I would like to try out ggtree as it appears to be very flexible. However, after the install via Bioconductor, I can neither load the sample trees nor any other trees. Install was on Ubuntu 16.04 and there were no errors. Any idea what is going on? I have no clues about R and I am probably missing something obvious...
> library("ape") > library("Biostrings") > library("ggplot2") > library("ggtree") > nwk <- system.file("extdata", "/home/ubuntuser/Desktop/Geospiza.nex", package="treeio") > tree <- read.tree(nwk) 1: Warning message: In read.tree(nwk) : empty character string.
> sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  ggtree_1.10.5 treeio_1.2.2 ggplot2_2.2.1  Biostrings_2.46.0 XVector_0.18.0 IRanges_2.12.0  S4Vectors_0.16.0 BiocGenerics_0.24.0 ape_5.1 loaded via a namespace (and not attached):  Rcpp_0.12.16 magrittr_1.5 zlibbioc_1.24.0 munsell_0.4.3  colorspace_1.3-2 lattice_0.20-35 rlang_0.2.0 plyr_1.8.4  grid_3.4.4 gtable_0.2.0 nlme_3.1-137 lazyeval_0.2.1  tibble_1.4.2 purrr_0.2.4 tidyr_0.8.0 glue_1.2.0  compiler_3.4.4 pillar_1.2.1 rvcheck_0.0.9 scales_0.5.0  jsonlite_1.5