drwxr-xr-x root/root usr/ drwxr-xr-x root/root usr/lib/ drwxr-xr-x root/root usr/lib/R/ drwxr-xr-x root/root usr/lib/R/library/ drwxr-xr-x root/root usr/lib/R/library/RNeXML/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/CITATION -rw-r--r-- root/root usr/lib/R/library/RNeXML/DESCRIPTION -rw-r--r-- root/root usr/lib/R/library/RNeXML/INDEX -rw-r--r-- root/root usr/lib/R/library/RNeXML/LICENSE drwxr-xr-x root/root usr/lib/R/library/RNeXML/Meta/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/Meta/Rd.rds -rw-r--r-- root/root usr/lib/R/library/RNeXML/Meta/features.rds -rw-r--r-- root/root usr/lib/R/library/RNeXML/Meta/hsearch.rds -rw-r--r-- root/root usr/lib/R/library/RNeXML/Meta/links.rds -rw-r--r-- root/root usr/lib/R/library/RNeXML/Meta/nsInfo.rds -rw-r--r-- root/root usr/lib/R/library/RNeXML/Meta/package.rds -rw-r--r-- root/root usr/lib/R/library/RNeXML/Meta/vignette.rds -rw-r--r-- root/root usr/lib/R/library/RNeXML/NAMESPACE -rw-r--r-- root/root usr/lib/R/library/RNeXML/NEWS.md drwxr-xr-x root/root usr/lib/R/library/RNeXML/R/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/R/RNeXML -rw-r--r-- root/root usr/lib/R/library/RNeXML/R/RNeXML.rdb -rw-r--r-- root/root usr/lib/R/library/RNeXML/R/RNeXML.rdx -rw-r--r-- root/root usr/lib/R/library/RNeXML/WORDLIST drwxr-xr-x root/root usr/lib/R/library/RNeXML/doc/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/S4.Rmd -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/S4.html -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/index.html -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/intro.Rmd -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/intro.html -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/metadata.Rmd -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/metadata.html -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/simmap.Rmd -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/simmap.html -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/sparql.Rmd -rw-r--r-- root/root usr/lib/R/library/RNeXML/doc/sparql.html drwxr-xr-x root/root usr/lib/R/library/RNeXML/examples/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/RDFa2RDFXML.xsl -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/biophylo.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/characters.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/coal.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/comp_analysis.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/gardiner_1984.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/geospiza.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/jsonld-ex.R -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/mbank_X962_11-22-2013_1534.nex -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/merge_data.Rmd -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/merge_data.md -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/meta_example.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/meta_taxa.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/missing_some_branchlengths.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/multitrees.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/ncbii.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/no-base-ns.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/ontotrace-result.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/phenex.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/phenoscape.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/primates.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/primates_from_R.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/primates_meta.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/primates_meta_xslt.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/simmap.nex -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/simmap.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/simmap_ex.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/some_missing_branchlengths.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/sparql.newick -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/taxa.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/treebase-record.xml -rw-r--r-- root/root usr/lib/R/library/RNeXML/examples/trees.xml drwxr-xr-x root/root usr/lib/R/library/RNeXML/help/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/AnIndex -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/RNeXML.rdb -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/RNeXML.rdx -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/aliases.rds drwxr-xr-x root/root usr/lib/R/library/RNeXML/help/figures/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/figures/Figure1-1.png -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/figures/logo.svg -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/figures/unnamed-chunk-5-1.png -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/figures/unnamed-chunk-8-1.png -rw-r--r-- root/root usr/lib/R/library/RNeXML/help/paths.rds drwxr-xr-x root/root usr/lib/R/library/RNeXML/html/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/html/00Index.html -rw-r--r-- root/root usr/lib/R/library/RNeXML/html/R.css -rw-r--r-- root/root usr/lib/R/library/RNeXML/simmap.md drwxr-xr-x root/root usr/lib/R/library/RNeXML/xsd/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/LICENSE -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/README.txt -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/abstract.xsd drwxr-xr-x root/root usr/lib/R/library/RNeXML/xsd/characters/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/README.txt -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/abstractcharacters.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/characters.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/continuous.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/dna.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/protein.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/restriction.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/rna.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/characters/standard.xsd drwxr-xr-x root/root usr/lib/R/library/RNeXML/xsd/external/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/external/sawsdl.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/external/xhtml-datatypes-1.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/external/xlink.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/external/xml.xsd drwxr-xr-x root/root usr/lib/R/library/RNeXML/xsd/meta/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/meta/README.txt -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/meta/annotations.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/meta/sets.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/nexml.xsd drwxr-xr-x root/root usr/lib/R/library/RNeXML/xsd/taxa/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/taxa/README.txt -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/taxa/taxa.xsd drwxr-xr-x root/root usr/lib/R/library/RNeXML/xsd/trees/ -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/trees/README.txt -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/trees/abstracttrees.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/trees/network.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/trees/tree.xsd -rw-r--r-- root/root usr/lib/R/library/RNeXML/xsd/trees/trees.xsd