nat

Package: nat
Type: Package
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Version: 1.8.1
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis@gmail.com>
URL: https://github.com/jefferis/nat http://jefferislab.org
BugReports: https://github.com/jefferis/nat/issues
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Depends: R (>= 2.15.1), rgl
Imports: nabor, igraph, methods, filehash, digest, nat.utils (>=
0.4.2), plyr, yaml
Suggests: Rvcg, testthat, httr, XML
License: GPL-3
LazyData: yes
Collate: 'amiralandmarks-io.R' 'amiramesh-io.R' 'cmtk-reformat.R'
'cmtk.R' 'cmtk_geometry.R' 'cmtk_io.R' 'cmtkreg.R'
'coordinates.R' 'dist3D_Segment_to_Segment.R' 'neuron.R'
'dotprops.R' 'graph-nodes.R' 'hxsurf.R' 'im3d.R' 'nat-data.R'
'nat-package.R' 'ndigest.R' 'neuron-io-amira.R'
'neuron-io-fiji.R' 'neuron-io-neuroml.R' 'neuron-io.R'
'neuron-plot.R' 'neuronlist.R' 'neuronlist_interactive_3d.R'
'neuronlist_sets.R' 'neuronlistfh.R' 'ngraph.R' 'nrrd-io.R'
'pop3d.R' 'potential_synapses.R' 'seglist.R' 'summary.R'
'vaa3draw-io.R' 'xform.R' 'xformimage.R' 'xformpoints.R'
'zzz.R'
NeedsCompilation: no
Packaged: 2015-12-30 17:14:07 UTC; jefferis
Repository: CRAN
Date/Publication: 2015-12-30 23:24:38

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'nat' ...
** package 'nat' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'nat'
    finding HTML links ... done
    Cell07PNs                               html  
    MBL.surf                                html  
    affmat2cmtkparams                       html  
    all.equal.dotprops                      html  
    all.equal.im3d                          html  
    all.equal.neuron                        html  
    amiramesh-io                            html  
    amiratype                               html  
    as.im3d                                 html  
    as.mesh3d                               html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/as.mesh3d.Rd:28: missing file link 'tmesh3d'
    as.neuronlist                           html  
    as.neuronlist.neuronlistfh              html  
    boundingbox                             html  
    finding level-2 HTML links ... done

    c.neuronlist                            html  
    clampmax                                html  
    cmtk.bindir                             html  
    cmtk.call                               html  
    cmtk.dof2mat                            html  
    cmtk.extract_affine                     html  
    cmtk.mat2dof                            html  
    cmtk.reformatx                          html  
    cmtk.statistics                         html  
    cmtk.targetvolume                       html  
    cmtk.version                            html  
    cmtkparams2affmat                       html  
    cmtkreg                                 html  
    cmtkreglist                             html  
    coord2ind                               html  
    dotprops-arithmetic                     html  
    dotprops                                html  
    fileformats                             html  
    find.neuron                             html  
    find.soma                               html  
    flip                                    html  
    get-set-neuronlist-data.frame           html  
    graph.nodes                             html  
    im3d-coords                             html  
    im3d-io                                 html  
    im3d                                    html  
    image.im3d                              html  
    imexpand.grid                           html  
    imscalebar                              html  
    imslice                                 html  
    ind2coord                               html  
    intersect                               html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/intersect.Rd:34: missing file link 'intersect'
    is.amiramesh                            html  
    is.fijitraces                           html  
    is.im3d                                 html  
    is.neuroml                              html  
    is.neuronlist                           html  
    is.nrrd                                 html  
    is.swc                                  html  
    is.vaa3draw                             html  
    kcs20                                   html  
    materials                               html  
    mirror                                  html  
    nat-internal                            html  
    nat-package                             html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/nat-package.Rd:35: missing file link 'graph'
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/nat-package.Rd:111: missing file link 'rgl'
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/nat-package.Rd:118: missing file link 'rgl'
    ndigest                                 html  
    neuron-arithmetic                       html  
    neuron                                  html  
    neuronlist-arithmetic                   html  
    neuronlist-dataframe-methods            html  
    neuronlist                              html  
    neuronlistfh                            html  
    ngraph                                  html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/ngraph.Rd:41: missing file link 'set.vertex.attribute'
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/ngraph.Rd:110: missing file link 'set.vertex.attribute'
    nlapply                                 html  
    nlscan                                  html  
    nopen3d                                 html  
    normalise_swc                           html  
    npop3d                                  html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/npop3d.Rd:21: missing file link 'pop3d'
    nrrd.voxdims                            html  
    origin                                  html  
    pan3d                                   html  
    plot.neuron                             html  
    plot.neuronlist                         html  
    plot3d                                  html  
    plot3d.boundingbox                      html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/plot3d.boundingbox.Rd:12: missing file link 'segments3d'
    plot3d.dotprops                         html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/plot3d.dotprops.Rd:60: missing file link 'points3d'
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/plot3d.dotprops.Rd:61: missing file link 'segments3d'
    plot3d.hxsurf                           html  
    plot3d.neuron                           html  
    plot3d.neuronlist                       html  
    pointsinside                            html  
    potential_synapses                      html  
    projection                              html  
    prune                                   html  
    prune_strahler                          html  
    prune_vertices                          html  
    read.cmtk                               html  
    read.cmtkreg                            html  
    read.hxsurf                             html  
    read.landmarks                          html  
    read.morphml                            html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/read.morphml.Rd:11: missing file link 'xmlParse'
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/read.morphml.Rd:13: missing file link 'xmlParse'
    read.neuron                             html  
    read.neuron.fiji                        html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/read.neuron.fiji.Rd:12: missing file link 'xmlParse'
    read.neuron.neuroml                     html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/read.neuron.neuroml.Rd:13: missing file link 'xmlParse'
    read.neuron.swc                         html  
    read.neuronlistfh                       html  
    read.neurons                            html  
    read.nrrd                               html  
    read.vaa3draw                           html  
    remotesync                              html  
    resample                                html  
    rootpoints                              html  
    scale.neuron                            html  
    seglengths                              html  
    seglist                                 html  
    seglist2swc                             html  
    segmentgraph                            html  
    setdiff                                 html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/setdiff.Rd:37: missing file link 'setdiff'
    spine                                   html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/spine.Rd:40: missing file link 'shortest.paths'
    strahler_order                          html  
    sub-.neuronlistfh                       html  
    sub2ind                                 html  
    subset                                  html  
    subset.dotprops                         html  
    subset.hxsurf                           html  
    subset.neuron                           html  
    subset.neuronlist                       html  
    summary.neuron                          html  
    threshold                               html  
    union                                   html  
Rd warning: /tmp/RtmpNWMq4S/R.INSTALL1dd05c0a1b99/nat/man/union.Rd:34: missing file link 'union'
    unmask                                  html  
    voxdims                                 html  
    write.amiramesh                         html  
    write.cmtk                              html  
    write.cmtkreg                           html  
    write.hxsurf                            html  
    write.neuron                            html  
    write.neuronlistfh                      html  
    write.neurons                           html  
    write.nrrd                              html  
    xform                                   html  
    xformimage                              html  
    xformpoints                             html  
    xyzmatrix                               html  
** building package indices
** testing if installed package can be loaded
* DONE (nat)
Making 'packages.html' ... done