could not find function "%>%"

[alvinopler]

in R 4.3.2 GUI 1.80 Big Sur ARM build (8281)
I get the error :
Error in seq(min(values(CHM_g), na.rm = T) + min_H, max(values(CHM_g), :
could not find function "%>%"
chm is from lidR

[DijoG]

Have you required tidyverse? require(tidyverse)

…

On Mon, 17 Jun 2024, 16:27 alvinopler, ***@***.***> wrote: in R 4.3.2 GUI 1.80 Big Sur ARM build (8281) I get the error : Error in seq(min(values(CHM_g), na.rm = T) + min_H, max(values(CHM_g), : could not find function "%>%" chm is from lidR — Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIGOLAZTJK765MFH352B4Y3ZH3W5NAVCNFSM6AAAAABJOD7HZGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM2TONBZGQ3TIMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[alvinopler]

Yes ! I loaded all libraries, now getting another error:
Error in (function (cond) :
error in evaluating the argument 'x' in selecting a method for function 'deepcopy': subscript out of bounds

[DijoG]

Can you provide a reproducible R code with the example chm data (I think it is accessible via the lidR library). Out of boundary-error can hint at terra objects (vect or rast) that are not properly read in. I will be able to check your issue on Sunday, am on vacation without my laptop.

…

On Tue, 18 Jun 2024, 10:16 alvinopler, ***@***.***> wrote: Yes ! I loaded all libraries, now getting another error: Error in (function (cond) : error in evaluating the argument 'x' in selecting a method for function 'deepcopy': subscript out of bounds — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIGOLA4KYGHSWLBN5Y5KVYLZH7UGFAVCNFSM6AAAAABJOD7HZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZVGQ4DQNRYHA> . You are receiving this because you commented.Message ID: ***@***.***>

[alvinopler]

R version: 4.3.3
terra 1.7.78
lidR 4.1.1

library(lidR)
library(terre)
library(tidyverse)
library(sf)
library(data.table)
library(crayon)

LASfile <- system.file("extdata", "MixedConifer.laz", package="lidR")
las <- readLAS(LASfile, select = "xyzr", filter = "-drop_z_below 0")
chm <- rasterize_canopy(las, 0.5, pitfree(subcircle = 0.2))
ttops <- get_TREETOPS(chm, 3)

Error in (function (cond) :
error in evaluating the argument 'x' in selecting a method for function 'deepcopy': subscript out of bounds

at every step of library I tried and it does not work giving the same error (except when loading tidyverse)

[DijoG]

There was a small compatible issue with terra::cells().
It should work now.

Please try:

remove.packages("TREETOPS")
devtools::install_github("DijoG/TREETOPS")

library(lidR)
library(terra)
library(tidyverse)
library(sf)
library(data.table)
library(crayon)

LASfile <- system.file("extdata", "MixedConifer.laz", package="lidR")
las <- readLAS(LASfile, select = "xyzr", filter = "-drop_z_below 0")
chm <- rasterize_canopy(las, 0.5, pitfree(subcircle = 0.2))
plot(chm)
ttops <- TREETOPS::get_TREETOPS(chm, 25)
points(vect(ttops))

[alvinopler]

Perfect thanks a lot !

[alvinopler]

Actually (sorry about that) got an error in finalize_treetops:

fttops <- TREETOPS::finalize_TREETOPS(ttops, 5, 5)
Error in st_as_sf():
ℹ In argument: ..2 = Z.
Caused by error:
! object 'Z' not found
Run rlang::last_trace() to see where the error occurred.

[DijoG]

Am truly sorry for the late reply, I completely missed the e-mail containing your request sent by github.

I forgot to adjust terra::cells() output attribute in the get_MARKER() function. It is done and
finalize_TREETOPS() works again.

All you have to do is:
remove.packages("TREETOPS")
devtools::install_github("DijoG/TREETOPS")

Thank you very much for using the tool and pointing out its errors!
Please let me know whether it works and I can close your issue.

Best,
Gergo