✨ Pixi task (install-r in r-phylo2vec): Rscript ./r-phylo2vec/scripts/install-package.R
ℹ Updating phylo2vec documentation
ℹ Loading phylo2vec
ℹ Re-compiling phylo2vec (debug build)
── R CMD INSTALL ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─  installing *source* package ‘phylo2vec’ ...
   ** using staged installation
   ** libs
   using C compiler: ‘x86_64-conda-linux-gnu-cc (conda-forge gcc 12.4.0-1) 12.4.0’
   rm -Rf phylo2vec.so ./rust/target/release/libphylo2vec.a entrypoint.o
   x86_64-conda-linux-gnu-cc -I"/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/include -I/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/include -Wl,-rpath-link,/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib    -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1728291269090/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec=/usr/local/src/conda-prefix  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c entrypoint.c -o entrypoint.o
   # In some environments, ~/.cargo/bin might not be included in PATH, so we need
   # to set it here to ensure cargo can be invoked. It is appended to PATH and
   # therefore is only used if cargo is absent from the user's PATH.
   if [ "true" != "true" ]; then \
        export CARGO_HOME=/home/nclow23/src/phylo2vec/public_fork2/r-phylo2vec/src/.cargo; \
   fi && \
        export PATH="/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/bin:/home/nclow23/.vscode-server/extensions/ms-python.python-2025.4.0-linux-x64/python_files/deactivate/bash:/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/py-phylo2vec/bin:/home/nclow23//.cargo/bin:/usr/local/texlive/2024/bin/x86_64-linux:/usr/local/cuda-12.6/bin:/home/nclow23/.cargo/bin:/home/nclow23/.pixi/bin:/home/nclow23/miniforge3/bin:/home/nclow23/tools/hal/bin:/home/nclow23/tools/ASTER/bin:/home/nclow23/tools/beast2.6/bin:/home/nclow23/.vscode-server/extensions/ms-python.python-2025.4.0-linux-x64/python_files/deactivate/bash:/home/nclow23/miniforge3/bin:/home/nclow23/.vscode-server/cli/servers/Stable-17baf841131aa23349f217ca7c570c76ee87b957/server/bin/remote-cli:/home/nclow23/.cargo/bin:/usr/local/texlive/2024/bin/x86_64-linux:/usr/local/cuda-12.6/bin:/home/nclow23/.cargo/bin:/home/nclow23/.pixi/bin:/home/nclow23/miniforge3/bin:/home/nclow23/tools/hal/bin:/home/nclow23/tools/ASTER/bin:/home/nclow23/tools/beast2.6/bin:/home/nclow23/.cargo/bin:/home/nclow23/miniforge3/bin:/home/nclow23/miniforge3/condabin:/usr/local/texlive/2024/bin/x86_64-linux:/usr/local/cuda-12.6/bin:/home/nclow23/.cargo/bin:/home/nclow23/.pixi/bin:/home/nclow23/miniforge3/bin:/home/nclow23/tools/hal/bin:/home/nclow23/tools/ASTER/bin:/home/nclow23/tools/beast2.6/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/nclow23//.cargo/bin" && \
        cargo build --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target
      Compiling r-phylo2vec v0.1.0 (/home/nclow23/src/phylo2vec/public_fork2/r-phylo2vec/src/rust)
       Finished `release` profile [optimized] target(s) in 0.28s
   if [ "true" != "true" ]; then \
        rm -Rf /home/nclow23/src/phylo2vec/public_fork2/r-phylo2vec/src/.cargo && \
        rm -Rf ./rust/target/release/build; \
   fi
   x86_64-conda-linux-gnu-cc -shared -L/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib -Wl,-rpath-link,/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib -L/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib -o phylo2vec.so entrypoint.o -L./rust/target/release -lphylo2vec -L/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib/R/lib -lR
   installing to /tmp/RtmpKrTA53/devtools_install_17b33712089cf2/00LOCK-r-phylo2vec/00new/phylo2vec/libs
   ** checking absolute paths in shared objects and dynamic libraries
─  DONE (phylo2vec)
── R CMD INSTALL ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─  installing to library ‘/tmp/RtmpKrTA53/temp_libpath17b33717d5c719’
─  installing *source* package ‘phylo2vec’ ...
   ** using staged installation
   ** libs
   using C compiler: ‘x86_64-conda-linux-gnu-cc (conda-forge gcc 12.4.0-1) 12.4.0’
   rm -Rf phylo2vec.so ./rust/target/release/libphylo2vec.a entrypoint.o
   x86_64-conda-linux-gnu-cc -I"/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/include -I/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/include -Wl,-rpath-link,/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib    -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1728291269090/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec=/usr/local/src/conda-prefix  -Wall -pedantic -fdiagnostics-color=always -c entrypoint.c -o entrypoint.o
   # In some environments, ~/.cargo/bin might not be included in PATH, so we need
   # to set it here to ensure cargo can be invoked. It is appended to PATH and
   # therefore is only used if cargo is absent from the user's PATH.
   if [ "" != "true" ]; then \
        export CARGO_HOME=/home/nclow23/src/phylo2vec/public_fork2/r-phylo2vec/src/.cargo; \
   fi && \
        export PATH="/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/bin:/home/nclow23/.vscode-server/extensions/ms-python.python-2025.4.0-linux-x64/python_files/deactivate/bash:/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/py-phylo2vec/bin:/home/nclow23//.cargo/bin:/usr/local/texlive/2024/bin/x86_64-linux:/usr/local/cuda-12.6/bin:/home/nclow23/.cargo/bin:/home/nclow23/.pixi/bin:/home/nclow23/miniforge3/bin:/home/nclow23/tools/hal/bin:/home/nclow23/tools/ASTER/bin:/home/nclow23/tools/beast2.6/bin:/home/nclow23/.vscode-server/extensions/ms-python.python-2025.4.0-linux-x64/python_files/deactivate/bash:/home/nclow23/miniforge3/bin:/home/nclow23/.vscode-server/cli/servers/Stable-17baf841131aa23349f217ca7c570c76ee87b957/server/bin/remote-cli:/home/nclow23/.cargo/bin:/usr/local/texlive/2024/bin/x86_64-linux:/usr/local/cuda-12.6/bin:/home/nclow23/.cargo/bin:/home/nclow23/.pixi/bin:/home/nclow23/miniforge3/bin:/home/nclow23/tools/hal/bin:/home/nclow23/tools/ASTER/bin:/home/nclow23/tools/beast2.6/bin:/home/nclow23/.cargo/bin:/home/nclow23/miniforge3/bin:/home/nclow23/miniforge3/condabin:/usr/local/texlive/2024/bin/x86_64-linux:/usr/local/cuda-12.6/bin:/home/nclow23/.cargo/bin:/home/nclow23/.pixi/bin:/home/nclow23/miniforge3/bin:/home/nclow23/tools/hal/bin:/home/nclow23/tools/ASTER/bin:/home/nclow23/tools/beast2.6/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/nclow23//.cargo/bin" && \
        cargo build --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target
       Updating crates.io index
    Downloading crates ...
     Downloaded byteorder v1.5.0
     Downloaded getrandom v0.2.15
     Downloaded rand_core v0.6.4
     Downloaded zerocopy-derive v0.7.35
     Downloaded unicode-ident v1.0.13
     Downloaded quote v1.0.37
     Downloaded rand v0.8.5
     Downloaded aho-corasick v1.1.3
     Downloaded memchr v2.7.4
     Downloaded syn v2.0.87
     Downloaded regex v1.11.1
     Downloaded rand_chacha v0.3.1
     Downloaded zerocopy v0.7.35
     Downloaded extendr-api v0.7.1
     Downloaded proc-macro2 v1.0.88
     Downloaded ppv-lite86 v0.2.20
     Downloaded paste v1.0.15
     Downloaded once_cell v1.20.2
     Downloaded libR-sys v0.7.1
     Downloaded cfg-if v1.0.0
     Downloaded extendr-macros v0.7.1
     Downloaded regex-automata v0.4.8
     Downloaded regex-syntax v0.8.5
     Downloaded libc v0.2.172
      Compiling proc-macro2 v1.0.88
      Compiling unicode-ident v1.0.13
      Compiling libc v0.2.172
      Compiling cfg-if v1.0.0
      Compiling byteorder v1.5.0
      Compiling libR-sys v0.7.1
      Compiling memchr v2.7.4
      Compiling regex-syntax v0.8.5
      Compiling paste v1.0.15
      Compiling extendr-api v0.7.1
      Compiling once_cell v1.20.2
      Compiling aho-corasick v1.1.3
      Compiling quote v1.0.37
      Compiling syn v2.0.87
      Compiling getrandom v0.2.15
      Compiling rand_core v0.6.4
      Compiling regex-automata v0.4.8
      Compiling zerocopy-derive v0.7.35
      Compiling extendr-macros v0.7.1
      Compiling regex v1.11.1
      Compiling zerocopy v0.7.35
      Compiling ppv-lite86 v0.2.20
      Compiling rand_chacha v0.3.1
      Compiling rand v0.8.5
      Compiling phylo2vec v0.1.0 (/home/nclow23/src/phylo2vec/public_fork2/phylo2vec)
      Compiling r-phylo2vec v0.1.0 (/home/nclow23/src/phylo2vec/public_fork2/r-phylo2vec/src/rust)
       Finished `release` profile [optimized] target(s) in 5.34s
   if [ "" != "true" ]; then \
        rm -Rf /home/nclow23/src/phylo2vec/public_fork2/r-phylo2vec/src/.cargo && \
        rm -Rf ./rust/target/release/build; \
   fi
   x86_64-conda-linux-gnu-cc -shared -L/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib -Wl,-rpath-link,/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib -L/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib -o phylo2vec.so entrypoint.o -L./rust/target/release -lphylo2vec -L/home/nclow23/src/phylo2vec/public_fork2/.pixi/envs/r-phylo2vec/lib/R/lib -lR
   installing to /tmp/RtmpKrTA53/temp_libpath17b33717d5c719/00LOCK-r-phylo2vec/00new/phylo2vec/libs
   ** R
   ** byte-compile and prepare package for lazy loading
   ** help
   *** installing help indices
   ** building package indices
   ** testing if installed package can be loaded from temporary location
   ** checking absolute paths in shared objects and dynamic libraries
   ** testing if installed package can be loaded from final location
   ** testing if installed package keeps a record of temporary installation path
─  creating tarball
   packaged installation of ‘phylo2vec’ as ‘phylo2vec_0.1.0_R_x86_64-conda-linux-gnu.tar.gz’
─  DONE (phylo2vec)
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpKrTA53/remotes17b3377a2fdde2/phylo2vec/DESCRIPTION’ ...
─  preparing ‘phylo2vec’:
✔  checking DESCRIPTION meta-information ...
   Warning in file(con, "r") :
     cannot open file 'man': No such file or directory
    ERROR
   computing Rd index failed:cannot open the connection
Error: Failed to install 'phylo2vec' from local:
  ! System command 'R' failed
Execution halted

===== SYSTEM INFO =====
Linux didelx02 5.15.0-133-generic #144-Ubuntu SMP Fri Feb 7 20:47:38 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
Distributor ID: Ubuntu
Description:    Ubuntu 22.04.4 LTS
Release:        22.04
Codename:       jammy
CPU: AMD Ryzen Threadripper PRO 5995WX 64-Cores
Memory: 251Gi
===== R VERSION =====
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
===== RUST VERSION =====
rustc 1.81.0 (eeb90cda1 2024-09-04)
cargo 1.81.0 (2dbb1af80 2024-08-20)
===== R PACKAGE DEBUG =====
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
[1] compiler_4.4.1
[1] "/home/nclow23/R/x86_64-pc-linux-gnu-library/4.4"
[2] "/usr/local/lib/R/site-library"                  
[3] "/usr/lib/R/site-library"                        
[4] "/usr/lib/R/library"