<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Chris,<div><br></div><div>Thanks for looking into this! I am also experiencing the same problem encountered by Shane.</div><div><br></div><div>Thanks,</div><div><br></div><div>Lili</div><div><br><div apple-content-edited="true">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1">Liliana Cano, PhD.</font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1">Postdoctoral Research Associate</font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1">Dept. Plant Pathology</font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1">North Carolina State University</font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1">Raleigh, NC 27695, USA.</font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1">Email: <a href="mailto:lcanomo@ncsu.edu">lcanomo@ncsu.edu</a></font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1">Phone: +1-919-513-1280</font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1">Mobile: +1-919-703-6147</font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><font face="Arial" size="1"><br></font></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><a href="https://twitter.com/ConchitaCano" style="font-size: 11px;">https://twitter.com/ConchitaCano</a></div><div><a href="http://plantpathology.ces.ncsu.edu/profile/liliana-cano/" style="font-size: 11px;">http://plantpathology.ces.ncsu.edu/profile/liliana-cano/</a></div></div></div></div></div></div></div></div>
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<br><div><div>On Jan 16, 2015, at 11:30 AM, Shane McCoy <<a href="mailto:shanemccoypdx@gmail.com">shanemccoypdx@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Thanks Chris!<div>appreciate you looking into this</div><div>shane</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 15, 2015 at 11:32 AM, Fields, Christopher J <span dir="ltr"><<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Just an update on this; I contacted Chris D. and Bundle::BioPerl is now on github:
<div><br>
</div>
<div><a href="https://github.com/bioperl/Bundle-BioPerl" target="_blank">https://github.com/bioperl/Bundle-BioPerl</a></div>
<div><br>
</div>
<div>I’ll work on pushing a new release up to CPAN, will post back when that is done.</div>
<div><br>
</div>
<div>chris (f)</div><div><div class="h5">
<div><br>
<div>
<blockquote type="cite">
<div>On Jan 14, 2015, at 2:14 PM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>> wrote:</div>
<br>
<div>
<div style="word-wrap:break-word">
<div>Bundle::BioPerl is out of date. I’ll have to check in with Chris Dagdigian to see if we can update that, as it’s not on github.</div>
<div><br>
</div>
<div>Unless you are using NCBI and the ‘gene’ database, you won’t need Bio::ASN1::EntrezGene. The latest CPAN releases for both should still resolve the circular dependency though; not sure why you are running into this problem.</div>
<div><br>
</div>
<div>The github master version should technically be ‘1.007000_001’ or similar, not ‘1.006925’. I’ll have a look at that.</div>
<div><br>
</div>
<div>chris</div>
<br>
<div>
<blockquote type="cite">
<div>On Jan 13, 2015, at 5:23 PM, Shane McCoy <<a href="mailto:shanemccoypdx@gmail.com" target="_blank">shanemccoypdx@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">Hello!
<div>Not too familiar w/ Bioperl and want to make sure i've properly installed on my VM ubuntu 14.4 server w/ git. </div>
<div>
<div><a href="http://www.bioperl.org/wiki/BioPerl_Dependencies" target="_blank">http://www.bioperl.org/wiki/BioPerl_Dependencies</a></div>
<div><a href="http://www.bioperl.org/wiki/Using_Git" target="_blank">http://www.bioperl.org/wiki/Using_Git</a></div>
<div><br>
</div>
<div>sudo apt-get update</div>
<div>sudo apt-get upgrade</div>
<div>sudo apt-get check</div>
<div>sudo apt-get autoclean</div>
<div><br>
</div>
<div>sudo apt-get install build-essential git gcc</div>
<div>sudo apt-get install libexpat1 expat</div>
<div>sudo apt-get install libgd-dev (unable to locate libgd recommended on
<a href="http://gmod.org/wiki/BioPerl" target="_blank">gmod.org/wiki/BioPerl</a> Dependencies Outside perl)</div>
<div>sudo apt-get install libssl-dev</div>
<div>sudo apt-get install libpq-dev</div>
<div>sudo apt-get install libdb-dev libperl-dev</div>
<div>sudo apt-get install libgd-gd2-perl</div>
<div>sudo apt-get install libxml2</div>
<div>sudo apt-get install libxml2-dev</div>
<div><br>
</div>
<div>Installed local::lib manually for perl modules. Set environment path </div>
<div>echo '[ $SHLVL -eq 1 ] && eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"' >>~/.bashrc</div>
<div><br>
</div>
<div>cpan> install Bundle::CPAN (archive::zip failed? pff!) </div>
<div>cpan> install Bundle::BioPerl</div>
<div>Failed during this command:</div>
<div> LDS/AcePerl-1.92.tar.gz : make_test NO</div>
<div> CJFIELDS/Bio-ASN1-EntrezGene-1.70.tar.gz : make_test NO</div>
<div> CAPTTOFU/DBD-mysql-4.029.tar.gz : writemakefile NO '/usr/bin/perl Makefile.PL </div>
<div>and several more. missing packages etc and successfully installed except the above 3. Don't think i need those.</div>
<div><br>
</div>
<div>sudo apt-get install libgd-gd2-perl</div>
<div><br>
</div>
<div>
git clone <a href="https://github.com/bioperl/bioperl-live.git" target="_blank">
https://github.com/bioperl/bioperl-live.git</a>
</div>
<div>cd bioperl-live
</div>
<div>perl Build.PL
--fails - needs more modules</div>
<div><br>
</div>
<div><br>
</div>
<div>Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL</div>
<div>Checking prerequisites...</div>
<div> recommends:</div>
<div><br>
</div>
<div>Algorithm::Munkres </div>
<div>Array::Compare </div>
<div>Bio::Phylo </div>
<div>Convert::Binary::C </div>
<div>GraphViz</div>
<div>HTML::TableExtract is not installed</div>
<div>PostScript::TextBlock is not installed</div>
<div>SOAP::Lite </div>
<div>Net::SSLeay Crypt::SSLeay IO::Socket::SSL</div>
<div>Sort::Naturally </div>
<div>XML::LibXML </div>
<div>DBD::Pg </div>
<div>DBD::SQLite</div>
<div>(all above installed via CPAN)</div>
<div><br>
</div>
<div>Checking optional features...</div>
<div>EntrezGene............disabled</div>
<div> requires:</div>
<div> ! Bio::ASN1::EntrezGene is not installed</div>
<div> - starts installing bioperl </div>
<div>i let it run and it installed Bioperl fine via CPAN. build OK. </div>
<div>Installed bio::asn1::entrezgene & bio::root::build</div>
<div>perl Build.PL</div>
<div>now needs Inline::C...</div>
<div>cpan>install Inline::C</div>
<div> cd bioperl-live </div>
<div>
perl Build.PL
-- fails. missing Manifest?</div>
<div>Build manifest</div>
<div>perl Build.PL --still fails</div>
<div>perl Build -- works</div>
<div>./Build test
--PASS</div>
<div>sudo ./Build install </div>
<div><br>
</div>
<div>Installed / passed tests OK. </div>
<div>Added;</div>
<div>export PERL5LIB="$HOME/bioperl-live:$PERL5LIB"</div>
<div>to .bashrc</div>
</div>
<div><br>
</div>
<div>So i've installed via CPAN which i didn't really want, but couldn't run Build.PL w/o prereq Bio::ASN1::EntrezGene which starts installing bioperl. What should i have done differently? </div>
<div>i still did Build w/ Git clone, but when i check Version i get 1.006924. I thought the bioperl-live version was 1.006925? i set the environment variable in bashrc for bioperl-live. </div>
<div>Ok, thanks for your time! Just want to make sure i'm doing this correctly. </div>
<div>Shane</div>
</div>
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