Home

Welcome to the preprocessing wiki! Here we add helpful notes and log troubleshooting

Training data sources

NEON site	Inventory source	actual inventory collection year	year_inventory	year_aop	notes
SJER	NEON	2017	2017	2017-03
SJER	NEON	2019	2019	2019-03
SJER	NEON	2021	2021	2021-03
SJER	UCLA	2023	2021	2021-03	using 2021 AOP data until NEON releases 2023 AOP data
SJER	UCLA/AIS	2024	2021	2021-03	using 2021 AOP data until NEON releases 2024 AOP data
SOAP	NEON	2019	2019	2019-06
TEAK	NEON	2021	2021	2021-07
TEAK	UCLA	2023	2021	2021-07	using 2021 AOP data until NEON releases 2023 AOP data
TEAK	UCLA	2024	2021	2021-07	using 2021 AOP data until NEON releases 2024 AOP data, also see shapes from Carissa that didn't overlap with imagery

Notes while troubleshooting workflow

• "Error in library.dynam(lib, package, package.lib) : shared object ‘rlang.dylib’ not found"

  • Solution: updated R version in conda-forge:
  • conda install -c conda-forge r-base=4.1.2
  • Source: https://stackoverflow.com/questions/73104543/how-to-install-different-versions-of-r-e-g-r-4-1-2-in-a-conda-environment

• Error: "rhdf5 library is not installed"

  • Solution: Installed rhdf5 via bioconductor in prismatic conda environment
  • conda install -c bioconda bioconductor-rhdf5
  • Source: https://odin.mdacc.tmc.edu/~wwang7/tutorial_conda.html

• I got this 'dylib' error again but for a different package: "Error in library.dynam(lib, package, package.lib) : shared object ‘dplyr.dylib’ not found"

  • Solution: in the R script where the package is loaded, add a line at the top installing the package (e.g. in line 1, install.packages("dplyr")). Then you can remove this line

• "Error in library(dplyr) : there is no package called ‘dplyr’"

  • Solution: Uninstall and re-install dplyr

• When troubleshooting various errors from rpy2, preceding the function with the package (package::function()) in the R script helped in many cases.

• Error: "/lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.35' not found (required by ./whitebox_tools) "

  • Needed to upgrade GLIBC for whitebox
  • solution source: https://tutorials.tinkink.net/en/linux/how-to-update-glibc.html

• Error: "Error in library.dynam(lib, package, package.lib) : shared object ‘methods.dylib’ not found"

  • solution: to main.py add os.environ['R_HOME'] = os.path.join(os.environ['CONDA_PREFIX'], 'lib/R'), and to inventory.py add import rpy2.robjects as robjects
  • solution source: https://github.com/rpy2/rpy2/issues/882
  • generalized with help from https://stackoverflow.com/questions/36539623/how-do-i-find-the-name-of-the-conda-environment-in-which-my-code-is-running

• Error "6: package ‘methods’ in options("defaultPackages") was not found"

  • Solution: Had conflicting R versions on my system versus my Conda environment.
  • Both were set to 4.3.3, and then the error disappeared.

• Error "(seaborn/fiona/r-neonutilities) not found"

  • Solution: Conda Forge installed seaborn, fiona, and r-neonutilities.
  • Used "conda install -c conda-forge X" in the prismatic environment to install them.

• These are the packages Dylan needed to download manually:

  • fiona
  • neonOS
  • geoNEON
  • neonUtilities
  • ggbiplot