<div dir="ltr"><div class="gmail_extra"><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,<div><br></div><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>
<div><br></div><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>
</div><div><br>
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>
</font></span></div><span class=""><font color="#888888"><div><br></div><div>-Evan Parker</div></font></span></div>
<br></blockquote></div><br></div><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? <br>
<br>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>
</div><div class="gmail_extra"><font><a href="http://packages.ubuntu.com/precise/t-coffee">http://packages.ubuntu.com/precise/t-coffee</a><br><br></font></div><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><br><br><br></div></div>