Warning: Permanently added '18.206.172.49' (ED25519) to the list of known hosts. Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-7h5p_ihj/R-CRAN-ClustAssess/R-CRAN-ClustAssess.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-7h5p_ihj/R-CRAN-ClustAssess --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1748397488.398721 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.1 starting (python version = 3.13.0, NVR = mock-6.1-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-7h5p_ihj/R-CRAN-ClustAssess/R-CRAN-ClustAssess.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-7h5p_ihj/R-CRAN-ClustAssess --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1748397488.398721 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-7h5p_ihj/R-CRAN-ClustAssess/R-CRAN-ClustAssess.spec) Config(fedora-42-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.1 INFO: Mock Version: 6.1 Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-42-x86_64-1748397488.398721/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (fallback) INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.20.1-1.fc41.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 python3-dnf-4.23.0-1.fc41.noarch python3-dnf-plugins-core-4.10.1-1.fc41.noarch dnf5-5.2.13.1-1.fc41.x86_64 dnf5-plugins-5.2.13.1-1.fc41.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: updates 100% | 105.4 KiB/s | 30.6 KiB | 00m00s fedora 100% | 1.0 MiB/s | 30.7 KiB | 00m00s Copr repository 100% | 102.6 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.37-1.fc42 fedora 8.2 MiB bzip2 x86_64 1.0.8-20.fc42 fedora 99.3 KiB coreutils x86_64 9.6-3.fc42 updates 5.4 MiB cpio x86_64 2.15-4.fc42 fedora 1.1 MiB diffutils x86_64 3.12-1.fc42 updates 1.6 MiB fedora-release-common noarch 42-26 updates 20.2 KiB findutils x86_64 1:4.10.0-5.fc42 fedora 1.9 MiB gawk x86_64 5.3.1-1.fc42 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.41-5.fc42 updates 0.0 B grep x86_64 3.11-10.fc42 fedora 1.0 MiB gzip x86_64 1.13-3.fc42 fedora 392.9 KiB info x86_64 7.2-3.fc42 fedora 357.9 KiB patch x86_64 2.8-1.fc42 updates 222.8 KiB redhat-rpm-config noarch 342-4.fc42 updates 185.5 KiB rpm-build x86_64 4.20.1-1.fc42 fedora 168.7 KiB sed x86_64 4.9-4.fc42 fedora 857.3 KiB shadow-utils x86_64 2:4.17.4-1.fc42 fedora 4.0 MiB tar x86_64 2:1.35-5.fc42 fedora 3.0 MiB unzip x86_64 6.0-66.fc42 fedora 390.3 KiB util-linux x86_64 2.40.4-7.fc42 fedora 3.4 MiB which x86_64 2.23-1.fc42 fedora 83.4 KiB xz x86_64 1:5.8.1-2.fc42 updates 1.3 MiB Installing dependencies: add-determinism x86_64 0.6.0-1.fc42 fedora 2.5 MiB alternatives x86_64 1.33-1.fc42 updates 62.2 KiB ansible-srpm-macros noarch 1-17.1.fc42 fedora 35.7 KiB audit-libs x86_64 4.0.3-2.fc42 fedora 351.3 KiB basesystem noarch 11-22.fc42 fedora 0.0 B binutils x86_64 2.44-3.fc42 fedora 25.9 MiB build-reproducibility-srpm-macros noarch 0.6.0-1.fc42 fedora 735.0 B bzip2-libs x86_64 1.0.8-20.fc42 fedora 84.6 KiB ca-certificates noarch 2024.2.69_v8.0.401-6.fc42 updates 2.6 MiB coreutils-common x86_64 9.6-3.fc42 updates 11.1 MiB crypto-policies noarch 20250214-1.gitff7551b.fc42 fedora 137.2 KiB curl x86_64 8.11.1-4.fc42 fedora 450.6 KiB cyrus-sasl-lib x86_64 2.1.28-30.fc42 fedora 2.3 MiB debugedit x86_64 5.1-6.fc42 updates 192.7 KiB dwz x86_64 0.15-9.fc42 fedora 291.0 KiB ed x86_64 1.21-2.fc42 fedora 146.5 KiB efi-srpm-macros noarch 6-3.fc42 updates 40.1 KiB elfutils x86_64 0.193-2.fc42 updates 2.9 MiB elfutils-debuginfod-client x86_64 0.193-2.fc42 updates 83.9 KiB elfutils-default-yama-scope noarch 0.193-2.fc42 updates 1.8 KiB elfutils-libelf x86_64 0.193-2.fc42 updates 1.2 MiB elfutils-libs x86_64 0.193-2.fc42 updates 683.4 KiB fedora-gpg-keys noarch 42-1 fedora 128.2 KiB fedora-release noarch 42-26 updates 0.0 B fedora-release-identity-basic noarch 42-26 updates 674.0 B fedora-repos noarch 42-1 fedora 4.9 KiB file x86_64 5.46-1.fc42 fedora 100.2 KiB file-libs x86_64 5.46-1.fc42 fedora 11.9 MiB filesystem x86_64 3.18-42.fc42 updates 112.0 B filesystem-srpm-macros noarch 3.18-42.fc42 updates 38.2 KiB fonts-srpm-macros noarch 1:2.0.5-21.fc42 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-2.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-14.fc42 fedora 144.0 B gdb-minimal x86_64 16.3-1.fc42 updates 13.2 MiB gdbm-libs x86_64 1:1.23-9.fc42 fedora 129.9 KiB ghc-srpm-macros noarch 1.9.2-2.fc42 fedora 779.0 B glibc x86_64 2.41-5.fc42 updates 6.6 MiB glibc-common x86_64 2.41-5.fc42 updates 1.0 MiB glibc-gconv-extra x86_64 2.41-5.fc42 updates 7.2 MiB gmp x86_64 1:6.3.0-4.fc42 fedora 811.3 KiB gnat-srpm-macros noarch 6-7.fc42 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-6.fc42 fedora 60.8 KiB jansson x86_64 2.14-2.fc42 fedora 93.1 KiB json-c x86_64 0.18-2.fc42 fedora 86.7 KiB kernel-srpm-macros noarch 1.0-25.fc42 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-5.fc42 fedora 58.3 KiB krb5-libs x86_64 1.21.3-5.fc42 fedora 2.3 MiB libacl x86_64 2.3.2-3.fc42 fedora 38.3 KiB libarchive x86_64 3.7.7-4.fc42 fedora 930.6 KiB libattr x86_64 2.5.2-5.fc42 fedora 27.1 KiB libblkid x86_64 2.40.4-7.fc42 fedora 262.4 KiB libbrotli x86_64 1.1.0-6.fc42 fedora 841.3 KiB libcap x86_64 2.73-2.fc42 fedora 207.1 KiB libcap-ng x86_64 0.8.5-4.fc42 fedora 72.9 KiB libcom_err x86_64 1.47.2-3.fc42 fedora 67.1 KiB libcurl x86_64 8.11.1-4.fc42 fedora 842.1 KiB libeconf x86_64 0.7.6-1.fc42 fedora 64.6 KiB libevent x86_64 2.1.12-15.fc42 fedora 903.1 KiB libfdisk x86_64 2.40.4-7.fc42 fedora 372.3 KiB libffi x86_64 3.4.6-5.fc42 fedora 82.3 KiB libgcc x86_64 15.1.1-2.fc42 updates 266.6 KiB libgomp x86_64 15.1.1-2.fc42 updates 539.1 KiB libidn2 x86_64 2.3.8-1.fc42 fedora 556.5 KiB libmount x86_64 2.40.4-7.fc42 fedora 356.3 KiB libnghttp2 x86_64 1.64.0-3.fc42 fedora 170.4 KiB libpkgconf x86_64 2.3.0-2.fc42 fedora 78.1 KiB libpsl x86_64 0.21.5-5.fc42 fedora 76.4 KiB libselinux x86_64 3.8-1.fc42 fedora 193.1 KiB libsemanage x86_64 3.8-1.fc42 fedora 308.4 KiB libsepol x86_64 3.8-1.fc42 fedora 826.0 KiB libsmartcols x86_64 2.40.4-7.fc42 fedora 180.4 KiB libssh x86_64 0.11.1-4.fc42 fedora 565.5 KiB libssh-config noarch 0.11.1-4.fc42 fedora 277.0 B libstdc++ x86_64 15.1.1-2.fc42 updates 2.8 MiB libtasn1 x86_64 4.20.0-1.fc42 fedora 176.3 KiB libtool-ltdl x86_64 2.5.4-4.fc42 fedora 70.1 KiB libunistring x86_64 1.1-9.fc42 fedora 1.7 MiB libuuid x86_64 2.40.4-7.fc42 fedora 37.3 KiB libverto x86_64 0.3.2-10.fc42 fedora 25.4 KiB libxcrypt x86_64 4.4.38-7.fc42 updates 284.5 KiB libxml2 x86_64 2.12.10-1.fc42 fedora 1.7 MiB libzstd x86_64 1.5.7-1.fc42 fedora 807.8 KiB lua-libs x86_64 5.4.7-3.fc42 fedora 280.8 KiB lua-srpm-macros noarch 1-15.fc42 fedora 1.3 KiB lz4-libs x86_64 1.10.0-2.fc42 fedora 157.4 KiB mpfr x86_64 4.2.2-1.fc42 fedora 828.8 KiB ncurses-base noarch 6.5-5.20250125.fc42 fedora 326.8 KiB ncurses-libs x86_64 6.5-5.20250125.fc42 fedora 946.3 KiB ocaml-srpm-macros noarch 10-4.fc42 fedora 1.9 KiB openblas-srpm-macros noarch 2-19.fc42 fedora 112.0 B openldap x86_64 2.6.9-3.fc42 fedora 655.1 KiB openssl-libs x86_64 1:3.2.4-3.fc42 fedora 7.8 MiB p11-kit x86_64 0.25.5-5.fc42 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-5.fc42 fedora 395.5 KiB package-notes-srpm-macros noarch 0.5-13.fc42 fedora 1.6 KiB pam-libs x86_64 1.7.0-5.fc42 updates 126.7 KiB pcre2 x86_64 10.45-1.fc42 fedora 697.7 KiB pcre2-syntax noarch 10.45-1.fc42 fedora 273.9 KiB perl-srpm-macros noarch 1-57.fc42 fedora 861.0 B pkgconf x86_64 2.3.0-2.fc42 fedora 88.5 KiB pkgconf-m4 noarch 2.3.0-2.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-2.fc42 fedora 989.0 B popt x86_64 1.19-8.fc42 fedora 132.8 KiB publicsuffix-list-dafsa noarch 20250116-1.fc42 fedora 68.5 KiB pyproject-srpm-macros noarch 1.18.1-1.fc42 fedora 1.9 KiB python-srpm-macros noarch 3.13-4.fc42 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.9.0-2.fc42 updates 464.0 B readline x86_64 8.2-13.fc42 fedora 485.0 KiB rpm x86_64 4.20.1-1.fc42 fedora 3.1 MiB rpm-build-libs x86_64 4.20.1-1.fc42 fedora 206.6 KiB rpm-libs x86_64 4.20.1-1.fc42 fedora 721.8 KiB rpm-sequoia x86_64 1.7.0-5.fc42 fedora 2.4 MiB rust-srpm-macros noarch 26.3-4.fc42 fedora 4.8 KiB setup noarch 2.15.0-13.fc42 fedora 720.9 KiB sqlite-libs x86_64 3.47.2-2.fc42 fedora 1.5 MiB systemd-libs x86_64 257.5-6.fc42 updates 2.2 MiB systemd-standalone-sysusers x86_64 257.5-6.fc42 updates 277.3 KiB tree-sitter-srpm-macros noarch 0.1.0-8.fc42 fedora 6.5 KiB util-linux-core x86_64 2.40.4-7.fc42 fedora 1.4 MiB xxhash-libs x86_64 0.8.3-2.fc42 fedora 90.2 KiB xz-libs x86_64 1:5.8.1-2.fc42 updates 217.8 KiB zig-srpm-macros noarch 1-4.fc42 fedora 1.1 KiB zip x86_64 3.0-43.fc42 fedora 698.5 KiB zlib-ng-compat x86_64 2.2.4-3.fc42 fedora 137.6 KiB zstd x86_64 1.5.7-1.fc42 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 148 packages Total size of inbound packages is 52 MiB. Need to download 0 B. After this operation, 177 MiB extra will be used (install 177 MiB, remove 0 B). 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100% | 85.9 MiB/s | 88.0 KiB | 00m00s [ 91/150] Installing libgomp-0:15.1.1-2 100% | 527.8 MiB/s | 540.5 KiB | 00m00s [ 92/150] Installing jansson-0:2.14-2.f 100% | 92.2 MiB/s | 94.4 KiB | 00m00s [ 93/150] Installing libpkgconf-0:2.3.0 100% | 0.0 B/s | 79.2 KiB | 00m00s [ 94/150] Installing pkgconf-0:2.3.0-2. 100% | 8.1 MiB/s | 91.0 KiB | 00m00s [ 95/150] Installing pkgconf-pkg-config 100% | 161.2 KiB/s | 1.8 KiB | 00m00s [ 96/150] Installing xxhash-libs-0:0.8. 100% | 89.4 MiB/s | 91.6 KiB | 00m00s [ 97/150] Installing libbrotli-0:1.1.0- 100% | 274.6 MiB/s | 843.6 KiB | 00m00s [ 98/150] Installing libnghttp2-0:1.64. 100% | 167.5 MiB/s | 171.5 KiB | 00m00s [ 99/150] Installing keyutils-libs-0:1. 100% | 0.0 B/s | 59.7 KiB | 00m00s [100/150] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 68.2 KiB | 00m00s [101/150] Installing libverto-0:0.3.2-1 100% | 0.0 B/s | 27.2 KiB | 00m00s [102/150] Installing libtool-ltdl-0:2.5 100% | 0.0 B/s | 71.2 KiB | 00m00s [103/150] Installing gdbm-libs-1:1.23-9 100% | 128.5 MiB/s | 131.6 KiB | 00m00s [104/150] Installing cyrus-sasl-lib-0:2 100% | 135.5 MiB/s | 2.3 MiB | 00m00s [105/150] Installing coreutils-common-0 100% | 446.1 MiB/s | 11.2 MiB | 00m00s [106/150] Installing openssl-libs-1:3.2 100% | 458.0 MiB/s | 7.8 MiB | 00m00s [107/150] Installing coreutils-0:9.6-3. 100% | 181.5 MiB/s | 5.4 MiB | 00m00s [108/150] Installing ca-certificates-0: 100% | 2.2 MiB/s | 2.4 MiB | 00m01s [109/150] Installing libarchive-0:3.7.7 100% | 303.6 MiB/s | 932.6 KiB | 00m00s [110/150] Installing krb5-libs-0:1.21.3 100% | 328.5 MiB/s | 2.3 MiB | 00m00s [111/150] Installing libssh-0:0.11.1-4. 100% | 277.1 MiB/s | 567.5 KiB | 00m00s [112/150] Installing gzip-0:1.13-3.fc42 100% | 29.9 MiB/s | 398.4 KiB | 00m00s [113/150] Installing rpm-sequoia-0:1.7. 100% | 402.4 MiB/s | 2.4 MiB | 00m00s [114/150] Installing rpm-libs-0:4.20.1- 100% | 353.2 MiB/s | 723.4 KiB | 00m00s [115/150] Installing rpm-build-libs-0:4 100% | 202.5 MiB/s | 207.4 KiB | 00m00s [116/150] Installing libevent-0:2.1.12- 100% | 295.2 MiB/s | 906.9 KiB | 00m00s [117/150] Installing openldap-0:2.6.9-3 100% | 214.5 MiB/s | 658.9 KiB | 00m00s [118/150] Installing libcurl-0:8.11.1-4 100% | 411.7 MiB/s | 843.2 KiB | 00m00s [119/150] Installing elfutils-debuginfo 100% | 7.0 MiB/s | 86.2 KiB | 00m00s [120/150] Installing elfutils-0:0.193-2 100% | 162.3 MiB/s | 2.9 MiB | 00m00s [121/150] Installing binutils-0:2.44-3. 100% | 354.8 MiB/s | 25.9 MiB | 00m00s [122/150] Installing gdb-minimal-0:16.3 100% | 323.1 MiB/s | 13.2 MiB | 00m00s [123/150] Installing debugedit-0:5.1-6. 100% | 15.9 MiB/s | 195.4 KiB | 00m00s [124/150] Installing curl-0:8.11.1-4.fc 100% | 22.1 MiB/s | 453.1 KiB | 00m00s [125/150] Installing rpm-0:4.20.1-1.fc4 100% | 104.1 MiB/s | 2.5 MiB | 00m00s [126/150] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [127/150] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 7.4 KiB | 00m00s [128/150] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [129/150] Installing efi-srpm-macros-0: 100% | 0.0 B/s | 41.1 KiB | 00m00s [130/150] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [131/150] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [132/150] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [133/150] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [134/150] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [135/150] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [136/150] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [137/150] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [138/150] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [139/150] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [140/150] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [141/150] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [142/150] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [143/150] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 62.0 KiB | 00m00s [144/150] Installing python-srpm-macros 100% | 0.0 B/s | 52.2 KiB | 00m00s [145/150] Installing redhat-rpm-config- 100% | 93.9 MiB/s | 192.2 KiB | 00m00s [146/150] Installing rpm-build-0:4.20.1 100% | 13.3 MiB/s | 177.4 KiB | 00m00s [147/150] Installing pyproject-srpm-mac 100% | 0.0 B/s | 2.5 KiB | 00m00s [148/150] Installing which-0:2.23-1.fc4 100% | 7.0 MiB/s | 85.6 KiB | 00m00s [149/150] Installing util-linux-0:2.40. 100% | 111.7 MiB/s | 3.5 MiB | 00m00s [150/150] Installing info-0:7.2-3.fc42. 100% | 241.7 KiB/s | 358.3 KiB | 00m01s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.6.0-1.fc42.x86_64 alternatives-1.33-1.fc42.x86_64 ansible-srpm-macros-1-17.1.fc42.noarch audit-libs-4.0.3-2.fc42.x86_64 basesystem-11-22.fc42.noarch bash-5.2.37-1.fc42.x86_64 binutils-2.44-3.fc42.x86_64 build-reproducibility-srpm-macros-0.6.0-1.fc42.noarch bzip2-1.0.8-20.fc42.x86_64 bzip2-libs-1.0.8-20.fc42.x86_64 ca-certificates-2024.2.69_v8.0.401-6.fc42.noarch coreutils-9.6-3.fc42.x86_64 coreutils-common-9.6-3.fc42.x86_64 cpio-2.15-4.fc42.x86_64 crypto-policies-20250214-1.gitff7551b.fc42.noarch curl-8.11.1-4.fc42.x86_64 cyrus-sasl-lib-2.1.28-30.fc42.x86_64 debugedit-5.1-6.fc42.x86_64 diffutils-3.12-1.fc42.x86_64 dwz-0.15-9.fc42.x86_64 ed-1.21-2.fc42.x86_64 efi-srpm-macros-6-3.fc42.noarch elfutils-0.193-2.fc42.x86_64 elfutils-debuginfod-client-0.193-2.fc42.x86_64 elfutils-default-yama-scope-0.193-2.fc42.noarch elfutils-libelf-0.193-2.fc42.x86_64 elfutils-libs-0.193-2.fc42.x86_64 fedora-gpg-keys-42-1.noarch fedora-release-42-26.noarch fedora-release-common-42-26.noarch fedora-release-identity-basic-42-26.noarch fedora-repos-42-1.noarch file-5.46-1.fc42.x86_64 file-libs-5.46-1.fc42.x86_64 filesystem-3.18-42.fc42.x86_64 filesystem-srpm-macros-3.18-42.fc42.noarch findutils-4.10.0-5.fc42.x86_64 fonts-srpm-macros-2.0.5-21.fc42.noarch forge-srpm-macros-0.4.0-2.fc42.noarch fpc-srpm-macros-1.3-14.fc42.noarch gawk-5.3.1-1.fc42.x86_64 gdb-minimal-16.3-1.fc42.x86_64 gdbm-libs-1.23-9.fc42.x86_64 ghc-srpm-macros-1.9.2-2.fc42.noarch glibc-2.41-5.fc42.x86_64 glibc-common-2.41-5.fc42.x86_64 glibc-gconv-extra-2.41-5.fc42.x86_64 glibc-minimal-langpack-2.41-5.fc42.x86_64 gmp-6.3.0-4.fc42.x86_64 gnat-srpm-macros-6-7.fc42.noarch go-srpm-macros-3.6.0-6.fc42.noarch gpg-pubkey-105ef944-65ca83d1 grep-3.11-10.fc42.x86_64 gzip-1.13-3.fc42.x86_64 info-7.2-3.fc42.x86_64 jansson-2.14-2.fc42.x86_64 json-c-0.18-2.fc42.x86_64 kernel-srpm-macros-1.0-25.fc42.noarch keyutils-libs-1.6.3-5.fc42.x86_64 krb5-libs-1.21.3-5.fc42.x86_64 libacl-2.3.2-3.fc42.x86_64 libarchive-3.7.7-4.fc42.x86_64 libattr-2.5.2-5.fc42.x86_64 libblkid-2.40.4-7.fc42.x86_64 libbrotli-1.1.0-6.fc42.x86_64 libcap-2.73-2.fc42.x86_64 libcap-ng-0.8.5-4.fc42.x86_64 libcom_err-1.47.2-3.fc42.x86_64 libcurl-8.11.1-4.fc42.x86_64 libeconf-0.7.6-1.fc42.x86_64 libevent-2.1.12-15.fc42.x86_64 libfdisk-2.40.4-7.fc42.x86_64 libffi-3.4.6-5.fc42.x86_64 libgcc-15.1.1-2.fc42.x86_64 libgomp-15.1.1-2.fc42.x86_64 libidn2-2.3.8-1.fc42.x86_64 libmount-2.40.4-7.fc42.x86_64 libnghttp2-1.64.0-3.fc42.x86_64 libpkgconf-2.3.0-2.fc42.x86_64 libpsl-0.21.5-5.fc42.x86_64 libselinux-3.8-1.fc42.x86_64 libsemanage-3.8-1.fc42.x86_64 libsepol-3.8-1.fc42.x86_64 libsmartcols-2.40.4-7.fc42.x86_64 libssh-0.11.1-4.fc42.x86_64 libssh-config-0.11.1-4.fc42.noarch libstdc++-15.1.1-2.fc42.x86_64 libtasn1-4.20.0-1.fc42.x86_64 libtool-ltdl-2.5.4-4.fc42.x86_64 libunistring-1.1-9.fc42.x86_64 libuuid-2.40.4-7.fc42.x86_64 libverto-0.3.2-10.fc42.x86_64 libxcrypt-4.4.38-7.fc42.x86_64 libxml2-2.12.10-1.fc42.x86_64 libzstd-1.5.7-1.fc42.x86_64 lua-libs-5.4.7-3.fc42.x86_64 lua-srpm-macros-1-15.fc42.noarch lz4-libs-1.10.0-2.fc42.x86_64 mpfr-4.2.2-1.fc42.x86_64 ncurses-base-6.5-5.20250125.fc42.noarch ncurses-libs-6.5-5.20250125.fc42.x86_64 ocaml-srpm-macros-10-4.fc42.noarch openblas-srpm-macros-2-19.fc42.noarch openldap-2.6.9-3.fc42.x86_64 openssl-libs-3.2.4-3.fc42.x86_64 p11-kit-0.25.5-5.fc42.x86_64 p11-kit-trust-0.25.5-5.fc42.x86_64 package-notes-srpm-macros-0.5-13.fc42.noarch pam-libs-1.7.0-5.fc42.x86_64 patch-2.8-1.fc42.x86_64 pcre2-10.45-1.fc42.x86_64 pcre2-syntax-10.45-1.fc42.noarch perl-srpm-macros-1-57.fc42.noarch pkgconf-2.3.0-2.fc42.x86_64 pkgconf-m4-2.3.0-2.fc42.noarch pkgconf-pkg-config-2.3.0-2.fc42.x86_64 popt-1.19-8.fc42.x86_64 publicsuffix-list-dafsa-20250116-1.fc42.noarch pyproject-srpm-macros-1.18.1-1.fc42.noarch python-srpm-macros-3.13-4.fc42.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.9.0-2.fc42.noarch readline-8.2-13.fc42.x86_64 redhat-rpm-config-342-4.fc42.noarch rpm-4.20.1-1.fc42.x86_64 rpm-build-4.20.1-1.fc42.x86_64 rpm-build-libs-4.20.1-1.fc42.x86_64 rpm-libs-4.20.1-1.fc42.x86_64 rpm-sequoia-1.7.0-5.fc42.x86_64 rust-srpm-macros-26.3-4.fc42.noarch sed-4.9-4.fc42.x86_64 setup-2.15.0-13.fc42.noarch shadow-utils-4.17.4-1.fc42.x86_64 sqlite-libs-3.47.2-2.fc42.x86_64 systemd-libs-257.5-6.fc42.x86_64 systemd-standalone-sysusers-257.5-6.fc42.x86_64 tar-1.35-5.fc42.x86_64 tree-sitter-srpm-macros-0.1.0-8.fc42.noarch unzip-6.0-66.fc42.x86_64 util-linux-2.40.4-7.fc42.x86_64 util-linux-core-2.40.4-7.fc42.x86_64 which-2.23-1.fc42.x86_64 xxhash-libs-0.8.3-2.fc42.x86_64 xz-5.8.1-2.fc42.x86_64 xz-libs-5.8.1-2.fc42.x86_64 zig-srpm-macros-1-4.fc42.noarch zip-3.0-43.fc42.x86_64 zlib-ng-compat-2.2.4-3.fc42.x86_64 zstd-1.5.7-1.fc42.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 warning: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Wrote: /builddir/build/SRPMS/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm RPM build warnings: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-42-x86_64-1748397488.398721/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-7h5p_ihj/R-CRAN-ClustAssess/R-CRAN-ClustAssess.spec) Config(child) 0 minutes 7 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm) Config(fedora-42-x86_64) Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-42-x86_64-1748397488.398721/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.20.1-1.fc41.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 python3-dnf-4.23.0-1.fc41.noarch python3-dnf-plugins-core-4.10.1-1.fc41.noarch dnf5-5.2.13.1-1.fc41.x86_64 dnf5-plugins-5.2.13.1-1.fc41.x86_64 Finish: chroot init Start: build phase for R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm Start: build setup for R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm Building target platforms: x86_64 Building for target x86_64 warning: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Wrote: /builddir/build/SRPMS/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm RPM build warnings: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Updating and loading repositories: updates 100% | 268.1 KiB/s | 30.6 KiB | 00m00s fedora 100% | 1.0 MiB/s | 30.7 KiB | 00m00s Copr repository 100% | 81.0 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 41.2 MiB/s | 12.9 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: R-CRAN-DT noarch 0.33-1.fc42.copr8935150 copr_base 5.3 MiB R-CRAN-Gmedian x86_64 1.2.7-1.fc42.copr8930360 copr_base 214.9 KiB R-CRAN-Matrix x86_64 1.7.3-1.fc42.copr8927562 copr_base 8.2 MiB R-CRAN-RANN x86_64 2.6.2-1.fc42.copr8922587 copr_base 91.5 KiB R-CRAN-Rcpp x86_64 1.0.14-1.fc42.copr8922423 copr_base 8.4 MiB R-CRAN-RcppEigen x86_64 0.3.4.0.2-1.fc42.copr8926104 copr_base 9.0 MiB R-CRAN-Seurat x86_64 5.3.0-1.fc42.copr8957487 copr_base 3.8 MiB R-CRAN-dplyr x86_64 1.1.4-1.fc42.copr8933752 copr_base 2.6 MiB R-CRAN-fastcluster x86_64 1.3.0-1.fc42.copr9009921 copr_base 276.0 KiB R-CRAN-foreach noarch 1.5.2-1.fc42.copr8926158 copr_base 379.5 KiB R-CRAN-ggnewscale noarch 0.5.1-1.fc42.copr8935470 copr_base 605.9 KiB R-CRAN-ggplot2 noarch 3.5.2-1.fc42.copr8933751 copr_base 7.2 MiB R-CRAN-ggrastr noarch 1.0.2-1.fc42.copr8938848 copr_base 3.5 MiB R-CRAN-ggrepel x86_64 0.9.6-1.fc42.copr8935154 copr_base 458.2 KiB R-CRAN-ggtext noarch 0.1.2-1.fc42.copr8936324 copr_base 1.6 MiB R-CRAN-glue x86_64 1.8.0-1.fc42.copr8922424 copr_base 345.2 KiB R-CRAN-gprofiler2 noarch 0.2.3-1.fc42.copr8940706 copr_base 4.4 MiB R-CRAN-igraph x86_64 2.1.4-1.fc42.copr8930309 copr_base 10.2 MiB R-CRAN-jsonlite x86_64 2.0.0-1.fc42.copr8922439 copr_base 2.3 MiB R-CRAN-leiden noarch 0.4.3.1-1.fc42.copr8932282 copr_base 5.4 MiB R-CRAN-matrixStats x86_64 1.5.0-1.fc42.copr8922425 copr_base 1.0 MiB R-CRAN-paletteer noarch 1.6.0-1.fc42.copr8935825 copr_base 503.8 KiB R-CRAN-plotly noarch 4.10.4-1.fc42.copr8937972 copr_base 6.6 MiB R-CRAN-progress noarch 1.2.3-1.fc42.copr8931984 copr_base 120.4 KiB R-CRAN-qualpalr x86_64 0.4.4-1.fc42.copr8930065 copr_base 889.8 KiB R-CRAN-reshape2 x86_64 1.4.4-3.fc42.copr8931977 copr_base 224.3 KiB R-CRAN-rlang x86_64 1.1.6-1.fc42.copr8922429 copr_base 2.6 MiB R-CRAN-shiny noarch 1.10.0-1.fc42.copr8931981 copr_base 13.6 MiB R-CRAN-shinyLP noarch 1.1.3-1.fc42.copr8934009 copr_base 63.0 KiB R-CRAN-shinyWidgets noarch 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fedora 349.5 KiB default-fonts-core-sans noarch 4.2-4.fc42 fedora 11.9 KiB desktop-file-utils x86_64 0.28-1.fc42 fedora 218.4 KiB emacs-filesystem noarch 1:30.0-4.fc42 fedora 0.0 B flexiblas x86_64 3.4.5-1.fc42 fedora 50.4 KiB flexiblas-devel x86_64 3.4.5-1.fc42 fedora 4.9 MiB flexiblas-netlib x86_64 3.4.5-1.fc42 fedora 10.9 MiB flexiblas-netlib64 x86_64 3.4.5-1.fc42 fedora 11.0 MiB flexiblas-openblas-openmp x86_64 3.4.5-1.fc42 fedora 39.2 KiB flexiblas-openblas-openmp64 x86_64 3.4.5-1.fc42 fedora 39.2 KiB fontconfig x86_64 2.16.0-2.fc42 fedora 764.7 KiB fonts-filesystem noarch 1:2.0.5-21.fc42 fedora 0.0 B freetype x86_64 2.13.3-2.fc42 fedora 858.2 KiB fribidi x86_64 1.0.16-2.fc42 fedora 194.3 KiB gcc x86_64 15.1.1-2.fc42 updates 111.1 MiB gcc-c++ x86_64 15.1.1-2.fc42 updates 41.3 MiB gcc-gfortran x86_64 15.1.1-2.fc42 updates 40.3 MiB gcc-plugin-annobin x86_64 15.1.1-2.fc42 updates 57.1 KiB glib2 x86_64 2.84.2-1.fc42 updates 14.7 MiB glibc-devel x86_64 2.41-5.fc42 updates 2.3 MiB glpk x86_64 5.0-13.fc42 fedora 914.6 KiB gnutls x86_64 3.8.9-3.fc42 fedora 3.6 MiB google-noto-fonts-common noarch 20250301-1.fc42 fedora 17.7 KiB google-noto-sans-vf-fonts noarch 20250301-1.fc42 fedora 1.4 MiB graphite2 x86_64 1.3.14-18.fc42 fedora 195.8 KiB harfbuzz x86_64 10.4.0-1.fc42 fedora 2.7 MiB harfbuzz-icu x86_64 10.4.0-1.fc42 fedora 15.4 KiB java-21-openjdk x86_64 1:21.0.7.0.6-1.fc42 updates 1.0 MiB java-21-openjdk-devel x86_64 1:21.0.7.0.6-1.fc42 updates 11.2 MiB java-21-openjdk-headless x86_64 1:21.0.7.0.6-1.fc42 updates 202.0 MiB javapackages-filesystem noarch 6.4.0-5.fc42 fedora 2.0 KiB jbigkit-libs x86_64 2.1-31.fc42 fedora 121.4 KiB kernel-headers x86_64 6.14.3-300.fc42 updates 6.5 MiB less x86_64 668-2.fc42 fedora 405.8 KiB libICE x86_64 1.1.2-2.fc42 fedora 198.4 KiB libRmath x86_64 4.5.0-3.fc42 updates 242.7 KiB libRmath-devel x86_64 4.5.0-3.fc42 updates 19.9 KiB libSM x86_64 1.2.5-2.fc42 fedora 105.0 KiB libX11 x86_64 1.8.11-1.fc42 fedora 1.3 MiB libX11-common noarch 1.8.11-1.fc42 fedora 1.2 MiB libX11-devel x86_64 1.8.11-1.fc42 fedora 1.0 MiB libX11-xcb x86_64 1.8.11-1.fc42 fedora 10.9 KiB libXau x86_64 1.0.12-2.fc42 fedora 76.9 KiB libXau-devel x86_64 1.0.12-2.fc42 fedora 7.5 KiB libXcomposite x86_64 0.4.6-5.fc42 fedora 44.4 KiB libXext x86_64 1.3.6-3.fc42 fedora 90.0 KiB libXft x86_64 2.3.8-8.fc42 fedora 168.4 KiB libXi x86_64 1.8.2-2.fc42 fedora 84.6 KiB libXmu x86_64 1.2.1-3.fc42 fedora 199.3 KiB libXrender x86_64 0.9.12-2.fc42 fedora 50.0 KiB libXt x86_64 1.3.1-2.fc42 fedora 429.7 KiB libXtst x86_64 1.2.5-2.fc42 fedora 33.5 KiB libdatrie x86_64 0.2.13-11.fc42 fedora 57.8 KiB libdeflate x86_64 1.24-1.fc42 updates 123.0 KiB libdeflate-devel x86_64 1.24-1.fc42 updates 26.0 KiB libfontenc x86_64 1.1.8-3.fc42 fedora 70.9 KiB libgfortran x86_64 15.1.1-2.fc42 updates 3.3 MiB libicu x86_64 76.1-4.fc42 fedora 36.3 MiB libicu-devel x86_64 76.1-4.fc42 fedora 5.0 MiB libjpeg-turbo x86_64 3.1.0-2.fc42 fedora 803.2 KiB liblerc x86_64 4.0.0-8.fc42 fedora 636.1 KiB libmpc x86_64 1.3.1-7.fc42 fedora 164.5 KiB libpng x86_64 2:1.6.44-2.fc42 fedora 241.7 KiB libquadmath x86_64 15.1.1-2.fc42 updates 317.9 KiB libquadmath-devel x86_64 15.1.1-2.fc42 updates 22.1 KiB libstdc++-devel x86_64 15.1.1-2.fc42 updates 16.1 MiB libthai x86_64 0.1.29-10.fc42 fedora 783.4 KiB libtiff x86_64 4.7.0-3.fc42 fedora 619.1 KiB libtirpc x86_64 1.3.6-1.rc3.fc42.2 fedora 199.0 KiB libtirpc-devel x86_64 1.3.6-1.rc3.fc42.2 fedora 251.6 KiB libwebp x86_64 1.5.0-2.fc42 fedora 947.6 KiB libxcb x86_64 1.17.0-5.fc42 fedora 1.1 MiB libxcb-devel x86_64 1.17.0-5.fc42 fedora 2.7 MiB libxcrypt-devel x86_64 4.4.38-7.fc42 updates 30.8 KiB libyaml x86_64 0.2.5-16.fc42 fedora 134.7 KiB libzstd-devel x86_64 1.5.7-1.fc42 fedora 208.0 KiB lksctp-tools x86_64 1.0.20-2.fc42 fedora 250.3 KiB make x86_64 1:4.4.1-10.fc42 fedora 1.8 MiB mkfontscale x86_64 1.2.3-2.fc42 fedora 45.0 KiB nettle x86_64 3.10.1-1.fc42 fedora 790.5 KiB nspr x86_64 4.36.0-8.fc42 updates 315.5 KiB nss x86_64 3.111.0-2.fc42 updates 1.9 MiB nss-softokn x86_64 3.111.0-2.fc42 updates 1.9 MiB nss-softokn-freebl x86_64 3.111.0-2.fc42 updates 848.3 KiB nss-sysinit x86_64 3.111.0-2.fc42 updates 18.1 KiB nss-util x86_64 3.111.0-2.fc42 updates 200.8 KiB openblas x86_64 0.3.29-1.fc42 fedora 111.7 KiB openblas-openmp x86_64 0.3.29-1.fc42 fedora 43.7 MiB openblas-openmp64 x86_64 0.3.29-1.fc42 fedora 43.9 MiB pandoc x86_64 3.1.11.1-33.fc42 fedora 185.0 MiB pandoc-common noarch 3.1.11.1-32.fc42 fedora 1.9 MiB pango x86_64 1.56.3-1.fc42 fedora 1.0 MiB pcre2-devel x86_64 10.45-1.fc42 fedora 2.1 MiB pcre2-utf16 x86_64 10.45-1.fc42 fedora 626.3 KiB pcre2-utf32 x86_64 10.45-1.fc42 fedora 598.2 KiB pixman x86_64 0.44.2-2.fc42 fedora 674.2 KiB suitesparse x86_64 7.8.3-1.fc42 fedora 114.7 MiB tcl8 x86_64 1:8.6.15-10.fc42 fedora 4.3 MiB tk8 x86_64 1:8.6.15-5.fc42 fedora 3.2 MiB tre x86_64 0.8.0-47.20140228gitc2f5d13.fc42 fedora 75.8 KiB tre-common noarch 0.8.0-47.20140228gitc2f5d13.fc42 fedora 81.0 KiB tre-devel x86_64 0.8.0-47.20140228gitc2f5d13.fc42 fedora 10.7 KiB ttmkfdir x86_64 3.0.9-72.fc42 fedora 118.5 KiB tzdata noarch 2025b-1.fc42 fedora 1.6 MiB tzdata-java noarch 2025b-1.fc42 fedora 100.1 KiB xdg-utils noarch 1.2.1-3.fc42 fedora 346.3 KiB xml-common noarch 0.6.3-66.fc42 fedora 78.4 KiB xorg-x11-fonts-Type1 noarch 7.5-40.fc42 fedora 863.3 KiB xorg-x11-proto-devel noarch 2024.1-4.fc42 fedora 1.7 MiB xz-devel x86_64 1:5.8.1-2.fc42 updates 258.8 KiB zlib-ng x86_64 2.2.4-3.fc42 fedora 157.0 KiB zlib-ng-compat-devel x86_64 2.2.4-3.fc42 fedora 107.0 KiB Transaction Summary: Installing: 309 packages Total size of inbound packages is 467 MiB. Need to download 173 MiB. After this operation, 1 GiB extra will be used (install 1 GiB, remove 0 B). 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R-CRAN-askpass-0:1.2.1-1.fc42 100% | 2.3 MiB/s | 35.0 KiB | 00m00s [301/309] R-CRAN-rprojroot-0:2.0.4-1.fc 100% | 39.5 MiB/s | 121.3 KiB | 00m00s [302/309] R-CRAN-caTools-0:1.18.3-1.fc4 100% | 5.3 MiB/s | 239.1 KiB | 00m00s [303/309] R-CRAN-dotCall64-0:1.2-1.fc42 100% | 1.1 MiB/s | 45.5 KiB | 00m00s [304/309] R-CRAN-litedown-0:0.7-1.fc42. 100% | 53.4 MiB/s | 382.6 KiB | 00m00s [305/309] R-littler-0:0.3.19-8.fc42.x86 100% | 11.5 MiB/s | 70.8 KiB | 00m00s [306/309] R-CRAN-tensor-0:1.5-3.fc42.co 100% | 823.1 KiB/s | 25.5 KiB | 00m00s [307/309] R-CRAN-sys-0:3.4.3-1.fc42.cop 100% | 2.0 MiB/s | 57.9 KiB | 00m00s [308/309] R-CRAN-data.table-0:1.17.4-1. 100% | 180.6 MiB/s | 2.3 MiB | 00m00s [309/309] R-CRAN-spatstat.utils-0:3.1.4 100% | 4.8 MiB/s | 445.8 KiB | 00m00s -------------------------------------------------------------------------------- [309/309] Total 100% | 60.2 MiB/s | 172.8 MiB | 00m03s Running transaction [ 1/311] Verify package files 100% | 228.0 B/s | 309.0 B | 00m01s >>> Running pre-transaction scriptlet: java-21-openjdk-headless-1:21.0.7.0.6-1.f >>> Finished pre-transaction scriptlet: java-21-openjdk-headless-1:21.0.7.0.6-1. >>> [RPM] /var/lib/mock/fedora-42-x86_64-1748397488.398721/root/var/cache/dnf/co [ 2/311] Prepare transaction 100% | 1.5 KiB/s | 309.0 B | 00m00s [ 3/311] Installing libgfortran-0:15.1 100% | 417.9 MiB/s | 3.3 MiB | 00m00s [ 4/311] Installing nspr-0:4.36.0-8.fc 100% | 309.9 MiB/s | 317.3 KiB | 00m00s [ 5/311] Installing libpng-2:1.6.44-2. 100% | 237.2 MiB/s | 242.9 KiB | 00m00s [ 6/311] Installing libicu-0:76.1-4.fc 100% | 443.1 MiB/s | 36.3 MiB | 00m00s [ 7/311] Installing nss-util-0:3.111.0 100% | 197.0 MiB/s | 201.8 KiB | 00m00s [ 8/311] Installing libquadmath-0:15.1 100% | 311.7 MiB/s | 319.2 KiB | 00m00s [ 9/311] Installing libmpc-0:1.3.1-7.f 100% | 162.2 MiB/s | 166.1 KiB | 00m00s [ 10/311] Installing libjpeg-turbo-0:3. 100% | 393.0 MiB/s | 804.9 KiB | 00m00s [ 11/311] Installing fonts-filesystem-1 100% | 0.0 B/s | 788.0 B | 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Finish: build setup for R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm Start: rpmbuild R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm Building target platforms: x86_64 Building for target x86_64 warning: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.icYBa3 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.uJIG3w + umask 022 + cd /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + cd /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + rm -rf ClustAssess + /usr/bin/mkdir -p ClustAssess + cd ClustAssess + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/ClustAssess_1.1.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + find -type f -executable -exec grep -Iq . '{}' ';' -exec sed -i -e '$a\' '{}' ';' + '[' -d ClustAssess/src ']' + find ClustAssess/src -type f -exec sed -i s@/usr/bin/strip@/usr/bin/true@g '{}' ';' + '[' -d ClustAssess/src ']' + find 'ClustAssess/src/Make*' -type f -exec sed -i s@-g0@@g '{}' ';' find: ‘ClustAssess/src/Make*’: No such file or directory + true + find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' '{}' ';' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.hIb2es + umask 022 + cd /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd ClustAssess + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.fhgTE5 + umask 022 + cd /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + '[' /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT ++ dirname /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT + mkdir -p /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + mkdir /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd ClustAssess + mkdir -p /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT/usr/local/lib/R/library + /usr/bin/R CMD INSTALL -l /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT/usr/local/lib/R/library ClustAssess * installing *source* package ‘ClustAssess’ ... ** this is package ‘ClustAssess’ version ‘1.1.0’ file ‘inst/CITATION’ has the wrong MD5 checksum ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c RcppExports.cpp -o RcppExports.o In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/Core:205, from /usr/local/lib/R/library/RcppEigen/include/Eigen/Dense:1, from /usr/local/lib/R/library/RcppEigen/include/RcppEigenForward.h:28, from /usr/local/lib/R/library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/Core:174: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/Core:165: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ 22 | typedef typename find_best_packet<_Scalar,size>::type PacketScalar; | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ 266 | Alignment = internal::traits::Alignment, | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here 24 | ResAlignment = traits >::Alignment | ^~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/Core:271: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ 302 | class DenseCoeffsBase : public DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ 555 | class DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ 41 | template class DenseBase | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ 48 | template class MatrixBase | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ 98 | class PlainObjectBase : public internal::dense_xpr_base::type | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ 178 | class Matrix | ^~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ 46 | typedef typename Coefficients::CoeffReturnType CoeffReturnType; | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ 273 | class Quaternion : public QuaternionBase > | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here 27 | { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ 22 | typedef typename find_best_packet<_Scalar,size>::type PacketScalar; | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ 266 | Alignment = internal::traits::Alignment, | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here 98 | ResAlignment = traits >::Alignment | ^~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ 302 | class DenseCoeffsBase : public DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ 555 | class DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ 41 | template class DenseBase | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ 48 | template class MatrixBase | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ 98 | class PlainObjectBase : public internal::dense_xpr_base::type | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ 178 | class Matrix | ^~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ 46 | typedef typename Coefficients::CoeffReturnType CoeffReturnType; | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ 273 | class Quaternion : public QuaternionBase > | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here 102 | { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/SparseCore:37, from /usr/local/lib/R/library/RcppEigen/include/Eigen/Sparse:26, from /usr/local/lib/R/library/RcppEigen/include/RcppEigenForward.h:29: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ 36 | class SparseCompressedBase | ^~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ 96 | class SparseMatrix | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here 61 | typedef Triplet T; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ 22 | typedef typename find_best_packet<_Scalar,size>::type PacketScalar; | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ 98 | class PlainObjectBase : public internal::dense_xpr_base::type | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ 178 | class Matrix | ^~~~~~ RcppExports.cpp:98:71: required from here 98 | rcpp_result_gen = Rcpp::wrap(getNNmatrix(nnRanked, k, start, prune)); | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ 302 | class DenseCoeffsBase : public DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ 555 | class DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ 41 | template class DenseBase | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ 48 | template class MatrixBase | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ 98 | class PlainObjectBase : public internal::dense_xpr_base::type | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ 178 | class Matrix | ^~~~~~ RcppExports.cpp:98:71: required from here 98 | rcpp_result_gen = Rcpp::wrap(getNNmatrix(nnRanked, k, start, prune)); | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ 336 | typedef typename DenseCoeffsBase::CoeffReturnType CoeffReturnType; | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ 1505 | struct evaluator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:77:20: required from ‘void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix]’ 77 | SrcEvaluatorType srcEvaluator(src); | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28: required from ‘static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix; Functor = Eigen::internal::assign_op; typename DstXprType::Scalar = double; typename SrcXprType::Scalar = double]’ 132 | assign_sparse_to_sparse(dst.derived(), src.derived()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::SparseMatrix; Src = Eigen::SparseMatrix; Func = assign_op]’ 890 | Assignment::run(actualDst, src, func); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:917:27: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:713:13: required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::SparseMatrix(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’ 713 | *this = other.derived(); | ~~~~~~^~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/RcppEigenWrap.h:387:24: required from ‘Eigen::SparseMatrix Rcpp::traits::Exporter >::get() [with T = double]’ 387 | return ans; | ^~~ /usr/local/lib/R/library/Rcpp/include/Rcpp/as.h:89:32: required from ‘T Rcpp::internal::as(SEXP, Rcpp::traits::r_type_generic_tag) [with T = Eigen::SparseMatrix; SEXP = SEXPREC*]’ 89 | return exporter.get(); | ~~~~~~~~~~~~^~ /usr/local/lib/R/library/Rcpp/include/Rcpp/as.h:152:31: required from ‘T Rcpp::as(SEXP) [with T = Eigen::SparseMatrix; SEXP = SEXPREC*]’ 152 | return internal::as(x, typename traits::r_type_traits::r_category()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/Rcpp/include/Rcpp/InputParameter.h:34:43: required from ‘Rcpp::InputParameter::operator T() [with T = Eigen::SparseMatrix]’ 34 | inline operator T() { return as(x) ; } | ~~~~~^~~ RcppExports.cpp:73:43: required from here 73 | rcpp_result_gen = Rcpp::wrap(pruneSNN(snnMatrix, prune)); | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c calculate_ecs.cpp -o calculate_ecs.o calculate_ecs.cpp: In function ‘double disjointECSaverage(Rcpp::IntegerVector, Rcpp::IntegerVector)’: calculate_ecs.cpp:52:13: warning: unused variable ‘cluster1’ [-Wunused-variable] 52 | int cluster1, cluster2; | ^~~~~~~~ calculate_ecs.cpp:52:23: warning: unused variable ‘cluster2’ [-Wunused-variable] 52 | int cluster1, cluster2; | ^~~~~~~~ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c calculate_pac.cpp -o calculate_pac.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c optimise_snn.cpp -o optimise_snn.o In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/Core:205, from /usr/local/lib/R/library/RcppEigen/include/Eigen/Dense:1, from /usr/local/lib/R/library/RcppEigen/include/RcppEigenForward.h:28, from /usr/local/lib/R/library/RcppEigen/include/RcppEigen.h:25, from optimise_snn.cpp:2: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/Core:174: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/Core:165: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ 22 | typedef typename find_best_packet<_Scalar,size>::type PacketScalar; | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ 266 | Alignment = internal::traits::Alignment, | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here 24 | ResAlignment = traits >::Alignment | ^~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/Core:271: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ 302 | class DenseCoeffsBase : public DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ 555 | class DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ 41 | template class DenseBase | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ 48 | template class MatrixBase | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ 98 | class PlainObjectBase : public internal::dense_xpr_base::type | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ 178 | class Matrix | ^~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ 46 | typedef typename Coefficients::CoeffReturnType CoeffReturnType; | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ 273 | class Quaternion : public QuaternionBase > | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here 27 | { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ 22 | typedef typename find_best_packet<_Scalar,size>::type PacketScalar; | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ 266 | Alignment = internal::traits::Alignment, | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here 98 | ResAlignment = traits >::Alignment | ^~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ 302 | class DenseCoeffsBase : public DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ 555 | class DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ 41 | template class DenseBase | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ 48 | template class MatrixBase | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ 98 | class PlainObjectBase : public internal::dense_xpr_base::type | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ 178 | class Matrix | ^~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ 46 | typedef typename Coefficients::CoeffReturnType CoeffReturnType; | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ 273 | class Quaternion : public QuaternionBase > | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here 102 | { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /usr/local/lib/R/library/RcppEigen/include/Eigen/SparseCore:37, from /usr/local/lib/R/library/RcppEigen/include/Eigen/Sparse:26, from /usr/local/lib/R/library/RcppEigen/include/RcppEigenForward.h:29: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ 36 | class SparseCompressedBase | ^~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ 96 | class SparseMatrix | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here 61 | typedef Triplet T; | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase > >’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase > >’ 36 | class SparseCompressedBase | ^~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:22:9: required from ‘class Eigen::internal::SparseTransposeImpl, 1024>’ 22 | class SparseTransposeImpl | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:45:37: required from ‘class Eigen::TransposeImpl, Eigen::Sparse>’ 45 | template class TransposeImpl | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37: required from ‘class Eigen::Transpose >’ 52 | template class Transpose | ^~~~~~~~~ optimise_snn.cpp:58:66: required from here 58 | Eigen::SparseMatrix SNN = nnMatrix * (nnMatrix.transpose()); | ~~~~~~~~~~~~~~~~~~^~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase, Eigen::Transpose >, 2> >’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Product.h:145:7: required from ‘class Eigen::ProductImpl, Eigen::Transpose >, 2, Eigen::Sparse>’ 145 | class ProductImpl : public internal::generic_xpr_base, MatrixXpr, StorageKind>::type | ^~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Product.h:71:7: required from ‘class Eigen::Product, Eigen::Transpose >, 2>’ 71 | class Product : public ProductImpl<_Lhs,_Rhs,Option, | ^~~~~~~ optimise_snn.cpp:58:68: required from here 58 | Eigen::SparseMatrix SNN = nnMatrix * (nnMatrix.transpose()); | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ 22 | typedef typename find_best_packet<_Scalar,size>::type PacketScalar; | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ 98 | class PlainObjectBase : public internal::dense_xpr_base::type | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ 178 | class Matrix | ^~~~~~ optimise_snn.cpp:92:87: required from here 92 | List getNNmatrix(Eigen::MatrixXd nnRanked, int k = -1, int start = 0, double prune = 0) { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ 302 | class DenseCoeffsBase : public DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ 555 | class DenseCoeffsBase | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ 41 | template class DenseBase | ^~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ 48 | template class MatrixBase | ^~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ 98 | class PlainObjectBase : public internal::dense_xpr_base::type | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ 178 | class Matrix | ^~~~~~ optimise_snn.cpp:92:87: required from here 92 | List getNNmatrix(Eigen::MatrixXd nnRanked, int k = -1, int start = 0, double prune = 0) { | ^ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ 336 | typedef typename DenseCoeffsBase::CoeffReturnType CoeffReturnType; | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ 1505 | struct evaluator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:96:8: required from ‘struct Eigen::internal::product_evaluator, Eigen::Transpose >, 2>, 8, Eigen::SparseShape, Eigen::SparseShape, double, double>’ 96 | struct product_evaluator, ProductTag, LhsShape, RhsShape> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:29:8: required from ‘struct Eigen::internal::evaluator, Eigen::Transpose >, 2> >’ 29 | struct evaluator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:687:97: required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::SparseMatrix(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::Product, Eigen::Transpose >, 2>; _Scalar = double; int _Options = 0; _StorageIndex = int]’ 687 | const bool needToTranspose = (Flags & RowMajorBit) != (internal::evaluator::Flags & RowMajorBit); | ^~~~~ optimise_snn.cpp:58:45: required from here 58 | Eigen::SparseMatrix SNN = nnMatrix * (nnMatrix.transpose()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ 36 | class SparseCompressedBase | ^~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ 96 | class SparseMatrix | ^~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1040:66: required from ‘void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]’ 1040 | SparseMatrix trMat(mat.rows(),mat.cols()); | ^~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from ‘void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ 1110 | internal::set_from_triplets >(begin, end, *this, internal::scalar_sum_op()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ optimise_snn.cpp:114:20: required from here 114 | NN.setFromTriplets(tripletList.begin(), tripletList.end()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator > >’ 336 | typedef typename DenseCoeffsBase::CoeffReturnType CoeffReturnType; | ^~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator >’ 1505 | struct evaluator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from ‘Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]’ 1181 | const bool needToTranspose = (Flags & RowMajorBit) != (internal::evaluator::Flags & RowMajorBit); | ^~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from ‘void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]’ 1063 | mat = trMat; | ~~~~^~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from ‘void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]’ 1110 | internal::set_from_triplets >(begin, end, *this, internal::scalar_sum_op()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ optimise_snn.cpp:114:20: required from here 114 | NN.setFromTriplets(tripletList.begin(), tripletList.end()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c update_connectivity.cpp -o update_connectivity.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppEigen/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c wilcox.cpp -o wilcox.o wilcox.cpp: In function ‘Rcpp::NumericVector wilcox_test(Rcpp::IntegerMatrix, int, int)’: wilcox.cpp:42:13: warning: unused variable ‘max’ [-Wunused-variable] 42 | int max = 0; | ^~~ g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o ClustAssess.so RcppExports.o calculate_ecs.o calculate_pac.o optimise_snn.o update_connectivity.o wilcox.o -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT/usr/local/lib/R/library/00LOCK-ClustAssess/00new/ClustAssess/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘ClustAssess’ finding HTML links ... done Clustering-class html add_metadata html assess_clustering_stability html assess_feature_stability html assess_nn_stability html automatic_stability_assessment html calculate_markers html calculate_markers_shiny html choose_stable_clusters html consensus_cluster html create_clustering html create_monocle_default html create_monocle_from_clustassess html create_monocle_from_clustassess_app html create_seurat_object_default html create_seurat_object_from_clustassess_app html element_agreement html element_consistency html element_sim html element_sim_elscore html element_sim_matrix html getNNmatrix html get_clusters_from_clustassess_object html get_colour_vector_from_palette html get_highest_prune_param html get_highest_prune_param_embedding html get_nn_conn_comps html length-Clustering-method html marker_overlap html merge_partitions html merge_resolutions html pac_convergence html pac_landscape html plot_clust_hierarchical html plot_clustering_difference_facet html plot_clustering_overall_stability html plot_clustering_per_value_stability html plot_connected_comps_evolution html plot_feature_overall_stability_boxplot html plot_feature_overall_stability_incremental html plot_feature_per_resolution_stability_boxplot html plot_feature_per_resolution_stability_incremental html plot_feature_stability_ecs_facet html plot_feature_stability_mb_facet html plot_k_n_partitions html plot_k_resolution_corresp html plot_n_neigh_ecs html plot_n_neigh_k_correspondence html print-Clustering-method html server_comparisons html server_dimensionality_reduction html server_graph_clustering html server_graph_construction html server_landing_page html server_sandbox html ui_comparisons html ui_dimensionality_reduction html ui_graph_clustering html ui_graph_construction html ui_landing_page html ui_sandbox html weighted_element_consistency html write_objects html write_shiny_app html ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ClustAssess) + test -d ClustAssess/src + cd ClustAssess/src + rm -f RcppExports.o calculate_ecs.o calculate_pac.o optimise_snn.o update_connectivity.o wilcox.o ClustAssess.so + rm -f /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT/usr/local/lib/R/library/R.css + find /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT/usr/local/lib/R/library -type f -exec sed -i s@/builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT@@g '{}' ';' + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.1.0-1.fc42.copr9094197 --unique-debug-suffix -1.1.0-1.fc42.copr9094197.x86_64 --unique-debug-src-base R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/ClustAssess find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/local/lib/R/library/ClustAssess/CITATION is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64/ClustAssess/src/RcppExports.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64/ClustAssess/src/calculate_ecs.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64/ClustAssess/src/calculate_pac.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64/ClustAssess/src/optimise_snn.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64/ClustAssess/src/update_connectivity.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64/ClustAssess/src/wilcox.cpp is executable but has no shebang, removing executable bit + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT Handler jar skipped: jar handler requires $SOURCE_DATE_EPOCH to be set Handler gzip skipped: gzip handler requires $SOURCE_DATE_EPOCH to be set Handler zip skipped: zip handler requires $SOURCE_DATE_EPOCH to be set Scanned 26 directories and 170 files, processed 141 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/SPECPARTS/rpm-debuginfo.specpart Processing files: R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64 Provides: R-CRAN-ClustAssess = 1.1.0-1.fc42.copr9094197 R-CRAN-ClustAssess(x86-64) = 1.1.0-1.fc42.copr9094197 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH) Processing files: R-CRAN-ClustAssess-debugsource-1.1.0-1.fc42.copr9094197.x86_64 Provides: R-CRAN-ClustAssess-debugsource = 1.1.0-1.fc42.copr9094197 R-CRAN-ClustAssess-debugsource(x86-64) = 1.1.0-1.fc42.copr9094197 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-CRAN-ClustAssess-debuginfo-1.1.0-1.fc42.copr9094197.x86_64 Provides: R-CRAN-ClustAssess-debuginfo = 1.1.0-1.fc42.copr9094197 R-CRAN-ClustAssess-debuginfo(x86-64) = 1.1.0-1.fc42.copr9094197 debuginfo(build-id) = 25c05d2c3f4917e20e0720cbe3c7a248b1d4e63f Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-CRAN-ClustAssess-debugsource(x86-64) = 1.1.0-1.fc42.copr9094197 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build/BUILDROOT Wrote: /builddir/build/RPMS/R-CRAN-ClustAssess-debugsource-1.1.0-1.fc42.copr9094197.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-ClustAssess-debuginfo-1.1.0-1.fc42.copr9094197.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.E89aAH + umask 022 + cd /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + test -d /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + rm -rf /builddir/build/BUILD/R-CRAN-ClustAssess-1.1.0-build + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: %source_date_epoch_from_changelog is set, but %changelog has no entries to take a date from Finish: rpmbuild R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm Finish: build phase for R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-42-x86_64-1748397488.398721/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/R-CRAN-ClustAssess-1.1.0-1.fc42.copr9094197.src.rpm) Config(child) 0 minutes 40 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "R-CRAN-ClustAssess", "epoch": null, "version": "1.1.0", "release": "1.fc42.copr9094197", "arch": "x86_64" }, { "name": "R-CRAN-ClustAssess-debugsource", "epoch": null, "version": "1.1.0", "release": "1.fc42.copr9094197", "arch": "x86_64" }, { "name": "R-CRAN-ClustAssess", "epoch": null, "version": "1.1.0", "release": "1.fc42.copr9094197", "arch": "src" }, { "name": "R-CRAN-ClustAssess-debuginfo", "epoch": null, "version": "1.1.0", "release": "1.fc42.copr9094197", "arch": "x86_64" } ] } RPMResults finished