Minor fix to CRAN complaints

Author: jdmanton

DESCRIPTION

@@ -2,7 +2,7 @@ Package: nat.nblast
 Type: Package
 Title: NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron Similarity
     and Clustering
-Version: 1.6.6
+Version: 1.6.7
 Authors@R: c(
     person("Gregory", "Jefferis", email= "jefferis@gmail.com",
       role = c("aut"), comment = c(ORCID = "0000-0002-0587-9355")),
@@ -11,7 +11,7 @@ Authors@R: c(
     )
 Description: Extends package 'nat' (NeuroAnatomy Toolbox) by providing a
     collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016) <doi: 10.1016/j.neuron.2016.06.012>).
-URL: https://github.com/natverse/nat.nblast, https://natverse.github.io
+URL: https://natverse.org/nat.nblast/
 BugReports: https://github.com/natverse/nat.nblast/issues
 Depends:
     R (>= 2.15.1),
@@ -33,6 +33,6 @@ Suggests:
 License: GPL-3
 LazyData: yes
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Language: en-GB
 Encoding: UTF-8

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method("dimnames<-",spam)
+S3method(WeightedNNBasedLinesetMatching,default)
 S3method(WeightedNNBasedLinesetMatching,dotprops)
 S3method(WeightedNNBasedLinesetMatching,neuron)
 S3method(diagonal,default)

R/DATA.r

@@ -5,8 +5,8 @@
 #' same type, rather than unrelated neurons.
 #'
 #' These scoring matrices were generated using all by all pairs from 150 DL2
-#' antennal lobe projection neurons from the \url{http://flycircuit.tw} dataset
-#' and 5000 random pairs from the same dataset.
+#' antennal lobe projection neurons from the FlyCircuit dataset and 5000 random
+#' pairs from the same dataset.
 #'
 #' \itemize{
 #'
@@ -34,27 +34,27 @@ NULL
 #'
 #' This R list (which has additional class \code{neuronlist}) contains 15
 #' skeletonized \emph{Drosophila} neurons as \code{dotprops} objects. Original
-#' data is due to Chiang et al. [1], who have generously shared their raw data
-#' at \url{http://flycircuit.tw}. Automated tracing of neuron skeletons was
-#' carried out by Lee et al [2]. Image registration and further processing was
-#' carried out by Greg Jefferis, Marta Costa and James Manton[3].
+#' data is due to Chiang et al. [1], who have generously shared their raw data.
+#' Automated tracing of neuron skeletons was carried out by Lee et al [2]. Image
+#' registration and further processing was carried out by Greg Jefferis, Marta
+#' Costa and James Manton[3].
 #' @name fctraces20
 #' @docType data
 #' @references [1] Chiang A.S., Lin C.Y., Chuang C.C., Chang H.M., Hsieh C.H.,
 #'   Yeh C.W., Shih C.T., Wu J.J., Wang G.T., Chen Y.C., Wu C.C., Chen G.Y.,
 #'   Ching Y.T., Lee P.C., Lin C.Y., Lin H.H., Wu C.C., Hsu H.W., Huang Y.A.,
 #'   Chen J.Y., et al. (2011). Three-dimensional reconstruction of brain-wide
 #'   wiring networks in Drosophila at single-cell resolution. Curr Biol 21 (1),
-#'   1--11. doi: \url{http://doi.org/10.1016/j.cub.2010.11.056}
+#'   1--11. doi: \doi{10.1016/j.cub.2010.11.056}
 #'
 #'   [2] P.-C. Lee, C.-C. Chuang, A.-S. Chiang, and Y.-T. Ching. (2012).
 #'   High-throughput computer method for 3d neuronal structure reconstruction
 #'   from the image stack of the Drosophila brain and its applications. PLoS
 #'   Comput Biol, 8(9):e1002658, Sep 2012. doi:
-#'   \url{http://doi.org/10.1371/journal.pcbi.1002658}.
+#'   \doi{10.1371/journal.pcbi.1002658}.
 #'
 #'   [3] NBLAST: Rapid, sensitive comparison of neuronal structure and
 #'   construction of neuron family databases. Marta Costa, Aaron D. Ostrovsky,
 #'   James D. Manton, Steffen Prohaska, Gregory S.X.E. Jefferis. bioRxiv doi:
-#'   \url{http://doi.org/10.1101/006346}.
+#'   \doi{10.1101/006346}.
 NULL

R/nat.nblast.r

@@ -1,5 +1,8 @@
 #' Neuron similarity, search and clustering tools
 #'
+#' \bold{nat.nblast} provides tools to compare neuronal morphology using the
+#' NBLAST algorithm (Costa et al. 2016).
+#'
 #' @section Similarity and search:
 #'
 #'   The main entry point for similarity and search functions is
@@ -82,7 +85,7 @@
 #' @references Costa, M., Ostrovsky, A.D., Manton, J.D., Prohaska, S., and
 #'   Jefferis, G.S.X.E. (2014). NBLAST: Rapid, sensitive comparison of neuronal
 #'   structure and construction of neuron family databases. bioRxiv preprint.
-#'   \href{http://dx.doi.org/10.1101/006346}{doi: 10.1101/006346}.
+#'   \doi{10.1101/006346}.
 #'
 #' @name nat.nblast-package
 #' @aliases nat.nblast

R/neuriteblast.r

@@ -105,19 +105,18 @@
 #' @references Kohl, J. Ostrovsky, A.D., Frechter, S., and Jefferis, G.S.X.E
 #'   (2013). A bidirectional circuit switch reroutes pheromone signals in male
 #'   and female brains. Cell 155 (7), 1610--23
-#'   \href{http://dx.doi.org/10.1016/j.cell.2013.11.025}{doi:
-#'   10.1016/j.cell.2013.11.025}.
+#'   \doi{10.1016/j.cell.2013.11.025}.
 #'
 #'   Costa, M., Ostrovsky, A.D., Manton, J.D., Prohaska, S., and Jefferis,
 #'   G.S.X.E. (2014). NBLAST: Rapid, sensitive comparison of neuronal structure
 #'   and construction of neuron family databases. bioRxiv preprint.
-#'   \href{http://dx.doi.org/10.1101/006346}{doi: 10.1101/006346}.
+#'   \doi{10.1101/006346}.
 #'
 #'   Jefferis G.S.X.E., Potter C.J., Chan A.M., Marin E.C., Rohlfing T., Maurer
 #'   C.R.J., and Luo L. (2007). Comprehensive maps of Drosophila higher
 #'   olfactory centers: spatially segregated fruit and pheromone representation.
 #'   Cell 128 (6), 1187--1203.
-#'   \href{http://dx.doi.org/10.1016/j.cell.2007.01.040}{doi:10.1016/j.cell.2007.01.040}
+#'   \doi{10.1016/j.cell.2007.01.040}
 #'
 #'
 #'
@@ -410,7 +409,7 @@ WeightedNNBasedLinesetMatching.neuron<-function(target, query, UseAlpha=FALSE,
   WeightedNNBasedLinesetMatching(target, query, ...)
 }
 
-
+#' @export
 WeightedNNBasedLinesetMatching.default<-function(target,query,dvs1=NULL,dvs2=NULL,alphas1=NULL,
                                         alphas2=NULL,NNDistFun=WeightedNNBasedLinesetDistFun,Verbose=FALSE,
                                         BothDirections=FALSE,BothDirectionsFun=list,OnlyClosestPoints=FALSE,...){

README.md

@@ -1,10 +1,10 @@
 # nat.nblast <img src="man/figures/logo.svg" align="right" height="139" />
 <!-- badges: start -->
-[![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.github.io)
+[![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.org/)
 [![Release Version](https://img.shields.io/github/release/natverse/nat.nblast.svg)](https://github.com/natverse/nat.nblast/releases/latest) 
 [![CRAN status](https://www.r-pkg.org/badges/version/nat.nblast)](https://CRAN.R-project.org/package=nat.nblast)
-[![Build Status](https://travis-ci.org/natverse/nat.nblast.svg?branch=master)](https://travis-ci.org/natverse/nat.nblast)
-[![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](https://natverse.github.io/nat.nblast/reference/)
+[![Build Status](https://travis-ci.org/natverse/nat.nblast.svg?branch=master)](https://app.travis-ci.com/natverse/nat.nblast)
+[![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](https://natverse.org/nat.nblast/reference/)
 <!-- badges: end -->
 
 **nat.nblast** is part of the [NeuroAnatomy Toolbox](https://jefferislab.github.io/)
@@ -52,13 +52,13 @@ databases of neurons. There is also support for all x all comparison for a group
 of neurons. This can produce a distance matrix suitable for hierarchical clustering,
 which is also implemented in the package.
 
-These tools are designed as an addon for the [NeuroAnatomy Toolbox](https://natverse.github.io/nat)
+These tools are designed as an addon for the [NeuroAnatomy Toolbox](https://natverse.org/nat/)
 (nat) R package, which will be installed as dependency.
 
 You will probably find the following online documentation helpful:
 
-* https://natverse.github.io/nat.nblast - Online documentation for this R package
-* http://jefferislab.org/si/nblast - Overview of NBLAST algorithm and online tools 
+* https://natverse.org/nat.nblast/ - Online documentation for this R package
+* https://jefferislab.org/si/nblast/ - Overview of NBLAST algorithm and online tools 
 
 ## Installation
 This package has been released to [CRAN](https://cran.r-project.org/package=nat.nblast)
@@ -81,6 +81,6 @@ devtools::install_github("natverse/nat.nblast")
 ```
 Note that this will also update the [nat package](https://github.com/natverse/nat)
 to the latest development version from github. Windows users need 
-[Rtools](http://www.murdoch-sutherland.com/Rtools/) to install this way.
+[Rtools](https://www.murdoch-sutherland.com/Rtools/) to install this way.