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caitiecollins / treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
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install error.. #31

Closed ghost closed 5 years ago

ghost commented 5 years ago 

install.packages("devtools", dep=TRUE)
library(devtools)
install_github("caitiecollins/treeWAS", build_vignettes = TRUE)
library(treeWAS)

Then R says:
ERROR: lazy loading failed for package ‘treeWAS’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/treeWAS’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/treeWAS’
installation of package ‘/var/folders/7g/r76zj5p11tn812ys0v9p89200000gn/T//RtmpsCCHox/file3d41667052cc/treeWAS_1.0.tar.gz’ had non-zero exit status
> library(treeWAS)
Error in library(treeWAS) : there is no package called ‘treeWAS’

I don't know what can i do.. 
help me
sekhwal commented 5 years ago

Same error here .....

xavierdidelot commented 5 years ago

Could you please execute each of the four lines one at a time, and let us know if any error is returned when executing the first line, etc?

sekhwal commented 5 years ago

Hi, I am trying to run following command but showing error..

dna <- read.dna(file = "filename", format = "fasta")

Error in read.dna(file = "/home/science/TreeWas/uniprot.fasta", format = "fasta"): could not find function "read.dna"

Traceback:

Also, please let me know what type of files is required to get the results from TreeWas.

Thank you,

Manoj

On Thu, May 9, 2019 at 12:39 AM Xavier Didelot notifications@github.com wrote:

Could you please execute each of the four lines one at a time, and let us know if any error is returned when executing the first line, etc?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/caitiecollins/treeWAS/issues/31#issuecomment-490789202, or mute the thread https://github.com/notifications/unsubscribe-auth/AGHR4LRLLF6YTJYPAXXENPLPUPIMXANCNFSM4HBKZPCA .

xavierdidelot commented 5 years ago

Maybe you need to first load the R package ape from which the read.dna function comes from? Try: library(ape)

sekhwal commented 5 years ago

Hi,

It is treeWas still showing error with the following command.

tree <- read.nexus(file = "../TreeWas/tree.newick")

error########

Error in start:end: argument of length 0 Traceback:

  1. read.nexus(file = "../TreeWas/tree.newick")

On Fri, May 10, 2019 at 8:42 AM Xavier Didelot notifications@github.com wrote:

Closed #31 https://github.com/caitiecollins/treeWAS/issues/31.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/caitiecollins/treeWAS/issues/31#event-2333504535, or mute the thread https://github.com/notifications/unsubscribe-auth/AGHR4LS3W56MHWP77R7M5GTPUWJW5ANCNFSM4HBKZPCA .

xavierdidelot commented 5 years ago

read.nexus is part of the ape package, not treeWAS, but if your file is in newick format you should use read.tree, also from ape.