Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-10-07

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All times shown according to UTC.

Time Nick Message
01:41 towodo joined #opentreeoflife
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01:47 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
11:43 mtholder joined #opentreeoflife
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13:29 towodo oh no… the leaf blowers…
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17:09 towodo mtholder, were you ever able to build a taxonomy?
17:10 mtholder yes. thanks.
17:10 mtholder cool stuff.
17:11 towodo if you say ‘make works’ you get additional reports
17:12 towodo although currently it’s getting the list of OTUs-in-studies from phylografter… need to fix that
17:14 towodo sorry that’s OTT ids-in-studies
17:17 mtholder one tiny annoyance when rebuilding is having to answer to the prompt:
17:17 mtholder (cd feed/gbif/in && (unzip checklist1.zip || true))
17:17 mtholder Archive:  checklist1.zip
17:17 mtholder warning:  stripped absolute path spec from /eml.xml
17:17 mtholder replace eml.xml? [y]es, [n]o, [A]ll, [N]one, [r]ename: N
17:17 mtholder I'm not sure if that is avoidable.
17:18 towodo probably there’s an unzip option for this
17:18 mtholder but overall it was quite smooth
17:19 towodo I had totally forgotten about it, since I downloaded GBIF a long time ago & downloading is lazy
17:31 towodo -o     overwrite existing files without prompting.  This is a dangerous option, so use it  with  care.
17:31 mtholder Oh. And running "make works" just now resulted in:
17:31 mtholder 500000
17:31 mtholder Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
17:31 mtholder at java.lang.String.split(String.java:2364)
17:31 mtholder at org.opentreeoflife.smasher.QualifiedId.<init>(Taxonomy.java:3541)
17:31 mtholder at org.opentreeoflife.smasher.Taxon.setSourceIds(Taxon.java:66)
17:31 mtholder at org.opentreeoflife.smasher.Taxonomy.initTaxon(Taxonomy.java:493)
17:31 mtholder at org.opentreeoflife.smasher.Taxonomy.loadTaxonomyProper(Taxonomy.java:411)
17:31 mtholder at org.opentreeoflife.smasher.Taxonomy.loadTaxonomy(Taxonomy.java:284)
17:31 mtholder at org.opentreeoflife.smasher.Taxonomy.getTaxonomy(Taxonomy.java:250)
17:32 mtholder at org.opentreeoflife.smasher.Smasher.main(Smasher.java:61)
17:32 mtholder trying with more memory in the BIGJAVA var in Makefile
17:32 mtholder ...
17:32 towodo I would really like to redo the makefile so that retrieved files are dated & you can keep multiple versions
17:32 towodo funny, I didn’t get that…
17:33 mtholder java -version
17:33 mtholder java version "1.8.0_20"
17:33 mtholder Java(TM) SE Runtime Environment (build 1.8.0_20-b26)
17:33 mtholder Java HotSpot(TM) 64-Bit Server VM (build 25.20-b23, mixed mode)
17:33 mtholder FWIW
17:34 towodo that could be it, I’m still at 1.7
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