Klaus Schliep mentioned this and a solution in a post in December:
https://stat.ethz.ch/pipermail/r-sig-phylo/2015-December/004478.html
>From the post:
> To solve the problem simply install the Biostrings package first
>
> source("http://bioconductor.org/biocLite.R";)
> biocLite("Biostrings")
>
> and in a fresh session of R try again to install phytools or phangorn.
>
>
On Sat, Jan 9, 2016 at 1:29 PM, Donald Miles <urosau...@gmail.com> wrote:
> 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 <vo...@trapa.cz> 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
> >
> > _______________________________________________
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at
> > http://www.mail-archive.com/r-sig-phylo@r-project.org/
> >
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
William Gearty
PhD Student, Paleobiology
Department of Geological Sciences
Stanford School of Earth, Energy & Environmental Sciences
people.stanford.edu/wgearty
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
