Error installing rTASSEL

[Eduardo Beche]

I am using the source

if (!require("devtools")) install.packages("devtools")
  devtools::install_github(
    repo = "maize-genetics/rTASSEL",
    ref = "master",
    build_vignettes = TRUE,
    dependencies = TRUE
  )

ERROR MESSAGE BELOW

The downloaded binary packages are in C:\Users\RDBECHEED\AppData\Local\Temp\RtmpInRJ4q\downloaded_packages ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file 'C:\Users\RDBECHEED\AppData\Local\Temp\RtmpInRJ4q\remotes289c9014b2b\maize-genetics-rTASSEL-80e7c0e/DESCRIPTION' (447ms) ─ preparing 'rTASSEL': (3.5s) ✔ checking DESCRIPTION meta-information ... ─ installing the package to build vignettes (383ms) ----------------------------------- ─ installing *source* package 'rTASSEL' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace 'S4Arrays' 1.0.5 is being loaded, but >= 1.1.1 is required Calls: <Anonymous> ... asNamespace -> loadNamespace -> namespaceImport -> loadNamespace Execution halted ERROR: lazy loading failed for package 'rTASSEL' ─ removing 'C:/Users/RDBECH~1/AppData/Local/Temp/Rtmpw3l7kF/Rinst95fc721b5244/rTASSEL' ----------------------------------- ERROR: package installation failed Error: Failed to install 'rTASSEL' from GitHub: ! System command 'Rcmd.exe' failed In addition: There were 18 warnings (use warnings() to see them)

[Brandon Monier]

Hi Eduardo,

To make sure this is not a problem with compiling the local vignettes (by the way, all of these are hosted on our site, rtassel.maizegenetics.net), can you run this simplified version of your command? See below:

devtools::install_github("maize-genetics/rTASSEL")

Best,

Brandon M.

[Eduardo Beche]

if (!require("devtools")) install.packages("devtools")

devtools::install_github("maize-genetics/rTASSEL")

If I use the code above the following error shows up

The downloaded binary packages are in C:\Users\RDBECHEED\AppData\Local\Temp\Rtmp65vV8b\downloaded_packages Warning message: package ‘devtools’ was built under R version 4.3.2 > devtools::install_github("maize-genetics/rTASSEL") Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘htmltools’ 0.5.5 is already loaded, but >= 0.5.7 is required

Thanks,

Eduardo

[Brandon Monier]

Looks like one of the dependencies needs at least version 0.5.7 of htmltools, so updating that package should solve that error message.

Best,

Brandon M.

[Brandon Monier]

Regarding your rJava installation issue: This may be a 32-bit vs. 64-bit version conflict. Can you check what version of R you are running on your machine:

Sys.info()[["machine"]]

...you should see something like "x86_32" or "x86_64" being 32-bit and 64-bit, respectively.

[Eduardo Beche]

Sys.info()[["machine"]] [1] "x86-64"

Looks like I have an x86-64, should I reinstall Java or rJava?

[Eduardo Beche]

installing *source* package 'rTASSEL' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error: .onLoad failed in loadNamespace() for 'rJava', details: call: fun(libname, pkgname) error: JAVA_HOME cannot be determined from the Registry Execution halted ERROR: lazy loading failed for package 'rTASSEL' ─ removing 'C:/Users/RDBECH~1/AppData/Local/Temp/RtmpicBaik/Rinst60701c3b5c2d/rTASSEL' ----------------------------------- ERROR: package installation failed Error: Failed to install 'rTASSEL' from GitHub: ! System command 'Rcmd.exe' failed

[Brandon Monier]

It looks like you have a 64-bit version of R installed. I suggest reinstalling Java to ensure you also have a compatible 64-bit version of that. Places like adoptium.com are great for getting OpenJDK binaries automatically tailored to your system.