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caitiecollins / treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
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Launching error TreeWas #35

Closed sekhwal closed 5 years ago

sekhwal commented 5 years ago

install.packages("devtools", dep=TRUE) #################ERROR################## Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning message in install.packages("devtools", dep = TRUE): “'lib = "/usr/local/lib/R/site-library"' is not writable” Error in install.packages("devtools", dep = TRUE): unable to install packages Traceback:

  1. install.packages("devtools", dep = TRUE)
  2. stop("unable to install packages") ############################################################ install_github("caitiecollins/treeWAS", build_vignettes = TRUE)

Error in install_github("caitiecollins/treeWAS", build_vignettes = TRUE): could not find function "install_github" Traceback:

xavierdidelot commented 5 years ago

This looks like an error when trying to install devtools, which is a prerequisite to installing treeWAS. It might help to specify where packages are installed, using the lib argument of the "install.packages function, see for example details at https://www.rdocumentation.org/packages/utils/versions/3.6.0/topics/install.packages

sekhwal commented 5 years ago

Hi, I want to load my data by following commands to RUN treeWAS, it is showing error.

Load example data:

data(sequence.fasta) data(phenotype) data(seq.newick)

Warning message in data(sequence.fasta): “data set ‘sequence.fasta’ not found”

Could you please suggest me steps to run treeWAS. I have a sequence file, a tree file and a phenotype file.

Thank you,

On Thu, May 9, 2019 at 12:46 AM Xavier Didelot notifications@github.com wrote:

This looks like an error when trying to install devtools, which is a prerequisite to installing treeWAS. It might help to specify where packages are installed, using the lib argument of the "install.packages function, see for example details at https://www.rdocumentation.org/packages/utils/versions/3.6.0/topics/install.packages

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/caitiecollins/treeWAS/issues/35#issuecomment-490791024, or mute the thread https://github.com/notifications/unsubscribe-auth/AGHR4LR2DRTTLGB25ISUHWDPUPJFNANCNFSM4HKCSDUQ .

xavierdidelot commented 5 years ago

See the read.FASTA function of the ape package to read a fasta file into R, and the read.tree function to read trees.