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
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