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Question: Something wrong with my Bioconductor installation? ggtree cannot read any tree
0
gravatar for martin
4 weeks ago by
martin0
martin0 wrote:

Hi,

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.

Thanks,

M.

> 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:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] ggtree_1.10.5       treeio_1.2.2        ggplot2_2.2.1      
[4] Biostrings_2.46.0   XVector_0.18.0      IRanges_2.12.0     
[7] S4Vectors_0.16.0    BiocGenerics_0.24.0 ape_5.1            

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16     magrittr_1.5     zlibbioc_1.24.0  munsell_0.4.3   
 [5] colorspace_1.3-2 lattice_0.20-35  rlang_0.2.0      plyr_1.8.4      
 [9] grid_3.4.4       gtable_0.2.0     nlme_3.1-137     lazyeval_0.2.1  
[13] tibble_1.4.2     purrr_0.2.4      tidyr_0.8.0      glue_1.2.0      
[17] compiler_3.4.4   pillar_1.2.1     rvcheck_0.0.9    scales_0.5.0    
[21] jsonlite_1.5    

 

ADD COMMENTlink modified 4 weeks ago by markus.riester90 • written 4 weeks ago by martin0
2
gravatar for markus.riester
4 weeks ago by
markus.riester90 wrote:

See the documentation of ?system.file.

nwk <- "/home/ubuntuser/Desktop/Geospiza.nex"

ADD COMMENTlink written 4 weeks ago by markus.riester90

Oops. Working now! Thanks.

ADD REPLYlink written 4 weeks ago by martin0
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