Error in unzip(file, exdir = tmp) : ‘exdir’ does not exist
gitIssues2018 opened this issue · 5 comments
Sorry, I think I have finally found the correct platform to submit a qiime2R issue.
Hello, I have installed the qiime2R package into R on my windows machine. I am able to successfully run commands which only have a single argument since I can designate the exdir path. The following two commands work fine.
otus<-read_qza(“table.qza” , tmp=“C:\tmp”)
otus<-read_qza(“table.qza” , tmp=“C:/tmp”)
When I run the qza_to_phyloseq command…
physeq<-qza_to_phyloseq(“table.qza”,“rooted-tree.qza”,“taxonomy.qza”, “sample-metadata.tsv”)
I receive the the error…
Error in unzip(file, exdir = tmp) : ‘exdir’ does not exist
How best can the exdir be designated in a windows R environment?
Hi there,
Apologies for the delay, I can make this option available for the qza_to_phyloseq function. In the meanwhile you can build the object manually as outlined in the readme or qiime community tutorial.
Jordan
I have added the tmp argument to qza_to_phyloseq which should fix your issue on windows now.
Jordan
physeq<-qza_to_phyloseq("table.qza","rooted-tree.qza","taxonomy.qza", "sample-metadata.tsv")
Error in unzip(file, exdir = tmp, list = TRUE) :
zip file 'table.qza' cannot be opened
In addition: Warning message:
In unzip(file, exdir = tmp) : error 1 in extracting from zip file
tree<-read_qza("rooted-tree.qza", tmp="C:\tmp")
Error in unzip(file, exdir = tmp, list = TRUE) :
zip file 'rooted-tree.qza' cannot be opened
In addition: Warning message:
In unzip(file, exdir = tmp) : error 1 in extracting from zip file
Can you create a new folder in your current working directory called testfolder then try with tmp="testfolder" and tell me if it still is throwing an error? My apologies I do not have a windows (i'm assuming its windows) machine to test on.
specifically try:
dir.create("testfolder")
tree<-read_qza("rooted-tree.qza", tmp="testfolder")