Add notebook showing COPC access in R using lasR by omshinde · Pull Request #576 · MAAP-Project/maap-documentation

omshinde · 2026-04-13T21:14:09Z

Addresses NASA-IMPACT/science-support#25

Install devel branch of lasR and from r-universe into hub image
Test partial read of COPC
Write a notebook in anticipation of release
plan for next R workspace release after this lands in released version
provide feedback if any bugs found

review-notebook-app · 2026-04-13T21:14:16Z

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wildintellect · 2026-04-13T23:12:27Z

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Make sure it's clear this only works on the MAAP Hub, and the R pyrocket-geospatial workspace.

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wildintellect · 2026-04-13T23:12:27Z

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Line #14. dyn.load("/srv/conda/envs/notebook/lib/libgdal.so.36"),
Hmm, what image are you working in? on pyrocket-geospatial this should not be using conda.

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I removed this part to avoid confusion. It was forcing the libgdal from conda to resolve package dependency issues. Thanks

hrodmn · 2026-04-14T16:39:08Z

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Line #8. # Fetch first page of items (limit=10 to get a representative sample)
We should use rstac to do STAC queries in R!

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Thanks. Updated

hrodmn · 2026-04-14T16:39:08Z

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What is going on with these bounding boxes? the lon values are out of bounds.

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They are in local coordinate reference system.

hrodmn · 2026-04-14T16:39:08Z

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+{


Line #6. full <- exec(reader_las() + summarise(), on = url)
is exec a lasR function?

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Yes. It's the pdal's pipeline.execute equivalent for lasR. Updated the code to specifically show lasR::exec()

omshinde · 2026-04-16T16:55:32Z

@wildintellect @hrodmn Thanks for the comments. I updated the notebook and requested re-review.

wildintellect · 2026-04-16T20:45:41Z

@omshinde how did you get lasR upgraded install to work? when I tried to build it takes a long time, and then links to the conda gdal which causes issues.

omshinde · 2026-04-16T21:51:51Z

I tested it again in a fresh R image and it works wit the following commands-

Notebook

# Install lasR 0.20.0 from r-universe
install.packages(
  "lasR",
  repos = c("https://r-lidar.r-universe.dev", "https://cloud.r-project.org")
)

Verify

library(lasR)
packageVersion("lasR")  # should return 0.20.0

From terminal

Rscript -e "install.packages('lasR', repos = c('https://r-lidar.r-universe.dev', 'https://cloud.r-project.org'))"

Verify:

Rscript -e "library(lasR); cat(as.character(packageVersion('lasR')), '\n')"

wildintellect · 2026-04-17T21:19:03Z

It's building against the conda versions of packages, which we don't want.

checking for gdal-config... /srv/conda/envs/notebook/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.10.2
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc -std=gnu2x
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /srv/conda/envs/notebook/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available for running:... yes
configure: GDAL: 3.10.2
configure: pkg-config proj exists, will use it
configure: using proj.h.
configure: PROJ: 9.4.0
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes
checking for geos-config... /srv/conda/envs/notebook/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.13.1
checking GEOS version >= 3.4.0... yes
checking for geos_c.h... yes
checking geos: linking with -L/srv/conda/envs/notebook/lib -lgeos_c... yes

omshinde · 2026-04-17T21:26:28Z

This is what I see-

(notebook) jovyan@jupyter-omshinde23--r-test:~$ Rscript -e "install.packages('lasR', repos = c('https://r-lidar.r-universe.dev', 'https://cloud.r-project.org'))"
Use py_require() for Python interoperability without altering PATH.
Use use_condaenv('notebook') to use conda environment but this will alter PATH and may break R functions.
Restart R to reset PATH or store PATH before calling use_condaenv('notebook') and restore when done.
python:         /srv/conda/envs/notebook/bin/python
libpython:      /srv/conda/envs/notebook/lib/libpython3.12.so
pythonhome:     /srv/conda/envs/notebook:/srv/conda/envs/notebook
version:        3.12.12 | packaged by conda-forge | (main, Oct 22 2025, 23:25:55) [GCC 14.3.0]
numpy:          /srv/conda/envs/notebook/lib/python3.12/site-packages/numpy
numpy_version:  2.3.5

NOTE: Python version was forced by use_python() function
Installing package into ‘/home/jovyan/R/x86_64-pc-linux-gnu-library/4.5’
(as ‘lib’ is unspecified)
trying URL 'https://r-lidar.r-universe.dev/src/contrib/sha256-0fa743c14663c2fffc66c4742ba4fe770b8969ea8a28879035ee3813019bba16'
Content type 'application/gzip' length 27180486 bytes (25.9 MB)
==================================================
downloaded 25.9 MB

Use py_require() for Python interoperability without altering PATH.
Use use_condaenv('notebook') to use conda environment but this will alter PATH and may break R functions.
Restart R to reset PATH or store PATH before calling use_condaenv('notebook') and restore when done.
python:         /srv/conda/envs/notebook/bin/python
libpython:      /srv/conda/envs/notebook/lib/libpython3.12.so
pythonhome:     /srv/conda/envs/notebook:/srv/conda/envs/notebook
version:        3.12.12 | packaged by conda-forge | (main, Oct 22 2025, 23:25:55) [GCC 14.3.0]
numpy:          /srv/conda/envs/notebook/lib/python3.12/site-packages/numpy
numpy_version:  2.3.5

NOTE: Python version was forced by use_python() function
ERROR: failed to lock directory ‘/home/jovyan/R/x86_64-pc-linux-gnu-library/4.5’ for modifying
Try removing ‘/home/jovyan/R/x86_64-pc-linux-gnu-library/4.5/00LOCK-lasR’

The downloaded source packages are in
        ‘/tmp/Rtmp2CgHFh/downloaded_packages’
Warning message:
In install.packages("lasR", repos = c("https://r-lidar.r-universe.dev",  :
  installation of package ‘lasR’ had non-zero exit status
(notebook) jovyan@jupyter-omshinde23--r-test:~$ Rscript -e "library(lasR); cat(as.character(packageVersion('lasR')), '\n')"
Use py_require() for Python interoperability without altering PATH.
Use use_condaenv('notebook') to use conda environment but this will alter PATH and may break R functions.
Restart R to reset PATH or store PATH before calling use_condaenv('notebook') and restore when done.
python:         /srv/conda/envs/notebook/bin/python
libpython:      /srv/conda/envs/notebook/lib/libpython3.12.so
pythonhome:     /srv/conda/envs/notebook:/srv/conda/envs/notebook
version:        3.12.12 | packaged by conda-forge | (main, Oct 22 2025, 23:25:55) [GCC 14.3.0]
numpy:          /srv/conda/envs/notebook/lib/python3.12/site-packages/numpy
numpy_version:  2.3.5

NOTE: Python version was forced by use_python() function
0.20.0 
(notebook) jovyan@jupyter-omshinde23--r-test:~$ Rscript -e "library(lasR); cat(as.character(packageVersion('lasR')), '\n')"

omshinde · 2026-04-20T18:23:26Z

MoM from lasR discussion with Sam G.

Tidyverse, terra, lasR, ~~lidR~~ should be enough for processing
R scripts working with Quarto and proposed package

Actions:

Rajat to look into custom image options for lasR setup. tracked here Create custom image for lasR latest version in MAAP Pyrocker geospatial R image maap-workspaces#203
TBD on MAAP default image

wildintellect · 2026-04-20T22:53:41Z

@omshinde let's move the install/container image with lasR to it's own ticket in a workspace related repo.

omshinde · 2026-04-28T20:34:10Z

@HarshiniGirish @hrodmn @wildintellect Are there any more comments on this doc (not worrying about the installation)? Thanks

HarshiniGirish · 2026-04-28T21:00:12Z

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+{


Line #3. install.packages("rstac", repos = "https://cloud.r-project.org")
already had a dependency cell earlier. do we need it?

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HarshiniGirish · 2026-04-28T21:00:12Z

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+{


Line #3. url <- "/vsis3/nasa-maap-data-store/file-staging/nasa-map/GEDI_CalVal_Lidar_COPC/usa_tepeecreek_2809704010602.copc.laz"
do we need to hardcode this as it is connected to the STAC discovery step

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HarshiniGirish · 2026-04-28T21:04:57Z

looks good to me. just came across 2 minor suggestions, feel free to ignore them @omshinde

wildintellect · 2026-04-28T21:21:37Z

I think we should close this PR. Even with the fixes it's not actually usable by users without us providing a permalink to boot the correct custom image. We're also not clearly showing the times - so we're sort of half solving the 2 things we need.

How to use lasR on MAAP to read COPC efficiently
Demonstrating efficient use of COPC vs previous methods

We can then rework in stages, what's ready for release and what's not. This might have been premature when all we wanted was to prove COPC access works as expected with the latest library.

Add COPC access in R using lasR

f1a0fdc

omshinde requested review from HarshiniGirish and wildintellect April 13, 2026 21:14

omshinde self-assigned this Apr 13, 2026

omshinde requested a review from hrodmn April 13, 2026 21:15

wildintellect reviewed Apr 13, 2026

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hrodmn reviewed Apr 14, 2026

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update COPC access in R notebook

1282aff

omshinde requested review from hrodmn and wildintellect April 16, 2026 16:54

omshinde mentioned this pull request Apr 28, 2026

Test lasR remote read capability NASA-IMPACT/science-support#25

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HarshiniGirish reviewed Apr 28, 2026

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HarshiniGirish approved these changes Apr 28, 2026

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omshinde closed this Apr 29, 2026

omshinde reopened this Apr 29, 2026

omshinde mentioned this pull request Apr 29, 2026

Add MAAP documentation showing COPC access in R using lasR NASA-IMPACT/science-support#35

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