‘TreeLS’ is not available (for R version XYZ)

[mansi-aggarwal-2504]

I have been trying to install this package since a long time now and I keep getting this error: Installing package into ‘/usr/local/lib/R/site-library’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘TreeLS’ is not available (for R version 4.0.2)

Also, the package has been removed from CRAN. I am all trying to get install it using devtools::install_github('tiagodc/TreeLS', ref='old') but no luck.

How can I use this package in R now?

[amygresham]

You can install the package to an older version of R by changing the version of R you are using in the global options.

[Jean-Romain]

but no luck.

What does it mean? What is the error message?

[mansi-aggarwal-2504]

You can install the package to an older version of R by changing the version of R you are using in the global options.

@amygresham I tried to install it to older versions also. It didn't work. I get the same error: Warning in install.packages : package ‘TreeLS’ is not available (for R version 3.6.2)

What does it mean? What is the error message?

@Jean-Romain I get an error like this: installation of package had non-zero exit status

I managed when I copied the library from the lib path of a system I was using TreeLS on, and pasted the folder to the new VM and it worked somehow. But this is a workaround. I want to know what the reason for this problem is, if anyone could tell.

[Jean-Romain]

installation of package had non-zero exit status

This is not the error. This is only the "conclusion". You have an error displayed somewhere in the output of the installation

[mansi-aggarwal-2504]

@Jean-Romain I was somehow able to reproduce the error while using devtools::install_github('tiagodc/TreeLS') Please let me know if this helps:

`Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rgl/libs/rgl.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rgl/libs/rgl.so
  Reason: image not found
Error: .onLoad failed in loadNamespace() for 'rgl', details:
  call: NULL
  error:    Loading rgl's DLL failed. 
    On MacOS, rgl depends on XQuartz, which you can download from xquartz.org.
Execution halted
ERROR: lazy loading failed for package ‘TreeLS’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/TreeLS’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/TreeLS’
Error: Failed to install 'TreeLS' from GitHub:
  (converted from warning) installation of package ‘/var/folders/vp/s7zhrkrd3x954qk3xw00krxc0000gn/T//Rtmp7WKwiW/file302a1db54e59/TreeLS_1.0.1.tar.gz’ had non-zero exit status`

[Jean-Romain]

Never seen that. It seems that your installation of rgl is incorrect and it seems to be a MacOS specific issue.

[amygresham]

I have been having the same issue. I am only able to access TreeLS on an earlier version of R because I installed it before it was removed from CRAN. As far as I can see, the package is no longer available for download.

If you google the CRAN documentation for TreeLS this text appears:

"Package ‘TreeLS’ was removed from the CRAN repository.

Formerly available versions can be obtained from the archive.

Archived on 2020-07-05 as check issues were not corrected in time.

Please use the canonical form https://CRAN.R-project.org/package=TreeLS to link to this page."

[stefanoch90]

Hello, I have the same problem too, it says so: Warning in install.packages : package ‘TreeLS’ is not available (for R version 4.0.2). How can i solve this issue? I have installed it in Windows 10.

[Jean-Romain]

The package is no longer on CRAN for the moment. There is nothing to "fix" on the user side. You can install it from the source.

[stefanoch90]

Thank you for the quick reply. Can you advise me what procedure to do to install from the source?

[Jean-Romain]

https://stackoverflow.com/questions/1474081/how-do-i-install-an-r-package-from-source

[stefanoch90]

Thank you very much. Where can I find the package file to download?

[Jean-Romain]

Have you read the README?

[stefanoch90]

Hi, i have followed your suggests and now i can processing my .LAS file with the TreeLs library. I thank you for your kindness.

[mansi-aggarwal-2504]

Hi, i have followed your suggests and now i can processing my .LAS file with the TreeLs library. I thank you for your kindness.

Hello, @stefanoch90, could you tell what worked for you? Did you check the archive file from CRAN page " Formerly available versions can be obtained from the archive. " and installed library from source?

EDIT Tried using install_github and got an error:

`trying URL 'https://cran.rstudio.com/src/contrib/sf_0.9-5.tar.gz'
Content type 'application/x-gzip' length 9001885 bytes (8.6 MB)
downloaded 8.6 MB

Error in strptime(xx, f, tz = tz) : 
  (converted from warning) unable to identify current timezone 'C':
please set environment variable 'TZ'
Error: Failed to install 'TreeLS' from GitHub:
  (converted from warning) installation of package ‘sf’ had non-zero exit status`

[stefanoch90]

Hello @mansi-aggarwal-2504 , i have followed the following list:

• devtools: run install.packages('devtools', dependencies = TRUE) from the R console;
• Rcpp compiler: on Windows: install Rtools for your R version - make sure to add it to your system's path (because i have got Windows 10);
• devtools::install_github('tiagodc/TreeLS')
• library(TreeLS). I made in this way and now i can work in an efficiently way.

[tiagodc]

Hi there, TreeLS is out of CRAN at the moment indeed, I already reviewed and fixed all dependency issues, most of the documentation and have a few tweaks and tests to do, but I intend to release a new version still this month. Sorry about the inconveniences and thanks @Jean-Romain for helping out!