Dear All,
I receive the same error as Gabriela when I try to load phytools in R or R
Studio.
Here is the text:
library("phytools",
lib.loc="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck
= vI[[j]]) :
there is no package called ‘Biostrings’
Error: package or namespace load failed for ‘phytools’
I am running R v 3.2.3 and phytools v 0.5-10.
If I try to load Biostrings I receive an error message that Biostrings is
not compatible with R 3.2.3.
Cheers,
Don Miles
Ohio University
On Sat, Jan 9, 2016 at 12:50 PM, Vojtěch Zeisek wrote:
> Hello
>
> Dne So 9. ledna 2016 13:11:45, Gabriela Wofkova napsal(a):
> > Hello,
> >
> > I have an problem with loading package "phytools". I have the newest
> > version of R studio and it cannot load package "Biostrings" which is
> > reqired to package "phytools". Also it not works in R program, too. Can
> you
> > have any idea, how to evade this?
> >
> > I need to use "read.newick" and load phylogenetic tree.
>
> What exactly are You doing? phytools does not require Biostrings and
> Biostrings does not require phytools. :-)
> Which operating system are You running? Which error did You get? Errors are
> keys to solutions... Do You have newest versions of the packages (I'd try
> to
> reinstall them first to see if they weren't corrupted)?
> Both load fine for me (on Linux):
>
> > library(phytools)
> Loading required package: ape
> Loading required package: maps
>
> # ATTENTION: maps v3.0 has an updated 'world' map.#
> # Many country borders and names have changed since 1990. #
> # Type '?world' or 'news(package="maps")'. See README_v3. #
>
> > library(Biostrings)
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
> clusterMap, parApply, parCapply, parLapply, parLapplyLB,
> parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
> anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
> do.call,
> duplicated, eval, evalq, Filter, Find, get, grep, grepl,
> intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
> order,
> paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
> rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
> unique, unlist, unsplit
>
> Loading required package: S4Vectors
> Loading required package: stats4
> Loading required package: IRanges
> Loading required package: XVector
>
> You do not need Biostrings to use read.newick.
> Note there is also read.tree in ape package reading trees in Newick format.
>
> > Thanks a lot for any useful answer!
> >
> > Gabriela, Charles University in Prague
>
> Sincerely,
> Vojtěch
>
> --
> Vojtěch Zeisek
> http://trapa.cz/en/
>
> Department of Botany, Faculty of Science
> Charles University in Prague
> Benátská 2, Prague, 12801, CZ
> http://botany.natur.cuni.cz/en/
>
> Institute of Botany, Academy of Science
> Zámek 1, Průhonice, 25243, CZ
> http://www.ibot.cas.cz/en/
>
> Czech Republic
>
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