issues installing version 0.99.20 about qiime2r HOT 10 CLOSED

This ended up working! The folder was within another folder of the same name once it was unzipped, so I think that was giving me some issues before.
In case it is useful to anyone else, the command that worked was
devtools::install(pkg = "C:/Users/Emilie/Documents/qiime2R-master/qiime2R-master")
Thanks so much for your help :)

from qiime2r.

Hi Emilie, I'm not sure why this didn't work for you. One idea: perhaps the quotation marks are copy/pasting oddly into your session. Alternatively, there is something off with the network connection of the computer you are trying to install on. You can get around this by downloading the source of the package and then installing manually as detailed here. Let me know if this works for you.

from qiime2r.

Thanks for the speedy reply! I was able to download the file, and then I tried install.packages("qiime2R-master.zip", repos=NULL, type="source") (after changing my working directory to downloads, as that is where the file is).
The only feedback on the screen was Installing package into ‘C:/Users/Emilie/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified)
But the package doesn't show up in my list of packages, and I can't load the library. So I don't think it worked. I've never installed a package this way before, so maybe I'm missing something else?

from qiime2r.

It is strange that there would be no error message but you could try manually installing the dependencies using install.packages() and BiocManager::install() and then try reinstalling again. You could also take a step back and look at using devtools::install_github(). Do you have a working install of devtools?

from qiime2r.

All the dependencies listed for it on github I have installed. I tried again with install.packages("../Downloads/qiime2R-master.zip", repos=NULL, type="source")
No error message. I can see the folder in C:\Users\Emilie\Documents\R\win-library\3.6, (as a qiime2R-master folder) but it does not show up in the list of packages with library().

I tried your suggestion of using devtools. I installed that package today (an downloaded RTools) and then loaded it via library, then:
> install_github("jbisanz/qiime2R") Downloading GitHub repo jbisanz/qiime2R@master Error in utils::download.file(url, path, method = method, quiet = quiet, : cannot open URL 'https://api.github.com/repos/jbisanz/qiime2R/tarball/master'
At least there is an error message this time.
Though I tried again (new R session) and got this

 > library(devtools)
Loading required package: usethis
> install_github("jbisanz/qiime2R")
Error: Failed to install 'unknown package' from GitHub:
  Timeout was reached: [api.github.com] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received

from qiime2r.

I also just tried with BiocManager
BiocManager::install("qiime2R")
It asked me to update some packages:
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29) Installing package(s) 'qiime2R' Installation path not writeable, unable to update packages: class, foreign, lattice, nlme, nnet, survival Old packages: 'igraph', 'locfit', 'Rcpp'
I said update all, and it did that but then there was this: Warning message: package ‘qiime2R’ is not available (for R version 3.6.3)
Is my R version the issue?

from qiime2r.

I don't think the issue is with your version of R (and note that qiime2R is not in bioconductor so the BiocMAnager::install("qiime2R") wouldn't be expected to work. Maybe try unzipping master.zip and then running: install.packages("qiime2R-master", repos=NULL, type="source").

from qiime2r.

Hello Jordan
I moved the zip folder to my default working directory (Documents) and then unzipped it. I then tried to command as suggested:install.packages("qiime2R-master", repos=NULL, type="source")
I got a different error message this time:
Installing package into ‘C:/Users/Emilie/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) Warning: invalid package 'qiime2R-master' Error: ERROR: no packages specified Warning in install.packages : installation of package ‘qiime2R-master’ had non-zero exit status
And I can see it did not get installed into the library.

So I tried with the zip file (in Documents this time) and it installed it , but R doesn't recognize it as a valid package. I tried this both in R studio and in R itself. The folder is installed in C:/Users/Emilie/Documents/R/win-library/3.6 but when I try to load it, I get the same message I saw before: library('qiime2R-master')
Error in library("qiime2R-master") : there is no package called ‘qiime2R-master’
I thought maybe the hyphen was the issue, so I changed the folder name and tried again:
library('qiime2R')
Error in library("qiime2R") : ‘qiime2R’ is not a valid installed package
So I think R isn't recognizing it as a valid package for some reason.

from qiime2r.

Installing package into ‘C:/Users/Emilie/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) Warning: invalid package 'qiime2R-master' Error: ERROR: no packages specified Warning in install.packages : installation of package ‘qiime2R-master’ had non-zero exit status

Probably means it could not find the folder. If you use list.files() do you see it listed in your working directory? If not use setwd() to change to the directory that contains the qiime2R-master. Idea: try removing the folder from C:/Users/Emilie/Documents/R/win-library/3.6. Then try installing the package as:

devtools::install("C:\\path\to\qiime2R-master")

from qiime2r.

I had the same problem with R4.0.1 on Windows10.
It was solved when I tried the last command you shared as below.
devtools::install("C:/Users/maruyama/Documents/qiime2R-master/")
Thank you for the very helpful information!

from qiime2r.