1. ggtree
  2. Commit da0f0f7f9513165bad61f20a4e98c8729f9745f7
Browse code

fixed R check

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122173 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 11/10/2016 01:31:56
Showing 15 changed files
DESCRIPTION
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@@ -1,7 +1,7 @@
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 Package: ggtree
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 Type: Package
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 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.5.15
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+Version: 1.5.16
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 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
NAMESPACE
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@@ -244,3 +244,4 @@ importFrom(stats4,plot)
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 importFrom(tidyr,gather)
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 importFrom(utils,download.file)
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 importFrom(utils,modifyList)
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+importFrom(utils,packageVersion)
NEWS
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@@ -1,3 +1,8 @@
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+CHANGES IN VERSION 1.5.16
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+------------------------
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+ o fixed R check <2016-10-10, Mon>
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+   + check.aes parameter is not available in release version of ggplot2 yet
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+
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 CHANGES IN VERSION 1.5.15
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 ------------------------
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  o check.aes for layers defined in ggtree <2016-10-07, Fri>
R/geom_balance.R
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@@ -14,6 +14,7 @@
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 #' @export
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 #' @importFrom ggplot2 aes_
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 #' @importFrom ggplot2 GeomRect
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+#' @importFrom utils packageVersion
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 #' @author Justin Silverman
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 #' @references J. Silverman, et al. \emph{A phylogenetic transform enhances
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 #'   analysis of compositional microbiota data}. (in preparation)
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@@ -45,7 +46,7 @@ geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend
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                   extendto=extendto,
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                   direction=1,
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                   na.rm = na.rm),
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-    check.aes = FALSE
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+    if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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   )
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   l2 <- layer(
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     stat=StatBalance,
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@@ -63,7 +64,7 @@ geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend
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                   extendto=extendto,
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                   direction=2,
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                   na.rm = na.rm),
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-    check.aes = FALSE
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+    if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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   )
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   return(c(l1,l2))
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 }
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@@ -116,7 +117,7 @@ stat_balance <- function(mapping=NULL, data=NULL, geom="rect",
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                   extendto=extendto,
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                   direction=1,
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                   ...),
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-    check.aes = FALSE
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+    if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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   )
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   l2 <- layer(
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     stat=StatBalance,
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@@ -134,7 +135,7 @@ stat_balance <- function(mapping=NULL, data=NULL, geom="rect",
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                   extendto=extendto,
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                   direction=2,
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                   ...),
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-    check.aes = FALSE
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+    if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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   )
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   return(c(l1,l2))
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 }
R/geom_cladelabel.R
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@@ -129,7 +129,7 @@ stat_cladeText <- function(mapping=NULL, data=NULL,
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                       na.rm  = na.rm,
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                       parse  = parse,
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                       ...),
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-          check.aes = FALSE
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+          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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           )
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 }
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@@ -157,7 +157,7 @@ stat_cladeBar <- function(mapping=NULL, data=NULL,
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                       align=align,
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                       na.rm=na.rm,
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                       ...),
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-          check.aes = FALSE
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+          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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           )
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 }
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R/geom_hilight.R
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@@ -40,7 +40,7 @@ geom_hilight <- function(node, fill="steelblue", alpha=.5, extend=0, extendto=NU
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                       extend=extend,
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                       extendto=extendto,
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                       na.rm = na.rm),
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-        check.aes = FALSE
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+        if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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     )
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 }
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R/geom_label.R
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@@ -67,7 +67,7 @@ geom_label2 <- function(mapping = NULL, data = NULL,
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             na.rm = na.rm,
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             ...
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         ),
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-        check.aes = FALSE
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+        if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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     )
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 }
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R/geom_point.R
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@@ -126,7 +126,7 @@ geom_point2 <- function(mapping = NULL, data = NULL,
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             na.rm = na.rm,
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             ...
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         ),
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-        check.aes = FALSE
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+        if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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     )
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 }
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R/geom_segment.R
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@@ -68,7 +68,7 @@ geom_segment2 <- function(mapping = NULL, data = NULL,
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             na.rm = na.rm,
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             ...
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         ),
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-        check.aes = FALSE
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+        if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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     )
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 }
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R/geom_strip.R
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@@ -98,7 +98,7 @@ stat_stripText <- function(mapping=NULL, data=NULL,
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                       na.rm=na.rm,
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                       parse=parse,
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                       ...),
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-          check.aes = FALSE
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+          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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           )
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 }
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@@ -134,7 +134,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL,
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                       barextend=barextend,
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                       na.rm=na.rm,
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                       ...),
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-          check.aes = FALSE
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+          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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           )
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 }
R/geom_taxalink.R
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@@ -31,7 +31,7 @@ geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {
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                         curvature = curvature,
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                         na.rm = na.rm,
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                         ...),
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-          check.aes = FALSE
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+          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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           )
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 }
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R/geom_text.R
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@@ -55,7 +55,7 @@ geom_text2 <- function(mapping = NULL, data = NULL,
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           na.rm = na.rm,
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           ...
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         ),
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-        check.aes = FALSE
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+        if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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     )
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 }
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R/geom_tiplab.R
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@@ -111,7 +111,7 @@ geom_tipsegment <- function(mapping=NULL, data=NULL,
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           params = list(offset = offset,
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                         na.rm = na.rm,
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                         ...),
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-          check.aes = FALSE
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+          if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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           )
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 }
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R/geom_tree.R
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@@ -47,7 +47,7 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit
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                                lineend = lineend,
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                                na.rm = na.rm,
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                                ...),
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-                   check.aes = FALSE
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+                   if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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                    ),
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              layer(data=data,
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                    mapping=mapping,
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@@ -60,7 +60,7 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit
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                                lineend = lineend,
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                                na.rm = na.rm,
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                                ...),
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-                   check.aes = FALSE
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+                   if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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                    )
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              )
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     } else if (layout %in% c("slanted", "radial", "unrooted")) {
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                           lineend = lineend,
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                           na.rm = na.rm,
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                           ...),
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-              check.aes = FALSE
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+              if (packageVersion('ggplot2') > '2.1.0') check.aes = FALSE
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               )
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     }
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 }
README.md
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1 1 
 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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 ===========================================================================================================================
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.15-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-14686/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.16-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-14940/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--07-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--10-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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@@ -17,7 +17,7 @@ Please cite the following article when using `ggtree`:
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 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. *accepted*
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-168-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-171-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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@@ -50,7 +50,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-14686/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-14940/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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          +-------------------------+------------------------+-------------------------+----------------+
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          |                                                                                         *   |