Dne So 9. ledna 2016 13:29:46, Donald Miles napsal(a):
> 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’
Did You recently (I mean prior past usage of phytools/Biostrings) update to R
3.2.X from R 3.1.X or earlier version? If yes, You have to reinstall packages
(well, some do not require so, but it seems to be safer to do it). This may be
bit painful procedure and it is little bit silly. Well, at least I, as using
source packages, must to it.
I usually do something like
packages <- installed.packages()[,"Package"]
install.packages(pkgs=packages, repos=c("http://cran.at.r-project.org";,
"http://cran.at.r-project.org";, "http://R-Forge.R-project.org";,
"http://cran.rstudio.com/";, "http://www.rforge.net/";,
"http://bioconductor.statistik.tu-dortmund.de/packages/3.2/bioc";,
"http://bioconductor.statistik.tu-dortmund.de/packages/3.2/data/annotation";,
"http://bioconductor.statistik.tu-dortmund.de/packages/3.2/data/experiment";,
"http://bioconductor.statistik.tu-dortmund.de/packages/3.2/extra";,
"http://www.stats.ox.ac.uk/pub/RWin";, "http://www.omegahat.org/R";,
"http://rkward.sf.net/R/";, "http://files.kde.org/rkward/R/";), lib="~/R/x86_64-
suse-linux-gnu-library/3.2", dependencies="Enhances", clean=TRUE)
update.packages(lib.loc="~/R/x86_64-suse-linux-gnu-library/3.2/",
repos=c("http://cran.at.r-project.org";, "http://cran.at.r-project.org";,
"http://R-Forge.R-project.org";, "http://cran.rstudio.com/";,
"http://www.rforge.net/";,
"http://bioconductor.statistik.tu-dortmund.de/packages/3.2/bioc";,
"http://bioconductor.statistik.tu-dortmund.de/packages/3.2/data/annotation";,
"http://bioconductor.statistik.tu-dortmund.de/packages/3.2/data/experiment";,
"http://bioconductor.statistik.tu-dortmund.de/packages/3.2/extra";,
"http://www.stats.ox.ac.uk/pub/RWin";,
"http://www.omegahat.org/R";, "http://rkward.sf.net/R/";,
"http://files.kde.org/rkward/R/";), instlib="~/R/x86_64-suse-linux-gnu-
library/3.2/", ask=FALSE, dependencies=“Enhances“)
Note I have little bit long list of repositories including R-Forge,
Bioconductor etc. You can shorten it of course. :-) And You'd need to modify
instlib according to Your placement.
> I am running R v 3.2.3 and phytools v 0.5-10.
$ R --version
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
> packageVersion("phytools")
[1] ‘0.5.10’
> packageVersion("Biostrings")
[1] ‘2.38.3’
And I do not see any dependency for Biostrings in phytools...
> 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
Vojtěch
> 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
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