### Starting build.
# Target: common_src/base.ml.depends, tags: { annot, extension:ml, file:common_src/base.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules common_src/base.ml > common_src/base.ml.depends # cached
# Target: common_src/mapsSets.ml.depends, tags: { annot, extension:ml, file:common_src/mapsSets.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules common_src/mapsSets.ml > common_src/mapsSets.ml.depends # cached
# Target: common_src/ppr.ml.depends, tags: { annot, extension:ml, file:common_src/ppr.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules common_src/ppr.ml > common_src/ppr.ml.depends # cached
# Target: common_src/ppr.cmo, tags: { annot, byte, compile, extension:ml, file:common_src/ppr.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I common_src -I tests -I prunetre_src -I pplacer_src -I json_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o common_src/ppr.cmo common_src/ppr.ml # cached
# Target: common_src/mapsSets.cmo, tags: { annot, byte, compile, extension:ml, file:common_src/mapsSets.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I common_src -I tests -I prunetre_src -I pplacer_src -I json_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o common_src/mapsSets.cmo common_src/mapsSets.ml # cached
# Target: common_src/base.cmo, tags: { annot, byte, compile, extension:ml, file:common_src/base.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I common_src -I tests -I prunetre_src -I pplacer_src -I json_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o common_src/base.cmo common_src/base.ml # cached
# Target: common_src/fam_batteries.ml.depends, tags: { annot, extension:ml, file:common_src/fam_batteries.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules common_src/fam_batteries.ml > common_src/fam_batteries.ml.depends # cached
# Target: common_src/fam_batteries.cmo, tags: { annot, byte, compile, extension:ml, file:common_src/fam_batteries.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I common_src -I tests -I prunetre_src -I pplacer_src -I json_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o common_src/fam_batteries.cmo common_src/fam_batteries.ml # cached
# Target: common_src/file_parsing.ml.depends, tags: { annot, extension:ml, file:common_src/file_parsing.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules common_src/file_parsing.ml > common_src/file_parsing.ml.depends # cached
# Target: common_src/file_parsing.cmo, tags: { annot, byte, compile, extension:ml, file:common_src/file_parsing.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I common_src -I tests -I prunetre_src -I pplacer_src -I json_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o common_src/file_parsing.cmo common_src/file_parsing.ml # cached
# Target: pplacer_src/bark_map.ml.depends, tags: { annot, extension:ml, file:pplacer_src/bark_map.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/bark_map.ml > pplacer_src/bark_map.ml.depends # cached
# Target: pplacer_src/newick_bark.ml.depends, tags: { annot, extension:ml, file:pplacer_src/newick_bark.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/newick_bark.ml > pplacer_src/newick_bark.ml.depends # cached
# Target: pplacer_src/myxml.ml.depends, tags: { annot, extension:ml, file:pplacer_src/myxml.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/myxml.ml > pplacer_src/myxml.ml.depends # cached
# Target: pplacer_src/myxml.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/myxml.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/myxml.cmo pplacer_src/myxml.ml # cached
# Target: pplacer_src/newick_bark.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/newick_bark.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/newick_bark.cmo pplacer_src/newick_bark.ml # cached
# Target: pplacer_src/bark_map.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/bark_map.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/bark_map.cmo pplacer_src/bark_map.ml # cached
# Target: pplacer_src/gentrees.ml.depends, tags: { annot, extension:ml, file:pplacer_src/gentrees.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/gentrees.ml > pplacer_src/gentrees.ml.depends # cached
# Target: pplacer_src/gtree.ml.depends, tags: { annot, extension:ml, file:pplacer_src/gtree.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/gtree.ml > pplacer_src/gtree.ml.depends # cached
# Target: pplacer_src/stree.ml.depends, tags: { annot, extension:ml, file:pplacer_src/stree.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/stree.ml > pplacer_src/stree.ml.depends # cached
# Target: pplacer_src/stree.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/stree.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/stree.cmo pplacer_src/stree.ml # cached
# Target: pplacer_src/gtree.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/gtree.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/gtree.cmo pplacer_src/gtree.ml # cached
# Target: pplacer_src/newick_gtree.ml.depends, tags: { annot, extension:ml, file:pplacer_src/newick_gtree.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/newick_gtree.ml > pplacer_src/newick_gtree.ml.depends # cached
# Target: pplacer_src/newick_lexer.mll, tags: { extension:mll, file:pplacer_src/newick_lexer.mll, lexer, ocaml, ocamllex, pkg_batteries, pkg_str, pkg_threads, quiet, traverse }
/Users/habnabit/fhcrc/godi/bin/ocamllex.opt -q pplacer_src/newick_lexer.mll # cached
# Target: pplacer_src/newick_lexer.ml.depends, tags: { annot, extension:ml, file:pplacer_src/newick_lexer.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/newick_lexer.ml > pplacer_src/newick_lexer.ml.depends # cached
# Target: pplacer_src/newick_parser.mly, tags: { extension:mly, file:pplacer_src/newick_parser.mly, ocaml, ocamlyacc, parser, pkg_batteries, pkg_str, pkg_threads, quiet, traverse }
/Users/habnabit/fhcrc/godi/bin/ocamlyacc pplacer_src/newick_parser.mly # cached
# Target: pplacer_src/newick_parser.mli.depends, tags: { extension:mli, file:pplacer_src/newick_parser.mli, ocaml, ocamldep, pkg_batteries, pkg_str, pkg_threads, quiet, traverse }
ocamlfind ocamldep -package batteries -package str -package threads -modules pplacer_src/newick_parser.mli > pplacer_src/newick_parser.mli.depends # cached
# Target: pplacer_src/newick_parser.cmi, tags: { byte, compile, extension:mli, file:pplacer_src/newick_parser.mli, interf, ocaml, pkg_batteries, pkg_str, pkg_threads, quiet, traverse }
ocamlfind ocamlc -c -package batteries -package str -package threads -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/newick_parser.cmi pplacer_src/newick_parser.mli # cached
# Target: pplacer_src/newick_lexer.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/newick_lexer.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/newick_lexer.cmo pplacer_src/newick_lexer.ml # cached
# Target: pplacer_src/newick_gtree.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/newick_gtree.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/newick_gtree.cmo pplacer_src/newick_gtree.ml # cached
# Target: pplacer_src/gentrees.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/gentrees.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/gentrees.cmo pplacer_src/gentrees.ml # cached
# Target: pplacer_src/newick_parser.ml.depends, tags: { annot, extension:ml, file:pplacer_src/newick_parser.ml, ocaml, ocamldep, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamldep -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -modules pplacer_src/newick_parser.ml > pplacer_src/newick_parser.ml.depends # cached
# Target: pplacer_src/newick_parser.cmo, tags: { annot, byte, compile, extension:ml, file:pplacer_src/newick_parser.ml, implem, ocaml, pkg_batteries, pkg_csv, pkg_gsl, pkg_pplacer, pkg_sqlite3, pkg_str, pkg_threads, pkg_xml-light, quiet, traverse, warn_Z }
ocamlfind ocamlc -c -annot -w Z -package batteries -package csv -package gsl -package sqlite3 -package str -package threads -package xml-light -thread -I pplacer_src -I tests -I prunetre_src -I json_src -I common_src -I tests/rppr -I tests/pplacer -I tests/json -I tests/guppy -o pplacer_src/newick_parser.cmo pplacer_src/newick_parser.ml # cached
# Target: gentrees.top, tags: { byte, extension:top, file:gentrees.top, link, ocaml, pkg_batteries, pkg_bigarray, pkg_csv, pkg_gsl, pkg_pplacer, pkg_str, pkg_threads, pkg_unix, pkg_xml-light, quiet, toplevel, traverse }
ocamlfind ocamlmktop -verbose -package batteries -package bigarray -package csv -package gsl -package str -package threads -package unix -package xml-light -thread common_src/ppr.cmo common_src/mapsSets.cmo common_src/base.cmo common_src/fam_batteries.cmo common_src/file_parsing.cmo pplacer_src/myxml.cmo pplacer_src/newick_bark.cmo pplacer_src/bark_map.cmo pplacer_src/stree.cmo pplacer_src/gtree.cmo pplacer_src/newick_parser.cmo pplacer_src/newick_lexer.cmo pplacer_src/newick_gtree.cmo pplacer_src/gentrees.cmo -o gentrees.top
+ ocamlfind ocamlmktop -verbose -package batteries -package bigarray -package csv -package gsl -package str -package threads -package unix -package xml-light -thread common_src/ppr.cmo common_src/mapsSets.cmo common_src/base.cmo common_src/fam_batteries.cmo common_src/file_parsing.cmo pplacer_src/myxml.cmo pplacer_src/newick_bark.cmo pplacer_src/bark_map.cmo pplacer_src/stree.cmo pplacer_src/gtree.cmo pplacer_src/newick_parser.cmo pplacer_src/newick_lexer.cmo pplacer_src/newick_gtree.cmo pplacer_src/gentrees.cmo -o gentrees.top
Effective set of compiler predicates: pkg_unix,pkg_threads.posix,pkg_threads,pkg_num.core,pkg_num,pkg_bigarray,pkg_str,pkg_findlib,pkg_camomile,pkg_batteries,pkg_csv,pkg_gsl,pkg_xml-light,autolink,mt,mt_posix,byte,create_toploop
+ ocamlmktop -verbose -o gentrees.top -thread -I /Users/habnabit/fhcrc/godi/lib/ocaml/pkg-lib/num -I /Users/habnabit/fhcrc/godi/lib/ocaml/pkg-lib/findlib -I /Users/habnabit/fhcrc/godi/lib/ocaml/pkg-lib/camomile -I /Users/habnabit/.odb/lib/batteries -I /Users/habnabit/fhcrc/godi/lib/ocaml/pkg-lib/csv -I /Users/habnabit/fhcrc/godi/lib/ocaml/pkg-lib/gsl -I /Users/habnabit/fhcrc/godi/lib/ocaml/pkg-lib/xml-light common_src/ppr.cmo common_src/mapsSets.cmo common_src/base.cmo common_src/fam_batteries.cmo common_src/file_parsing.cmo pplacer_src/myxml.cmo pplacer_src/newick_bark.cmo pplacer_src/bark_map.cmo pplacer_src/stree.cmo pplacer_src/gtree.cmo pplacer_src/newick_parser.cmo pplacer_src/newick_lexer.cmo pplacer_src/newick_gtree.cmo pplacer_src/gentrees.cmo
File "_none_", line 1, characters 0-1:
Error: Error while linking common_src/base.cmo:
Reference to undefined global `Str'
ocamlmktop returned with exit code 2
Command exited with code 2.
# Compilation unsuccessful.