is sdsl currently broken?

from gramtools.

Yes, it is broken, have raised an issue there

from gramtools.

I'm not using the latest version of sdsl.

Sent from my iPhone

On 27 Jan 2016, at 09:50, Zamin Iqbal <[email protected]mailto:[email protected]> wrote:

Yes, it is broken, have raised an issue there

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Reply to this email directly or view it on GitHubhttps://github.com//issues/5#issuecomment-175517975.

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OK, but makes it hard for me to compile...
Can I copy yours?

from gramtools.

Sure, can you see /home/sm0179/sdsl-lite?

Sent from my iPhone

On 27 Jan 2016, at 10:26, Zamin Iqbal <[email protected]mailto:[email protected]> wrote:

OK, but makes it hard for me to compile...
Can I copy yours?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/5#issuecomment-175535678.

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But the whole thing can't compile yet as I haven't got a make file to link the functions

Sent from my iPhone

On 27 Jan 2016, at 10:26, Zamin Iqbal <[email protected]mailto:[email protected]> wrote:

OK, but makes it hard for me to compile...
Can I copy yours?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/5#issuecomment-175535678.

from gramtools.

Ah - ok, so you'd like me to code review for the moment, not try compile?

from gramtools.

Longer term if this became an issue, you could modify gramtools so it pulls sorina/sdsl-lite instead of simongog/sdsl-lite, and have a fork of sdsl-lite that is yours, and periodically update your version

from gramtools.

So the reason I’m using an old version is because Jerome modified some of their code to make the SSE stuff work and then I couldn’t pull the newer versions. Now I’m not sure whether I should ask Jerome to tell them about his hacks and merge them or to separately get the newest version of sdsl and see if that makes the SSE work without Jerome’s thing

From: Zamin Iqbal <[email protected]mailto:[email protected]>
Reply-To: iqbal-lab/gramtools <[email protected]mailto:[email protected]>
Date: Wed, 27 Jan 2016 05:19:56 -0800
To: iqbal-lab/gramtools <[email protected]mailto:[email protected]>
Cc: Sorina Maciuca <[email protected]mailto:[email protected]>
Subject: Re: [gramtools] Install/compile fails (#5)

Longer term if this became an issue, you could modify gramtools so it pulls sorina/sdsl-lite instead of simongog/sdsl-lite, and have a fork of sdsl-lite that is yours, and periodically update your version

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/5#issuecomment-175621600.

from gramtools.

Yeah I'm ok to use yours for now. But we should probably chat to Sgog

from gramtools.

Agreed, for the moment it’s not pressing issue. Code review would be good, and thinking all the wrong ways the input data might come in so I make good assertions.

From: Zamin Iqbal <[email protected]mailto:[email protected]>
Reply-To: iqbal-lab/gramtools <[email protected]mailto:[email protected]>
Date: Wed, 27 Jan 2016 05:46:51 -0800
To: iqbal-lab/gramtools <[email protected]mailto:[email protected]>
Cc: Sorina Maciuca <[email protected]mailto:[email protected]>
Subject: Re: [gramtools] Install/compile fails (#5)

Yeah I'm ok to use yours for now. But we should probably chat to Sgog

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/5#issuecomment-175634671.

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Yeah, I'll code review. Trying to understand the algo + how to use the API+ how we might test. We can start gramtools meetings nextweek

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