orxgboost 1.1.0

Error log

The package failed to build. The error log from opam follows.

Opam plugin "depext" may require upgrading/reinstalling. Reinstall the plugin on the current switch? [Y/n] y
The following actions will be performed:
  - recompile opam-depext 1.2.3

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved opam-depext.1.2.3  (cached)
-> removed   opam-depext.1.2.3
-> installed opam-depext.1.2.3
Done.

<><> opam-depext.1.2.3 installed successfully <><><><><><><><><><><><><><><><><>
=> opam-depext is unnecessary when used with opam >= 2.1. Please use opam install directly instead
# Run eval $(opam env) to update the current shell environment

<><> Carrying on to "opam depext -viy orxgboost.1.1.0 dune.3.16.0 conf-r.1.0.0" 

Since version 2.1, opam now handles external dependencies alongside OCaml ones, and the `depext` plugin interface is provided for backwards compatibility only. Consider using your usual `opam install` command to install both OCaml and system dependencies, or `opam install <pkg> --depext-only` if you want to only install external dependencies.
# Detecting depexts using vars: arch=x86_64, os=linux, os-distribution=debian, os-family=debian
# The following system packages are needed:
r-base-core
[NOTE] Package dune is already installed (current version is 3.16.0).
The following actions will be performed:
  - install conf-r    1.0.0
  - install orxgboost 1.1.0
===== 2 to install =====

The following system packages will first need to be installed:
    r-base-core

<><> Handling external dependencies <><><><><><><><><><><><><><><><><><><><><><>
Let opam run your package manager to install the required system packages?
(answer 'n' for other options) [Y/n] y
+ /usr/bin/sudo "apt-get" "install" "-qq" "-yy" "r-base-core"
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- Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ...
- Setting up icu-devtools (72.1-3) ...
- Setting up pkgconf-bin (1.8.1-1) ...
- Setting up libsensors5:amd64 (1:3.6.0-7.1) ...
- Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ...
- Setting up libgfortran5:amd64 (12.2.0-14) ...
- Setting up libtimedate-perl (2.3300-2) ...
- Setting up libregexp-ipv6-perl (0.03-3) ...
- Setting up liblzma-dev:amd64 (5.4.1-0.2) ...
- Setting up libxcb-dri2-0:amd64 (1.15-1) ...
- Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ...
- Setting up libpcre2-posix3:amd64 (10.42-1) ...
- Setting up sensible-utils (0.0.17+nmu1) ...
- Setting up libxshmfence1:amd64 (1.3-1) ...
- Setting up libxcb-randr0:amd64 (1.15-1) ...
- Setting up dbus-session-bus-common (1.14.10-1~deb12u1) ...
- Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ...
- Setting up libthai-data (0.1.29-1) ...
- Setting up libxss1:amd64 (1:1.2.3-1) ...
- Setting up libxkbfile1:amd64 (1:1.1.0-1) ...
- Setting up dbus-system-bus-common (1.14.10-1~deb12u1) ...
- Setting up libdrm-common (2.4.114-1) ...
- Setting up libelf1:amd64 (0.188-2.1) ...
- Setting up libxcomposite1:amd64 (1:0.4.5-1) ...
- Setting up libicu-dev:amd64 (72.1-3) ...
- Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ...
- Setting up xdg-utils (1.1.3-4.1) ...
- update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
- Setting up liburi-perl (5.17-1) ...
- Setting up dbus-bin (1.14.10-1~deb12u1) ...
- Setting up libx11-protocol-perl (0.56-9) ...
- Setting up libblas-dev:amd64 (3.11.0-2) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
- Setting up libbz2-dev:amd64 (1.0.8-5+b1) ...
- Setting up libwayland-client0:amd64 (1.21.0-1) ...
- Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ...
- Setting up libpcrecpp0v5:amd64 (2:8.39-15) ...
- Setting up libice6:amd64 (2:1.0.10-1) ...
- Setting up libhttp-date-perl (6.05-2) ...
- Setting up liblapack3:amd64 (3.11.0-2) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
- Setting up libxft2:amd64 (2.3.6-1) ...
- Setting up libncurses-dev:amd64 (6.4-4) ...
- Setting up libfile-basedir-perl (0.09-2) ...
- Setting up libfile-listing-perl (6.15-1) ...
- Setting up libpcre2-dev:amd64 (10.42-1) ...
- Setting up libpcre3-dev:amd64 (2:8.39-15) ...
- Setting up libxtst6:amd64 (2:1.2.3-1.1) ...
- Setting up libtk8.6:amd64 (8.6.13-2) ...
- Setting up libxcursor1:amd64 (1:1.2.1-1) ...
- Setting up libpng-dev:amd64 (1.6.39-2) ...
- Setting up libjpeg-dev:amd64 (1:2.1.5-2) ...
- Setting up libnet-http-perl (6.22-1) ...
- Setting up libgfortran-12-dev:amd64 (12.2.0-14) ...
- Setting up dbus-daemon (1.14.10-1~deb12u1) ...
- Setting up libreadline-dev:amd64 (8.2-1.3) ...
- Setting up pkgconf:amd64 (1.8.1-1) ...
- Setting up libthai0:amd64 (0.1.29-1) ...
- Setting up gfortran-12 (12.2.0-14) ...
- Setting up dbus (1.14.10-1~deb12u1) ...
- invoke-rc.d: could not determine current runlevel
- invoke-rc.d: policy-rc.d denied execution of start.
- Setting up shared-mime-info (2.2-1) ...
- Setting up liblapack-dev:amd64 (3.11.0-2) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
- Setting up pkg-config:amd64 (1.8.1-1) ...
- Setting up ucf (3.0043+nmu1) ...
- Setting up libfile-desktopentry-perl (0.22-3) ...
- Setting up libwww-robotrules-perl (6.02-1) ...
- Setting up libdrm2:amd64 (2.4.114-1+b1) ...
- Setting up libhtml-parser-perl:amd64 (3.81-1) ...
- Setting up libllvm15:amd64 (1:15.0.6-4+b1) ...
- Setting up libncurses5-dev:amd64 (6.4-4) ...
- Setting up libsm6:amd64 (2:1.2.3-1) ...
- Setting up libio-socket-ssl-perl (2.081-2) ...
- Setting up libhttp-message-perl (6.44-1) ...
- Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ...
- Setting up libhtml-form-perl (6.11-1) ...
- Setting up libfile-mimeinfo-perl (0.33-1) ...
- Setting up libpaper1:amd64 (1.1.29) ...
- 
- Creating config file /etc/papersize with new version
- Setting up libhttp-negotiate-perl (6.01-2) ...
- Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ...
- Setting up libgbm1:amd64 (22.3.6-1+deb12u1) ...
- Setting up libhttp-cookies-perl (6.10-1) ...
- Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ...
- Setting up libhtml-tree-perl (5.07-3) ...
- Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ...
- Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ...
- Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ...
- Setting up libhtml-format-perl (2.16-2) ...
- Setting up libpaper-utils (1.1.29) ...
- Setting up gfortran (4:12.2.0-3) ...
- update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
- update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
- Setting up libegl-mesa0:amd64 (22.3.6-1+deb12u1) ...
- Setting up libnet-smtp-ssl-perl (1.04-2) ...
- Setting up libmailtools-perl (2.21-2) ...
- Setting up libxt6:amd64 (1:1.2.1-1.1) ...
- Setting up libhttp-daemon-perl (6.16-1) ...
- Setting up libegl1:amd64 (1.6.0-1) ...
- Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ...
- Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ...
- Setting up libxmu6:amd64 (2:1.1.3-3) ...
- Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ...
- Setting up libglx0:amd64 (1.6.0-1) ...
- Setting up libxaw7:amd64 (2:1.0.14-1) ...
- Setting up x11-xserver-utils (7.7+9+b1) ...
- Setting up libgl1:amd64 (1.6.0-1) ...
- Setting up r-base-core (4.2.2.20221110-2) ...
- 
- Creating config file /etc/R/Renviron with new version
- Setting up r-cran-lattice (0.20-45-3) ...
- Setting up r-cran-nlme (3.1.162-1) ...
- Setting up zutty (0.14.0.20230218+dfsg1-1) ...
- update-alternatives: using /usr/bin/zutty to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode
- Setting up r-cran-cluster (2.1.4-1) ...
- Setting up x11-utils (7.7+5) ...
- Setting up r-cran-nnet (7.3-18-1) ...
- Setting up r-cran-codetools (0.2-19-1) ...
- Setting up r-cran-boot (1.3-28.1-1) ...
- Setting up r-base-dev (4.2.2.20221110-2) ...
- Setting up r-cran-spatial (7.3-16-1) ...
- Setting up r-cran-mass (7.3-58.2-1) ...
- Setting up r-cran-foreign (0.8.84-1) ...
- Setting up r-cran-matrix (1.5-3-1) ...
- Setting up r-cran-kernsmooth (2.23-20-1) ...
- Setting up r-cran-mgcv (1.8-41-1) ...
- Setting up r-cran-class (7.3-21-1) ...
- Setting up r-cran-survival (3.5-3-1) ...
- Setting up r-cran-rpart (4.1.19-1) ...
- Setting up r-recommended (4.2.2.20221110-2) ...
- Setting up liblwp-protocol-https-perl (6.10-1) ...
- Setting up libwww-perl (6.68-1) ...
- Setting up libxml-parser-perl (2.46-4) ...
- Setting up libxml-twig-perl (1:3.52-2) ...
- Setting up libnet-dbus-perl (1.2.0-2) ...
- Processing triggers for libc-bin (2.36-9+deb12u8) ...

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved conf-r.1.0.0  (cached)
Processing  2/6:
Processing  3/6: [conf-r: R CMD]
-> retrieved orxgboost.1.1.0  (cached)
+ /usr/bin/R "CMD" "BATCH" "check.r" (CWD=/home/opam/.opam/5.1/.opam-switch/build/conf-r.1.0.0)
-> compiled  conf-r.1.0.0
-> installed conf-r.1.0.0
Processing  5/6: [orxgboost: R CMD]
+ /usr/bin/R "CMD" "BATCH" "install_matrix.r" (CWD=/home/opam/.opam/5.1/.opam-switch/build/orxgboost.1.1.0)
+ /usr/bin/R "CMD" "BATCH" "install_xgboost.r" (CWD=/home/opam/.opam/5.1/.opam-switch/build/orxgboost.1.1.0)
[ERROR] The compilation of orxgboost.1.1.0 failed at "R CMD BATCH install_xgboost.r".

#=== ERROR while compiling orxgboost.1.1.0 ====================================#
# context              2.1.6 | linux/x86_64 | ocaml-base-compiler.5.1.1 | file:///src
# path                 ~/.opam/5.1/.opam-switch/build/orxgboost.1.1.0
# command              /usr/bin/R CMD BATCH install_xgboost.r
# exit-code            1
# env-file             ~/.opam/log/orxgboost-115-bb0578.env
# output-file          ~/.opam/log/orxgboost-115-bb0578.out



<><> Error report <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
+- The following actions failed
| - build orxgboost 1.1.0
+- 
+- The following changes have been performed
| - install conf-r 1.0.0
+- 

<><> orxgboost.1.1.0 troubleshooting ><><><><><><><><><><><><><><><><><><><><><>
=> Please interact with R to install needed things in user-space:
   R
   install.packages('Marix', repos='http://cran.r-project.org')
   install.packages('xgboost', repos='http://cran.r-project.org')
# Run eval $(opam env) to update the current shell environment

The former state can be restored with:
    /usr/bin/opam switch import "/home/opam/.opam/5.1/.opam-switch/backup/state-20240912093326.export"
'opam --cli=2.1 install orxgboost.1.1.0 dune.3.16.0 conf-r.1.0.0 --verbose --yes --confirm-level=unsafe-yes' failed.