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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 1.2.1-1 <><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><> -> retrieved opam-depext.1.2.1-1 (cached) -> removed opam-depext.1.2.1-1 -> installed opam-depext.1.2.1-1 Done. <><> opam-depext.1.2.1-1 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 ocaml-r.0.2.0 stdio.v0.13.0 sexplib0.v0.13.0 jbuilder.1.0+beta20.2 dune-configurator.3.15.2 dune.3.15.2 csexp.1.5.2 configurator.v0.11.0 conf-r-mathlib.1 conf-r.1.0.0 conf-pkg-config.3 base.v0.13.2" 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: pkg-config r-base-core r-mathlib [NOTE] Package dune is already installed (current version is 3.15.2). The following actions will be performed: - install conf-r 1.0.0 - install jbuilder 1.0+beta20.2 - install csexp 1.5.2 - install conf-pkg-config 3 - install sexplib0 v0.13.0 - install dune-configurator 3.15.2 - install conf-r-mathlib 1 - install base v0.13.2 - install stdio v0.13.0 - install configurator v0.11.0 - install ocaml-r 0.2.0 ===== 11 to install ===== The following system packages will first need to be installed: pkg-config r-base-core r-mathlib <><> 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" "pkg-config" "r-base-core" "r-mathlib" - debconf: delaying package configuration, since apt-utils is not installed - Selecting previously unselected package libdbus-1-3:amd64. - (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18735 files and directories currently installed.) - Preparing to unpack .../000-libdbus-1-3_1.14.10-1~deb12u1_amd64.deb ... - Unpacking libdbus-1-3:amd64 (1.14.10-1~deb12u1) ... - Selecting previously unselected package dbus-bin. - Preparing to unpack .../001-dbus-bin_1.14.10-1~deb12u1_amd64.deb ... - Unpacking dbus-bin (1.14.10-1~deb12u1) ... - Selecting previously unselected package dbus-session-bus-common. - Preparing to unpack .../002-dbus-session-bus-common_1.14.10-1~deb12u1_all.deb ... - Unpacking dbus-session-bus-common (1.14.10-1~deb12u1) ... - Selecting previously unselected package libapparmor1:amd64. - Preparing to unpack .../003-libapparmor1_3.0.8-3_amd64.deb ... - Unpacking libapparmor1:amd64 (3.0.8-3) ... - Selecting previously unselected package dbus-daemon. - Preparing to unpack .../004-dbus-daemon_1.14.10-1~deb12u1_amd64.deb ... - Unpacking dbus-daemon (1.14.10-1~deb12u1) ... - Selecting previously unselected package dbus-system-bus-common. - Preparing to unpack .../005-dbus-system-bus-common_1.14.10-1~deb12u1_all.deb ... - Unpacking dbus-system-bus-common (1.14.10-1~deb12u1) ... - Selecting previously unselected package dbus. - Preparing to unpack .../006-dbus_1.14.10-1~deb12u1_amd64.deb ... - Unpacking dbus (1.14.10-1~deb12u1) ... - Selecting previously unselected package sensible-utils. - Preparing to unpack .../007-sensible-utils_0.0.17+nmu1_all.deb ... - Unpacking sensible-utils (0.0.17+nmu1) ... - Selecting previously unselected package ucf. - Preparing to unpack .../008-ucf_3.0043+nmu1_all.deb ... - 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Unpacking gfortran (4:12.2.0-3) ... - Selecting previously unselected package libicu72:amd64. - Preparing to unpack .../015-libicu72_72.1-3_amd64.deb ... - Unpacking libicu72:amd64 (72.1-3) ... - Selecting previously unselected package icu-devtools. - Preparing to unpack .../016-icu-devtools_72.1-3_amd64.deb ... - Unpacking icu-devtools (72.1-3) ... - Selecting previously unselected package libauthen-sasl-perl. - Preparing to unpack .../017-libauthen-sasl-perl_2.1600-3_all.deb ... - Unpacking libauthen-sasl-perl (2.1600-3) ... - Selecting previously unselected package libblas3:amd64. - Preparing to unpack .../018-libblas3_3.11.0-2_amd64.deb ... - Unpacking libblas3:amd64 (3.11.0-2) ... - Selecting previously unselected package libblas-dev:amd64. - Preparing to unpack .../019-libblas-dev_3.11.0-2_amd64.deb ... - Unpacking libblas-dev:amd64 (3.11.0-2) ... - Selecting previously unselected package libbz2-dev:amd64. - Preparing to unpack .../020-libbz2-dev_1.0.8-5+b1_amd64.deb ... - Unpacking libbz2-dev:amd64 (1.0.8-5+b1) ... - 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Selecting previously unselected package libdata-dump-perl. - Preparing to unpack .../027-libdata-dump-perl_1.25-1_all.deb ... - Unpacking libdata-dump-perl (1.25-1) ... - Selecting previously unselected package libdatrie1:amd64. - Preparing to unpack .../028-libdatrie1_0.2.13-2+b1_amd64.deb ... - Unpacking libdatrie1:amd64 (0.2.13-2+b1) ... - Selecting previously unselected package libdrm-common. - Preparing to unpack .../029-libdrm-common_2.4.114-1_all.deb ... - Unpacking libdrm-common (2.4.114-1) ... - Selecting previously unselected package libdrm2:amd64. - Preparing to unpack .../030-libdrm2_2.4.114-1+b1_amd64.deb ... - Unpacking libdrm2:amd64 (2.4.114-1+b1) ... - Selecting previously unselected package libdrm-amdgpu1:amd64. - Preparing to unpack .../031-libdrm-amdgpu1_2.4.114-1+b1_amd64.deb ... - Unpacking libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... - Selecting previously unselected package libpciaccess0:amd64. - Preparing to unpack .../032-libpciaccess0_0.17-2_amd64.deb ... - Unpacking libpciaccess0:amd64 (0.17-2) ... - 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Unpacking libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... - Selecting previously unselected package libwayland-client0:amd64. - Preparing to unpack .../039-libwayland-client0_1.21.0-1_amd64.deb ... - Unpacking libwayland-client0:amd64 (1.21.0-1) ... - Selecting previously unselected package libx11-xcb1:amd64. - Preparing to unpack .../040-libx11-xcb1_2%3a1.8.4-2+deb12u2_amd64.deb ... - Unpacking libx11-xcb1:amd64 (2:1.8.4-2+deb12u2) ... - Selecting previously unselected package libxcb-dri2-0:amd64. - Preparing to unpack .../041-libxcb-dri2-0_1.15-1_amd64.deb ... - Unpacking libxcb-dri2-0:amd64 (1.15-1) ... - Selecting previously unselected package libxcb-dri3-0:amd64. - Preparing to unpack .../042-libxcb-dri3-0_1.15-1_amd64.deb ... - Unpacking libxcb-dri3-0:amd64 (1.15-1) ... - Selecting previously unselected package libxcb-present0:amd64. - Preparing to unpack .../043-libxcb-present0_1.15-1_amd64.deb ... - Unpacking libxcb-present0:amd64 (1.15-1) ... - Selecting previously unselected package libxcb-randr0:amd64. - 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Selecting previously unselected package libtimedate-perl. - Preparing to unpack .../056-libtimedate-perl_2.3300-2_all.deb ... - Unpacking libtimedate-perl (2.3300-2) ... - Selecting previously unselected package libhttp-date-perl. - Preparing to unpack .../057-libhttp-date-perl_6.05-2_all.deb ... - Unpacking libhttp-date-perl (6.05-2) ... - Selecting previously unselected package libfile-listing-perl. - Preparing to unpack .../058-libfile-listing-perl_6.15-1_all.deb ... - Unpacking libfile-listing-perl (6.15-1) ... - Selecting previously unselected package libglib2.0-0:amd64. - Preparing to unpack .../059-libglib2.0-0_2.74.6-2+deb12u2_amd64.deb ... - Unpacking libglib2.0-0:amd64 (2.74.6-2+deb12u2) ... - Selecting previously unselected package libxml2:amd64. - Preparing to unpack .../060-libxml2_2.9.14+dfsg-1.3~deb12u1_amd64.deb ... - Unpacking libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... - Selecting previously unselected package shared-mime-info. - Preparing to unpack .../061-shared-mime-info_2.2-1_amd64.deb ... - 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Unpacking libsensors5:amd64 (1:3.6.0-7.1) ... - Selecting previously unselected package libgl1-mesa-dri:amd64. - Preparing to unpack .../074-libgl1-mesa-dri_22.3.6-1+deb12u1_amd64.deb ... - Unpacking libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... - Selecting previously unselected package libglx-mesa0:amd64. - Preparing to unpack .../075-libglx-mesa0_22.3.6-1+deb12u1_amd64.deb ... - Unpacking libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... - Selecting previously unselected package libglx0:amd64. - Preparing to unpack .../076-libglx0_1.6.0-1_amd64.deb ... - Unpacking libglx0:amd64 (1.6.0-1) ... - Selecting previously unselected package libgl1:amd64. - Preparing to unpack .../077-libgl1_1.6.0-1_amd64.deb ... - Unpacking libgl1:amd64 (1.6.0-1) ... - Selecting previously unselected package libgles2:amd64. - Preparing to unpack .../078-libgles2_1.6.0-1_amd64.deb ... - Unpacking libgles2:amd64 (1.6.0-1) ... - Selecting previously unselected package libglib2.0-data. - Preparing to unpack .../079-libglib2.0-data_2.74.6-2+deb12u2_all.deb ... - Unpacking libglib2.0-data (2.74.6-2+deb12u2) ... - Selecting previously unselected package libgraphite2-3:amd64. - Preparing to unpack .../080-libgraphite2-3_1.3.14-1_amd64.deb ... - Unpacking libgraphite2-3:amd64 (1.3.14-1) ... - Selecting previously unselected package libharfbuzz0b:amd64. - Preparing to unpack .../081-libharfbuzz0b_6.0.0+dfsg-3_amd64.deb ... - Unpacking libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... - Selecting previously unselected package libhtml-tagset-perl. - Preparing to unpack .../082-libhtml-tagset-perl_3.20-6_all.deb ... - Unpacking libhtml-tagset-perl (3.20-6) ... - Selecting previously unselected package libhtml-parser-perl:amd64. - Preparing to unpack .../083-libhtml-parser-perl_3.81-1_amd64.deb ... - Unpacking libhtml-parser-perl:amd64 (3.81-1) ... - Selecting previously unselected package libio-html-perl. - Preparing to unpack .../084-libio-html-perl_1.004-3_all.deb ... - Unpacking libio-html-perl (1.004-3) ... - Selecting previously unselected package liblwp-mediatypes-perl. - 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Setting up libtie-ixhash-perl (1.23-4) ... - Setting up libicu72:amd64 (72.1-3) ... - Setting up libxcb-xfixes0:amd64 (1.15-1) ... - Setting up r-doc-html (4.2.2.20221110-2) ... - Setting up libpcre16-3:amd64 (2:8.39-15) ... - Setting up libxi6:amd64 (2:1.8-1+b1) ... - Setting up libfont-afm-perl (1.20-4) ... - Setting up libxrender1:amd64 (1:0.9.10-1.1) ... - Setting up libdatrie1:amd64 (0.2.13-2+b1) ... - Setting up xdg-user-dirs (0.18-1) ... - Setting up libpng-tools (1.6.39-2) ... - Setting up libxcb-render0:amd64 (1.15-1) ... - Setting up libclone-perl:amd64 (0.46-1) ... - Setting up libglib2.0-0:amd64 (2.74.6-2+deb12u2) ... - No schema files found: doing nothing. - Setting up libglvnd0:amd64 (1.6.0-1) ... - Setting up libio-stringy-perl (2.111-3) ... - Setting up libhtml-tagset-perl (3.20-6) ... - Setting up libauthen-sasl-perl (2.1600-3) ... - Setting up libxcb-glx0:amd64 (1.15-1) ... - Setting up liblwp-mediatypes-perl (6.04-2) ... - Setting up libxcb-shape0:amd64 (1.15-1) ... - Setting up x11-common (1:7.7+23) ... - invoke-rc.d: could not determine current runlevel - invoke-rc.d: policy-rc.d denied execution of restart. - Setting up libtry-tiny-perl (0.31-2) ... - Setting up libsensors-config (1:3.6.0-7.1) ... - Setting up libxxf86dga1:amd64 (2:1.1.5-1) ... - Setting up perl-openssl-defaults:amd64 (7+b1) ... - Setting up libencode-locale-perl (1.05-3) ... - Setting up libxcb-shm0:amd64 (1.15-1) ... - Setting up libcairo2:amd64 (1.16.0-7) ... - Setting up libpcre2-16-0:amd64 (10.42-1) ... - Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... - Setting up libxcb-present0:amd64 (1.15-1) ... - Setting up libpcre3:amd64 (2:8.39-15) ... - Setting up zip (3.0-13) ... - Setting up libfontenc1:amd64 (1:1.1.4-1) ... - Setting up libz3-4:amd64 (4.8.12-3.1) ... - Setting up libpcre2-32-0:amd64 (10.42-1) ... - Setting up libblas3:amd64 (3.11.0-2) ... - 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 (2.74.6-2+deb12u2) ... - Setting up libpkgconf3:amd64 (1.8.1-1) ... - Setting up libgles2:amd64 (1.6.0-1) ... - Setting up libdata-dump-perl (1.25-1) ... - Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2) ... - Setting up libxfixes3:amd64 (1:6.0.0-2) ... - Setting up libxcb-sync1:amd64 (1.15-1) ... - Setting up libipc-system-simple-perl (1.30-2) ... - Setting up libxml-xpathengine-perl (0.14-2) ... - Setting up libncurses6:amd64 (6.4-4) ... - Setting up libdbus-1-3:amd64 (1.14.10-1~deb12u1) ... - Setting up libfribidi0:amd64 (1.0.8-2.1) ... - Setting up libxinerama1:amd64 (2:1.1.4-3) ... - Setting up libxv1:amd64 (2:1.0.11-1.1) ... - Setting up libpcre32-3:amd64 (2:8.39-15) ... - Setting up libio-html-perl (1.004-3) ... - Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... - 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 r-mathlib (4.2.2.20221110-2) ... - 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+deb12u7) ... <><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><> Processing 1/33: Processing 2/33: Processing 3/33: Processing 4/33: Processing 5/33: Processing 6/33: Processing 7/33: [conf-pkg-config: pkg-config] Processing 8/33: [conf-pkg-config: pkg-config] [conf-r: R CMD] -> retrieved base.v0.13.2 (cached) Processing 9/33: [conf-pkg-config: pkg-config] [conf-r: R CMD] -> retrieved configurator.v0.11.0 (cached) Processing 10/33: [conf-pkg-config: pkg-config] [conf-r: R CMD] -> retrieved csexp.1.5.2 (cached) Processing 11/33: [conf-pkg-config: pkg-config] [conf-r: R CMD] Processing 12/33: [conf-pkg-config: pkg-config] [conf-r: R CMD] [csexp: dune build] - usage: pkgconf [OPTIONS] [LIBRARIES] - - basic options: - - --help this message - --about print pkgconf version and license to stdout - --version print supported pkg-config version to stdout - --atleast-pkgconfig-version check whether or not pkgconf is compatible - with a specified pkg-config version - --errors-to-stdout print all errors on stdout instead of stderr - --print-errors ensure all errors are printed - --short-errors be less verbose about some errors - --silence-errors explicitly be silent about errors - --list-all list all known packages - --list-package-names list all known package names - --simulate simulate walking the calculated dependency graph - --no-cache do not cache already seen packages when - walking the dependency graph - --log-file=filename write an audit log to a specified file - --with-path=path adds a directory to the search path - --define-prefix override the prefix variable with one that is guessed based on - the location of the .pc file - --dont-define-prefix do not override the prefix variable under any circumstances - --prefix-variable=varname sets the name of the variable that pkgconf considers - to be the package prefix - --relocate=path relocates a path and exits (mostly for testsuite) - --dont-relocate-paths disables path relocation support - - cross-compilation personality support: - - --personality=triplet|filename sets the personality to 'triplet' or a file named 'filename' - --dump-personality dumps details concerning selected personality - - checking specific pkg-config database entries: - - --atleast-version require a specific version of a module - --exact-version require an exact version of a module - --max-version require a maximum version of a module - --exists check whether or not a module exists - --uninstalled check whether or not an uninstalled module will be used - --no-uninstalled never use uninstalled modules when satisfying dependencies - --no-provides do not use 'provides' rules to resolve dependencies - --maximum-traverse-depth maximum allowed depth for dependency graph - --static be more aggressive when computing dependency graph - (for static linking) - --shared use a simplified dependency graph (usually default) - --pure optimize a static dependency graph as if it were a normal - dependency graph - --env-only look only for package entries in PKG_CONFIG_PATH - --ignore-conflicts ignore 'conflicts' rules in modules - --validate validate specific .pc files for correctness - - querying specific pkg-config database fields: - - --define-variable=varname=value define variable 'varname' as 'value' - --variable=varname print specified variable entry to stdout - --cflags print required CFLAGS to stdout - --cflags-only-I print required include-dir CFLAGS to stdout - --cflags-only-other print required non-include-dir CFLAGS to stdout - --libs print required linker flags to stdout - --libs-only-L print required LDPATH linker flags to stdout - --libs-only-l print required LIBNAME linker flags to stdout - --libs-only-other print required other linker flags to stdout - --print-requires print required dependency frameworks to stdout - --print-requires-private print required dependency frameworks for static - linking to stdout - --print-provides print provided dependencies to stdout - --print-variables print all known variables in module to stdout - --digraph print entire dependency graph in graphviz 'dot' format - --keep-system-cflags keep -I/usr/include entries in cflags output - --keep-system-libs keep -L/lib:/lib/i386-linux-gnu:/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnux32:/lib32:/libx32:/usr/lib:/usr/lib/i386-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnux32:/usr/lib32:/usr/libx32 entries in libs output - --path show the exact filenames for any matching .pc files - --modversion print the specified module's version to stdout - --internal-cflags do not filter 'internal' cflags from output - - filtering output: - - --msvc-syntax print translatable fragments in MSVC syntax - --fragment-filter=types filter output fragments to the specified types - - report bugs to <https://github.com/pkgconf/pkgconf/issues/new>. -> compiled conf-pkg-config.3 Processing 12/33: [conf-r: R CMD] [csexp: dune build] -> installed conf-pkg-config.3 Processing 13/33: [conf-r: R CMD] [csexp: dune build] Processing 14/33: [conf-r: R CMD] [conf-r-mathlib: pkg-config libRmath] [csexp: dune build] -> retrieved ocaml-r.0.2.0 (cached) Processing 15/33: [conf-r: R CMD] [conf-r-mathlib: pkg-config libRmath] [csexp: dune build] -> compiled conf-r-mathlib.1 Processing 15/33: [conf-r: R CMD] [csexp: dune build] -> installed conf-r-mathlib.1 Processing 16/33: [conf-r: R CMD] [csexp: dune build] -> retrieved sexplib0.v0.13.0 (cached) Processing 17/33: [conf-r: R CMD] [csexp: dune build] Processing 18/33: [conf-r: R CMD] [csexp: dune build] [sexplib0: dune build] -> retrieved stdio.v0.13.0 (cached) -> retrieved jbuilder.1.0+beta20.2 (cached) Processing 19/33: [conf-r: R CMD] [csexp: dune build] [jbuilder: ocaml configure.ml] [sexplib0: dune build] -> compiled conf-r.1.0.0 Processing 19/33: [csexp: dune build] [jbuilder: ocaml configure.ml] [sexplib0: dune build] -> installed conf-r.1.0.0 Processing 20/33: [csexp: dune build] [jbuilder: ocaml configure.ml] [sexplib0: dune build] Processing 20/33: [csexp: dune build] [jbuilder: ocaml bootstrap.ml] [sexplib0: dune build] -> compiled csexp.1.5.2 Processing 20/33: [jbuilder: ocaml bootstrap.ml] [sexplib0: dune build] -> installed csexp.1.5.2 Processing 21/33: [jbuilder: ocaml bootstrap.ml] [sexplib0: dune build] -> compiled sexplib0.v0.13.0 Processing 21/33: [jbuilder: ocaml bootstrap.ml] -> installed sexplib0.v0.13.0 Processing 22/33: [jbuilder: ocaml bootstrap.ml] -> retrieved dune-configurator.3.15.2 (cached) Processing 23/33: [dune-configurator: rm] [jbuilder: ocaml bootstrap.ml] Processing 23/33: [dune-configurator: dune build] [jbuilder: ocaml bootstrap.ml] - '/home/opam/.opam/4.11/bin/ocamllex.opt' -q src/meta_lexer.mll - '/home/opam/.opam/4.11/bin/ocamldep.opt' -modules src/action.ml src/action_intf.ml src/arg_spec.ml src/artifacts.ml src/bin.ml src/binary_kind.ml src/build.ml src/build_interpret.ml src/build_system.ml src/clflags.ml src/cm_kind.ml src/colors.ml src/config.ml src/context.ml src/dep_path.ml src/env.ml src/errors.ml src/exe.ml src/file_tree.ml src/findlib.ml src/gen_meta.ml src/gen_rules.ml src/glob_lexer.boot.ml src/import.ml src/inline_tests.ml src/install.ml src/install_rules.ml src/installed_dune_file.ml src/interned.ml src/jbuild.ml src/jbuild_load.ml vendor/boot/jbuilder_opam_file_format.ml vendor/boot/jbuilder_re.ml src/js_of_ocaml_rules.ml src/lib.ml src/loc.ml src/log.ml src/main.ml src/menhir.ml src/merlin.ml src/meta.ml src/meta_lexer.ml src/ml_kind.ml src/mode.ml src/module.ml src/module_compilation.ml src/modules_partitioner.ml src/ocaml_flags.ml src/ocamldep.ml src/odoc.boot.ml src/opam_file.ml src/ordered_set_lang.ml src/package.ml src/path.ml src/per_item.ml src/preprocessing.ml src/print_diff.ml src/process.ml src/report_error.ml src/scheduler.ml src/scope.ml src/setup.boot.ml src/sexp.ml src/string_with_vars.ml src/sub_system.ml src/sub_system_intf.ml src/sub_system_name.ml src/super_context.ml src/syntax.ml src/top_closure.ml src/utils.ml src/utop.ml src/variant.ml src/vfile_kind.ml src/watermarks.ml src/workspace.ml > boot-depends.txt - '/home/opam/.opam/4.11/bin/ocamldep.opt' -modules src/stdune/caml/caml.ml src/stdune/caml/result.ml src/stdune/caml/result_compat.ml > boot-depends.txt - '/home/opam/.opam/4.11/bin/ocamldep.opt' -modules src/fiber/fiber.ml > boot-depends.txt - '/home/opam/.opam/4.11/bin/ocamldep.opt' -modules src/ocaml-config/ocaml_config.ml > boot-depends.txt - '/home/opam/.opam/4.11/bin/ocamldep.opt' -modules src/stdune/stdune.ml src/stdune/ansi_color.ml src/stdune/array.ml src/stdune/char.ml src/stdune/common.ml src/stdune/comparable.ml src/stdune/either.ml src/stdune/exn.ml src/stdune/filename.ml src/stdune/hashtbl.ml src/stdune/import.ml src/stdune/int.ml src/stdune/io.ml src/stdune/list.ml src/stdune/map.ml src/stdune/map_intf.ml src/stdune/option.ml src/stdune/or_exn.ml src/stdune/ordering.ml src/stdune/pp.ml src/stdune/result.ml src/stdune/set.ml src/stdune/set_intf.ml src/stdune/staged.ml src/stdune/string.ml > boot-depends.txt - '/home/opam/.opam/4.11/bin/ocamldep.opt' -modules src/usexp/usexp.ml src/usexp/parser_automaton_internal.ml src/usexp/sexp_ast.ml src/usexp/table.ml > boot-depends.txt - '/home/opam/.opam/4.11/bin/ocamldep.opt' -modules src/xdg/xdg.ml > boot-depends.txt - '/home/opam/.opam/4.11/bin/ocamlc.opt' -g -w -40 -o boot.exe unix.cma boot.ml - File "src/stdune/caml/result.ml", line 4, characters 7-17: - Alert deprecated: module Stdlib.Pervasives - Use Stdlib instead. - - If you need to stay compatible with OCaml < 4.07, you can use the - stdlib-shims library: https://github.com/ocaml/stdlib-shims - File "src/stdune/caml/result.mli", line 6, characters 7-17: - Alert deprecated: module Stdlib.Pervasives - Use Stdlib instead. - - If you need to stay compatible with OCaml < 4.07, you can use the - stdlib-shims library: https://github.com/ocaml/stdlib-shims - File "src/stdune/pp.ml", line 98, characters 7-18: - Alert deprecated: Stdlib.Format.pp_open_tag - Use Format.pp_open_stag. - File "src/stdune/pp.ml", line 100, characters 7-19: - Alert deprecated: Stdlib.Format.pp_close_tag - Use Format.pp_close_stag. - File "src/stdune/pp.ml", line 103, characters 18-48: - Alert deprecated: Stdlib.Format.pp_get_formatter_tag_functions - Use Format.pp_get_formatter_stag_functions. - File "src/stdune/pp.ml", line 105, characters 6-36: - Alert deprecated: Stdlib.Format.pp_set_formatter_tag_functions - This function will erase non-string tag formatting functions. Use Format.pp_set_formatter_stag_functions. - File "src/stdune/io.ml", line 1, characters 11-21: - Alert deprecated: module Stdlib.Pervasives - Use Stdlib instead. - - If you need to stay compatible with OCaml < 4.07, you can use the - stdlib-shims library: https://github.com/ocaml/stdlib-shims - File "src/usexp/usexp.ml", line 209, characters 15-52: - Alert deprecated: Stdlib.Format.pp_get_formatter_tag_functions - Use Format.pp_get_formatter_stag_functions. - File "src/usexp/usexp.ml", line 210, characters 2-39: - Alert deprecated: Stdlib.Format.pp_set_formatter_tag_functions - This function will erase non-string tag formatting functions. Use Format.pp_set_formatter_stag_functions. - File "src/colors.ml", line 105, characters 18-48: - Alert deprecated: Stdlib.Format.pp_get_formatter_tag_functions - Use Format.pp_get_formatter_stag_functions. - File "src/colors.ml", line 107, characters 6-36: - Alert deprecated: Stdlib.Format.pp_set_formatter_tag_functions - This function will erase non-string tag formatting functions. Use Format.pp_set_formatter_stag_functions. Processing 23/33: [dune-configurator: dune build] [jbuilder: ./boot.exe 31] -> compiled dune-configurator.3.15.2 Processing 23/33: [jbuilder: ./boot.exe 31] -> installed dune-configurator.3.15.2 Processing 24/33: [jbuilder: ./boot.exe 31] Processing 25/33: [base: dune build] [jbuilder: ./boot.exe 31] - ocamlc src/stdune/caml/.caml.objs/caml__Result.{cmi,cmti} - File "src/stdune/caml/result.mli", line 6, characters 7-17: - 6 | open Pervasives - ^^^^^^^^^^ - Alert deprecated: module Stdlib.Pervasives - Use Stdlib instead. - - If you need to stay compatible with OCaml < 4.07, you can use the - stdlib-shims library: https://github.com/ocaml/stdlib-shims - ocamlopt src/stdune/caml/.caml.objs/caml__Result.{cmx,o} - File "src/stdune/caml/result.ml", line 4, characters 7-17: - 4 | open Pervasives - ^^^^^^^^^^ - Alert deprecated: module Stdlib.Pervasives - Use Stdlib instead. - - If you need to stay compatible with OCaml < 4.07, you can use the - stdlib-shims library: https://github.com/ocaml/stdlib-shims - ocamlopt src/stdune/.stdune.objs/stdune__Io.{cmx,o} - File "src/stdune/io.ml", line 1, characters 11-21: - 1 | module P = Pervasives - ^^^^^^^^^^ - Alert deprecated: module Stdlib.Pervasives - Use Stdlib instead. - - If you need to stay compatible with OCaml < 4.07, you can use the - stdlib-shims library: https://github.com/ocaml/stdlib-shims - ocamlopt src/stdune/.stdune.objs/stdune__Pp.{cmx,o} - File "src/stdune/pp.ml", line 98, characters 7-18: - 98 | pp_open_tag ppf (embed_tag ~opening ~closing); - ^^^^^^^^^^^ - Alert deprecated: Stdlib.Format.pp_open_tag - Use Format.pp_open_stag. - File "src/stdune/pp.ml", line 100, characters 7-19: - 100 | pp_close_tag ppf () - ^^^^^^^^^^^^ - Alert deprecated: Stdlib.Format.pp_close_tag - Use Format.pp_close_stag. - File "src/stdune/pp.ml", line 103, characters 18-48: - 103 | let funcs = pp_get_formatter_tag_functions ppf () in - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Alert deprecated: Stdlib.Format.pp_get_formatter_tag_functions - Use Format.pp_get_formatter_stag_functions. - File "src/stdune/pp.ml", line 105, characters 6-36: - 105 | pp_set_formatter_tag_functions ppf - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Alert deprecated: Stdlib.Format.pp_set_formatter_tag_functions - This function will erase non-string tag formatting functions. Use Format.pp_set_formatter_stag_functions. - ocamlopt src/usexp/.usexp.objs/usexp.{cmx,o} - File "src/usexp/usexp.ml", line 209, characters 15-52: - 209 | let tfuncs = Format.pp_get_formatter_tag_functions ppf () in - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Alert deprecated: Stdlib.Format.pp_get_formatter_tag_functions - Use Format.pp_get_formatter_stag_functions. - File "src/usexp/usexp.ml", line 210, characters 2-39: - 210 | Format.pp_set_formatter_tag_functions ppf - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Alert deprecated: Stdlib.Format.pp_set_formatter_tag_functions - This function will erase non-string tag formatting functions. Use Format.pp_set_formatter_stag_functions. - ocamlopt src/.jbuilder.objs/jbuilder__Colors.{cmx,o} - File "src/colors.ml", line 105, characters 18-48: - 105 | let funcs = pp_get_formatter_tag_functions ppf () in - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Alert deprecated: Stdlib.Format.pp_get_formatter_tag_functions - Use Format.pp_get_formatter_stag_functions. - File "src/colors.ml", line 107, characters 6-36: - 107 | pp_set_formatter_tag_functions ppf - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Alert deprecated: Stdlib.Format.pp_set_formatter_tag_functions - This function will erase non-string tag formatting functions. Use Format.pp_set_formatter_stag_functions. -> compiled jbuilder.1.0+beta20.2 Processing 25/33: [base: dune build] -> installed jbuilder.1.0+beta20.2 Processing 26/33: [base: dune build] + /home/opam/.opam/4.11/bin/dune "build" "-p" "base" "-j" "31" (CWD=/home/opam/.opam/4.11/.opam-switch/build/base.v0.13.2) -> compiled base.v0.13.2 -> installed base.v0.13.2 Processing 28/33: [stdio: dune build] + /home/opam/.opam/4.11/bin/dune "build" "-p" "stdio" "-j" "31" (CWD=/home/opam/.opam/4.11/.opam-switch/build/stdio.v0.13.0) -> compiled stdio.v0.13.0 -> installed stdio.v0.13.0 Processing 30/33: [configurator: jbuilder build] + /home/opam/.opam/4.11/bin/jbuilder "build" "-p" "configurator" "-j" "31" (CWD=/home/opam/.opam/4.11/.opam-switch/build/configurator.v0.11.0) - ocamlc src/.configurator.objs/configurator.{cmo,cmt} - File "src/configurator.ml", line 8, characters 20-35: - 8 | module Pervasives = Caml.Pervasives - ^^^^^^^^^^^^^^^ - Alert deprecated: module Caml.Pervasives - Use Stdlib instead. - - If you need to stay compatible with OCaml < 4.07, you can use the - stdlib-shims library: https://github.com/ocaml/stdlib-shims - ocamlopt src/.configurator.objs/configurator.{cmx,o} - File "src/configurator.ml", line 8, characters 20-35: - 8 | module Pervasives = Caml.Pervasives - ^^^^^^^^^^^^^^^ - Alert deprecated: module Caml.Pervasives - Use Stdlib instead. - - If you need to stay compatible with OCaml < 4.07, you can use the - stdlib-shims library: https://github.com/ocaml/stdlib-shims -> compiled configurator.v0.11.0 -> installed configurator.v0.11.0 Processing 32/33: [ocaml-r: dune build] + /home/opam/.opam/4.11/bin/dune "build" "-p" "ocaml-r" "-j" "31" (CWD=/home/opam/.opam/4.11/.opam-switch/build/ocaml-r.0.2.0) - File "lib/dune", line 9, characters 19-37: - 9 | read_internal_stub - ^^^^^^^^^^^^^^^^^^ - (cd _build/default/lib && /usr/bin/gcc -O2 -fno-strict-aliasing -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_REENTRANT -I/usr/share/R/include -g -I /home/opam/.opam/4.11/lib/ocaml -o read_internal_stub.o -c read_internal_stub.c) - In file included from read_internal_stub.c:32: - read_internal_stub.c: In function 'ocamlr_inspect_primsxp_offset': - read_internal_stub.c:108:32: error: invalid use of undefined type 'struct SEXPREC' - 108 | return(Val_int(Sexp_val(sexp)->u.primsxp.offset)); - | ^~ - /home/opam/.opam/4.11/lib/ocaml/caml/mlvalues.h:75:47: note: in definition of macro 'Val_long' - 75 | #define Val_long(x) ((intnat) (((uintnat)(x) << 1)) + 1) - | ^ - read_internal_stub.c:108:10: note: in expansion of macro 'Val_int' - 108 | return(Val_int(Sexp_val(sexp)->u.primsxp.offset)); - | ^~~~~~~ - read_internal_stub.c: In function 'ocamlr_inspect_promsxp_value': - read_internal_stub.c:241:33: error: invalid use of undefined type 'struct SEXPREC' - 241 | return(Val_sexp(Sexp_val(sexp)->u.promsxp.value)); - | ^~ - read_internal_stub.c: In function 'ocamlr_inspect_promsxp_expr': - read_internal_stub.c:254:33: error: invalid use of undefined type 'struct SEXPREC' - 254 | return(Val_sexp(Sexp_val(sexp)->u.promsxp.expr)); - | ^~ - read_internal_stub.c: In function 'ocamlr_inspect_promsxp_env': - read_internal_stub.c:267:33: error: invalid use of undefined type 'struct SEXPREC' - 267 | return(Val_sexp(Sexp_val(sexp)->u.promsxp.env)); - | ^~ - File "lib/dune", line 10, characters 19-38: - 10 | write_internal_stub - ^^^^^^^^^^^^^^^^^^^ - (cd _build/default/lib && /usr/bin/gcc -O2 -fno-strict-aliasing -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_REENTRANT -I/usr/share/R/include -g -I /home/opam/.opam/4.11/lib/ocaml -o write_internal_stub.o -c write_internal_stub.c) - write_internal_stub.c: In function 'ocamlr_write_lisplist_carval': - write_internal_stub.c:50:21: error: invalid use of undefined type 'struct SEXPREC' - 50 | Sexp_val(lisplist)->u.listsxp.carval = Sexp_val(elmnt); - | ^~ - write_internal_stub.c: In function 'ocamlr_write_lisplist_tagval': - write_internal_stub.c:55:21: error: invalid use of undefined type 'struct SEXPREC' - 55 | Sexp_val(lisplist)->u.listsxp.tagval = Sexp_val(tag); - | ^~ - (cd _build/default/lib && /usr/bin/gcc -O2 -fno-strict-aliasing -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_REENTRANT -I/usr/share/R/include -g -I /home/opam/.opam/4.11/lib/ocaml -o initialisation_stub.o -c initialisation_stub.c) - initialisation_stub.c: In function 'ocamlr_initEmbeddedR': - initialisation_stub.c:70:35: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] - 70 | for (i=0; i<length; i++) argv[i]=String_val(Field(ml_argv, i)); - | ^ [ERROR] The compilation of ocaml-r.0.2.0 failed at "dune build -p ocaml-r -j 31". #=== ERROR while compiling ocaml-r.0.2.0 ======================================# # context 2.1.5 | linux/x86_64 | ocaml-base-compiler.4.11.2 | file:///src # path ~/.opam/4.11/.opam-switch/build/ocaml-r.0.2.0 # command ~/.opam/4.11/bin/dune build -p ocaml-r -j 31 # exit-code 1 # env-file ~/.opam/log/ocaml-r-114-8aa744.env # output-file ~/.opam/log/ocaml-r-114-8aa744.out ### output ### # File "lib/dune", line 9, characters 19-37: # 9 | read_internal_stub # ^^^^^^^^^^^^^^^^^^ # (cd _build/default/lib && /usr/bin/gcc -O2 -fno-strict-aliasing -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_REENTRANT -I/usr/share/R/include -g -I /home/opam/.opam/4.11/lib/ocaml -o read_internal_stub.o -c read_internal_stub.c) # In file included from read_internal_stub.c:32: # read_internal_stub.c: In function 'ocamlr_inspect_primsxp_offset': # read_internal_stub.c:108:32: error: invalid use of undefined type 'struct SEXPREC' # 108 | return(Val_int(Sexp_val(sexp)->u.primsxp.offset)); # | ^~ # /home/opam/.opam/4.11/lib/ocaml/caml/mlvalues.h:75:47: note: in definition of macro 'Val_long' # 75 | #define Val_long(x) ((intnat) (((uintnat)(x) << 1)) + 1) # | ^ # read_internal_stub.c:108:10: note: in expansion of macro 'Val_int' # 108 | return(Val_int(Sexp_val(sexp)->u.primsxp.offset)); # | ^~~~~~~ # read_internal_stub.c: In function 'ocamlr_inspect_promsxp_value': # read_internal_stub.c:241:33: error: invalid use of undefined type 'struct SEXPREC' # 241 | return(Val_sexp(Sexp_val(sexp)->u.promsxp.value)); # | ^~ # read_internal_stub.c: In function 'ocamlr_inspect_promsxp_expr': # read_internal_stub.c:254:33: error: invalid use of undefined type 'struct SEXPREC' # 254 | return(Val_sexp(Sexp_val(sexp)->u.promsxp.expr)); # | ^~ # read_internal_stub.c: In function 'ocamlr_inspect_promsxp_env': # read_internal_stub.c:267:33: error: invalid use of undefined type 'struct SEXPREC' # 267 | return(Val_sexp(Sexp_val(sexp)->u.promsxp.env)); # | ^~ # File "lib/dune", line 10, characters 19-38: # 10 | write_internal_stub # ^^^^^^^^^^^^^^^^^^^ # (cd _build/default/lib && /usr/bin/gcc -O2 -fno-strict-aliasing -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_REENTRANT -I/usr/share/R/include -g -I /home/opam/.opam/4.11/lib/ocaml -o write_internal_stub.o -c write_internal_stub.c) # write_internal_stub.c: In function 'ocamlr_write_lisplist_carval': # write_internal_stub.c:50:21: error: invalid use of undefined type 'struct SEXPREC' # 50 | Sexp_val(lisplist)->u.listsxp.carval = Sexp_val(elmnt); # | ^~ # write_internal_stub.c: In function 'ocamlr_write_lisplist_tagval': # write_internal_stub.c:55:21: error: invalid use of undefined type 'struct SEXPREC' # 55 | Sexp_val(lisplist)->u.listsxp.tagval = Sexp_val(tag); # | ^~ # (cd _build/default/lib && /usr/bin/gcc -O2 -fno-strict-aliasing -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_REENTRANT -I/usr/share/R/include -g -I /home/opam/.opam/4.11/lib/ocaml -o initialisation_stub.o -c initialisation_stub.c) # initialisation_stub.c: In function 'ocamlr_initEmbeddedR': # initialisation_stub.c:70:35: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] # 70 | for (i=0; i<length; i++) argv[i]=String_val(Field(ml_argv, i)); # | ^ <><> Error report <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> +- The following actions failed | - build ocaml-r 0.2.0 +- +- The following changes have been performed | - install base v0.13.2 | - install conf-pkg-config 3 | - install conf-r 1.0.0 | - install conf-r-mathlib 1 | - install configurator v0.11.0 | - install csexp 1.5.2 | - install dune-configurator 3.15.2 | - install jbuilder 1.0+beta20.2 | - install sexplib0 v0.13.0 | - install stdio v0.13.0 +- <><> configurator.v0.11.0 installed successfully ><><><><><><><><><><><><><><><> => configurator is deprecated. Please use dune-configurator in new code and consider switching to it in existing projects. # 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/4.11/.opam-switch/backup/state-20240517134300.export" 'opam --cli=2.1 install ocaml-r.0.2.0 stdio.v0.13.0 sexplib0.v0.13.0 jbuilder.1.0+beta20.2 dune-configurator.3.15.2 dune.3.15.2 csexp.1.5.2 configurator.v0.11.0 conf-r-mathlib.1 conf-r.1.0.0 conf-pkg-config.3 base.v0.13.2 --verbose --yes --confirm-level=unsafe-yes' failed.