#117 Change how trees are assigned into PFTs #123

arne-exe · 2025-10-06T08:05:42Z

This PR will provide a set of scripts to implement a new way to assign trees into PFTs:

add PFT species classification script based on Dobert et al., 2017 data
generate 2 new csv files (to be uploaded in Globus)
add new cohort distribution script, that takes the Dobert species classification and applies it to the SAFE tree census data
generate new cohort distribution csv file (also to be uploaded in Globus)

arne-exe · 2025-10-06T08:09:16Z

Hi @davidorme, it's the first time pushing a commit from a new laptop, I think I set up everything except for the pre-commit tool. Can you please remind me how this is done or where I can read how to do this?

Note to self:
Think I found it: https://virtual-ecosystem.readthedocs.io/en/latest/development/contributing/overview.html#installing-and-using-pre-commit

for more information, see https://pre-commit.ci

arne-exe · 2025-10-06T08:54:59Z

Hi @davidorme, it's the first time pushing a commit from a new laptop, I think I set up everything except for the pre-commit tool. Can you please remind me how this is done or where I can read how to do this?

Note to self: Think I found it: https://virtual-ecosystem.readthedocs.io/en/latest/development/contributing/overview.html#installing-and-using-pre-commit

install poetry

install pre-commit

add R to path

make sure Rtools is installed

add Rtools to path

$ git commit -m "Recommit after installing poetry and precommit"
[INFO] Installing environment for https://github.com/lorenzwalthert/precommit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('C:\\Program Files\\R\\R-4.5.1\\bin\\Rscript.EXE', '--vanilla', 'C:\\Users\\User\\AppData\\Local\\Temp\\tmpbxrpzqmr\\script.R')
return code: 1
stdout:
    # Bootstrapping renv 1.0.11 --------------------------------------------------
    - Downloading renv ... OK
    - Installing renv  ... OK

    - One or more packages recorded in the lockfile are not installed.
    - Use `renv::status()` for more details.
    The following package(s) will be updated:

    # RSPM -----------------------------------------------------------------------
    - backports      [* -> 1.5.0]
    - brew           [* -> 1.0-10]
    - callr          [* -> 3.7.6]
    - cli            [* -> 3.6.3]
    - commonmark     [* -> 1.9.2]
    - cpp11          [* -> 0.5.1]
    - crayon         [* -> 1.5.3]
    - curl           [* -> 6.2.0]
    - cyclocomp      [* -> 1.1.1]
    - desc           [* -> 1.4.3]
    - digest         [* -> 0.6.37]
    - docopt         [* -> 0.7.1]
    - evaluate       [* -> 1.0.3]
    - fs             [* -> 1.6.5]
    - glue           [* -> 1.8.0]
    - here           [* -> 1.0.1]
    - highr          [* -> 0.11]
    - hunspell       [* -> 3.0.5]
    - jsonlite       [* -> 1.8.9]
    - jsonvalidate   [* -> 1.3.2]
    - knitr          [* -> 1.49]
    - lazyeval       [* -> 0.2.2]
    - lifecycle      [* -> 1.0.4]
    - lintr          [* -> 3.1.2]
    - magrittr       [* -> 2.0.3]
    - pkgbuild       [* -> 1.4.6]
    - pkgload        [* -> 1.4.0]
    - processx       [* -> 3.8.5]
    - ps             [* -> 1.8.1]
    - purrr          [* -> 1.0.2]
    - R.cache        [* -> 0.16.0]
    - R.methodsS3    [* -> 1.8.2]
    - R.oo           [* -> 1.27.0]
    - R.utils        [* -> 2.12.3]
    - R6             [* -> 2.5.1]
    - Rcpp           [* -> 1.0.14]
    - remotes        [* -> 2.5.0]
    - rex            [* -> 1.2.1]
    - rlang          [* -> 1.1.5]
    - roxygen2       [* -> 7.3.2]
    - rprojroot      [* -> 2.0.4]
    - spelling       [* -> 2.3.1]
    - stringi        [* -> 1.8.4]
    - stringr        [* -> 1.5.1]
    - styler         [* -> 1.10.3]
    - V8             [* -> 6.0.0]
    - vctrs          [* -> 0.6.5]
    - withr          [* -> 3.0.2]
    - xfun           [* -> 0.50]
    - xml2           [* -> 1.3.6]
    - xmlparsedata   [* -> 1.0.5]
    - yaml           [* -> 2.3.10]

    # Downloading packages -------------------------------------------------------
    - Downloading V8 from RSPM ...                  OK [file is up to date]
    - Downloading jsonlite from RSPM ...            OK [file is up to date]
    - Downloading curl from RSPM ...                OK [file is up to date]
    - Downloading backports from RSPM ...           OK [file is up to date]
    - Downloading brew from RSPM ...                OK [file is up to date]
    - Downloading callr from RSPM ...               OK [file is up to date]
    - Downloading processx from RSPM ...            OK [file is up to date]
    - Downloading ps from RSPM ...                  OK [file is up to date]
    - Downloading cli from RSPM ...                 OK [file is up to date]
    - Downloading commonmark from RSPM ...          OK [file is up to date]
    - Downloading cpp11 from RSPM ...               OK [file is up to date]
    - Downloading crayon from RSPM ...              OK [file is up to date]
    - Downloading cyclocomp from RSPM ...           OK [file is up to date]
    - Downloading desc from RSPM ...                OK [file is up to date]
    - Downloading remotes from RSPM ...             OK [file is up to date]
    - Downloading withr from RSPM ...               OK [file is up to date]
    - Downloading docopt from RSPM ...              OK [file is up to date]
    - Downloading evaluate from RSPM ...            OK [file is up to date]
    - Downloading fs from RSPM ...                  OK [file is up to date]
    - Downloading glue from RSPM ...                OK [file is up to date]
    - Downloading here from RSPM ...                OK [file is up to date]
    - Downloading rprojroot from RSPM ...           OK [file is up to date]
    - Downloading highr from RSPM ...               OK [file is up to date]
    - Downloading xfun from RSPM ...                OK [file is up to date]
    - Downloading hunspell from RSPM ...            OK [file is up to date]
    - Downloading jsonvalidate from RSPM ...        OK [file is up to date]
    - Downloading knitr from RSPM ...               OK [file is up to date]
    - Downloading yaml from RSPM ...                OK [file is up to date]
    - Downloading lazyeval from RSPM ...            OK [file is up to date]
    - Downloading lifecycle from RSPM ...           OK [file is up to date]
    - Downloading rlang from RSPM ...               OK [file is up to date]
    - Downloading lintr from RSPM ...               OK [file is up to date]
    - Downloading rex from RSPM ...                 OK [file is up to date]
    - Downloading xml2 from RSPM ...                OK [file is up to date]
    - Downloading xmlparsedata from RSPM ...        OK [file is up to date]
    - Downloading magrittr from RSPM ...            OK [file is up to date]
    - Downloading pkgbuild from RSPM ...            OK [file is up to date]
    - Downloading pkgload from RSPM ...             OK [file is up to date]
    - Downloading purrr from RSPM ...               OK [file is up to date]
    - Downloading vctrs from RSPM ...               OK [file is up to date]
    - Downloading roxygen2 from RSPM ...            OK [file is up to date]
    - Downloading stringi from RSPM ...             OK [file is up to date]
    - Downloading stringr from RSPM ...             OK [file is up to date]
    - Downloading spelling from RSPM ...            OK [file is up to date]
    - Downloading styler from RSPM ...              OK [file is up to date]
    Successfully downloaded 45 packages in 56 seconds.

    # Installing packages --------------------------------------------------------
    - Installing R.methodsS3 ...                    OK [linked from cache]
    - Installing R.oo ...                           OK [linked from cache]
    - Installing R.utils ...                        OK [linked from cache]
    - Installing digest ...                         OK [linked from cache]
    - Installing R.cache ...                        OK [linked from cache]
    - Installing R6 ...                             OK [linked from cache]
    - Installing Rcpp ...                           OK [linked from cache]
    - Installing jsonlite ...                       FAILED
    Traceback (most recent calls last):
    13: renv::restore()
    12: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
    11: renv_install_impl(records)
    10: renv_install_staged(records)
     9: renv_install_default(records)
     8: handler(package, renv_install_package(record))
     7: renv_install_package(record)
     6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
     5: renv_install_package_impl(record)
     4: r_cmd_install(package, path)
     3: r_exec_error(package, output, "install", status)
     2: abort(all)
     1: stop(fallback)
stderr:
    Error: Error installing package 'jsonlite':
    ====================================

    * installing *source* package 'jsonlite' ...
    ** this is package 'jsonlite' version '1.8.9'
    ** package 'jsonlite' successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    using C compiler: 'gcc.exe (GCC) 14.2.0'
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -Iyajl/api    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"    -D__USE_MINGW_ANSI_STDIO   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c base64.c -o base64.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -Iyajl/api    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"    -D__USE_MINGW_ANSI_STDIO   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c collapse_array.c -o collapse_array.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -Iyajl/api    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"    -D__USE_MINGW_ANSI_STDIO   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c collapse_object.c -o collapse_object.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -Iyajl/api    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"    -D__USE_MINGW_ANSI_STDIO   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c collapse_pretty.c -o collapse_pretty.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -Iyajl/api    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"    -D__USE_MINGW_ANSI_STDIO   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c escape_chars.c -o escape_chars.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -Iyajl/api    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"    -D__USE_MINGW_ANSI_STDIO   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c integer64_to_na.c -o integer64_to_na.o
    In file included from modp_numtoa.h:34,
                     from integer64_to_na.c:2:
    modp_stdint.h:37:23: error: two or more data types in declaration specifiers
       37 | typedef unsigned char bool;
          |                       ^~~~
    modp_stdint.h:37:1: warning: useless type name in empty declaration
       37 | typedef unsigned char bool;
          | ^~~~~~~
    make: *** [C:/PROGRA~1/R/R-45~1.1/etc/x64/Makeconf:289: integer64_to_na.o] Error 1
    ERROR: compilation failed for package 'jsonlite'
    * removing 'C:/Users/User/.cache/pre-commit/repog6trpveh/renv-default/renv/staging/1/jsonlite'
    install of package 'jsonlite' failed [error code 1]
    Execution halted
Check the log at C:\Users\User\.cache\pre-commit\pre-commit.log

Hi @davidorme, I'm stuck here, do you have any suggestions on how to fix this?

davidorme · 2025-10-06T10:21:40Z

@arne-exe We also have the ve_data_science website here:

https://imperialcollegelondon.github.io/ve_data_science/getting_started/

Although that page is a little out of date and doesn't say anything much different from the VE site. We do need to improve this though - some people are relying on the GitHub CI to catch pre-commit issues and it is better to trap them locally!

On this specific issue... I'm not sure but I think the first thing to do is to update the pre-commit chain. I'm going to put in an issue (#124) and PR for that now.

davidorme · 2025-10-06T12:13:41Z

@arne-exe that PR is now in.

Try switching to main and then git pull to get the updates and then pre-commit run -a to see what happens. It should install the new setup and run all the checks. If that goes well, you should be able to git merge main into this branch and then re-try your local commit.

arne-exe · 2025-10-07T03:41:29Z

Hi @davidorme, thanks for looking into this. I still can't get it to work, even after the following:

installed poetry (and pre-commit)
set the correct virtual environment
cleaned the pre-commit cache
installed R and Rtools (and added them to system path)
installed the "digest package"

I've attached a copy of the error below:

$ poetry run pre-commit run --all-files
[INFO] Initializing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Initializing environment for https://github.com/astral-sh/ruff-pre-commit.
[INFO] Initializing environment for https://github.com/igorshubovych/markdownlint-cli.
[INFO] Initializing environment for https://github.com/lorenzwalthert/precommit.
[INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/astral-sh/ruff-pre-commit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/igorshubovych/markdownlint-cli.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/lorenzwalthert/precommit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('C:\\Program Files\\R\\R-4.5.1\\bin\\Rscript.EXE', '--vanilla', 'C:\\Users\\User\\AppData\\Local\\Temp\\tmphvy19zw8\\script.R')
return code: 1
stdout:
    # Bootstrapping renv 1.0.5 ---------------------------------------------------
    - Downloading renv ... OK
    - Installing renv  ... OK

    - One or more packages recorded in the lockfile are not installed.
    - Use `renv::status()` for more details.
    The following package(s) will be updated:

    # RSPM -----------------------------------------------------------------------
    - backports      [* -> 1.5.0]
    - brew           [* -> 1.0-10]
    - callr          [* -> 3.7.6]
    - cli            [* -> 3.6.3]
    - commonmark     [* -> 1.9.1]
    - cpp11          [* -> 0.4.7]
    - crayon         [* -> 1.5.3]
    - cyclocomp      [* -> 1.1.1]
    - desc           [* -> 1.4.3]
    - digest         [* -> 0.6.36]
    - docopt         [* -> 0.7.1]
    - evaluate       [* -> 0.24.0]
    - fs             [* -> 1.6.4]
    - glue           [* -> 1.7.0]
    - here           [* -> 1.0.1]
    - highr          [* -> 0.11]
    - hunspell       [* -> 3.0.3]
    - knitr          [* -> 1.48]
    - lazyeval       [* -> 0.2.2]
    - lifecycle      [* -> 1.0.4]
    - lintr          [* -> 3.1.2]
    - magrittr       [* -> 2.0.3]
    - pkgbuild       [* -> 1.4.4]
    - pkgload        [* -> 1.4.0]
    - processx       [* -> 3.8.4]
    - ps             [* -> 1.7.7]
    - purrr          [* -> 1.0.2]
    - R.cache        [* -> 0.16.0]
    - R.methodsS3    [* -> 1.8.2]
    - R.oo           [* -> 1.26.0]
    - R.utils        [* -> 2.12.3]
    - R6             [* -> 2.5.1]
    - Rcpp           [* -> 1.0.12]
    - remotes        [* -> 2.5.0]
    - rex            [* -> 1.2.1]
    - rlang          [* -> 1.1.4]
    - roxygen2       [* -> 7.3.2]
    - rprojroot      [* -> 2.0.4]
    - spelling       [* -> 2.3.0]
    - stringi        [* -> 1.8.4]
    - stringr        [* -> 1.5.1]
    - styler         [* -> 1.10.3]
    - vctrs          [* -> 0.6.5]
    - withr          [* -> 3.0.0]
    - xfun           [* -> 0.45]
    - xml2           [* -> 1.3.6]
    - xmlparsedata   [* -> 1.0.5]
    - yaml           [* -> 2.3.9]

    # Downloading packages -------------------------------------------------------
    - Downloading R.cache from RSPM ...             OK [file is up to date]
    - Downloading digest from RSPM ...              OK [file is up to date]
    - Downloading R6 from RSPM ...                  OK [file is up to date]
    - Downloading Rcpp from RSPM ...                OK [file is up to date]
    - Downloading backports from RSPM ...           OK [file is up to date]
    - Downloading brew from RSPM ...                OK [file is up to date]
    - Downloading callr from RSPM ...               OK [file is up to date]
    - Downloading processx from RSPM ...            OK [file is up to date]
    - Downloading ps from RSPM ...                  OK [file is up to date]
    - Downloading cli from RSPM ...                 OK [file is up to date]
    - Downloading commonmark from RSPM ...          OK [file is up to date]
    - Downloading cpp11 from RSPM ...               OK [file is up to date]
    - Downloading crayon from RSPM ...              OK [file is up to date]
    - Downloading cyclocomp from RSPM ...           OK [file is up to date]
    - Downloading desc from RSPM ...                OK [file is up to date]
    - Downloading remotes from RSPM ...             OK [file is up to date]
    - Downloading withr from RSPM ...               OK [file is up to date]
    - Downloading docopt from RSPM ...              OK [file is up to date]
    - Downloading evaluate from RSPM ...            OK [file is up to date]
    - Downloading fs from RSPM ...                  OK [file is up to date]
    - Downloading glue from RSPM ...                OK [file is up to date]
    - Downloading here from RSPM ...                OK [file is up to date]
    - Downloading rprojroot from RSPM ...           OK [file is up to date]
    - Downloading highr from RSPM ...               OK [file is up to date]
    - Downloading xfun from RSPM ...                OK [file is up to date]
    - Downloading hunspell from RSPM ...            OK [file is up to date]
    - Downloading knitr from RSPM ...               OK [file is up to date]
    - Downloading yaml from RSPM ...                OK [file is up to date]
    - Downloading lazyeval from RSPM ...            OK [file is up to date]
    - Downloading lifecycle from RSPM ...           OK [file is up to date]
    - Downloading rlang from RSPM ...               OK [file is up to date]
    - Downloading lintr from RSPM ...               OK [file is up to date]
    - Downloading rex from RSPM ...                 OK [file is up to date]
    - Downloading xml2 from RSPM ...                OK [file is up to date]
    - Downloading xmlparsedata from RSPM ...        OK [file is up to date]
    - Downloading magrittr from RSPM ...            OK [file is up to date]
    - Downloading pkgbuild from RSPM ...            OK [file is up to date]
    - Downloading pkgload from RSPM ...             OK [file is up to date]
    - Downloading purrr from RSPM ...               OK [file is up to date]
    - Downloading vctrs from RSPM ...               OK [file is up to date]
    - Downloading roxygen2 from RSPM ...            OK [file is up to date]
    - Downloading stringi from RSPM ...             OK [file is up to date]
    - Downloading stringr from RSPM ...             OK [file is up to date]
    - Downloading spelling from RSPM ...            OK [file is up to date]
    - Downloading styler from RSPM ...              OK [file is up to date]
    Successfully downloaded 45 packages in 55 seconds.

    # Installing packages --------------------------------------------------------
    - Installing R.methodsS3 ...                    OK [linked from cache]
    - Installing R.oo ...                           OK [linked from cache]
    - Installing R.utils ...                        OK [linked from cache]
    - Installing digest ...                         FAILED
    Traceback (most recent calls last):
    13: renv::restore()
    12: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
    11: renv_install_impl(records)
    10: renv_install_staged(records)
     9: renv_install_default(records)
     8: handler(package, renv_install_package(record))
     7: renv_install_package(record)
     6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
     5: renv_install_package_impl(record)
     4: r_cmd_install(package, path)
     3: r_exec_error(package, output, "install", status)
     2: abort(all)
     1: stop(fallback)
stderr:
    Error: Error installing package 'digest':
    ==================================

    * installing *source* package 'digest' ...
    ** this is package 'digest' version '0.6.36'
    ** package 'digest' successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    using C compiler: 'gcc.exe (GCC) 14.2.0'
    using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
    g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c SpookyV2.cpp -o SpookyV2.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c aes.c -o aes.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c blake3.c -o blake3.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c blake3_dispatch.c -o blake3_dispatch.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c blake3_portable.c -o blake3_portable.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c crc32.c -o crc32.o
    g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c crc32c.cpp -o crc32c.o
    g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c crc32c_portable.cpp -o crc32c_portable.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c digest.c -o digest.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c digest2int.c -o digest2int.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c init.c -o init.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c md5.c -o md5.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c pmurhash.c -o pmurhash.o
    gcc  -I"C:/PROGRA~1/R/R-45~1.1/include" -DNDEBUG -I.    -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c raes.c -o raes.o
    raes.c: In function 'AESFinalizer':
    raes.c:25:3: error: implicit declaration of function 'Free'; did you mean 'free'? [-Wimplicit-function-declaration]
       25 |   Free(ctx);
          |   ^~~~
          |   free
    raes.c: In function 'AESinit':
    raes.c:42:23: error: implicit declaration of function 'Calloc'; did you mean 'calloc'? [-Wimplicit-function-declaration]
       42 |   ctx = (aes_context*)Calloc(sizeof(*ctx), char);
          |                       ^~~~~~
          |                       calloc
    raes.c:42:44: error: expected expression before 'char'
       42 |   ctx = (aes_context*)Calloc(sizeof(*ctx), char);
          |                                            ^~~~
    make: *** [C:/PROGRA~1/R/R-45~1.1/etc/x64/Makeconf:289: raes.o] Error 1
    ERROR: compilation failed for package 'digest'
    * removing 'C:/Users/User/.cache/pre-commit/repo_een0mgj/renv-default/renv/staging/1/digest'
    install of package 'digest' failed [error code 1]
    Execution halted
Check the log at C:\Users\User\.cache\pre-commit\pre-commit.log
(ve-data-science-py3.12)

nickwctan · 2025-10-07T04:11:44Z

@arne-exe We also have the ve_data_science website here:

https://imperialcollegelondon.github.io/ve_data_science/getting_started/

Sorry for budging in this PR, but Arne and I found out that the Getting Started from the ve_data_science
/README.md does not work anymore. It seems like the ending url is different, so maybe README.md file just needs updating?

Same for the link to GitHub overview

I have created a PR to change the links. See PR #126

Created PFT species classification using Dobert data

15c0084

arne-exe linked an issue Oct 6, 2025 that may be closed by this pull request

Change how trees are assigned into PFTs #117

Open

arne-exe self-assigned this Oct 6, 2025

[pre-commit.ci] auto fixes from pre-commit.com hooks

f406f0c

for more information, see https://pre-commit.ci

This was referenced Oct 6, 2025

Issues with pre-commit setup #124

Closed

Updating pre-commit #125

Merged

Merge branch 'main' into 117-change-how-trees-are-assigned-into-pfts

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#117 Change how trees are assigned into PFTs #123

#117 Change how trees are assigned into PFTs #123

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nickwctan commented Oct 7, 2025

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#117 Change how trees are assigned into PFTs #123

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#117 Change how trees are assigned into PFTs #123

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