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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 1.2.3 <><> 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 oplsr.8.0.1 parany.14.0.1 ocamlfind.1.9.6 num.1.5-1 minicli.5.0.2 dune.3.16.0 dolog.6.0.0 cpu.2.0.0 cpm.12.2.0 conf-r.1.0.0 conf-gnuplot.0.1 conf-autoconf.0.2 camlp-streams.5.0.1 batteries.3.8.0" 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: autoconf gnuplot-x11 r-base-core [NOTE] Package dune is already installed (current version is 3.16.0). [NOTE] Package ocamlfind is already installed (current version is 1.9.6). The following actions will be performed: - install conf-autoconf 0.2 - install conf-r 1.0.0 - install minicli 5.0.2 - install conf-gnuplot 0.1 - install camlp-streams 5.0.1 - install num 1.5-1 - install dolog 6.0.0 - install cpu 2.0.0 - install batteries 3.8.0 - install parany 14.0.1 - install cpm 12.2.0 - install oplsr 8.0.1 ===== 12 to install ===== The following system packages will first need to be installed: autoconf gnuplot-x11 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" "autoconf" "gnuplot-x11" "r-base-core" - debconf: delaying package configuration, since apt-utils is not installed - Selecting previously unselected package libargon2-1: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 ... 18764 files and directories currently installed.) - Preparing to unpack .../00-libargon2-1_0~20171227-0.3+deb12u1_amd64.deb ... - Unpacking libargon2-1:amd64 (0~20171227-0.3+deb12u1) ... - Selecting previously unselected package dmsetup. - Preparing to unpack .../01-dmsetup_2%3a1.02.185-2_amd64.deb ... - Unpacking dmsetup (2:1.02.185-2) ... - Selecting previously unselected package libdevmapper1.02.1:amd64. - Preparing to unpack .../02-libdevmapper1.02.1_2%3a1.02.185-2_amd64.deb ... - Unpacking libdevmapper1.02.1:amd64 (2:1.02.185-2) ... - Selecting previously unselected package libjson-c5:amd64. - Preparing to unpack .../03-libjson-c5_0.16-2_amd64.deb ... - Unpacking libjson-c5:amd64 (0.16-2) ... - Selecting previously unselected package libcryptsetup12:amd64. - Preparing to unpack .../04-libcryptsetup12_2%3a2.6.1-4~deb12u2_amd64.deb ... - Unpacking libcryptsetup12:amd64 (2:2.6.1-4~deb12u2) ... - Selecting previously unselected package libfdisk1:amd64. - Preparing to unpack .../05-libfdisk1_2.38.1-5+deb12u1_amd64.deb ... - Unpacking libfdisk1:amd64 (2.38.1-5+deb12u1) ... - Selecting previously unselected package libkmod2:amd64. - Preparing to unpack .../06-libkmod2_30+20221128-1_amd64.deb ... - Unpacking libkmod2:amd64 (30+20221128-1) ... - Selecting previously unselected package libapparmor1:amd64. - Preparing to unpack .../07-libapparmor1_3.0.8-3_amd64.deb ... - Unpacking libapparmor1:amd64 (3.0.8-3) ... - Selecting previously unselected package libip4tc2:amd64. - Preparing to unpack .../08-libip4tc2_1.8.9-2_amd64.deb ... - Unpacking libip4tc2:amd64 (1.8.9-2) ... - Selecting previously unselected package libsystemd-shared:amd64. - Preparing to unpack .../09-libsystemd-shared_252.30-1~deb12u2_amd64.deb ... - Unpacking libsystemd-shared:amd64 (252.30-1~deb12u2) ... - Selecting previously unselected package systemd. - Preparing to unpack .../10-systemd_252.30-1~deb12u2_amd64.deb ... - Unpacking systemd (252.30-1~deb12u2) ... - Setting up libargon2-1:amd64 (0~20171227-0.3+deb12u1) ... - Setting up libjson-c5:amd64 (0.16-2) ... - Setting up libfdisk1:amd64 (2.38.1-5+deb12u1) ... - Setting up libkmod2:amd64 (30+20221128-1) ... - Setting up libapparmor1:amd64 (3.0.8-3) ... - Setting up libip4tc2:amd64 (1.8.9-2) ... - Setting up libsystemd-shared:amd64 (252.30-1~deb12u2) ... - Setting up libdevmapper1.02.1:amd64 (2:1.02.185-2) ... - Setting up libcryptsetup12:amd64 (2:2.6.1-4~deb12u2) ... - Setting up systemd (252.30-1~deb12u2) ... - Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service → /lib/systemd/system/getty@.service. - Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target → /lib/systemd/system/remote-fs.target. - Created symlink /etc/systemd/system/sysinit.target.wants/systemd-pstore.service → /lib/systemd/system/systemd-pstore.service. - Initializing machine ID from random generator. - Creating group 'systemd-journal' with GID 999. - Creating group 'systemd-network' with GID 998. - Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. - Setting up dmsetup (2:1.02.185-2) ... - Selecting previously unselected package systemd-sysv. - (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 ... 19679 files and directories currently installed.) - Preparing to unpack .../000-systemd-sysv_252.30-1~deb12u2_amd64.deb ... - Unpacking systemd-sysv (252.30-1~deb12u2) ... - Selecting previously unselected package libdbus-1-3:amd64. - Preparing to unpack .../001-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 .../002-dbus-bin_1.14.10-1~deb12u1_amd64.deb ... - 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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 libxkbcommon0:amd64 (1.5.0-1) ... - Setting up libwayland-client0:amd64 (1.21.0-1) ... - Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... - Setting up automake (1:1.16.5-1.3) ... - update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode - Setting up libpcrecpp0v5:amd64 (2:8.39-15) ... - Setting up gnuplot-data (5.4.4+dfsg1-2) ... - 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 libavahi-common3:amd64 (0.8-10) ... - 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 libatspi2.0-0:amd64 (2.46.0-5) ... - Setting up libreadline-dev:amd64 (8.2-1.3) ... - Setting up libwxbase3.2-1:amd64 (3.2.2+dfsg-2) ... - Setting up pkgconf:amd64 (1.8.1-1) ... - Setting up libatk-bridge2.0-0:amd64 (2.46.0-5) ... - 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 libwayland-cursor0:amd64 (1.21.0-1) ... - 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 libpam-systemd:amd64 (252.30-1~deb12u2) ... - Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+deb12u1) ... - Setting up libsm6:amd64 (2:1.2.3-1) ... - Setting up libavahi-client3:amd64 (0.8-10) ... - 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 gtk-update-icon-cache (3.24.38-2~deb12u2) ... - 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 dbus-user-session (1.14.10-1~deb12u1) ... - Setting up libegl-mesa0:amd64 (22.3.6-1+deb12u1) ... - Setting up libnet-smtp-ssl-perl (1.04-2) ... - Setting up adwaita-icon-theme (43-1) ... - 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 (2.21-2) ... - Setting up libnotify4:amd64 (0.8.1-1) ... - Setting up libxt6:amd64 (1:1.2.1-1.1) ... - Setting up libcups2:amd64 (2.4.2-3+deb12u7) ... - Setting up libhttp-daemon-perl (6.16-1) ... - Setting up libgdk-pixbuf2.0-bin (2.42.10+dfsg-1+deb12u1) ... - 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 dconf-service (0.40.0-4) ... - Setting up libxaw7:amd64 (2:1.0.14-1) ... - Setting up x11-xserver-utils (7.7+9+b1) ... - Setting up librsvg2-2:amd64 (2.54.7+dfsg-1~deb12u1) ... - 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 librsvg2-common:amd64 (2.54.7+dfsg-1~deb12u1) ... - 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 dconf-gsettings-backend:amd64 (0.40.0-4) ... - 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 libgtk-3-common (3.24.38-2~deb12u2) ... - Setting up gsettings-desktop-schemas (43.0-1) ... - Setting up r-cran-class (7.3-21-1) ... - Setting up libgtk-3-0:amd64 (3.24.38-2~deb12u2) ... - Setting up r-cran-survival (3.5-3-1) ... - Setting up libgtk-3-bin (3.24.38-2~deb12u2) ... - Setting up at-spi2-core (2.46.0-5) ... - Setting up libwxgtk3.2-1:amd64 (3.2.2+dfsg-2) ... - Setting up r-cran-rpart (4.1.19-1) ... - Setting up r-recommended (4.2.2.20221110-2) ... - Setting up gnuplot-x11 (5.4.4+dfsg1-2+b2) ... - update-alternatives: using /usr/bin/gnuplot-x11 to provide /usr/bin/gnuplot (gnuplot) in auto mode - 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 triggers for libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+deb12u1) ... <><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><> Processing 1/36: Processing 2/36: Processing 3/36: Processing 4/36: -> retrieved conf-r.1.0.0 (cached) Processing 5/36: Processing 6/36: Processing 7/36: [conf-autoconf: autoconf] Processing 8/36: [conf-autoconf: autoconf] [conf-gnuplot: gnuplot] Processing 9/36: [conf-autoconf: autoconf] [conf-gnuplot: gnuplot] [conf-r: R CMD] -> retrieved batteries.3.8.0 (cached) Processing 10/36: [conf-autoconf: autoconf] [conf-gnuplot: gnuplot] [conf-r: R CMD] -> retrieved camlp-streams.5.0.1 (cached) Processing 11/36: [conf-autoconf: autoconf] [conf-gnuplot: gnuplot] [conf-r: R CMD] Processing 12/36: [camlp-streams: dune build] [conf-autoconf: autoconf] [conf-gnuplot: gnuplot] [conf-r: R CMD] -> retrieved cpm.12.2.0 (cached) Processing 13/36: [camlp-streams: dune build] [conf-autoconf: autoconf] [conf-gnuplot: gnuplot] [conf-r: R CMD] - autoconf (GNU Autoconf) 2.71 - Copyright (C) 2021 Free Software Foundation, Inc. - License GPLv3+/Autoconf: GNU GPL version 3 or later - <https://gnu.org/licenses/gpl.html>, <https://gnu.org/licenses/exceptions.html> - This is free software: you are free to change and redistribute it. - There is NO WARRANTY, to the extent permitted by law. - - Written by David J. MacKenzie and Akim Demaille. -> compiled conf-autoconf.0.2 Processing 13/36: [camlp-streams: dune build] [conf-gnuplot: gnuplot] [conf-r: R CMD] -> installed conf-autoconf.0.2 Processing 14/36: [camlp-streams: dune build] [conf-gnuplot: gnuplot] [conf-r: R CMD] - gnuplot 5.4 patchlevel 4 -> compiled conf-gnuplot.0.1 Processing 14/36: [camlp-streams: dune build] [conf-r: R CMD] -> installed conf-gnuplot.0.1 Processing 15/36: [camlp-streams: dune build] [conf-r: R CMD] -> retrieved cpu.2.0.0 (cached) Processing 16/36: [camlp-streams: dune build] [conf-r: R CMD] Processing 17/36: [camlp-streams: dune build] [conf-r: R CMD] [cpu: autoconf] -> retrieved dolog.6.0.0 (cached) Processing 18/36: [camlp-streams: dune build] [conf-r: R CMD] [cpu: autoconf] Processing 19/36: [camlp-streams: dune build] [conf-r: R CMD] [cpu: autoconf] [dolog: dune build] -> retrieved minicli.5.0.2 (cached) Processing 20/36: [camlp-streams: dune build] [conf-r: R CMD] [cpu: autoconf] [dolog: dune build] Processing 21/36: [camlp-streams: dune build] [conf-r: R CMD] [cpu: autoconf] [dolog: dune build] [minicli: dune build] -> retrieved num.1.5-1 (cached) [num: patch] applying num-in-findlib-dir.patch Processing 22/36: [camlp-streams: dune build] [conf-r: R CMD] [cpu: autoconf] [dolog: dune build] [minicli: dune build] [num: patch] -> retrieved oplsr.8.0.1 (cached) -> retrieved parany.14.0.1 (cached) Processing 22/36: [camlp-streams: dune build] [conf-r: R CMD] [cpu: autoconf] [dolog: dune build] [minicli: dune build] [num: make opam-modern] -> compiled conf-r.1.0.0 Processing 22/36: [camlp-streams: dune build] [cpu: autoconf] [dolog: dune build] [minicli: dune build] [num: make opam-modern] -> installed conf-r.1.0.0 Processing 23/36: [camlp-streams: dune build] [cpu: autoconf] [dolog: dune build] [minicli: dune build] [num: make opam-modern] - configure.ac:8: warning: The macro `AC_HEADER_STDC' is obsolete. - configure.ac:8: You should run autoupdate. - ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... - configure.ac:8: the top level Processing 23/36: [camlp-streams: dune build] [cpu: autoheader] [dolog: dune build] [minicli: dune build] [num: make opam-modern] -> compiled dolog.6.0.0 Processing 23/36: [camlp-streams: dune build] [cpu: autoheader] [minicli: dune build] [num: make opam-modern] -> installed dolog.6.0.0 Processing 24/36: [camlp-streams: dune build] [cpu: autoheader] [minicli: dune build] [num: make opam-modern] -> compiled minicli.5.0.2 Processing 24/36: [camlp-streams: dune build] [cpu: autoheader] [num: make opam-modern] -> installed minicli.5.0.2 Processing 25/36: [camlp-streams: dune build] [cpu: autoheader] [num: make opam-modern] -> compiled camlp-streams.5.0.1 Processing 25/36: [cpu: autoheader] [num: make opam-modern] -> installed camlp-streams.5.0.1 Processing 26/36: [cpu: autoheader] [num: make opam-modern] Processing 26/36: [cpu: ./configure] [num: make opam-modern] - checking for ocamlc... ocamlc - OCaml version is 5.1.1 - OCaml library path is /home/opam/.opam/5.1/lib/ocaml - checking for ocamlopt... ocamlopt - checking for ocamlc.opt... ocamlc.opt - checking for ocamlopt.opt... ocamlopt.opt - checking for dynlink.cmxa... no - checking for ocaml... ocaml - checking for ocamldep... ocamldep - checking for ocamlmktop... ocamlmktop - checking for ocamlmklib... ocamlmklib - checking for ocamldoc... ocamldoc - checking for ocamlbuild... no - checking for gcc... gcc - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... - checking whether we are cross compiling... no - checking for suffix of object files... o - checking whether the compiler supports GNU C... yes - checking whether gcc accepts -g... yes - checking for gcc option to enable C11 features... none needed - checking for stdio.h... yes - checking for stdlib.h... yes - checking for string.h... yes - checking for inttypes.h... yes - checking for stdint.h... yes - checking for strings.h... yes - checking for sys/stat.h... yes - checking for sys/types.h... yes - checking for unistd.h... yes - checking for grep that handles long lines and -e... /usr/bin/grep - checking for egrep... /usr/bin/grep -E - checking for sched.h... yes - checking for gcc options needed to detect all undeclared functions... none needed - checking whether sched_setaffinity is declared... yes - checking for mach/thread_policy.h... no - checking whether thread_policy_set is declared... no - configure: creating ./config.status - config.status: creating src/config.h Processing 26/36: [cpu: dune build] [num: make opam-modern] - /usr/bin/make -C src all - make[1]: Entering directory '/home/opam/.opam/5.1/.opam-switch/build/num.1.5-1/src' - ocamlc -ccopt -DBNG_ARCH_amd64 -c bng.c - ocamlc -ccopt -DBNG_ARCH_amd64 -c nat_stubs.c - ocamlmklib -oc nums bng.o nat_stubs.o - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c int_misc.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c int_misc.ml - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c nat.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c nat.ml - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c big_int.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c big_int.ml - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c arith_flags.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c arith_flags.ml - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c ratio.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c ratio.ml - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c num.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c num.ml - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c arith_status.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c arith_status.ml - ocamlmklib -o nums -oc nums -linkall int_misc.cmo nat.cmo big_int.cmo arith_flags.cmo ratio.cmo num.cmo arith_status.cmo - cp ../toplevel/num_top_printers.mli ../toplevel/num_top.mli ../toplevel/num_top_printers.ml ../toplevel/num_top.ml . - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c num_top_printers.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c num_top_printers.ml - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c num_top.mli - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c num_top.ml - ocamlc -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -a -o num_top.cma num_top_printers.cmo num_top.cmo - echo 'version = "1.6~dev"' > META.top - cat META.num-top.in >> META.top - ocamlopt -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c int_misc.ml - ocamlopt -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c nat.ml - ocamlopt -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c big_int.ml - ocamlopt -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c arith_flags.ml - ocamlopt -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c ratio.ml - ocamlopt -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c num.ml - ocamlopt -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -c arith_status.ml - ocamlmklib -o nums -oc nums -linkall int_misc.cmx nat.cmx big_int.cmx arith_flags.cmx ratio.cmx num.cmx arith_status.cmx - ocamlopt -w +a-4-9-41-42-44-45-48 -bin-annot -g -safe-string -strict-sequence -strict-formats -I +compiler-libs -I . -shared -o nums.cmxs nums.cmxa - make[1]: Leaving directory '/home/opam/.opam/5.1/.opam-switch/build/num.1.5-1/src' - cp src/num-modern.install num.install -> compiled num.1.5-1 Processing 26/36: [cpu: dune build] -> installed num.1.5-1 Processing 27/36: [cpu: dune build] Processing 28/36: [batteries: dune build] [cpu: dune build] -> compiled cpu.2.0.0 Processing 28/36: [batteries: dune build] -> installed cpu.2.0.0 Processing 29/36: [batteries: dune build] Processing 30/36: [batteries: dune build] [parany: dune build] -> compiled parany.14.0.1 Processing 30/36: [batteries: dune build] -> installed parany.14.0.1 Processing 31/36: [batteries: dune build] + /home/opam/.opam/5.1/bin/dune "build" "-p" "batteries" "-j" "39" "@install" (CWD=/home/opam/.opam/5.1/.opam-switch/build/batteries.3.8.0) -> compiled batteries.3.8.0 -> installed batteries.3.8.0 Processing 33/36: [cpm: dune build] + /home/opam/.opam/5.1/bin/dune "build" "-p" "cpm" "-j" "39" (CWD=/home/opam/.opam/5.1/.opam-switch/build/cpm.12.2.0) -> compiled cpm.12.2.0 -> installed cpm.12.2.0 Processing 35/36: [oplsr: dune build] + /home/opam/.opam/5.1/bin/dune "build" "-p" "oplsr" "-j" "39" (CWD=/home/opam/.opam/5.1/.opam-switch/build/oplsr.8.0.1) -> compiled oplsr.8.0.1 Processing 36/36: [oplsr: R CMD] + /usr/bin/R "CMD" "BATCH" "install_pls.r" (CWD=/home/opam/.opam/5.1/.opam-switch/build/oplsr.8.0.1) [ERROR] The installation of oplsr failed at "R CMD BATCH install_pls.r". #=== ERROR while installing oplsr.8.0.1 =======================================# # context 2.1.6 | linux/x86_64 | ocaml-base-compiler.5.1.1 | file:///src # path ~/.opam/5.1/.opam-switch/build/oplsr.8.0.1 # command /usr/bin/R CMD BATCH install_pls.r # exit-code 1 # env-file ~/.opam/log/oplsr-115-7be9ca.env # output-file ~/.opam/log/oplsr-115-7be9ca.out <><> Error report <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> +- The following actions failed | - install oplsr 8.0.1 +- +- The following changes have been performed | - install batteries 3.8.0 | - install camlp-streams 5.0.1 | - install conf-autoconf 0.2 | - install conf-gnuplot 0.1 | - install conf-r 1.0.0 | - install cpm 12.2.0 | - install cpu 2.0.0 | - install dolog 6.0.0 | - install minicli 5.0.2 | - install num 1.5-1 | - install parany 14.0.1 +- <><> oplsr.8.0.1 troubleshooting ><><><><><><><><><><><><><><><><><><><><><><><> => Please interact with R to install needed things in user-space: R install.packages('pls', 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-20240912112010.export" 'opam --cli=2.1 install oplsr.8.0.1 parany.14.0.1 ocamlfind.1.9.6 num.1.5-1 minicli.5.0.2 dune.3.16.0 dolog.6.0.0 cpu.2.0.0 cpm.12.2.0 conf-r.1.0.0 conf-gnuplot.0.1 conf-autoconf.0.2 camlp-streams.5.0.1 batteries.3.8.0 --verbose --yes --confirm-level=unsafe-yes' failed.