fix check issues

DESCRIPTION

@@ -18,7 +18,7 @@ Description: A pipeline for the identification, within taxonomic groups,
     search tool and is, therefore, not dependent on differences in gene
     naming conventions and naming errors.
 License: MIT + file LICENSE
-URL: https://docs.ropensci.org/phylotaR,
+URL: https://docs.ropensci.org/phylotaR/,
     https://github.com/ropensci/phylotaR#readme
 BugReports: https://github.com/ropensci/phylotaR/issues
 Depends:
@@ -44,8 +44,6 @@ Suggests:
     testthat
 VignetteBuilder: 
     knitr
-Remotes:
-    ropensci/restez
 Encoding: UTF-8
 RoxygenNote: 7.2.3
 SystemRequirements: BLAST+ (>=2.0)

README.md

@@ -1,7 +1,7 @@
 # Automated Retrieval of Orthologous DNA Sequences from GenBank <img src="https://raw.githubusercontent.com/ropensci/phylotaR/master/logo.png" height="300" align="right"/>
-[![R-CMD-check](https://github.com/ropensci/phylotaR/actions/workflows/r-check.yml/badge.svg)](https://github.com/ropensci/phylotaR/actions/workflows/r-check.yml) [![Coverage Status](https://coveralls.io/repos/github/ropensci/phylotaR/badge.svg?branch=master)](https://coveralls.io/github/ropensci/phylotaR?branch=master) [![](https://badges.ropensci.org/187_status.svg)](https://github.com/ropensci/onboarding/issues/187) [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/phylotaR)](https://CRAN.R-project.org/package=phylotaR)
+[![R-CMD-check](https://github.com/ropensci/phylotaR/actions/workflows/r-check.yml/badge.svg)](https://github.com/ropensci/phylotaR/actions/workflows/r-check.yml) [![Coverage Status](https://coveralls.io/repos/github/ropensci/phylotaR/badge.svg?branch=master)](https://coveralls.io/github/ropensci/phylotaR?branch=master) [![](https://badges.ropensci.org/187_status.svg)](https://github.com/ropensci/software-review/issues/187) [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/phylotaR)](https://CRAN.R-project.org/package=phylotaR)
 
-R implementation of the PhyLoTa sequence cluster pipeline. For more information see the accompanying website. Tested and demonstrated on Unix and Windows. **Find out more by visiting the [phylotaR website](https://ropensci.github.io/phylotaR/).**
+R implementation of the PhyLoTa sequence cluster pipeline. For more information see the accompanying website. Tested and demonstrated on Unix and Windows. **Find out more by visiting the [phylotaR website](https://docs.ropensci.org/phylotaR/).**
 
 ## Install
 

vignettes/phylotaR.Rmd

@@ -11,7 +11,7 @@ vignette: >
 
 The first step to running a phylogenetic analysis is the identification of overlapping sequences. Often orthology is determined by pairing sequences whose gene names match (e.g. COI sequences with COI sequences, rbcl sequences with rbcl sequences). Problems can arise however if gene names differ between authors, if different gene sections are represented or if sequences are mislabelled. These issues can be especially problematic for large-scale analyses where individual errors cannot be detected.
 
-[PhyLoTa](https://www.ncbi.nlm.nih.gov/pubmed/18570030) is a pipeline that uses an alignment search tool to identify orthologous sequences without the need for gene name matching. For a given parental taxonomic group, the pipeline will search through available sequences hosted on GenBank and identify orthologous sequence clusters. A user is then able to survey the identified clusters and select the ones which best suit their phylogenetic analysis needs, e.g. by selecting the clusters that maximise the number of taxonomic groups.
+[PhyLoTa](https://pubmed.ncbi.nlm.nih.gov/18570030/) is a pipeline that uses an alignment search tool to identify orthologous sequences without the need for gene name matching. For a given parental taxonomic group, the pipeline will search through available sequences hosted on GenBank and identify orthologous sequence clusters. A user is then able to survey the identified clusters and select the ones which best suit their phylogenetic analysis needs, e.g. by selecting the clusters that maximise the number of taxonomic groups.
 
 This R pacakge, `phylotaR`, is an R implementation of this pipeline. In this vignette we will demonstrate how to run PhyLoTa using a small taxonomic group. The pipeline is composed of four automated stages (taxise, download, cluster, cluster2) and a final user-performed stage of cluster selection.
 

vignettes/phylotaR.Rmd.orig

@@ -11,7 +11,7 @@ vignette: >
 
 The first step to running a phylogenetic analysis is the identification of overlapping sequences. Often orthology is determined by pairing sequences whose gene names match (e.g. COI sequences with COI sequences, rbcl sequences with rbcl sequences). Problems can arise however if gene names differ between authors, if different gene sections are represented or if sequences are mislabelled. These issues can be especially problematic for large-scale analyses where individual errors cannot be detected.
 
-[PhyLoTa](https://www.ncbi.nlm.nih.gov/pubmed/18570030) is a pipeline that uses an alignment search tool to identify orthologous sequences without the need for gene name matching. For a given parental taxonomic group, the pipeline will search through available sequences hosted on GenBank and identify orthologous sequence clusters. A user is then able to survey the identified clusters and select the ones which best suit their phylogenetic analysis needs, e.g. by selecting the clusters that maximise the number of taxonomic groups.
+[PhyLoTa](https://pubmed.ncbi.nlm.nih.gov/18570030/) is a pipeline that uses an alignment search tool to identify orthologous sequences without the need for gene name matching. For a given parental taxonomic group, the pipeline will search through available sequences hosted on GenBank and identify orthologous sequence clusters. A user is then able to survey the identified clusters and select the ones which best suit their phylogenetic analysis needs, e.g. by selecting the clusters that maximise the number of taxonomic groups.
 
 This R pacakge, `phylotaR`, is an R implementation of this pipeline. In this vignette we will demonstrate how to run PhyLoTa using a small taxonomic group. The pipeline is composed of four automated stages (taxise, download, cluster, cluster2) and a final user-performed stage of cluster selection.