readLAS crashes when reading ALS las files, after previously working

[Joe-StPeter]

I have previously been using the lidR package and it was working great (great work!). However today I simply tried to open an airborne las file and the R sessions crashed. Here is the code, it ain't complicated.

library(lidR)
las = readLAS("Las_files/e1054n0839.las")

I have uploaded the example las file here.

This crashes the R session, either in R or R studio (grey bomb). I have tried to open multiple airborne LiDAR las files from this same dataset and they all crash R. However, when I open much larger las files (100 times larger) from a different project they load into R just fine. I have updated my R version to 3.6.2, updated to the latest version of lidR, checked my filepaths, had the las file on my C drive, and on an external hard drive, doesn't matter.

I have checked the las files in other programs such as PDQ viewer and ArcGIS and they look fine and perform fine in those software programs. And like I said everything was working fine yesterday. I would also note that I had similar experience on a different computer, when I tried to readLAS or put into a las catalog the session crashed. I would be happy to learn that this behavior is due to something I, the user, is doing.

[Jean-Romain]

This file is read on my computer GNU/linux, rlas v1.3.5. Please check your version of rlas. Check also your version of lidR. Current release is 2.2.2

[Joe-StPeter]

Thanks for the quick reply. Both rlas and lidR are updated versions -
other attached packages:

[1] lidR_2.2.2 raster_3.0-12 sp_1.4-0 rlas_1.3.5 

I am sorry this is not reproducing.

[Jean-Romain]

So it is a Windows or Mac specific issue. Please report your sessionInfo()

[Joe-StPeter]

R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lidR_2.2.2    raster_3.0-12 sp_1.4-0      rlas_1.3.5   

loaded via a namespace (and not attached):
[1] compiler_3.6.2    tools_3.6.2       Rcpp_1.0.3        codetools_0.2-16  grid_3.6.2        data.table_1.12.8
[7] lattice_0.20-38 

[Jean-Romain]

I read your file on Windows 7, R 3.5.3 32 bits rlas 1.3.5, lidR 2.2.2

x = rlas::read.las("H://issue46/e1054n0839.las") # ok
x = lidR::readLAS("H:/Téléchargements/issue46/e1054n0839.las") # ok

Then on Windows 7, R 3.6.1 64 bits rlas 1.3.5, lidR 2.2.2

x = rlas::read.las("H://issue46/e1054n0839.las") # ok
x = lidR::readLAS("H:/Téléchargements/issue46/e1054n0839.las") # crash
x = rlas:::stream.las("H://Téléchargements/issue46/e1054n0839.las") # ok

I confirm the bug. However on Windows tools to debug such kind of trouble do not exist so I don't know how and when I will be able to fix it.

Other tests

x = rlas:::stream.las("H://Téléchargements/issue46/e1054n0839.las") # ok
x = rlas:::C_reader("H:/Téléchargements/issue46/e1054n0839.las", "", select = "*", filter = "", filter_wkt = ) # ok

I'm moving the question to lidR it seems it comes from it. Minimal reproducible example:

data =  rlas::read.las("H://Téléchargements/issue46/e1054n0839.las")                   
header= rlas::read.lasheader("H:/Téléchargements/issue46/e1054n0839.las")
las = lidR::LAS(data, header) # crash

[Jean-Romain]

I spotted the issue

header <- rlas::read.lasheader("H:/Téléchargements/issue46/e1054n0839.las")
header <- lidR::LASheader(header)
proj4string <- lidR::projection(header, asText = FALSE)  # crash

[Jean-Romain]

Minimal reproducible example

wkt = "PROJCS[\"NAD83 (2011) / Conus Albers\",GEOGCS[\"GCS_NAD_1983_2011\",DATUM[\"D_NAD_1983_2011\",SPHEROID[\"GRS_1980\",6378137.0,298.257222101,AUTHORITY[\"EPSG\",7019]],AUTHORITY[\"EPSG\",1116]],PRIMEM[\"Greenwich\",0.0,AUTHORITY[\"EPSG\",8901]],UNIT[\"Degree\",0.0174532925199433,AUTHORITY[\"EPSG\",9102]],AUTHORITY[\"EPSG\",6318]],PROJECTION[\"Albers\",AUTHORITY[\"Esri\",43007]],PARAMETER[\"False_Easting\",0.0,AUTHORITY[\"Esri\",100001]],PARAMETER[\"False_Northing\",0.0,AUTHORITY[\"Esri\",100002]],PARAMETER[\"Central_Meridian\",-96.0,AUTHORITY[\"Esri\",100010]],PARAMETER[\"Standard_Parallel_1\",29.5,AUTHORITY[\"Esri\",100025]],PARAMETER[\"Standard_Parallel_2\",45.5,AUTHORITY[\"Esri\",100026]],PARAMETER[\"Latitude_Of_Origin\",23.0,AUTHORITY[\"Esri\",100021]],UNIT[\"Meter\",1.0,AUTHORITY[\"EPSG\",9001]]],VERTCS[\"NAVD_1988\",VDATUM[\"North_American_Vertical_Datum_1988\",AUTHORITY[\"EPSG\",5103]],PARAMETER[\"Vertical_Shift\",0.0,AUTHORITY[\"Esri\",100006]],PARAMETER[\"Direction\",1.0,AUTHORITY[\"Esri\",100007]],UNIT[\"Meter\",1.0,AUTHORITY[\"EPSG\",9001]],AUTHORITY[\"EPSG\",5703]]"
proj4 = rgdal::showP4(wkt)
crs = sp::CRS(proj4)  # crash

I'm closing the issue because it is not related to lidR

[Jean-Romain]

Fixed in v2.2.4

[Joe-StPeter]

Thank you!

[Jean-Romain]

For your information the conclusion is that the coordinate reference in your file is invalid. The issue went upstream to sp edzer/sp#75 then upstream again to libproj OSGeo/PROJ#2022