orxgboost

Gradient boosting for OCaml using the R xgboost package

Error log

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

You are using opam 2.1+, where external dependency handling has been integrated: consider calling opam directly, the 'depext' plugin interface is provided for backwards compatibility only
# 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 3.4.1).
The following actions will be performed:
  - install conf-r    1.0.0
  - install orxgboost 1.2.0
===== 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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- Preparing to unpack .../195-mesa-vulkan-drivers_20.3.5-1_amd64.deb ...
- Unpacking mesa-vulkan-drivers:amd64 (20.3.5-1) ...
- Selecting previously unselected package pkg-config.
- Preparing to unpack .../196-pkg-config_0.29.2-1_amd64.deb ...
- Unpacking pkg-config (0.29.2-1) ...
- Selecting previously unselected package zip.
- Preparing to unpack .../197-zip_3.0-12_amd64.deb ...
- Unpacking zip (3.0-12) ...
- Selecting previously unselected package xdg-utils.
- Preparing to unpack .../198-xdg-utils_1.1.3-4.1_all.deb ...
- Unpacking xdg-utils (1.1.3-4.1) ...
- Selecting previously unselected package r-base-core.
- Preparing to unpack .../199-r-base-core_4.0.4-1_amd64.deb ...
- Unpacking r-base-core (4.0.4-1) ...
- Selecting previously unselected package r-base-dev.
- Preparing to unpack .../200-r-base-dev_4.0.4-1_all.deb ...
- Unpacking r-base-dev (4.0.4-1) ...
- Selecting previously unselected package r-cran-boot.
- Preparing to unpack .../201-r-cran-boot_1.3-27-1_all.deb ...
- Unpacking r-cran-boot (1.3-27-1) ...
- Selecting previously unselected package r-cran-mass.
- Preparing to unpack .../202-r-cran-mass_7.3-53.1-1_amd64.deb ...
- Unpacking r-cran-mass (7.3-53.1-1) ...
- Selecting previously unselected package r-cran-class.
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- Unpacking r-cran-class (7.3-18-1) ...
- Selecting previously unselected package r-cran-cluster.
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- Unpacking r-cran-cluster (2.1.1-1) ...
- Selecting previously unselected package r-cran-codetools.
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- Unpacking r-cran-codetools (0.2-18-1) ...
- Selecting previously unselected package r-cran-foreign.
- Preparing to unpack .../206-r-cran-foreign_0.8.81-1_amd64.deb ...
- Unpacking r-cran-foreign (0.8.81-1) ...
- Selecting previously unselected package r-cran-kernsmooth.
- Preparing to unpack .../207-r-cran-kernsmooth_2.23-18-1_amd64.deb ...
- Unpacking r-cran-kernsmooth (2.23-18-1) ...
- Selecting previously unselected package r-cran-lattice.
- Preparing to unpack .../208-r-cran-lattice_0.20-41-1+b1_amd64.deb ...
- Unpacking r-cran-lattice (0.20-41-1+b1) ...
- Selecting previously unselected package r-cran-matrix.
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- Unpacking r-cran-matrix (1.3-2-1) ...
- Selecting previously unselected package r-cran-nlme.
- Preparing to unpack .../210-r-cran-nlme_3.1.152-1_amd64.deb ...
- Unpacking r-cran-nlme (3.1.152-1) ...
- Selecting previously unselected package r-cran-mgcv.
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- Unpacking r-cran-mgcv (1.8-34-1) ...
- Selecting previously unselected package r-cran-nnet.
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- Unpacking r-cran-nnet (7.3-15-1) ...
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- Unpacking r-cran-survival (3.2-7-1) ...
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- Unpacking r-cran-rpart (4.1-15-2+b1) ...
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- Unpacking r-recommended (4.0.4-1) ...
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- Unpacking termit (3.1-1) ...
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- Unpacking libglx0:amd64 (1.3.2-1) ...
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- Unpacking libgl1:amd64 (1.3.2-1) ...
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- Unpacking x11-utils (7.7+5) ...
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- Selecting previously unselected package xdg-user-dirs.
- Preparing to unpack .../223-xdg-user-dirs_0.17-2_amd64.deb ...
- Unpacking xdg-user-dirs (0.17-2) ...
- Setting up libpcrecpp0v5:amd64 (2:8.39-13) ...
- Setting up libtext-iconv-perl (1.7-7+b1) ...
- Setting up libgraphite2-3:amd64 (1.3.14-1) ...
- Setting up libxcb-dri3-0:amd64 (1.14-3) ...
- Setting up liblcms2-2:amd64 (2.12~rc1-2) ...
- Setting up libpixman-1-0:amd64 (0.40.0-1.1~deb11u1) ...
- Setting up bzip2-doc (1.0.8-4) ...
- Setting up libpaper1:amd64 (1.1.28+b1) ...
- 
- Creating config file /etc/papersize with new version
- Setting up libx11-xcb1:amd64 (2:1.7.2-1) ...
- Setting up libpciaccess0:amd64 (0.16-1) ...
- Setting up fontconfig (2.13.1-4.2) ...
- Regenerating fonts cache... 
- done.
- Setting up systemd-sysv (247.3-7+deb11u1) ...
- Setting up libproxy1v5:amd64 (0.4.17-1) ...
- Setting up libncurses-dev:amd64 (6.2+20201114-2) ...
- Setting up libtie-ixhash-perl (1.23-2.1) ...
- Setting up libxdamage1:amd64 (1:1.1.5-2) ...
- Setting up libxcb-xfixes0:amd64 (1.14-3) ...
- Setting up r-doc-html (4.0.4-1) ...
- Setting up libpcre16-3:amd64 (2:8.39-13) ...
- Setting up hicolor-icon-theme (0.17-2) ...
- Setting up libxi6:amd64 (2:1.7.10-1) ...
- Setting up libfont-afm-perl (1.20-3) ...
- Setting up libxrender1:amd64 (1:0.9.10-1) ...
- Setting up libvte-2.91-common (0.62.3-1) ...
- Setting up libicu67:amd64 (67.1-7) ...
- Setting up libdatrie1:amd64 (0.2.13-1) ...
- Setting up xdg-user-dirs (0.17-2) ...
- Setting up libpng-tools (1.6.37-3) ...
- Setting up libxcb-render0:amd64 (1.14-3) ...
- Setting up libclone-perl (0.45-1+b1) ...
- Setting up libglib2.0-0:amd64 (2.66.8-1) ...
- Setting up libglvnd0:amd64 (1.3.2-1) ...
- Setting up libio-stringy-perl (2.111-3) ...
- Setting up libhtml-tagset-perl (3.20-4) ...
- Setting up libauthen-sasl-perl (2.1600-1.1) ...
- Setting up libxcb-glx0:amd64 (1.14-3) ...
- Setting up liblwp-mediatypes-perl (6.04-1) ...
- Setting up libgdk-pixbuf2.0-common (2.42.2+dfsg-1+deb11u1) ...
- Setting up libxcb-shape0:amd64 (1.14-3) ...
- Setting up x11-common (1:7.7+22) ...
- invoke-rc.d: could not determine current runlevel
- invoke-rc.d: policy-rc.d denied execution of start.
- Setting up libtry-tiny-perl (0.30-1) ...
- Setting up libsensors-config (1:3.6.0-7) ...
- Setting up libxxf86dga1:amd64 (2:1.1.4-1+b3) ...
- Setting up perl-openssl-defaults:amd64 (5) ...
- Setting up libnss-systemd:amd64 (247.3-7+deb11u1) ...
- First installation detected...
- Checking NSS setup...
- Setting up xkb-data (2.29-2) ...
- Setting up libencode-locale-perl (1.05-1.1) ...
- Setting up libxcb-shm0:amd64 (1.14-3) ...
- Setting up libpaper-utils (1.1.28+b1) ...
- Setting up libreadline-dev:amd64 (8.1-1) ...
- Setting up libcairo2:amd64 (1.16.0-5) ...
- Setting up libpcre2-16-0:amd64 (10.36-2+deb11u1) ...
- Setting up libcolord2:amd64 (1.4.5-3) ...
- Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
- Setting up libxcb-present0:amd64 (1.14-3) ...
- Setting up libdconf1:amd64 (0.38.0-2) ...
- Setting up zip (3.0-12) ...
- Setting up libfontenc1:amd64 (1:1.1.4-1) ...
- Setting up libz3-4:amd64 (4.8.10-1) ...
- Setting up libpcre2-32-0:amd64 (10.36-2+deb11u1) ...
- Setting up libblas3:amd64 (3.9.0-3) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
- Setting up libglib2.0-data (2.66.8-1) ...
- Setting up libllvm11:amd64 (1:11.0.1-2) ...
- Setting up libdata-dump-perl (1.23-1.1) ...
- Setting up libjpeg62-turbo-dev:amd64 (1:2.0.6-4) ...
- Setting up libepoxy0:amd64 (1.5.5-1) ...
- Setting up libxfixes3:amd64 (1:5.0.3-2) ...
- Setting up libxcb-sync1:amd64 (1.14-3) ...
- Setting up libipc-system-simple-perl (1.30-1) ...
- Setting up libxml-xpathengine-perl (0.14-1) ...
- Setting up libavahi-common-data:amd64 (0.8-5+deb11u1) ...
- Setting up libdbus-1-3:amd64 (1.12.24-0+deb11u1) ...
- Setting up dbus (1.12.24-0+deb11u1) ...
- invoke-rc.d: could not determine current runlevel
- invoke-rc.d: policy-rc.d denied execution of start.
- Setting up libfribidi0:amd64 (1.0.8-2+deb11u1) ...
- Setting up libxinerama1:amd64 (2:1.1.4-2) ...
- Setting up libxv1:amd64 (2:1.0.11-1) ...
- Setting up libpcre32-3:amd64 (2:8.39-13) ...
- Setting up systemd-timesyncd (247.3-7+deb11u1) ...
- Created symlink /etc/systemd/system/dbus-org.freedesktop.timesync1.service → /lib/systemd/system/systemd-timesyncd.service.
- Created symlink /etc/systemd/system/sysinit.target.wants/systemd-timesyncd.service → /lib/systemd/system/systemd-timesyncd.service.
- Setting up libio-html-perl (1.004-2) ...
- Setting up libxrandr2:amd64 (2:1.5.1-1) ...
- Setting up libtcl8.6:amd64 (8.6.11+dfsg-1) ...
- Setting up icu-devtools (67.1-7) ...
- Setting up pkg-config (0.29.2-1) ...
- Setting up libpcre2-posix2:amd64 (10.36-2+deb11u1) ...
- Setting up libsensors5:amd64 (1:3.6.0-7) ...
- Setting up libglapi-mesa:amd64 (20.3.5-1) ...
- Setting up libgfortran5:amd64 (10.2.1-6) ...
- Setting up libvulkan1:amd64 (1.2.162.0-1) ...
- Setting up libtimedate-perl (2.3300-2) ...
- Setting up liblzma-dev:amd64 (5.2.5-2.1~deb11u1) ...
- Setting up libxcb-dri2-0:amd64 (1.14-3) ...
- Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ...
- Setting up libatk1.0-data (2.36.0-2) ...
- Setting up libxshmfence1:amd64 (1.3-1) ...
- Setting up libxcb-randr0:amd64 (1.14-3) ...
- Setting up liblua5.3-0:amd64 (5.3.3-1.1+b1) ...
- Setting up libncurses5-dev:amd64 (6.2+20201114-2) ...
- Setting up libpam-systemd:amd64 (247.3-7+deb11u1) ...
- Setting up libharfbuzz0b:amd64 (2.7.4-1) ...
- Setting up libthai-data (0.1.28-3) ...
- Setting up libgfortran-10-dev:amd64 (10.2.1-6) ...
- Setting up libjson-glib-1.0-common (1.6.2-1) ...
- Setting up libcairo-gobject2:amd64 (1.16.0-5) ...
- Setting up libatk1.0-0:amd64 (2.36.0-2) ...
- Setting up libwayland-egl1:amd64 (1.18.0-2~exp1.1) ...
- Setting up libxss1:amd64 (1:1.2.3-1) ...
- Setting up libxkbfile1:amd64 (1:1.1.0-1) ...
- Setting up glib-networking-common (2.66.0-2) ...
- Setting up libdrm-common (2.4.104-1) ...
- Setting up libelf1:amd64 (0.183-1) ...
- Setting up libxcomposite1:amd64 (1:0.4.5-1) ...
- Setting up libicu-dev:amd64 (67.1-7) ...
- Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u3) ...
- 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 (5.08-1) ...
- Setting up libx11-protocol-perl (0.56-7.1) ...
- Setting up libblas-dev:amd64 (3.9.0-3) ...
- 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 (1.0.8-4) ...
- Setting up libxkbcommon0:amd64 (1.0.3-2) ...
- Setting up libwayland-client0:amd64 (1.18.0-2~exp1.1) ...
- Setting up libnet-ssleay-perl (1.88-3+b1) ...
- Setting up glib-networking-services (2.66.0-2) ...
- Setting up libice6:amd64 (2:1.0.10-1) ...
- Setting up libhttp-date-perl (6.05-1) ...
- Setting up liblapack3:amd64 (3.9.0-3) ...
- 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 (2.3.2-2) ...
- Setting up libfile-basedir-perl (0.08-1) ...
- Setting up libfile-listing-perl (6.14-1) ...
- Setting up libpcre2-dev:amd64 (10.36-2+deb11u1) ...
- Setting up libpcre3-dev:amd64 (2:8.39-13) ...
- Setting up libxtst6:amd64 (2:1.2.3-1) ...
- Setting up libtk8.6:amd64 (8.6.11-2) ...
- Setting up libxcursor1:amd64 (1:1.2.0-2) ...
- Setting up libpng-dev:amd64 (1.6.37-3) ...
- Setting up libavahi-common3:amd64 (0.8-5+deb11u1) ...
- Setting up libjpeg-dev:amd64 (1:2.0.6-4) ...
- Setting up libnet-http-perl (6.20-1) ...
- Setting up libatspi2.0-0:amd64 (2.38.0-4) ...
- Setting up libjson-glib-1.0-0:amd64 (1.6.2-1) ...
- Setting up libatk-bridge2.0-0:amd64 (2.38.0-1) ...
- Setting up libthai0:amd64 (0.1.28-3) ...
- Setting up dbus-user-session (1.12.24-0+deb11u1) ...
- Setting up shared-mime-info (2.0-1) ...
- Setting up liblapack-dev:amd64 (3.9.0-3) ...
- 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 gfortran-10 (10.2.1-6) ...
- Setting up libfile-desktopentry-perl (0.22-2) ...
- Setting up libwww-robotrules-perl (6.02-1) ...
- Setting up libdrm2:amd64 (2.4.104-1) ...
- Setting up at-spi2-core (2.38.0-4) ...
- Setting up libwayland-cursor0:amd64 (1.18.0-2~exp1.1) ...
- Setting up libhtml-parser-perl (3.75-1+b1) ...
- Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.2+dfsg-1+deb11u1) ...
- Setting up libsm6:amd64 (2:1.2.3-1) ...
- Setting up libavahi-client3:amd64 (0.8-5+deb11u1) ...
- Setting up libio-socket-ssl-perl (2.069-1) ...
- Setting up libhttp-message-perl (6.28-1) ...
- Setting up libdrm-amdgpu1:amd64 (2.4.104-1) ...
- Setting up libhtml-form-perl (6.07-1) ...
- Setting up mesa-vulkan-drivers:amd64 (20.3.5-1) ...
- Setting up libfile-mimeinfo-perl (0.30-1) ...
- Setting up gtk-update-icon-cache (3.24.24-4+deb11u2) ...
- Setting up libhttp-negotiate-perl (6.01-1) ...
- Setting up libdrm-nouveau2:amd64 (2.4.104-1) ...
- Setting up libhttp-cookies-perl (6.10-1) ...
- Setting up libdrm-radeon1:amd64 (2.4.104-1) ...
- Setting up libhtml-tree-perl (5.07-2) ...
- Setting up libpango-1.0-0:amd64 (1.46.2-3) ...
- Setting up libdrm-intel1:amd64 (2.4.104-1) ...
- Setting up libgl1-mesa-dri:amd64 (20.3.5-1) ...
- Setting up dconf-service (0.38.0-2) ...
- Setting up libhtml-format-perl (2.12-1.1) ...
- Setting up gfortran (4:10.2.1-1) ...
- 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 libnet-smtp-ssl-perl (1.04-1) ...
- Setting up adwaita-icon-theme (3.38.0-1) ...
- update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
- Setting up libmailtools-perl (2.21-1) ...
- Setting up libxt6:amd64 (1:1.2.0-1) ...
- Setting up libcups2:amd64 (2.3.3op2-3+deb11u2) ...
- Setting up libhttp-daemon-perl (6.12-1+deb11u1) ...
- Setting up libgdk-pixbuf2.0-bin (2.42.2+dfsg-1+deb11u1) ...
- Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ...
- Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ...
- Setting up libxmu6:amd64 (2:1.1.2-2+b3) ...
- Setting up libglx-mesa0:amd64 (20.3.5-1) ...
- Setting up libglx0:amd64 (1.3.2-1) ...
- Setting up dconf-gsettings-backend:amd64 (0.38.0-2) ...
- Setting up libxaw7:amd64 (2:1.0.13-1.1) ...
- Setting up x11-xserver-utils (7.7+8) ...
- Setting up librsvg2-2:amd64 (2.50.3+dfsg-1) ...
- Setting up libgl1:amd64 (1.3.2-1) ...
- Setting up r-base-core (4.0.4-1) ...
- 
- Creating config file /etc/R/Renviron with new version
- Setting up librsvg2-common:amd64 (2.50.3+dfsg-1) ...
- Setting up r-cran-lattice (0.20-41-1+b1) ...
- Setting up r-cran-nlme (3.1.152-1) ...
- Setting up r-cran-cluster (2.1.1-1) ...
- Setting up x11-utils (7.7+5) ...
- Setting up r-cran-nnet (7.3-15-1) ...
- Setting up libgtk-3-common (3.24.24-4+deb11u2) ...
- Setting up gsettings-desktop-schemas (3.38.0-2) ...
- Setting up r-cran-codetools (0.2-18-1) ...
- Setting up r-cran-boot (1.3-27-1) ...
- Setting up r-base-dev (4.0.4-1) ...
- Setting up r-cran-spatial (7.3-13-1) ...
- Setting up r-cran-mass (7.3-53.1-1) ...
- Setting up r-cran-foreign (0.8.81-1) ...
- Setting up r-cran-matrix (1.3-2-1) ...
- Setting up r-cran-kernsmooth (2.23-18-1) ...
- Setting up r-cran-mgcv (1.8-34-1) ...
- Setting up glib-networking:amd64 (2.66.0-2) ...
- Setting up libsoup2.4-1:amd64 (2.72.0-2) ...
- Setting up r-cran-class (7.3-18-1) ...
- Setting up r-cran-survival (3.2-7-1) ...
- Setting up libsoup-gnome2.4-1:amd64 (2.72.0-2) ...
- Setting up librest-0.7-0:amd64 (0.8.1-1.1) ...
- Setting up libgtk-3-0:amd64 (3.24.24-4+deb11u2) ...
- Setting up r-cran-rpart (4.1-15-2+b1) ...
- Setting up libgtk-3-bin (3.24.24-4+deb11u2) ...
- Setting up libvte-2.91-0:amd64 (0.62.3-1) ...
- Setting up r-recommended (4.0.4-1) ...
- Setting up termit (3.1-1) ...
- update-alternatives: using /usr/bin/termit to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode
- Setting up liblwp-protocol-https-perl (6.10-1) ...
- Setting up libwww-perl (6.52-1) ...
- Setting up libxml-parser-perl:amd64 (2.46-2) ...
- Setting up libxml-twig-perl (1:3.52-1) ...
- Setting up libnet-dbus-perl (1.2.0-1+b1) ...
- Processing triggers for libc-bin (2.31-13+deb11u5) ...
- Processing triggers for libgdk-pixbuf-2.0-0:amd64 (2.42.2+dfsg-1+deb11u1) ...

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing  2/6:
Processing  3/6: [conf-r: R CMD]
-> retrieved orxgboost.1.2.0  (cached)
+ /usr/bin/R "CMD" "BATCH" "check.r" (CWD=/home/opam/.opam/4.14/.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/4.14/.opam-switch/build/orxgboost.1.2.0)
+ /usr/bin/R "CMD" "BATCH" "install_xgboost.r" (CWD=/home/opam/.opam/4.14/.opam-switch/build/orxgboost.1.2.0)
[ERROR] The compilation of orxgboost.1.2.0 failed at "R CMD BATCH install_xgboost.r".

#=== ERROR while compiling orxgboost.1.2.0 ====================================#
# context              2.1.3 | linux/x86_64 | ocaml-base-compiler.4.14.0 | file:///src
# path                 ~/.opam/4.14/.opam-switch/build/orxgboost.1.2.0
# command              /usr/bin/R CMD BATCH install_xgboost.r
# exit-code            1
# env-file             ~/.opam/log/orxgboost-260-1df665.env
# output-file          ~/.opam/log/orxgboost-260-1df665.out



<><> Error report <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
+- The following actions failed
| - build orxgboost 1.2.0
+- 
+- The following changes have been performed
| - install conf-r 1.0.0
+- 

<><> orxgboost.1.2.0 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/4.14/.opam-switch/backup/state-20221210192010.export"
'opam --cli=2.1 install orxgboost.1.2.0 conf-r.1.0.0 dune.3.4.1 --verbose --yes --confirm-level=unsafe-yes' failed.