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<div>Can you run cpanm to install those? I think that's what we do for bioperl. </div>
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<div>Chris</div>
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Sent from a Phone of Ingenuity (+3)<br>
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<div>-------- Original message --------</div>
<div>From: Eric Talevich </div>
<div>Date:08/03/2014 11:46 AM (GMT-06:00) </div>
<div>To: Evan Parker </div>
<div>Cc: BioPython-Dev Mailing List </div>
<div>Subject: Re: [Biopython-dev] Travis-CI failing due to t-coffee dependency </div>
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<div class="gmail_quote">On Sat, Aug 2, 2014 at 9:56 PM, Evan Parker <span dir="ltr">
<<a href="mailto:eparker05@gmail.com" target="_blank">eparker05@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="ltr">Hey Biopython-Dev,
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<div>I was pushing some commits today and I noticed failures on Travis-CI due to dependency failures. Travis was giving me the following error:</div>
<div>* > The command "sudo apt-get install t-coffee</div>
<div>* muscle mafft probcons wise emboss" failed</div>
<div>* and exited with 100 during .</div>
<div>I have a link to the error below. I broke apart the dependencies and tried again and I identified t-coffee as the issue. I'm not exactly sure of how to proceed from this point or if others have experienced this or are currently experiencing this.</div>
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<div>A Travis-CI job that failed due to this error:</div>
<div><a href="https://travis-ci.org/eparker05/biopython/jobs/31520799" target="_blank">https://travis-ci.org/eparker05/biopython/jobs/31520799</a><br>
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My latest feature-branch commit that identified the specific Travis-CI dependency failure<br>
<a href="https://github.com/eparker05/biopython/commit/2149fa15e89bb6833097b8db74e3a77badac2ccd" target="_blank">https://github.com/eparker05/biopython/commit/2149fa15e89bb6833097b8db74e3a77badac2ccd</a><span class=""><font color="#888888"><br>
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<div>-Evan Parker</div>
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<div class="gmail_extra">It looks like this affected all 5 builds on the two commits before your fix (beginning within the last day), so I suppose it's not just a transient network error on Travis's side?
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The apt-get failure is for only one package in the main Ubuntu US repository, <font>
libxml-sax-perl, which is a dependency of </font><font><a href="http://packages.ubuntu.com/precise/libxml-simple-perl">libxml-simple-perl</a> which t-coffee "recommends":</font><br>
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<div class="gmail_extra"><font><a href="http://packages.ubuntu.com/precise/t-coffee">http://packages.ubuntu.com/precise/t-coffee</a><br>
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<div class="gmail_extra">What if we tried adding the "--no-install-recommends" flag to the Travis configuration?<br>
<span class="">"sudo apt-get install </span><span class="">--no-install-recommends t-coffee</span>"<br>
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