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jbisanz / qiime2R

Import qiime2 artifacts to R
MIT License
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Issue Installing qiime2R on R4.0.4 #35

Open angepoch opened 3 years ago

angepoch commented 3 years ago

Hello,

I've had a lot of issues trying to install this package into RStudio (4.0.4). I am currently working in Windows 10 and here are the steps I've taken.

1) Using if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")} devtools::install_github("jbisanz/qiime2R") I receive this message:

Downloading GitHub repo jbisanz/qiime2R@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update? 1: All
2: CRAN packages only
3: None
4: ade4 (1.7-17 -> 1.7-18) [CRAN] Enter one or more numbers, or an empty line to skip updates: 2 ade4 (1.7-17 -> 1.7-18) [CRAN] Installing 1 packages: ade4 Installing package into ‘C:/Users/angel/OneDrive/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) There is a binary version available but the source version is later: binary source needs_compilation ade4 1.7-17 1.7-18 TRUE trying URL 'http://cran.rstudio.com/bin/windows/contrib/4.0/ade4_1.7-17.zip' Content type 'application/zip' length 5226980 bytes (5.0 MB) downloaded 5.0 MB package ‘ade4’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\angel\AppData\Local\Temp\Rtmp69Vana\downloaded_packages Error: Failed to install 'qiime2R' from GitHub: System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr empty

2) Then I tried downloading it from the source using download.file("https://github.com/jbisanz/qiime2R/archive/master.zip", "source.zip") unzip("source.zip") install.packages("qiime2R-master", repos = NULL, type="source")

Getting an error saying:

Installing package into ‘C:/Users/angel/OneDrive/Documents/R/win-library/4.0’ (as ‘lib’ is unspecified) Warning in install.packages : installation of package ‘qiime2R-master’ had non-zero exit status

3) I tried unzipping the master file myself and using devtools::install("C:/Users/angel/OneDrive/Documents/qiime2R-master/"), but I still receive

Error in (function (command = NULL, args = character(), error_on_status = TRUE, : System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr empty

I made sure to have Rtools installed and pathed correctly and am still receiving the same errors. Please advise on what I could do about this!

BisanzLab commented 3 years ago

I have the sneaking suspicion it is because you are trying to install it on to a onedrive shared folder. I have seen this cause issues before. Try changing your library to a local folder and I suspect your problem will go away.