Running with gitlab-runner 13.8.0 (775dd39d)  on dsop-shared-gitlab-runner-f887cbcbd-srgz6 E82_g8RG section_start:1630431921:resolve_secrets Resolving secrets section_end:1630431921:resolve_secrets section_start:1630431921:prepare_executor Preparing the "kubernetes" executor Using Kubernetes namespace: gitlab-runner-ironbank-dsop WARNING: Pulling GitLab Runner helper image from Docker Hub. Helper image is migrating to registry.gitlab.com, for more information see https://docs.gitlab.com/runner/configuration/advanced-configuration.html#migrating-helper-image-to-registrygitlabcom Using Kubernetes executor with image registry1.dso.mil/ironbank/ironbank-pipelines/rootless-podman:0.2 ... section_end:1630431921:prepare_executor section_start:1630431921:prepare_script Preparing environment Waiting for pod gitlab-runner-ironbank-dsop/runner-e82g8rg-project-6549-concurrent-0hzpfr to be running, status is Pending Waiting for pod gitlab-runner-ironbank-dsop/runner-e82g8rg-project-6549-concurrent-0hzpfr to be running, status is Pending ContainersNotInitialized: "containers with incomplete status: [istio-init]" ContainersNotReady: "containers with unready status: [build helper istio-proxy]" ContainersNotReady: "containers with unready status: [build helper istio-proxy]" Running on runner-e82g8rg-project-6549-concurrent-0hzpfr via dsop-shared-gitlab-runner-f887cbcbd-srgz6... section_end:1630431927:prepare_script section_start:1630431927:get_sources Getting source from Git repository $ until [ $(curl --fail --silent --output /dev/stderr --write-out "%{http_code}" localhost:15020/healthz/ready) -eq 200 ]; do echo Waiting for Sidecar; sleep 3 ; done ; echo Sidecar available; Waiting for Sidecar Sidecar available Fetching changes with git depth set to 50... Initialized empty Git repository in /builds/dsop/opensource/r/r-studio/.git/ Created fresh repository. Checking out 29e02e63 as master... Skipping object checkout, Git LFS is not installed. Skipping Git submodules setup section_end:1630431931:get_sources section_start:1630431931:download_artifacts Downloading artifacts Downloading artifacts for hardening-manifest (6111649)... Downloading artifacts from coordinator... ok  id=6111649 responseStatus=200 OK token=gKexfqXv Downloading artifacts for import-artifacts (6111635)... WARNING: ci-artifacts/preflight/: lchown ci-artifacts/preflight/: operation not permitted (suppressing repeats) Downloading artifacts from coordinator... ok  id=6111635 responseStatus=200 OK token=5X9mefx2 WARNING: ci-artifacts/import-artifacts/: lchown ci-artifacts/import-artifacts/: operation not permitted (suppressing repeats) Downloading artifacts for load-scripts (6111630)... Downloading artifacts from coordinator... ok  id=6111630 responseStatus=200 OK token=7GFF36hS WARNING: ci-artifacts/[MASKED]/: lchown ci-artifacts/[MASKED]/: operation not permitted (suppressing repeats) Downloading artifacts for wl-compare-lint (6111634)... Downloading artifacts from coordinator... ok  id=6111634 responseStatus=200 OK token=KhhVxNwQ WARNING: ci-artifacts/lint/: lchown ci-artifacts/lint/: operation not permitted (suppressing repeats) section_end:1630431933:download_artifacts section_start:1630431933:step_script Executing "step_script" stage of the job script $ "${PIPELINE_REPO_DIR}/stages/build/build-run.sh" Determine source registry based on branch Load any images used in Dockerfile build Load HTTP and S3 external resources 'ci-artifacts/import-artifacts/external-resources/ModelMetrics_1.2.2.2.tar.gz' -> './ModelMetrics_1.2.2.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/R6_2.5.1.tar.gz' -> './R6_2.5.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/RColorBrewer_1.1-2.tar.gz' -> './RColorBrewer_1.1-2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/RcppArmadillo_0.10.6.0.0.tar.gz' -> './RcppArmadillo_0.10.6.0.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/Rcpp_1.0.7.tar.gz' -> './Rcpp_1.0.7.tar.gz' 'ci-artifacts/import-artifacts/external-resources/RhpcBLASctl_0.20-137.tar.gz' -> './RhpcBLASctl_0.20-137.tar.gz' 'ci-artifacts/import-artifacts/external-resources/SQUAREM_2021.1.tar.gz' -> './SQUAREM_2021.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/askpass_1.1.tar.gz' -> './askpass_1.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/caret_6.0-88.tar.gz' -> './caret_6.0-88.tar.gz' 'ci-artifacts/import-artifacts/external-resources/cli_3.0.1.tar.gz' -> './cli_3.0.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/colorspace_2.0-2.tar.gz' -> './colorspace_2.0-2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/compat-openssl10-1.0.2o-3.el8.x86_64.rpm' -> './compat-openssl10-1.0.2o-3.el8.x86_64.rpm' 'ci-artifacts/import-artifacts/external-resources/cpp11_0.3.1.tar.gz' -> './cpp11_0.3.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/crayon_1.4.1.tar.gz' -> './crayon_1.4.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/curl_4.3.2.tar.gz' -> './curl_4.3.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/data.table_1.14.0.tar.gz' -> './data.table_1.14.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/digest_0.6.27.tar.gz' -> './digest_0.6.27.tar.gz' 'ci-artifacts/import-artifacts/external-resources/dplyr_1.0.7.tar.gz' -> './dplyr_1.0.7.tar.gz' 'ci-artifacts/import-artifacts/external-resources/ellipsis_0.3.2.tar.gz' -> './ellipsis_0.3.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/evaluate_0.14.tar.gz' -> './evaluate_0.14.tar.gz' 'ci-artifacts/import-artifacts/external-resources/fansi_0.5.0.tar.gz' -> './fansi_0.5.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/farver_2.1.0.tar.gz' -> './farver_2.1.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/float_0.2-4.tar.gz' -> './float_0.2-4.tar.gz' 'ci-artifacts/import-artifacts/external-resources/foreach_1.5.1.tar.gz' -> './foreach_1.5.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/generics_0.1.0.tar.gz' -> './generics_0.1.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/ggplot2_3.3.5.tar.gz' -> './ggplot2_3.3.5.tar.gz' 'ci-artifacts/import-artifacts/external-resources/glue_1.4.2.tar.gz' -> './glue_1.4.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/gower_0.2.2.tar.gz' -> './gower_0.2.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/gtable_0.3.0.tar.gz' -> './gtable_0.3.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/highr_0.9.tar.gz' -> './highr_0.9.tar.gz' 'ci-artifacts/import-artifacts/external-resources/httr_1.4.2.tar.gz' -> './httr_1.4.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/ipred_0.9-11.tar.gz' -> './ipred_0.9-11.tar.gz' 'ci-artifacts/import-artifacts/external-resources/isoband_0.2.5.tar.gz' -> './isoband_0.2.5.tar.gz' 'ci-artifacts/import-artifacts/external-resources/iterators_1.0.13.tar.gz' -> './iterators_1.0.13.tar.gz' 'ci-artifacts/import-artifacts/external-resources/jsonlite_1.7.2.tar.gz' -> './jsonlite_1.7.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/knitr_1.33.tar.gz' -> './knitr_1.33.tar.gz' 'ci-artifacts/import-artifacts/external-resources/labeling_0.4.2.tar.gz' -> './labeling_0.4.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/lava_1.6.9.tar.gz' -> './lava_1.6.9.tar.gz' 'ci-artifacts/import-artifacts/external-resources/lgr_0.4.2.tar.gz' -> './lgr_0.4.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/lifecycle_1.0.0.tar.gz' -> './lifecycle_1.0.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/lubridate_1.7.10.tar.gz' -> './lubridate_1.7.10.tar.gz' Trying to pull registry1.dso.mil/ironbank/opensource/r/r-base:4.0.3... 'ci-artifacts/import-artifacts/external-resources/magrittr_2.0.1.tar.gz' -> './magrittr_2.0.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/markdown_1.1.tar.gz' -> './markdown_1.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/mime_0.11.tar.gz' -> './mime_0.11.tar.gz' 'ci-artifacts/import-artifacts/external-resources/mlapi_0.1.0.tar.gz' -> './mlapi_0.1.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/munsell_0.5.0.tar.gz' -> './munsell_0.5.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/numDeriv_2016.8-1.1.tar.gz' -> './numDeriv_2016.8-1.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/openssl_1.4.4.tar.gz' -> './openssl_1.4.4.tar.gz' 'ci-artifacts/import-artifacts/external-resources/oysteR_0.1.1.tar.gz' -> './oysteR_0.1.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/pROC_1.17.0.1.tar.gz' -> './pROC_1.17.0.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/pillar_1.6.2.tar.gz' -> './pillar_1.6.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/pkgconfig_2.0.3.tar.gz' -> './pkgconfig_2.0.3.tar.gz' 'ci-artifacts/import-artifacts/external-resources/plyr_1.8.6.tar.gz' -> './plyr_1.8.6.tar.gz' 'ci-artifacts/import-artifacts/external-resources/prodlim_2019.11.13.tar.gz' -> './prodlim_2019.11.13.tar.gz' 'ci-artifacts/import-artifacts/external-resources/purrr_0.3.4.tar.gz' -> './purrr_0.3.4.tar.gz' 'ci-artifacts/import-artifacts/external-resources/recipes_0.1.16.tar.gz' -> './recipes_0.1.16.tar.gz' 'ci-artifacts/import-artifacts/external-resources/reshape2_1.4.4.tar.gz' -> './reshape2_1.4.4.tar.gz' 'ci-artifacts/import-artifacts/external-resources/rjson_0.2.20.tar.gz' -> './rjson_0.2.20.tar.gz' 'ci-artifacts/import-artifacts/external-resources/rlang_0.4.11.tar.gz' -> './rlang_0.4.11.tar.gz' 'ci-artifacts/import-artifacts/external-resources/rsparse_0.4.0.tar.gz' -> './rsparse_0.4.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/rstudio-server-rhel-1.4.1717-x86_64.rpm' -> './rstudio-server-rhel-1.4.1717-x86_64.rpm' 'ci-artifacts/import-artifacts/external-resources/scales_1.1.1.tar.gz' -> './scales_1.1.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/stringi_1.7.4.tar.gz' -> './stringi_1.7.4.tar.gz' 'ci-artifacts/import-artifacts/external-resources/stringr_1.4.0.tar.gz' -> './stringr_1.4.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/sys_3.4.tar.gz' -> './sys_3.4.tar.gz' 'ci-artifacts/import-artifacts/external-resources/text2vec_0.6.tar.gz' -> './text2vec_0.6.tar.gz' 'ci-artifacts/import-artifacts/external-resources/tibble_3.1.4.tar.gz' -> './tibble_3.1.4.tar.gz' 'ci-artifacts/import-artifacts/external-resources/tidyr_1.1.3.tar.gz' -> './tidyr_1.1.3.tar.gz' 'ci-artifacts/import-artifacts/external-resources/tidyselect_1.1.1.tar.gz' -> './tidyselect_1.1.1.tar.gz' 'ci-artifacts/import-artifacts/external-resources/timeDate_3043.102.tar.gz' -> './timeDate_3043.102.tar.gz' 'ci-artifacts/import-artifacts/external-resources/utf8_1.2.2.tar.gz' -> './utf8_1.2.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/vctrs_0.3.8.tar.gz' -> './vctrs_0.3.8.tar.gz' 'ci-artifacts/import-artifacts/external-resources/viridisLite_0.4.0.tar.gz' -> './viridisLite_0.4.0.tar.gz' 'ci-artifacts/import-artifacts/external-resources/withr_2.4.2.tar.gz' -> './withr_2.4.2.tar.gz' 'ci-artifacts/import-artifacts/external-resources/xfun_0.25.tar.gz' -> './xfun_0.25.tar.gz' 'ci-artifacts/import-artifacts/external-resources/yaml_2.2.1.tar.gz' -> './yaml_2.2.1.tar.gz' Converting labels from hardening manifest into command line args Converting build args from hardening manifest into command line args Build the image STEP 1: FROM registry1.dso.mil/ironbank/opensource/r/r-base:4.0.3 Getting image source signatures Copying blob sha256:96476a77b28db43fcb170401c287700d91d95cdff9c06e5ea7b48289d40a8e57 Copying blob sha256:612731bd4073ce3a4b81a4cba66d261924ba75b5ce327bb37f3e0e3f4aced605 Copying blob sha256:db2f50b75fc09a20e8d9c497d96ad384fbeacf7e77df71e4c7b578d4c07fccce Copying blob sha256:83e99d40cd69b35e854123b47ffe6f80efe70a43e3e4afa3974a5b835a0443f7 Copying config sha256:5f718611d9ccbcadf88d31ee270128d3d4961c635cb46e7c6dedfd73d5944ada Writing manifest to image destination Storing signatures STEP 2: USER root STEP 3: ENV RSTUDIO_VERSION=1.4.1717 STEP 4: COPY *.rpm /tmp STEP 5: RUN dnf upgrade -y && dnf install -y --nogpgcheck glibc-langpack-en initscripts procps-ng /tmp/rstudio-server-rhel-${RSTUDIO_VERSION}-x86_64.rpm /tmp/compat-openssl10-1.0.2o-3.el8.x86_64.rpm binutils curl glibc-devel glibc-headers libcurl-devel libX11 libX11-common kernel-headers && mkdir -p /local/libs && chown -R $USER /var/lib/rstudio-server /var/run/rstudio-server && chmod -R g=u /var/lib/rstudio-server && chmod -R g=u /etc/rstudio && ln -s /usr/lib/rstudio-server/bin/rstudio-server /usr/local/bin/rstudio-server && chmod +t /var/run/rstudio-server && chkconfig rstudio-server off Red Hat Universal Base Image 8 (RPMs) - BaseOS 79 kB/s | 790 kB 00:10 Red Hat Universal Base Image 8 (RPMs) - AppStre 260 kB/s | 2.4 MB 00:09 Red Hat Universal Base Image 8 (RPMs) - CodeRea 1.4 kB/s | 14 kB 00:10 Dependencies resolved. Nothing to do. Complete! Package libX11-1.6.8-4.el8.x86_64 is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: binutils x86_64 2.30-93.el8 ubi-8-baseos 5.8 M compat-openssl10 x86_64 1:1.0.2o-3.el8 @commandline 1.1 M curl x86_64 7.61.1-18.el8 ubi-8-baseos 353 k glibc-devel x86_64 2.28-151.el8 ubi-8-baseos 1.0 M glibc-headers x86_64 2.28-151.el8 ubi-8-baseos 478 k glibc-langpack-en x86_64 2.28-151.el8 ubi-8-baseos 827 k initscripts x86_64 10.00.15-1.el8 ubi-8-baseos 339 k kernel-headers x86_64 4.18.0-305.12.1.el8_4 ubi-8-baseos 7.1 M libX11-common noarch 1.6.8-4.el8 ubi-8-appstream 158 k libcurl-devel x86_64 7.61.1-18.el8 ubi-8-baseos 833 k procps-ng x86_64 3.3.15-6.el8 ubi-8-baseos 329 k rstudio-server x86_64 1.4.1717-1 @commandline 63 M Installing dependencies: libpq x86_64 13.3-1.el8_4 ubi-8-appstream 197 k psmisc x86_64 23.1-5.el8 ubi-8-baseos 151 k sqlite x86_64 3.26.0-13.el8 ubi-8-baseos 667 k Transaction Summary ================================================================================ Install 15 Packages Total size: 82 M Total download size: 18 M Installed size: 604 M Downloading Packages: [MIRROR] procps-ng-3.3.15-6.el8.x86_64.rpm: Curl error (28): Timeout was reached for https://cdn-ubi.redhat.com/content/public/ubi/dist/ubi8/8/x86_64/baseos/os/Packages/p/procps-ng-3.3.15-6.el8.x86_64.rpm [Operation timed out after 5000 milliseconds with 0 out of 0 bytes received] [MIRROR] glibc-headers-2.28-151.el8.x86_64.rpm: Curl error (28): Timeout was reached for https://cdn-ubi.redhat.com/content/public/ubi/dist/ubi8/8/x86_64/baseos/os/Packages/g/glibc-headers-2.28-151.el8.x86_64.rpm [Operation timed out after 5000 milliseconds with 0 out of 0 bytes received] [MIRROR] glibc-langpack-en-2.28-151.el8.x86_64.rpm: Curl error (28): Timeout was reached for https://cdn-ubi.redhat.com/content/public/ubi/dist/ubi8/8/x86_64/baseos/os/Packages/g/glibc-langpack-en-2.28-151.el8.x86_64.rpm [Operation timed out after 5000 milliseconds with 0 out of 0 bytes received] (1/13): procps-ng-3.3.15-6.el8.x86_64.rpm 66 kB/s | 329 kB 00:05 (2/13): glibc-headers-2.28-151.el8.x86_64.rpm 95 kB/s | 478 kB 00:05 (3/13): glibc-langpack-en-2.28-151.el8.x86_64.r 164 kB/s | 827 kB 00:05 (4/13): curl-7.61.1-18.el8.x86_64.rpm 41 MB/s | 353 kB 00:00 (5/13): libcurl-devel-7.61.1-18.el8.x86_64.rpm 47 MB/s | 833 kB 00:00 (6/13): initscripts-10.00.15-1.el8.x86_64.rpm 43 MB/s | 339 kB 00:00 (7/13): psmisc-23.1-5.el8.x86_64.rpm 33 MB/s | 151 kB 00:00 (8/13): sqlite-3.26.0-13.el8.x86_64.rpm 57 MB/s | 667 kB 00:00 (9/13): glibc-devel-2.28-151.el8.x86_64.rpm 66 MB/s | 1.0 MB 00:00 (10/13): binutils-2.30-93.el8.x86_64.rpm 98 MB/s | 5.8 MB 00:00 (11/13): kernel-headers-4.18.0-305.12.1.el8_4.x 111 MB/s | 7.1 MB 00:00 [MIRROR] libpq-13.3-1.el8_4.x86_64.rpm: Curl error (35): SSL connect error for https://cdn-ubi.redhat.com/content/public/ubi/dist/ubi8/8/x86_64/appstream/os/Packages/l/libpq-13.3-1.el8_4.x86_64.rpm [OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to cdn-ubi.redhat.com:443 ] [MIRROR] libX11-common-1.6.8-4.el8.noarch.rpm: Curl error (35): SSL connect error for https://cdn-ubi.redhat.com/content/public/ubi/dist/ubi8/8/x86_64/appstream/os/Packages/l/libX11-common-1.6.8-4.el8.noarch.rpm [OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to cdn-ubi.redhat.com:443 ] (12/13): libX11-common-1.6.8-4.el8.noarch.rpm 32 kB/s | 158 kB 00:04 (13/13): libpq-13.3-1.el8_4.x86_64.rpm 40 kB/s | 197 kB 00:04 -------------------------------------------------------------------------------- Total 1.8 MB/s | 18 MB 00:10 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libpq-13.3-1.el8_4.x86_64 1/15 Installing : kernel-headers-4.18.0-305.12.1.el8_4.x86_64 2/15 Running scriptlet: glibc-headers-2.28-151.el8.x86_64 3/15 Installing : glibc-headers-2.28-151.el8.x86_64 3/15 Installing : sqlite-3.26.0-13.el8.x86_64 4/15 Installing : psmisc-23.1-5.el8.x86_64 5/15 Installing : procps-ng-3.3.15-6.el8.x86_64 6/15 Installing : initscripts-10.00.15-1.el8.x86_64 7/15 Running scriptlet: initscripts-10.00.15-1.el8.x86_64 7/15 Running scriptlet: rstudio-server-1.4.1717-1.x86_64 8/15 Installing : rstudio-server-1.4.1717-1.x86_64 8/15 Running scriptlet: rstudio-server-1.4.1717-1.x86_64 8/15 /usr/lib/rstudio-server/bin/rserver: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory Installing : glibc-devel-2.28-151.el8.x86_64 9/15 Running scriptlet: glibc-devel-2.28-151.el8.x86_64 9/15 Installing : compat-openssl10-1:1.0.2o-3.el8.x86_64 10/15 Running scriptlet: compat-openssl10-1:1.0.2o-3.el8.x86_64 10/15 Installing : libX11-common-1.6.8-4.el8.noarch 11/15 Installing : binutils-2.30-93.el8.x86_64 12/15 Running scriptlet: binutils-2.30-93.el8.x86_64 12/15 Installing : curl-7.61.1-18.el8.x86_64 13/15 Installing : libcurl-devel-7.61.1-18.el8.x86_64 14/15 Installing : glibc-langpack-en-2.28-151.el8.x86_64 15/15 Running scriptlet: glibc-langpack-en-2.28-151.el8.x86_64 15/15 Verifying : procps-ng-3.3.15-6.el8.x86_64 1/15 Verifying : glibc-headers-2.28-151.el8.x86_64 2/15 Verifying : glibc-langpack-en-2.28-151.el8.x86_64 3/15 Verifying : libcurl-devel-7.61.1-18.el8.x86_64 4/15 Verifying : curl-7.61.1-18.el8.x86_64 5/15 Verifying : binutils-2.30-93.el8.x86_64 6/15 Verifying : initscripts-10.00.15-1.el8.x86_64 7/15 Verifying : psmisc-23.1-5.el8.x86_64 8/15 Verifying : sqlite-3.26.0-13.el8.x86_64 9/15 Verifying : glibc-devel-2.28-151.el8.x86_64 10/15 Verifying : kernel-headers-4.18.0-305.12.1.el8_4.x86_64 11/15 Verifying : libpq-13.3-1.el8_4.x86_64 12/15 Verifying : libX11-common-1.6.8-4.el8.noarch 13/15 Verifying : rstudio-server-1.4.1717-1.x86_64 14/15 Verifying : compat-openssl10-1:1.0.2o-3.el8.x86_64 15/15 Installed products updated. Installed: binutils-2.30-93.el8.x86_64 compat-openssl10-1:1.0.2o-3.el8.x86_64 curl-7.61.1-18.el8.x86_64 glibc-devel-2.28-151.el8.x86_64 glibc-headers-2.28-151.el8.x86_64 glibc-langpack-en-2.28-151.el8.x86_64 initscripts-10.00.15-1.el8.x86_64 kernel-headers-4.18.0-305.12.1.el8_4.x86_64 libX11-common-1.6.8-4.el8.noarch libcurl-devel-7.61.1-18.el8.x86_64 libpq-13.3-1.el8_4.x86_64 procps-ng-3.3.15-6.el8.x86_64 psmisc-23.1-5.el8.x86_64 rstudio-server-1.4.1717-1.x86_64 sqlite-3.26.0-13.el8.x86_64 Complete! STEP 6: COPY *.tar.gz /local/libs STEP 7: COPY rpackages /tmp/rpackages STEP 8: RUN R -e "library(tools); write_PACKAGES('/local/libs')" && cat /tmp/rpackages | awk '{printf "\x27"$1"\x27,"}' | sed 's/.$//' | xargs -0 -I {} R -e "install.packages(c({}), contriburl='file:///local/libs')" && rpm -e --nodeps binutils curl glibc-devel glibc-headers libcurl-devel libX11 libX11-common kernel-headers && echo "auth-none=1" >> /etc/rstudio/disable_auth_rserver.conf && echo "server-daemonize=0" >> /etc/rstudio/rserver.conf && echo "[*]" > /etc/rstudio/logging.conf && echo "log-level=warn" >> /etc/rstudio/logging.conf && echo "logger-type=stderr" >> /etc/rstudio/logging.conf && dnf clean all && rm -rf /var/cache/dnf /tmp/* /local/libs/* R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(tools); write_PACKAGES('/local/libs') > > R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > install.packages(c('ggplot2','data.table','dplyr','tidyr','knitr','caret','text2vec','oysteR'), contriburl='file:///local/libs') also installing the dependencies 'numDeriv', 'SQUAREM', 'lava', 'sys', 'colorspace', 'prodlim', 'askpass', 'farver', 'labeling', 'munsell', 'RColorBrewer', 'viridisLite', 'fansi', 'pkgconfig', 'crayon', 'utf8', 'mime', 'iterators', 'gower', 'ipred', 'lubridate', 'timeDate', 'float', 'RhpcBLASctl', 'RcppArmadillo', 'curl', 'openssl', 'digest', 'glue', 'gtable', 'isoband', 'rlang', 'scales', 'tibble', 'withr', 'ellipsis', 'generics', 'lifecycle', 'magrittr', 'R6', 'tidyselect', 'vctrs', 'pillar', 'purrr', 'cpp11', 'evaluate', 'highr', 'markdown', 'stringr', 'yaml', 'xfun', 'foreach', 'plyr', 'ModelMetrics', 'reshape2', 'recipes', 'pROC', 'Rcpp', 'rsparse', 'stringi', 'mlapi', 'lgr', 'cli', 'httr', 'jsonlite', 'rjson' * installing *source* package 'numDeriv' ... ** package 'numDeriv' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'numDeriv' done 00.numDeriv.Intro html genD html grad html hessian html jacobian html numDeriv-package html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (numDeriv) Making 'packages.html' ... done * installing *source* package 'SQUAREM' ... ** package 'SQUAREM' successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'SQUAREM' done fpiter html internal html squarem html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SQUAREM) Making 'packages.html' ... done * installing *source* package 'sys' ... ** package 'sys' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c exec.c -o exec.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o sys.so exec.o init.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-sys/00new/sys/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'sys' done as_text html deprecated html exec html exec_r html quote ** building package indices html ** 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 (sys) Making 'packages.html' ... done * installing *source* package 'colorspace' ... ** package 'colorspace' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c colorspace.c -o colorspace.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o colorspace.so colorspace.o init.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-colorspace/00new/colorspace/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'colorspace' finding HTML links ... done HLS html HSV html LAB html LUV html RGB html USSouthPolygon html XYZ html adjust_transparency html choose_palette html color-class html contrast_ratio html coords html cvd html cvd_emulator html cvd_image html demoplot html desaturate html divergingx_hcl html Rd warning: /tmp/RtmpXtPURX/Rbuild1f8ff35ae999ad/colorspace/man/divergingx_hcl.Rd:125: file link 'sequential_hcl' in package 'colorspace' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpXtPURX/Rbuild1f8ff35ae999ad/colorspace/man/divergingx_hcl.Rd:125: file link 'diverging_hcl' in package 'colorspace' does not exist and so has been treated as a topic hcl_color_picker html hcl_palettes html hclplot html hex html hex2RGB html lighten html max_chroma html mixcolor html polarLAB html polarLUV html rainbow_hcl html Rd warning: /tmp/RtmpXtPURX/Rbuild1f8ff35ae999ad/colorspace/man/rainbow_hcl.Rd:108: file link 'heat.colors' in package 'grDevices' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpXtPURX/Rbuild1f8ff35ae999ad/colorspace/man/rainbow_hcl.Rd:118: file link 'cm.colors' in package 'grDevices' does not exist and so has been treated as a topic readRGB html readhex html sRGB html scale_colour_binned_diverging html scale_colour_binned_divergingx html scale_colour_binned_qualitative html scale_colour_binned_sequential html scale_colour_continuous_diverging html scale_colour_continuous_divergingx html scale_colour_continuous_qualitative html scale_colour_continuous_sequential html scale_colour_discrete_diverging html scale_colour_discrete_divergingx html scale_colour_discrete_qualitative html scale_colour_discrete_sequential html simulate_cvd html specplot html swatchplot html whitepoint html writehex html ** building package indices ** installing vignettes ** 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 (colorspace) Making 'packages.html' ... done * installing *source* package 'farver' ... ** package 'farver' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ColorSpace.cpp -o ColorSpace.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Comparison.cpp -o Comparison.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Conversion.cpp -o Conversion.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c encode.cpp -o encode.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c farver.cpp -o farver.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o farver.so ColorSpace.o Comparison.o Conversion.o encode.o farver.o init.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-farver/00new/farver/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'farver' done as_white_ref html compare_colour html convert_colour html decode_colour html encode_colour html farver-package html manip_channel html native_encoding html *** copying figures ** 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 (farver) Making 'packages.html' ... done * installing *source* package 'labeling' ... ** package 'labeling' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'labeling' done extended html extended.figures html gnuplot html heckbert html labeling-internal html labeling-package html matplotlib html nelder html rpretty html sparks html thayer html wilkinson html ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (labeling) Making 'packages.html' ... done * installing *source* package 'RColorBrewer' ... ** package 'RColorBrewer' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'RColorBrewer' ColorBrewer html done ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RColorBrewer) Making 'packages.html' ... done * installing *source* package 'viridisLite' ... ** package 'viridisLite' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'viridisLite' done viridis html viridis.map html *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (viridisLite) Making 'packages.html' ... done * installing *source* package 'fansi' ... ** package 'fansi' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c assumptions.c -o assumptions.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c has.c -o has.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nchar.c -o nchar.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c read.c -o read.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rnchar.c -o rnchar.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c state.c -o state.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c strip.c -o strip.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c strsplit.c -o strsplit.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabs.c -o tabs.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tohtml.c -o tohtml.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unhandled.c -o unhandled.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unique.c -o unique.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c utf8.c -o utf8.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c wrap.c -o wrap.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o fansi.so assumptions.o has.o init.o nchar.o read.o rnchar.o state.o strip.o strsplit.o tabs.o tohtml.o unhandled.o unique.o utf8.o utils.o wrap.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-fansi/00new/fansi/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'fansi' done fansi html fansi_lines html has_ctl html html_code_block html html_esc html in_html html make_styles html nchar_ctl html set_knit_hooks html sgr_256 html sgr_to_html html strip_ctl html strsplit_ctl html Rd warning: /tmp/RtmpJZyKr3/R.INSTALLc644ae732e8/fansi/man/strsplit_ctl.Rd:35: file link 'regular expression' in package 'base' does not exist and so has been treated as a topic strtrim_ctl html Rd warning: /tmp/RtmpJZyKr3/R.INSTALLc644ae732e8/fansi/man/strtrim_ctl.Rd:33: file link 'as.character' in package 'base' does not exist and so has been treated as a topic strwrap_ctl html Rd warning: /tmp/RtmpJZyKr3/R.INSTALLc644ae732e8/fansi/man/strwrap_ctl.Rd:72: file link 'as.character' in package 'base' does not exist and so has been treated as a topic substr_ctl html ** building package indices tabs_as_spaces html term_cap_test html unhandled_ctl html ** installing vignettes ** 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 (fansi) Making 'packages.html' ... done * installing *source* package 'pkgconfig' ... ** package 'pkgconfig' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'pkgconfig' done get_config html pkgconfig-package html set_config html set_config_in html ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pkgconfig) Making 'packages.html' ... done * installing *source* package 'crayon' ... ** package 'crayon' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'crayon' done chr html col_align html col_nchar html col_strsplit html col_substr html col_substring html combine_styles html concat html crayon html drop_style html has_color html has_style html hyperlink html make_style html num_ansi_colors html num_colors html show_ansi_colors html start.crayon html strip_style html style html styles html ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (crayon) Making 'packages.html' ... done * installing *source* package 'utf8' ... ** package 'utf8' successfully unpacked and MD5 sums checked ** using staged installation gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c as_utf8.c -o as_utf8.o ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c bytes.c -o bytes.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c context.c -o context.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c render.c -o render.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c render_table.c -o render_table.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c string.c -o string.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c text.c -o text.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_encode.c -o utf8_encode.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_format.c -o utf8_format.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_normalize.c -o utf8_normalize.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_valid.c -o utf8_valid.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_width.c -o utf8_width.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c util.c -o util.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/array.c -o utf8lite/src/array.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/char.c -o utf8lite/src/char.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/encode.c -o utf8lite/src/encode.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/error.c -o utf8lite/src/error.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/escape.c -o utf8lite/src/escape.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/graph.c -o utf8lite/src/graph.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/graphscan.c -o utf8lite/src/graphscan.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/normalize.c -o utf8lite/src/normalize.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/render.c -o utf8lite/src/render.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/text.c -o utf8lite/src/text.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/textassign.c -o utf8lite/src/textassign.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/textiter.c -o utf8lite/src/textiter.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/textmap.c -o utf8lite/src/textmap.o ar rcs libcutf8lite.a utf8lite/src/array.o utf8lite/src/char.o utf8lite/src/encode.o utf8lite/src/error.o utf8lite/src/escape.o utf8lite/src/graph.o utf8lite/src/graphscan.o utf8lite/src/normalize.o utf8lite/src/render.o utf8lite/src/text.o utf8lite/src/textassign.o utf8lite/src/textiter.o utf8lite/src/textmap.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o utf8.so as_utf8.o bytes.o context.o init.o render.o render_table.o string.o text.o utf8_encode.o utf8_format.o utf8_normalize.o utf8_valid.o utf8_width.o util.o -L. -lcutf8lite -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-utf8/00new/utf8/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'utf8' done as_utf8 html output html utf8-package html utf8_encode html utf8_format html utf8_normalize html utf8_print html utf8_width html ** building package indices ** installing vignettes ** 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 (utf8) Making 'packages.html' ... done * installing *source* package 'mime' ... ** package 'mime' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rawmatch.c -o rawmatch.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-mime/00new/mime/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'mime' done guess_type html mimemap html parse_multipart 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 (mime) Making 'packages.html' ... done * installing *source* package 'iterators' ... ** package 'iterators' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'iterators' done iapply html icount html idiv html iread.table html ireadLines html irnorm html isplit html iter html iterators-package html makeIwrapper html nextElem ** building package indices html ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (iterators) Making 'packages.html' ... done * installing *source* package 'gower' ... ** package 'gower' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c R_register_native.c -o R_register_native.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c gower.c -o gower.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o gower.so R_register_native.o gower.o -fopenmp -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-gower/00new/gower/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'gower' done gower-package html gower_dist html gower_topn html ** building package indices ** installing vignettes ** 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 (gower) Making 'packages.html' ... done * installing *source* package 'timeDate' ... ** package 'timeDate' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'sample' from package 'base' in package 'timeDate' Creating a generic function for 'getDataPart' from package 'methods' in package 'timeDate' Creating a generic function for 'abline' from package 'graphics' in package 'timeDate' ** help *** installing help indices finding HTML links ... converting help for package 'timeDate' done 00timeDate-package html base-c html base-diff html base-difftimeDate html base-format html base-length html base-rep html base-rev html base-round html base-sample html base-sort html base-start html base-subset html base-summary html base-unique html calendar-Easter html calendar-align html calendar-dayOfWeek html calendar-dayOfYear html calendar-endpoints html calendar-firstDay html calendar-isBizday html calendar-isRegular html calendar-isWeekday html calendar-julian html calendar-nDay html calendar-onOrAfter html calendar-periods html class-timeDate html graphics-plot html holiday-Dates html holiday-LONDON html holiday-Listing html holiday-NERC html holiday-NYSE html holiday-TSX html holiday-ZURICH html holiday html methods-as html methods-mathOps html methods-names html methods-show html options-RmetricsOptions html options-currentYear html options-myFinCenter html options-myUnits html stats-blockStart html stats-kurtosis html stats-na-fail html stats-skewness html stats-window html timeDate-Calendar html timeDate-DaylightSavingTime html timeDate-Sequence html timeDate-Sys.timeDate html timeDate-finCenter html timeDate-listFinCenter html timeDate-midnightStandard html timeDate-rulesFinCenter html timeDate-whichFormat html timeDate html ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (timeDate) Making 'packages.html' ... done * installing *source* package 'float' ... ** package 'float' successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gcc option to accept ISO C99... none needed checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++11 accepts -g... yes checking for sinf in -lm... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking size of int... 4 checking for gcc option to support OpenMP... -fopenmp checking for echo... yes checking for grep... yes checking for sgemm_ in -lRblas... yes checking for sgetrf_ in -lRblas... yes ******************* Results of float package configure ******************* * OpenMP Report: >> OPENMP_CFLAGS=-fopenmp >> OMPFLAGS_C=$(SHLIB_OPENMP_CFLAGS) * byte order: little endian * using system BLAS library >> BLAS_LIBS=-L/opt/R/4.0.3/lib/R/lib -lRblas * using system LAPACK library >> LAPACK_LIBS=-L/opt/R/4.0.3/lib/R/lib -lRlapack ************************************************************************* configure: creating ./config.status config.status: creating src/endianness.h configure: creating ./config.status config.status: creating src/endianness.h config.status: creating src/Makevars ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c backsolve.c -o backsolve.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c binary.c -o binary.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c chol.c -o chol.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c chol2inv.c -o chol2inv.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c colSums.c -o colSums.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c cond.c -o cond.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c converters.c -o converters.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c crossprod.c -o crossprod.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c eigen.c -o eigen.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c extremes.c -o extremes.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c float_native.c -o float_native.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c isSymmetric.c -o isSymmetric.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c machine.c -o machine.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c math.c -o math.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c matmult.c -o matmult.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c NA.c -o NA.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c norm.c -o norm.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c qr.c -o qr.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c rand.c -o rand.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c scale.c -o scale.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c sign.c -o sign.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c solve.c -o solve.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c sum.c -o sum.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c svd.c -o svd.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c sweep.c -o sweep.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c xpose.c -o xpose.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c utils/matmult.c -o utils/matmult.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c utils/symmetrize.c -o utils/symmetrize.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fpic -g -O2 -c utils/xpose.c -o utils/xpose.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -c slapack_wrap.f -o slapack_wrap.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o float.so backsolve.o binary.o chol.o chol2inv.o colSums.o cond.o converters.o crossprod.o eigen.o extremes.o float_native.o isSymmetric.o machine.o math.o matmult.o NA.o norm.o qr.o rand.o scale.o sign.o solve.o sum.o svd.o sweep.o xpose.o utils/matmult.o utils/symmetrize.o utils/xpose.o slapack_wrap.o -L/opt/R/4.0.3/lib/R/lib -lRlapack -L/opt/R/4.0.3/lib/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -lgfortran -lm -lquadmath -L/opt/R/4.0.3/lib/R/lib -lR ar crs libfloat.a backsolve.o binary.o chol.o chol2inv.o colSums.o cond.o converters.o crossprod.o eigen.o extremes.o float_native.o isSymmetric.o machine.o math.o matmult.o NA.o norm.o qr.o rand.o scale.o sign.o solve.o sum.o svd.o sweep.o xpose.o utils/matmult.o utils/symmetrize.o utils/xpose.o slapack_wrap.o ranlib libfloat.a installing via 'install.libs.R' to /opt/R/4.0.3/lib/R/library/00LOCK-float/00new/float ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help Creating a generic function for 'backsolve' from package 'base' in package 'float' Creating a generic function for 'forwardsolve' from package 'base' in package 'float' Creating a generic function for 'chol2inv' from 'base' in package 'float' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'float' Creating a generic function for 'colSums' from package 'base' in package 'float' Creating a generic function for 'rowSums' from package 'base' in package 'float' Creating a generic function for 'colMeans' from package 'base' in package 'float' Creating a generic function for 'rowMeans' from package 'base' in package 'float' Creating a generic function for 'rcond' from 'base' in package 'float' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'float' Creating a generic function for 'typeof' from package 'base' in package 'float' Creating a generic function for 'storage.mode' from package 'base' in package 'float' Creating a generic function for 'crossprod' from package 'base' in package 'float' Creating a generic function for 'tcrossprod' from package 'base' in package 'float' Creating a generic function for 'diag' from package 'base' in package 'float' Creating a generic function for 'nrow' from package 'base' in package 'float' Creating a generic function for 'ncol' from package 'base' in package 'float' Creating a generic function for 'NROW' from package 'base' in package 'float' Creating a generic function for 'NCOL' from package 'base' in package 'float' Creating a generic function for 'eigen' from package 'base' in package 'float' Creating a generic function for 'which.min' from package 'base' in package 'float' Creating a generic function for 'which.max' from package 'base' in package 'float' Creating a generic function for 'rownames' from package 'base' in package 'float' Creating a generic function for 'rownames<-' from package 'base' in package 'float' Creating a generic function for 'colnames' from package 'base' in package 'float' Creating a generic function for 'colnames<-' from package 'base' in package 'float' Creating a generic function for 'norm' from package 'base' in package 'float' Creating a generic function for 'qr.Q' from package 'base' in package 'float' Creating a generic function for 'qr.R' from package 'base' in package 'float' Creating a generic function for 'qr.qy' from package 'base' in package 'float' Creating a generic function for 'qr.qty' from package 'base' in package 'float' Creating a generic function for 'La.svd' from package 'base' in package 'float' Creating a generic function for 'svd' from 'base' in package 'float' (from the saved implicit definition) Creating a generic function for 'svd' from package 'base' in package 'float' Creating a generic function for 'sweep' from package 'base' in package 'float' *** installing help indices finding HTML links ... converting help for package 'float' done Machine_float html NA_float_ html NaNf html arithmetic html backsolve html bind html bracket html c html chol html chol2inv html colsums html comparison html converters html crossprod html diag html dims html eigen html extremes html float-package html float html float32-class html float32 html hyperbolic html is.float html isSymmetric html log html mathis html matmult html miscmath html na html names html norm html print-float32 html qr html rand html rcond html rep html round html scale html sign html solve html specialmath html sum html svd html sweep html trig html xpose html ** building package indices ** installing vignettes 'float.Rnw' ** 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 (float) Making 'packages.html' ... done * installing *source* package 'RhpcBLASctl' ... ** package 'RhpcBLASctl' successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking sys/sysctl.h usability... yes checking sys/sysctl.h presence... yes checking for sys/sysctl.h... yes checking for sysctl... yes checking for sysctlbyname... no checking sys/sysinfo.h usability... yes checking sys/sysinfo.h presence... yes checking for sys/sysinfo.h... yes checking for get_nprocs... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c blasctl.c -o blasctl.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o RhpcBLASctl.so blasctl.o registerDynamicSymbol.o -ldl -fopenmp -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-RhpcBLASctl/00new/RhpcBLASctl/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'RhpcBLASctl' done RhpcBLASctl-package 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 (RhpcBLASctl) Making 'packages.html' ... done * installing *source* package 'curl' ... ** package 'curl' successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-lcurl ** libs rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c callbacks.c -o callbacks.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c curl.c -o curl.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c download.c -o download.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c escape.c -o escape.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fetch.c -o fetch.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c form.c -o form.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c getdate.c -o getdate.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c handle.c -o handle.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ieproxy.c -o ieproxy.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c interrupt.c -o interrupt.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c multi.c -o multi.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c nslookup.c -o nslookup.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c reflist.c -o reflist.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c split.c -o split.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ssl.c -o ssl.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c typechecking.c -o typechecking.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c winidn.c -o winidn.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c writer.c -o writer.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-curl/00new/curl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'curl' done curl html curl_download html curl_echo html curl_escape html curl_fetch html curl_options html curl_upload html file_writer html handle html handle_cookies html ie_proxy html multi html multipart html nslookup html parse_date html parse_headers html send_mail html ** building package indices ** installing vignettes ** 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 (curl) Making 'packages.html' ... done * installing *source* package 'digest' ... ** package 'digest' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SpookyV2.cpp -o SpookyV2.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c aes.c -o aes.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c blake3.c -o blake3.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c blake3_dispatch.c -o blake3_dispatch.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c blake3_portable.c -o blake3_portable.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c crc32.c -o crc32.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c digest.c -o digest.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c digest2int.c -o digest2int.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c md5.c -o md5.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pmurhash.c -o pmurhash.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c raes.c -o raes.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sha1.c -o sha1.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sha2.c -o sha2.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sha256.c -o sha256.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c spooky_serialize.cpp -o spooky_serialize.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c xxhash.c -o xxhash.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o digest.so SpookyV2.o aes.o blake3.o blake3_dispatch.o blake3_portable.o crc32.o digest.o digest2int.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o spooky_serialize.o xxhash.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-digest/00new/digest/libs ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'digest' finding HTML links ... done AES html digest html digest2int html hmac html makeRaw html sha1 html vdigest html ** building package indices ** installing vignettes ** 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 (digest) Making 'packages.html' ... done * installing *source* package 'glue' ... ** package 'glue' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c glue.c -o glue.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c trim.c -o trim.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-glue/00new/glue/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'glue' done as_glue html glue-deprecated html glue html glue_col html glue_collapse html Rd warning: /tmp/Rtmp0fHeCb/R.INSTALL1a094317c5/glue/man/glue_collapse.Rd:13: file link 'NA_character_' in package 'base' does not exist and so has been treated as a topic glue_safe html glue_sql html identity_transformer html quoting html trim html *** copying figures ** building package indices ** installing vignettes ** 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 (glue) Making 'packages.html' ... done * installing *source* package 'gtable' ... ** package 'gtable' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'gtable' done bind html gtable-package html gtable html gtable_add_cols html gtable_add_grob html gtable_add_padding html gtable_add_rows html gtable_add_space html gtable_col html gtable_filter html gtable_height html gtable_matrix html gtable_row html gtable_show_layout html gtable_spacer html gtable_trim html gtable_width html is.gtable html print.gtable html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gtable) Making 'packages.html' ... done * installing *source* package 'isoband' ... ** package 'isoband' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -c clip-lines.cpp -o clip-lines.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -c isoband.cpp -o isoband.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -c polygon.cpp -o polygon.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -c separate-polygons.cpp -o separate-polygons.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -c test-clip-lines.cpp -o test-clip-lines.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -c test-runner.cpp -o test-runner.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -c test-separate-polygons.cpp -o test-separate-polygons.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o isoband.so clip-lines.o init.o isoband.o polygon.o separate-polygons.o test-clip-lines.o test-runner.o test-separate-polygons.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-isoband/00new/isoband/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'isoband' finding HTML links ... done angle_halfcircle_bottom html clip_lines html iso_to_sfg html isoband-package html isobands html isobands_grob html isolines_grob html label_placer html label_placer_simple html plot_iso html *** copying figures ** building package indices ** installing vignettes ** 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 (isoband) Making 'packages.html' ... done * installing *source* package 'rlang' ... ** package 'rlang' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c capture.c -o capture.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c export.c -o export.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c internal.c -o internal.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c lib.c -o lib.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o rlang.so capture.o export.o internal.o lib.o version.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-rlang/00new/rlang/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'rlang' done abort html are_na html arg_match html as_box html as_bytes html as_data_mask html as_env html as_environment html as_function html as_label html as_name html as_overscope html as_pairlist html as_quosure html as_string html as_utf8_character html bare-type-predicates html box html call2 html call_args html call_fn html call_inspect html call_modify html call_name html call_parse_type html call_standardise html caller_env html caller_fn html caller_frame html catch_cnd html chr_unserialise_unicode html cnd html cnd_message html cnd_muffle html cnd_signal html cnd_type html done html dots_definitions html dots_n html dots_values html duplicate html dyn-dots html empty_env html enquo0 html entrace html env html env_bind html env_bind_exprs html env_binding_are_active html env_binding_lock html env_browse html env_bury html env_clone html env_depth html env_get html env_has html env_inherits html env_lock html env_name html env_names html env_parent html env_poke html env_print html env_unbind html env_unlock html eval_bare html eval_tidy html exec html exiting html expr_interp html expr_label html expr_print html exprs_auto_name html f_rhs html f_text html faq-options html flatten html fn_body html fn_env html fn_fmls html format_error_bullets html frame_position html friendly_type html get_env html has_length html has_name html hash html inherits_any html inject html invoke html is_call html is_callable html is_condition html is_copyable html is_empty html is_env html is_environment html is_expr html is_expression html is_formula html is_frame html is_function html is_installed html is_integerish html is_interactive html is_lang html is_named html is_namespace html is_pairlist html is_reference html is_stack html is_symbol html is_true html is_weakref html lang html lang_head html lang_modify html last_error html lifecycle html list2 html local_bindings html local_options html missing html missing_arg html mut_node_car html names2 html new-vector-along-retired html new-vector html new_call html new_formula html new_function html new_node html new_quosures html new_weakref html ns_env html nse-defuse html nse-force html op-definition html op-get-attr html op-na-default html op-null-default html overscope_eval_next html pairlist2 html parse_expr html parse_quosure html prepend html prim_name html quo_expr html quo_label html quo_squash html quosure html raw_deparse_str html rep_along html restarting html return_from html rlang_backtrace_on_error html rst_abort html rst_list html scalar-type-predicates html scoped_env html scoped_interactive html search_envs html seq2 html set_attrs html set_expr html set_names html splice html stack html stack_trim html string html switch_type html sym html tidyeval-data html trace_back html type-predicates html type_of html vec_poke_n html vector-coercion html vector-construction html vector-old-ctors html with_abort html with_env html with_handlers html with_restarts html wref_key html zap html zap_srcref html *** copying figures ** 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 (rlang) Making 'packages.html' ... done * installing *source* package 'withr' ... ** package 'withr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'withr' finding HTML links ... done defer html devices html Rd warning: /tmp/RtmpyJeZmR/R.INSTALL1c301946b59a/withr/man/devices.Rd:228: file link 'X11' in package 'grDevices' does not exist and so has been treated as a topic makevars_user html set_makevars html with_ html with_collate html with_connection html with_db_connection html with_dir html with_envvar html with_file html with_gctorture2 html with_libpaths html with_locale html with_makevars html with_options html with_package html Rd warning: /tmp/RtmpyJeZmR/R.INSTALL1c301946b59a/withr/man/with_package.Rd:68: file link '.libPaths' in package 'base' does not exist and so has been treated as a topic with_par html with_path html with_rng_version html with_seed html with_sink html with_temp_libpaths html with_tempfile html with_timezone html withr html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (withr) Making 'packages.html' ... done * installing *source* package 'generics' ... ** package 'generics' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'generics' finding HTML links ... done augment html calculate html coercion-factor html coercion-time-difference html compile html components html equation html estfun html evaluate html explain html fit html fit_xy html generate html generics-package html glance html hypothesize html interpolate html learn html min_grid html prune html refit html required_pkgs html setops html specify html tidy html train html tunable html var_imp html varying_args html visualize html ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (generics) Making 'packages.html' ... done * installing *source* package 'magrittr' ... ** package 'magrittr' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pipe.c -o pipe.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o magrittr.so pipe.o utils.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-magrittr/00new/magrittr/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'magrittr' done aliases html compound html debug_fseq html debug_pipe html exposition html faq-pipe-gender html freduce html fseq html functions html magrittr-package html pipe html pipe_eager_lexical html *** copying figures print.fseq ** building package indices html tee html ** installing vignettes ** 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 (magrittr) Making 'packages.html' ... done * installing *source* package 'R6' ... ** package 'R6' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'R6' done R6Class html as.list.R6 html is.R6 html *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R6) Making 'packages.html' ... done * installing *source* package 'cpp11' ... ** package 'cpp11' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'cpp11' done cpp11-package html cpp_register html cpp_source html cpp_vendor html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cpp11) Making 'packages.html' ... done * installing *source* package 'evaluate' ... ** package 'evaluate' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'evaluate' done create_traceback html Rd warning: /tmp/RtmpUsQnQL/R.INSTALL1e8247c9fe9/evaluate/man/create_traceback.Rd:11: file link 'sys.calls' in package 'base' does not exist and so has been treated as a topic evaluate html flush_console html inject_funs html is.message html line_prompt html new_output_handler html parse_all html remove_hooks html replay html set_hooks html try_capture_stack html watchout html ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (evaluate) Making 'packages.html' ... done * installing *source* package 'yaml' ... ** package 'yaml' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api.c -o api.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dumper.c -o dumper.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c emitter.c -o emitter.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c implicit.c -o implicit.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c loader.c -o loader.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parser.c -o parser.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c r_emit.c -o r_emit.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c r_ext.c -o r_ext.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c r_parse.c -o r_parse.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c reader.c -o reader.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scanner.c -o scanner.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c writer.c -o writer.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-yaml/00new/yaml/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'yaml' done as.yaml html read_yaml html write_yaml html yaml.load 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 (yaml) Making 'packages.html' ... done * installing *source* package 'xfun' ... ** package 'xfun' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o xfun.so base64.o init.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-xfun/00new/xfun/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'xfun' done Rscript html Rscript_call html attr html base64_encode html base64_uri html bg_process html broken_packages html bump_version html cache_rds html del_empty_dir html dir_create html dir_exists html do_once html download_file html embed_file html exit_call html file_ext html file_string html format_bytes html from_root html github_releases html grep_sub html gsub_file html in_dir html install_dir html install_github html isFALSE html is_R_CMD_check html is_abs_path html is_ascii html is_sub_path html is_web_path html magic_path html mark_dirs html msg_cat html native_encode html news2md html normalize_path html numbers_to_words html optipng html os html parse_only html pkg_attach html proc_kill html process_file html proj_root html prose_index html protect_math html raw_string html read_bin html read_utf8 html relative_path html rename_seq html retry html rev_check html rstudio_type html same_path html session_info html set_envvar html split_lines html split_source html strict_list html stringsAsStrings html submit_cran html tinify html tojson html tree html try_silent html upload_ftp html url_filename html valid_syntax html ** building package indices ** installing vignettes ** 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 (xfun) Making 'packages.html' ... done * installing *source* package 'Rcpp' ... ** package 'Rcpp' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c api.cpp -o api.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c attributes.cpp -o attributes.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c barrier.cpp -o barrier.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c date.cpp -o date.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c module.cpp -o module.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c rcpp_init.cpp -o rcpp_init.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-Rcpp/00new/Rcpp/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'Rcpp' done CppClass-class html CppConstructor-class html CppField-class html CppFunction-class html CppObject-class html CppOverloadedMethods-class html DollarNames-methods html Module-class html Module html Rcpp-deprecated html Rcpp-internal html Rcpp-package html Rcpp.package.skeleton html Rcpp.plugin.maker html RcppLdFlags html RcppUnitTests html compileAttributes html compilerCheck html cppFunction html demangle html dependsAttribute html evalCpp html exportAttribute html exposeClass html formals html getRcppVersion html interfacesAttribute html loadModule html loadRcppModules-deprecated html pluginsAttribute html populate html registerPlugin html setRcppClass html sourceCpp html ** building package indices ** installing vignettes ** 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 (Rcpp) Making 'packages.html' ... done * installing *source* package 'stringi' ... ** package 'stringi' successfully unpacked and MD5 sums checked ** using staged installation checking for R_HOME... /opt/R/4.0.3/lib/R checking for R... /opt/R/4.0.3/lib/R/bin/R checking for endianness... little checking for R >= 3.1.0 for C++11 use... yes checking for R < 3.4.0 for CXX1X flag use... no checking for cat... /usr/bin/cat checking for local ICUDT_DIR... icu69/data checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++11 accepts -g... yes checking whether the C++ compiler supports the long long type... yes checking whether the compiler implements namespaces... yes checking whether the compiler supports Standard Template Library... yes checking whether std::map is available... yes checking for pkg-config... /usr/bin/pkg-config checking with pkg-config for the system ICU4C... 60.3 checking for ICU4C >= 55... yes checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done checking whether an ICU4C-based project can be built... yes checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes checking programmatically if U_CHARSET_IS_UTF8 is defined and set... no checking the capabilities of the ICU data library (ucnv, uloc, utrans)... yes checking the capabilities of the ICU data library (ucol)... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/uconfig_local.h config.status: creating src/install.libs.R *** stringi configure summary: ICU_FOUND=1 STRINGI_CXXSTD=CXX_STD=CXX11 STRINGI_CFLAGS= -fpic STRINGI_CPPFLAGS=-I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H STRINGI_CXXFLAGS= -fpic STRINGI_LDFLAGS=-L/usr/lib64 STRINGI_LIBS=-licui18n -licuuc -licudata *** Compiler settings used: CC=gcc LD=g++ -std=gnu++11 CFLAGS=-g -O2 -fpic CPPFLAGS=-I/usr/local/include -UDEBUG -DNDEBUG CXX=g++ -std=gnu++11 CXXFLAGS=-g -O2 -fpic LDFLAGS= LIBS= ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_brkiter.cpp -o stri_brkiter.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_collator.cpp -o stri_collator.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_common.cpp -o stri_common.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_compare.cpp -o stri_compare.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_base.cpp -o stri_container_base.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_listint.cpp -o stri_container_listint.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_listraw.cpp -o stri_container_listraw.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_listutf8.cpp -o stri_container_listutf8.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_regex.cpp -o stri_container_regex.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_usearch.cpp -o stri_container_usearch.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_utf16.cpp -o stri_container_utf16.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_utf8.cpp -o stri_container_utf8.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_encoding_detection.cpp -o stri_encoding_detection.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_encoding_management.cpp -o stri_encoding_management.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_escape.cpp -o stri_escape.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_exception.cpp -o stri_exception.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_ICU_settings.cpp -o stri_ICU_settings.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_join.cpp -o stri_join.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_length.cpp -o stri_length.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_pad.cpp -o stri_pad.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_prepare_arg.cpp -o stri_prepare_arg.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_random.cpp -o stri_random.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_reverse.cpp -o stri_reverse.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_count.cpp -o stri_search_class_count.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_detect.cpp -o stri_search_class_detect.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_extract.cpp -o stri_search_class_extract.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_locate.cpp -o stri_search_class_locate.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_replace.cpp -o stri_search_class_replace.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_split.cpp -o stri_search_class_split.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_startsendswith.cpp -o stri_search_class_startsendswith.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_subset.cpp -o stri_search_class_subset.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_trim.cpp -o stri_search_class_trim.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_common.cpp -o stri_search_common.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_count.cpp -o stri_search_coll_count.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_detect.cpp -o stri_search_coll_detect.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_extract.cpp -o stri_search_coll_extract.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_locate.cpp -o stri_search_coll_locate.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_replace.cpp -o stri_search_coll_replace.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_split.cpp -o stri_search_coll_split.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_startsendswith.cpp -o stri_search_coll_startsendswith.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_subset.cpp -o stri_search_coll_subset.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_boundaries_count.cpp -o stri_search_boundaries_count.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_boundaries_extract.cpp -o stri_search_boundaries_extract.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_boundaries_locate.cpp -o stri_search_boundaries_locate.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_boundaries_split.cpp -o stri_search_boundaries_split.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_count.cpp -o stri_search_fixed_count.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_detect.cpp -o stri_search_fixed_detect.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_extract.cpp -o stri_search_fixed_extract.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_locate.cpp -o stri_search_fixed_locate.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_replace.cpp -o stri_search_fixed_replace.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_split.cpp -o stri_search_fixed_split.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_subset.cpp -o stri_search_fixed_subset.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_startsendswith.cpp -o stri_search_fixed_startsendswith.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_in.cpp -o stri_search_in.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_other_split.cpp -o stri_search_other_split.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_count.cpp -o stri_search_regex_count.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_detect.cpp -o stri_search_regex_detect.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_extract.cpp -o stri_search_regex_extract.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_locate.cpp -o stri_search_regex_locate.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_match.cpp -o stri_search_regex_match.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_replace.cpp -o stri_search_regex_replace.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_split.cpp -o stri_search_regex_split.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_subset.cpp -o stri_search_regex_subset.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_sort.cpp -o stri_sort.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_sprintf.cpp -o stri_sprintf.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_stats.cpp -o stri_stats.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_stringi.cpp -o stri_stringi.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_sub.cpp -o stri_sub.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_test.cpp -o stri_test.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_time_zone.cpp -o stri_time_zone.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_time_calendar.cpp -o stri_time_calendar.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_time_symbols.cpp -o stri_time_symbols.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_time_format.cpp -o stri_time_format.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_trans_casemap.cpp -o stri_trans_casemap.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_trans_other.cpp -o stri_trans_other.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_trans_normalization.cpp -o stri_trans_normalization.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_ucnv.cpp -o stri_ucnv.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_uloc.cpp -o stri_uloc.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_utils.cpp -o stri_utils.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_wrap.cpp -o stri_wrap.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_sort.o stri_sprintf.o stri_stats.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib64 -licui18n -licuuc -licudata -L/opt/R/4.0.3/lib/R/lib -lR installing via 'install.libs.R' to /opt/R/4.0.3/lib/R/library/00LOCK-stringi/00new/stringi ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'stringi' done about_arguments html about_encoding html about_locale html about_search html about_search_boundaries html about_search_charclass html about_search_coll html about_search_fixed html about_search_regex html about_stringi html operator_add html operator_compare html operator_dollar html stri_compare html stri_count html stri_count_boundaries html stri_datetime_add html stri_datetime_create html stri_datetime_fields html stri_datetime_format html Rd warning: /tmp/Rtmpoh5Fka/R.INSTALL20b3129f2116/stringi/man/stri_datetime_format.Rd:55: file link 'strftime' in package 'base' does not exist and so has been treated as a topic stri_datetime_fstr html Rd warning: /tmp/Rtmpoh5Fka/R.INSTALL20b3129f2116/stringi/man/stri_datetime_fstr.Rd:21: file link 'strftime' in package 'base' does not exist and so has been treated as a topic stri_datetime_now html stri_datetime_symbols html stri_detect html stri_dup html stri_duplicated html stri_enc_detect html stri_enc_detect2 html stri_enc_fromutf32 html stri_enc_info html stri_enc_isascii html stri_enc_isutf16 html stri_enc_isutf8 html stri_enc_list html stri_enc_mark html stri_enc_set html stri_enc_toascii html stri_enc_tonative html stri_enc_toutf32 html stri_enc_toutf8 html stri_encode html stri_escape_unicode html stri_extract html stri_extract_boundaries html stri_flatten html stri_info html stri_isempty html stri_join html stri_join_list html stri_length html stri_list2matrix html stri_locale_info html stri_locale_list html stri_locale_set html stri_locate html stri_locate_boundaries html stri_match html stri_na2empty html stri_numbytes html stri_opts_brkiter html stri_opts_collator html stri_opts_fixed html stri_opts_regex html stri_order html stri_pad html stri_rand_lipsum html stri_rand_shuffle html stri_rand_strings html stri_rank html stri_read_lines html stri_read_raw html stri_remove_empty html stri_replace html stri_replace_na html stri_replace_rstr html Rd warning: /tmp/Rtmpoh5Fka/R.INSTALL20b3129f2116/stringi/man/stri_replace_rstr.Rd:16: file link 'gsub' in package 'base' does not exist and so has been treated as a topic stri_reverse html stri_sort html stri_sort_key html stri_split html stri_split_boundaries html stri_split_lines html stri_sprintf html stri_startsendswith html stri_stats_general html stri_stats_latex html stri_sub html stri_sub_all html stri_subset html stri_timezone_info html stri_timezone_list html stri_timezone_set html stri_trans_casemap html stri_trans_char html stri_trans_general html stri_trans_list html stri_trans_nf html stri_trim html stri_unescape_unicode html stri_unique html stri_width html stri_wrap html stri_write_lines 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 (stringi) Making 'packages.html' ... done * installing *source* package 'jsonlite' ... ** package 'jsonlite' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c base64.c -o base64.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c collapse_array.c -o collapse_array.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c collapse_object.c -o collapse_object.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c collapse_pretty.c -o collapse_pretty.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c escape_chars.c -o escape_chars.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c integer64_to_na.c -o integer64_to_na.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c is_datelist.c -o is_datelist.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c is_recordlist.c -o is_recordlist.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c is_scalarlist.c -o is_scalarlist.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c modp_numtoa.c -o modp_numtoa.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c null_to_na.c -o null_to_na.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c num_to_char.c -o num_to_char.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c parse.c -o parse.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c prettify.c -o prettify.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c push_parser.c -o push_parser.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c r-base64.c -o r-base64.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c register.c -o register.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c row_collapse.c -o row_collapse.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c transpose_list.c -o transpose_list.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c validate.c -o validate.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl.c -o yajl/yajl.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_buf.c -o yajl/yajl_buf.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_encode.c -o yajl/yajl_encode.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_gen.c -o yajl/yajl_gen.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_lex.c -o yajl/yajl_lex.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_parser.c -o yajl/yajl_parser.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c yajl/yajl_tree.c -o yajl/yajl_tree.o ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-jsonlite/00new/jsonlite/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help in method for 'asJSON' with signature '"blob"': no definition for class "blob" *** installing help indices finding HTML links ... converting help for package 'jsonlite' done base64 html flatten html fromJSON html prettify html rbind_pages html read_json html serializeJSON html stream_in html unbox html validate html ** building package indices ** installing vignettes ** 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 (jsonlite) Making 'packages.html' ... done * installing *source* package 'rjson' ... ** package 'rjson' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dump.cpp -o dump.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parser.c -o parser.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c register.c -o register.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o rjson.so dump.o parser.o register.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-rjson/00new/rjson/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rjson' finding HTML links ... done fromJSON html newJSONParser html rjson html toJSON html ** building package indices ** installing vignettes ** 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 (rjson) Making 'packages.html' ... done * installing *source* package 'data.table' ... ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation gcc 8.4.1 zlib 1.2.11 is available ok R CMD SHLIB supports OpenMP without any extra hint ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c assign.c -o assign.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c between.c -o between.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c bmerge.c -o bmerge.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c chmatch.c -o chmatch.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c cj.c -o cj.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c coalesce.c -o coalesce.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c dogroups.c -o dogroups.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fastmean.c -o fastmean.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fcast.c -o fcast.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fifelse.c -o fifelse.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fmelt.c -o fmelt.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c forder.c -o forder.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frank.c -o frank.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fread.c -o fread.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c freadR.c -o freadR.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c froll.c -o froll.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frollR.c -o frollR.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frolladaptive.c -o frolladaptive.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fsort.c -o fsort.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fwrite.c -o fwrite.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fwriteR.c -o fwriteR.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c gsumm.c -o gsumm.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c ijoin.c -o ijoin.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c inrange.c -o inrange.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c nafill.c -o nafill.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c nqrecreateindices.c -o nqrecreateindices.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c openmp-utils.c -o openmp-utils.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c quickselect.c -o quickselect.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c rbindlist.c -o rbindlist.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c reorder.c -o reorder.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c shift.c -o shift.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c snprintf.c -o snprintf.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c subset.c -o subset.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c transpose.c -o transpose.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c types.c -o types.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c uniqlist.c -o uniqlist.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c vecseq.c -o vecseq.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c wrappers.c -o wrappers.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/opt/R/4.0.3/lib/R/lib -lR PKG_CFLAGS = -fopenmp PKG_LIBS = -fopenmp -lz if [ "data.table.so" != "datatable.so" ]; then mv data.table.so datatable.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi installing to /opt/R/4.0.3/lib/R/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'data.table' done IDateTime html J html address html all.equal.data.table html as.data.table html as.data.table.xts html as.matrix html as.xts.data.table html assign html between html cdt html chmatch html coalesce html copy html data.table-class html data.table html datatable-optimize html dcast.data.table html deprecated html duplicated html fcase html fifelse html foverlaps html frank html fread html froll html fsort html fwrite html groupingsets html last html last.updated html like html melt.data.table html merge html na.omit.data.table html nafill html openmp-utils html patterns html print.data.table html rbindlist html rleid html rowid html setDF html setDT html setNumericRounding html setattr html setcolorder html setkey html setops html setorder html shift html shouldPrint html special-symbols html split html subset.data.table html tables html test html test.data.table html timetaken html transform.data.table html transpose html truelength html tstrsplit html update.dev.pkg html ** building package indices ** installing vignettes ** 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 (data.table) Making 'packages.html' ... done * installing *source* package 'lava' ... ** package 'lava' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'lava' done By html Col html Combine html Expand html Graph html Grep html Missing html Model html NA2x html NR html PD html Range.lvm html addvar html backdoor html baptize html binomial.rd html blockdiag html bmd html bmidata html bootstrap html bootstrap.lvm html brisa html calcium html cancel html children html click html closed.testing html colorbar html commutation html compare html complik html confband html confint.lvmfit html confpred html constrain-set html contr html correlation html covariance html csplit html curly html cv html devcoords html diagtest html dsep.lvm html equivalence html estimate.default html estimate.lvm html eventTime html fplot html getMplus html getSAS html gof html hubble html hubble2 html iid html images html indoorenv html intercept html internal html ksmooth2 html labels-set html lava-package html lava.options html lvm html makemissing html measurement.error html missingdata html mixture html modelsearch html multinomial html mvnmix html nldata html nsem html op_concat html op_match html ordinal-set html ordreg html parpos html partialcor html path html pcor html pdfconvert html plot.estimate html plot.lvm html plot.sim html plotConf html predict.lvm html predictlvm html rbind.Surv html regression-set html revdiag html rmvar html rotate2 html scheffe html semdata html serotonin html serotonin2 html sim html sim.default html spaghetti html stack.estimate html subset.lvm html summary.sim html timedep html toformula html tr html trim html twindata html twostage html twostage.lvmfit html twostageCV html vars html vec html wait html wkm html wrapvec html zibreg html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lava) Making 'packages.html' ... done * installing *source* package 'askpass' ... ** package 'askpass' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c askpass.c -o askpass.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-askpass/00new/askpass/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'askpass' done askpass html ssh_askpass 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 (askpass) Making 'packages.html' ... done * installing *source* package 'munsell' ... ** package 'munsell' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'munsell' done check_mnsl html chroma_slice html complement html complement_slice html darker html desaturate html fix_mnsl html hue_slice html hvc2mnsl html in_gamut html lighter html mnsl html mnsl2hvc html mnsl_hues html munsell html pbgyr html plot_closest html plot_hex html plot_mnsl html rgb2mnsl html rygbp html saturate html seq_mnsl html text_colour html theme_munsell html value_slice html *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (munsell) Making 'packages.html' ... done * installing *source* package 'lubridate' ... ** package 'lubridate' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cctz/src/time_zone_fixed.cc -o cctz/src/time_zone_fixed.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cctz/src/time_zone_if.cc -o cctz/src/time_zone_if.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cctz/src/time_zone_impl.cc -o cctz/src/time_zone_impl.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cctz/src/time_zone_info.cc -o cctz/src/time_zone_info.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cctz/src/time_zone_libc.cc -o cctz/src/time_zone_libc.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cctz/src/time_zone_lookup.cc -o cctz/src/time_zone_lookup.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cctz/src/time_zone_posix.cc -o cctz/src/time_zone_posix.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cctz/src/zone_info_source.cc -o cctz/src/zone_info_source.o ar rcs libcctz.a ./cctz/src/time_zone_fixed.o ./cctz/src/time_zone_if.o ./cctz/src/time_zone_impl.o ./cctz/src/time_zone_info.o ./cctz/src/time_zone_libc.o ./cctz/src/time_zone_lookup.o ./cctz/src/time_zone_posix.o ./cctz/src/zone_info_source.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c update.cpp -o update.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c datetime.c -o datetime.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c period.c -o period.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I. -I./cctz/src/ -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c tparse.c -o tparse.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o lubridate.so RcppExports.o update.o utils.o datetime.o period.o tparse.o -L. -lcctz -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-lubridate/00new/lubridate/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'lubridate' finding HTML links ... done DateCoercion html DateTimeUpdate html Deprecated html Duration-class html Interval-class html Period-class html Timespan-class html am html as.duration html as.interval html as.period html as_date html cyclic_encoding html date html date_decimal html date_utils html day html days_in_month html decimal_date html dst html duration html fit_to_timeline html force_tz html format_ISO8601 html format_ISO8601_precision_check html guess_formats html hidden_aliases html hms html hour html interval html is.difftime html is.instant html is.timespan html lakers html leap_year html local_time html lubridate-package html make_datetime html make_difftime html minute html month html mplus html now html origin html parse_date_time html period html period_to_seconds html posix_utils html pretty_dates html quarter html reclass_date html reclass_timespan html reexports html rollbackward html round_date html second html stamp html time_length html timespan html tz html week html with_tz html within-interval html year html ymd html ymd_hms html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location System has not been booted with systemd as init system (PID 1). Can't operate. Failed to create bus connection: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location System has not been booted with systemd as init system (PID 1). Can't operate. Failed to create bus connection: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 ** testing if installed package keeps a record of temporary installation path * DONE (lubridate) Making 'packages.html' ... done * installing *source* package 'RcppArmadillo' ... ** package 'RcppArmadillo' successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... g++ -std=gnu++11 -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ -std=gnu++11 accepts -g... (cached) yes checking whether we have a suitable tempdir... /tmp checking whether R CMD SHLIB can already compile programs using OpenMP... yes checking LAPACK_LIBS... R-supplied partial LAPACK found configure: WARNING: Some complex-valued LAPACK functions may not be available configure: creating ./config.status config.status: creating inst/include/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -c fastLm.cpp -o fastLm.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/opt/R/4.0.3/lib/R/lib -lRlapack -L/opt/R/4.0.3/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'RcppArmadillo' finding HTML links ... done RcppArmadillo-package html RcppArmadillo.package.skeleton html armadillo_set_seed html armadillo_set_seed_random html armadillo_version html fastLm html ** building package indices ** installing vignettes ** 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 (RcppArmadillo) Making 'packages.html' ... done * installing *source* package 'ellipsis' ... ** package 'ellipsis' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dots.c -o dots.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o ellipsis.so dots.o init.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-ellipsis/00new/ellipsis/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'ellipsis' done check_dots_empty html check_dots_unnamed html check_dots_used html dots_empty html dots_used html ellipsis-package html safe_median 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 (ellipsis) Making 'packages.html' ... done * installing *source* package 'lifecycle' ... ** package 'lifecycle' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'lifecycle' done badge html deprecate_soft html deprecated html expect_deprecated html last_warnings html lifecycle-package html signal_experimental html signal_stage html verbosity html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lifecycle) Making 'packages.html' ... done * installing *source* package 'purrr' ... ** package 'purrr' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c backports.c -o backports.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coerce.c -o coerce.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c conditions.c -o conditions.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c flatten.c -o flatten.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c map.c -o map.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pluck.c -o pluck.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c transpose.c -o transpose.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o purrr.so backports.o coerce.o conditions.o flatten.o init.o map.o pluck.o transpose.o utils.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-purrr/00new/purrr/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'purrr' done accumulate html along html array-coercion html as_mapper html as_vector html at_depth html attr_getter html compose html cross html detect html done html every html exec html faq-adverbs-export html flatten html get-attr html has_element html head_while html imap html insistently html invoke html is_numeric html keep html lift html list_modify html lmap html map html map2 html Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/map2.Rd:111: file link 'pmax' in package 'base' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/map2.Rd:111: file link 'pmin' in package 'base' does not exist and so has been treated as a topic map_if html modify html modify_in html negate html null-default html Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/null-default.Rd:13: file link '%||%' in package 'rlang' does not exist and so has been treated as a topic partial html pipe html pluck html prepend html purrr-package html rate-helpers html rate_sleep html rbernoulli html rdunif html reduce html reduce_right html reexports html Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_atomic' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_bare_atomic' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_bare_character' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_bare_double' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_bare_integer' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_bare_list' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_bare_logical' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_bare_numeric' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_bare_vector' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_character' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_double' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_integer' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_list' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_logical' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_null' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_scalar_atomic' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_scalar_character' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_scalar_double' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_scalar_integer' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_scalar_list' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_scalar_logical' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_scalar_vector' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpJ3FtIj/R.INSTALL2e3e4a167018/purrr/man/reexports.Rd:39: file link 'is_vector' in package 'rlang' does not exist and so has been treated as a topic rep_along html rerun html *** copying figures safely html set_names html ** building package indices splice html transpose html vec_depth html when html zap html ** installing vignettes ** 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 (purrr) Making 'packages.html' ... done * installing *source* package 'highr' ... ** package 'highr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'highr' done hi_andre html hilight html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (highr) Making 'packages.html' ... done * installing *source* package 'markdown' ... ** package 'markdown' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rbase64.c -o Rbase64.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rinit.c -o Rinit.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rmarkdown.c -o Rmarkdown.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c autolink.c -o autolink.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c buffer.c -o buffer.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c houdini_href_e.c -o houdini_href_e.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c houdini_html_e.c -o houdini_html_e.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c html.c -o html.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c html_smartypants.c -o html_smartypants.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c markdown.c -o markdown.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c stack.c -o stack.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o markdown.so Rbase64.o Rinit.o Rmarkdown.o autolink.o buffer.o houdini_href_e.o houdini_html_e.o html.o html_smartypants.o markdown.o stack.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-markdown/00new/markdown/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'markdown' done markdown html markdownExtensions html markdownHTMLOptions html markdownToHTML html registeredRenderers html renderMarkdown html rendererExists html rendererOutputType html rpubsUpload html smartypants html ** building package indices ** installing vignettes ** 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 (markdown) Making 'packages.html' ... done * installing *source* package 'stringr' ... ** package 'stringr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'stringr' done case html invert_match html modifiers html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/modifiers.Rd:102: file link 'stringi-search-boundaries' in package 'stringi' does not exist and so has been treated as a topic pipe html str_c html str_conv html str_count html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_count.Rd:16: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_detect html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_detect.Rd:16: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_dup html str_extract html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_extract.Rd:19: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_flatten html str_glue html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_glue.Rd:29: file link 'glue_data' in package 'glue' does not exist and so has been treated as a topic str_interp html str_length html str_locate html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_locate.Rd:19: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_match html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_match.Rd:17: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_order html str_pad html str_remove html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_remove.Rd:19: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic finding level-2 HTML links ... str_replace html done Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_replace.Rd:19: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_replace_na html str_split html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_split.Rd:19: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_starts html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_starts.Rd:20: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_sub html str_subset html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_subset.Rd:19: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_trim html str_trunc html str_view html Rd warning: /tmp/RtmpiPk267/R.INSTALL2ff09a36865/stringr/man/str_view.Rd:19: file link 'stringi-search-regex' in package 'stringi' does not exist and so has been treated as a topic str_wrap html stringr-data html stringr-package html word html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (stringr) Making 'packages.html' ... done * installing *source* package 'foreach' ... ** package 'foreach' successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'foreach' finding HTML links ... done foreach-ext html foreach-package html foreach html getDoParWorkers html getDoSeqWorkers html registerDoSEQ html setDoPar html setDoSeq html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (foreach) Making 'packages.html' ... done * installing *source* package 'plyr' ... ** package 'plyr' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c loop_apply.c -o loop_apply.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split-numeric.cpp -o split-numeric.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o plyr.so RcppExports.o loop_apply.o split-numeric.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-plyr/00new/plyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'plyr' finding HTML links ... done a_ply html aaply html adply html alply html amv_dim html amv_dimnames html arrange html as.data.frame.function html as.list.split html as.quoted html baseball html colwise html compact html count html create_progress_bar html d_ply html daply html ddply html defaults html desc html dims html dlply html each html empty html eval.quoted html failwith html get-split html here html id html id_var html idata.frame html indexed_array html indexed_df html is.discrete html is.formula html isplit2 html join html join.keys html join_all html l_ply html laply html ldply html liply html list_to_array html list_to_dataframe html list_to_vector html llply html loop_apply html m_ply html maply html mapvalues html match_df html mdply html mlply html mutate html name_rows html names.quoted html nunique html ozone html plyr-deprecated html plyr html print.quoted html print.split html progress_none html progress_text html progress_time html progress_tk html progress_win html quickdf html quoted html r_ply html raply html rbind.fill html rbind.fill.matrix html Rd warning: /tmp/RtmpST37gn/R.INSTALL30d449b736f6/plyr/man/rbind.fill.matrix.Rd:48: file link 'rbind' in package 'base' does not exist and so has been treated as a topic rdply html reduce_dim html rename html revalue html rlply html round_any html splat html split_indices html split_labels html splitter_a html splitter_d html strip_splits html summarise html take html true html try_default html tryapply html unrowname html vaggregate 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 (plyr) Making 'packages.html' ... done * installing *source* package 'ModelMetrics' ... ** package 'ModelMetrics' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c auc_.cpp -o auc_.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c confusionMatrix_.cpp -o confusionMatrix_.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c error.cpp -o error.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gini_.cpp -o gini_.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c logLoss_.cpp -o logLoss_.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o ModelMetrics.so RcppExports.o auc_.o confusionMatrix_.o error.o gini_.o logLoss_.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-ModelMetrics/00new/ModelMetrics/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'ModelMetrics' done auc html brier html ce html confusionMatrix html f1Score html fScore html gini html kappa html logLoss html mae html mauc html mcc html mlogLoss html mse html msle html npv html ppv html recall html rmse html rmsle html testDF html tnr 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 (ModelMetrics) Making 'packages.html' ... done * installing *source* package 'mlapi' ... ** package 'mlapi' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'mlapi' done fit html fit_transform html mlapiDecomposition html mlapiEstimation html mlapiEstimationOnline html mlapiTransformation html mlapiTransformationOnline html predict html transform html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mlapi) Making 'packages.html' ... done * installing *source* package 'lgr' ... ** package 'lgr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'lgr' done Appender html AppenderBuffer html AppenderConsole html AppenderFile html AppenderFileRotating html AppenderFileRotatingDate html AppenderFileRotatingTime html AppenderMemory html AppenderTable html CannotInitializeAbstractClassError html EventFilter html FilterForceLevel html FilterInject html Filterable html Layout html LayoutFormat html LayoutGlue html LayoutJson html LogEvent html Logger html LoggerGlue html as.data.frame.LogEvent html basic_config html colorize_levels html default_exception_handler html event_list html get_log_levels html get_logger html is_filter html label_levels html lgr-package html logger_config html logger_tree html pad_right html print.Appender html print.LogEvent html print.Logger html print.logger_tree html read_json_lines html simple_logging html standardize_threshold html suspend_logging html system_infos html toString.LogEvent html use_logger html with_log_level html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lgr) Making 'packages.html' ... done * installing *source* package 'cli' ... ** package 'cli' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cleancall.c -o cleancall.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c errors.c -o errors.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c progress-altrep.c -o progress-altrep.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c progress.c -o progress.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c thread.c -o thread.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tty.c -o tty.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c win-utf8.c -o win-utf8.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o cli.so cleancall.o errors.o init.o progress-altrep.o progress.o thread.o tty.o win-utf8.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-cli/00new/cli/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'cli' done ansi-styles html ansi_align html ansi_columns html ansi_has_any html ansi_hide_cursor html ansi_nchar html ansi_regex html ansi_strip html ansi_strsplit html ansi_strtrim html ansi_strwrap html ansi_substr html ansi_substring html ansi_toupper html ansi_trimws html boxx html builtin_theme html cat_line html cli-config html cli html cli_abort html cli_alert html cli_blockquote html cli_bullets html cli_code html cli_debug_doc html cli_div html cli_dl html cli_end html cli_format html cli_format_method html cli_h1 html cli_li html cli_list_themes html cli_ol html cli_output_connection html cli_par html cli_process_start html cli_progress_along html cli_progress_bar html cli_progress_builtin_handlers html cli_progress_demo html cli_progress_message html cli_progress_output html cli_progress_step html cli_progress_styles html cli_rule html cli_sitrep html cli_status html cli_status_clear html cli_status_update html cli_text html cli_ul html cli_vec html cli_verbatim html combine_ansi_styles html console_width html containers html demo_spinners html faq html format_error html format_inline html get_spinner html inline-markup html is_ansi_tty html is_dynamic_tty html is_utf8_output html list_spinners html make_ansi_style html make_spinner html match_selector html match_selector_node html num_ansi_colors html parse_selector html pluralization-helpers html pluralization html pluralize html progress-c html progress-utils html progress-variables html rule html simple_theme html spark_bar html spark_line html start_app html style_hyperlink html symbol html test_that_cli html themes html tree html unicode-width-workaround html *** copying figures ** 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 (cli) Making 'packages.html' ... done * installing *source* package 'prodlim' ... ** package 'prodlim' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c GMLE.c -o GMLE.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c IntIndex.c -o IntIndex.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c icens_prodlim.c -o icens_prodlim.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c icens_prodlim_ml.c -o icens_prodlim_ml.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c iindex.c -o iindex.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c life_table.c -o life_table.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c loo.c -o loo.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c neighborhood.c -o neighborhood.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c predict.c -o predict.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c predict_individual_survival.c -o predict_individual_survival.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c prodlim.c -o prodlim.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c prodlim_clustersurv.c -o prodlim_clustersurv.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c prodlim_comprisk.c -o prodlim_comprisk.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c prodlim_multistates.c -o prodlim_multistates.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c prodlim_surv.c -o prodlim_surv.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c sindex.c -o sindex.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c summary_prodlim.c -o summary_prodlim.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o prodlim.so GMLE.o IntIndex.o icens_prodlim.o icens_prodlim_ml.o iindex.o init.o life_table.o loo.o neighborhood.o predict.o predict_individual_survival.o prodlim.o prodlim_clustersurv.o prodlim_comprisk.o prodlim_multistates.o prodlim_surv.o sindex.o summary_prodlim.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-prodlim/00new/prodlim/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'prodlim' done EventHistory.frame html Hist html List2Matrix html PercentAxis html SimCompRisk html SimSurv html SmartControl html atRisk html backGround html checkCauses html confInt html crModel html dimColor html getEvent html getStates html jackknife html leaveOneOut html markTime html meanNeighbors html model.design html neighborhood html parseSpecialNames html plot.Hist html plot.prodlim html plotCompetingRiskModel html plotIllnessDeathModel html predict.prodlim html predictSurvIndividual html print.prodlim html prodlim html quantile.prodlim html redist html row.match html sindex html stopTime html strip.terms html summary.Hist html summary.prodlim html survModel 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 (prodlim) Making 'packages.html' ... done * installing *source* package 'openssl' ... ** package 'openssl' successfully unpacked and MD5 sums checked ** using staged installation Using PKG_CFLAGS= --------------------------- [ANTICONF] -------------------------------- Configuration failed because openssl was not found. Try installing: * deb: libssl-dev (Debian, Ubuntu, etc) * rpm: openssl-devel (Fedora, CentOS, RHEL) * csw: libssl_dev (Solaris) * brew: openssl@1.1 (Mac OSX) If openssl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------- [ERROR MESSAGE] --------------------------- tools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~~~ compilation terminated. ERROR: configuration failed for package 'openssl' -------------------------------------------------------------------- * removing '/opt/R/4.0.3/lib/R/library/openssl' * installing *source* package 'scales' ... ** package 'scales' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'scales' done Range html alpha html area_pal html asn_trans html atanh_trans html boxcox_trans html breaks_extended html breaks_log html breaks_pretty html breaks_width html brewer_pal html Rd warning: /tmp/RtmpKj28hX/R.INSTALL348654a1ab69/scales/man/brewer_pal.Rd:16: file link 'brewer.pal' in package 'RColorBrewer' does not exist and so has been treated as a topic cbreaks html col2hcl html col_numeric html colour_ramp html cscale html date_breaks html date_trans html demo_continuous html dichromat_pal html div_gradient_pal html dscale html exp_trans html expand_range html format_format html fullseq html gradient_n_pal html grey_pal html hms_trans html hue_pal html identity_pal html identity_trans html label_bytes html label_date html label_dollar html label_number html label_number_auto html label_number_si html label_ordinal html label_parse html label_percent html label_pvalue html label_scientific html label_wrap html linetype_pal html log_trans html manual_pal html minor_breaks_width html muted html number html number_bytes_format html oob html probability_trans html reciprocal_trans html regular_minor_breaks html rescale html rescale_max html rescale_mid html rescale_none html rescale_pal html reverse_trans html scales-package html seq_gradient_pal html shape_pal html show_col html sqrt_trans html time_trans html train_continuous html train_discrete html trans_breaks html trans_format html trans_new html trans_range html unit_format html viridis_pal html yj_trans html zero_range html *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scales) Making 'packages.html' ... done * installing *source* package 'vctrs' ... ** package 'vctrs' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c altrep-rle.c -o altrep-rle.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c arg-counter.c -o arg-counter.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c arg.c -o arg.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c bind.c -o bind.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c c-unchop.c -o c-unchop.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c c.c -o c.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c callables.c -o callables.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cast-bare.c -o cast-bare.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cast-dispatch.c -o cast-dispatch.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cast.c -o cast.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c compare.c -o compare.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c complete.c -o complete.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c conditions.c -o conditions.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c dictionary.c -o dictionary.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c dim.c -o dim.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c equal.c -o equal.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fields.c -o fields.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fill.c -o fill.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c group.c -o group.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c growable.c -o growable.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c hash.c -o hash.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c names.c -o names.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-groups.c -o order-groups.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-radix.c -o order-radix.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-sortedness.c -o order-sortedness.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-transform.c -o order-transform.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-truelength.c -o order-truelength.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c poly-op.c -o poly-op.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c proxy-restore.c -o proxy-restore.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c proxy.c -o proxy.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ptype2-dispatch.c -o ptype2-dispatch.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rep.c -o rep.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c runs.c -o runs.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c shape.c -o shape.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c size-common.c -o size-common.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c size.c -o size.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-array.c -o slice-array.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-assign-array.c -o slice-assign-array.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-assign.c -o slice-assign.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-chop.c -o slice-chop.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice.c -o slice.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c split.c -o split.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c subscript-loc.c -o subscript-loc.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c subscript.c -o subscript.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c translate.c -o translate.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-data-frame.c -o type-data-frame.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-date-time.c -o type-date-time.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-factor.c -o type-factor.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-info.c -o type-info.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-tibble.c -o type-tibble.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type.c -o type.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type2.c -o type2.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c typeof2-s3.c -o typeof2-s3.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c typeof2.c -o typeof2.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c unspecified.c -o unspecified.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils-dispatch.c -o utils-dispatch.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils-rlang.c -o utils-rlang.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o vctrs.so altrep-rle.o arg-counter.o arg.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o equal.o fields.o fill.o group.o growable.o hash.o init.o names.o order-groups.o order-radix.o order-sortedness.o order-transform.o order-truelength.o poly-op.o proxy-restore.o proxy.o ptype2-dispatch.o rep.o runs.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-tibble.o type.o type2.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils-rlang.o utils.o version.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-vctrs/00new/vctrs/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'vctrs' done as-is html data_frame html df_list html df_ptype2 html faq-compatibility-types html faq-error-incompatible-attributes html faq-error-scalar-type html fields html howto-faq-coercion-data-frame html howto-faq-coercion html howto-faq-fix-scalar-type-error html int64 html internal-faq-ptype2-identity html list_of html maybe_lossy_cast html name_spec html new_data_frame html new_date html new_factor html new_list_of html new_partial html new_rcrd html new_vctr html obj_print html op-empty-default html partial_factor html partial_frame html reference-faq-compatibility html s3_register html table html theory-faq-coercion html unspecified html vctrs-conditions html vctrs-data-frame html vctrs-package html vec-rep html vec_arith html vec_as_index html vec_as_location html vec_as_names html vec_as_names_legacy html vec_as_subscript html vec_assert html vec_bind html vec_c html vec_cast html vec_cbind_frame_ptype html vec_chop html vec_compare html vec_count html vec_data html vec_default_ptype2 html vec_detect_complete html vec_duplicate html vec_empty html vec_equal html vec_fill_missing html vec_group html vec_identify_runs html vec_init html vec_is_list html vec_list_cast html vec_match html vec_math html vec_names html vec_order html vec_proxy html vec_proxy_compare html vec_proxy_equal html vec_ptype html vec_ptype2 html vec_ptype_full html vec_recycle html vec_repeat html vec_seq_along html vec_size html vec_slice html vec_split html vec_type html vec_unique html *** copying figures ** building package indices ** installing vignettes ** 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 (vctrs) Making 'packages.html' ... done * installing *source* package 'reshape2' ... ** package 'reshape2' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c melt.cpp -o melt.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o reshape2.so RcppExports.o melt.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-reshape2/00new/reshape2/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'reshape2' done add_margins html cast html Rd warning: /tmp/RtmplDQmrW/R.INSTALL362d5617aa3e/reshape2/man/cast.Rd:77: file link '.' in package 'plyr' does not exist and so has been treated as a topic colsplit html french_fries html guess_value html margins html melt html melt.array html melt.data.frame html melt.default html melt.list html melt_check html parse_formula html recast html smiths html tips 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 (reshape2) Making 'packages.html' ... done * installing *source* package 'pROC' ... ** package 'pROC' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppVersion.cpp -o RcppVersion.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c delong.cpp -o delong.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c perfsAll.cpp -o perfsAll.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o pROC.so RcppExports.o RcppVersion.o delong.o perfsAll.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-pROC/00new/pROC/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'pROC' done aSAH html are.paired html auc html ci html ci.auc html ci.coords html ci.se html ci.sp html ci.thresholds html coords html coords_transpose html cov html ggroc html groupGeneric html has.partial.auc html lines.roc html multiclass html pROC-package html plot.ci html plot.roc html power.roc.test html print html roc html roc.test html smooth html var 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 (pROC) Making 'packages.html' ... done * installing *source* package 'rsparse' ... ** package 'rsparse' successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++11 accepts -g... yes checking whether g++ version is sufficient... yes, with OpenMP as version 8.4.1 checking for macOS... checking for OpenMP... found and suitable configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c FTRL.cpp -o FTRL.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c FactorizationMachine.cpp -o FactorizationMachine.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c GloVe.cpp -o GloVe.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c ProductSparseDense.cpp -o ProductSparseDense.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c SolverAlsWrmf.cpp -o SolverAlsWrmf.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c SolverRankMF.cpp -o SolverRankMF.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c TopProduct.cpp -o TopProduct.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c kmeans.cpp -o kmeans.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -DARMA_32BIT_WORD -fpic -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o rsparse.so FTRL.o FactorizationMachine.o GloVe.o ProductSparseDense.o RcppExports.o SolverAlsWrmf.o SolverRankMF.o TopProduct.o kmeans.o utils.o -fopenmp -L/opt/R/4.0.3/lib/R/library/float/libs -l:float.so -Wl,-rpath=/opt/R/4.0.3/lib/R/library/float/libs -L/opt/R/4.0.3/lib/R/lib -lRlapack -L/opt/R/4.0.3/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-rsparse/00new/rsparse/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'rsparse' done FTRL html FactorizationMachine html GloVe html LinearFlow html MatrixFactorizationRecommender html PureSVD html ScaleNormalize html WRMF html detect_number_omp_threads html matmult html metrics html movielens100k html slice html soft_impute html train_test_split html *** copying figures ** 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 (rsparse) Making 'packages.html' ... done * installing *source* package 'knitr' ... ** package 'knitr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'knitr' done Sweave2knitr html all_labels html all_patterns html asis_output html cache_engines html chunk_hook html clean_cache html combine_words html finding level-2 HTML links ... current_input html done dep_auto html dep_prev html engine_output html fig_chunk html fig_path html hook_animation html hook_document html hook_plot html image_uri html imgur_upload html include_graphics html include_url html inline_expr html is_low_change html kable html knit html knit2html html knit2pandoc html knit2pdf html knit2wp html knit_child html knit_code html knit_engines html knit_exit html knit_expand html knit_filter html knit_global html knit_hooks html knit_meta html knit_params html knit_params_yaml html knit_patterns html knit_print html knit_rd html knit_theme html knit_watch html knitr-package html load_cache html opts_chunk html opts_hooks html opts_knit html opts_template html output_hooks html output_type html pandoc html pat_fun html plot_crop html rand_seed html raw_block html raw_output html read_chunk html read_rforge html rocco html rst2pdf html set_alias html set_header html set_parent html sew html spin html spin_child html stitch html vignette_engines html wrap_rmd html write_bib html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (knitr) Making 'packages.html' ... done * installing *source* package 'ipred' ... ** package 'ipred' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SdiffKM.c -o SdiffKM.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o ipred.so SdiffKM.o init.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-ipred/00new/ipred/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'ipred' done DLBCL html GlaucomaMVF html Smoking html bagging html bootest html control.errorest html cv html dystrophy html errorest html inbagg html inclass html ipred-internal html ipredknn html kfoldcv html mypredict.lm html predict.bagging html predict.inbagg html predict.inclass html predict.ipredknn html predict.slda html print.bagging html print.cvclass html print.inbagg html print.inclass html prune.bagging html rsurv html sbrier html slda html summary.bagging html summary.inbagg html summary.inclass html varset html ** building package indices ** installing vignettes ** 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 (ipred) Making 'packages.html' ... done * installing *source* package 'tidyselect' ... ** package 'tidyselect' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'tidyselect' finding HTML links ... done all_of html eval_select html Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/eval_select.Rd:38: file link 'enquo' in package 'rlang' does not exist and so has been treated as a topic everything html faq-external-vector html faq-selection-context html language html Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/language.Rd:24: file link 'last_col' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/language.Rd:30: file link 'ends_with' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/language.Rd:31: file link 'contains' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/language.Rd:32: file link 'matches' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/language.Rd:33: file link 'num_range' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/language.Rd:41: file link 'any_of' in package 'tidyselect' does not exist and so has been treated as a topic one_of html ** building package indices peek_vars html poke_vars html reexports html Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/reexports.Rd:17: file link 'enquo' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/reexports.Rd:17: file link 'quo' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/reexports.Rd:17: file link 'quo_name' in package 'rlang' does not exist and so has been treated as a topic Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/reexports.Rd:17: file link 'quos' in package 'rlang' does not exist and so has been treated as a topic starts_with html tidyselect-package html vars_pull html Rd warning: /tmp/Rtmp7JHGLy/R.INSTALL3a9a5328c744/tidyselect/man/vars_pull.Rd:23: file link 'quasiquotation' in package 'rlang' does not exist and so has been treated as a topic vars_select html vars_select_helpers html where html ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tidyselect) Making 'packages.html' ... done * installing *source* package 'pillar' ... ** package 'pillar' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'pillar' done align html char html colonnade html ctl_new_pillar html deprecated html dim_desc html expect_known_display html extra_cols html format_glimpse html format_tbl html format_type_sum html get_extent html glimpse html new_ornament html finding level-2 HTML links ... done new_pillar html new_pillar_component html new_pillar_shaft html new_pillar_title html new_pillar_type html new_tbl_format_setup html num html pillar-package html pillar html pillar_options html pillar_shaft html squeeze html style_subtle html tbl_format_body html tbl_format_footer html tbl_format_header html tbl_format_setup html tbl_sum html type_sum html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pillar) Making 'packages.html' ... done ERROR: dependency 'openssl' is not available for package 'httr' * removing '/opt/R/4.0.3/lib/R/library/httr' * installing *source* package 'text2vec' ... ** package 'text2vec' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c HashCorpus.cpp -o HashCorpus.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c VocabCorpus.cpp -o VocabCorpus.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c Vocabulary.cpp -o Vocabulary.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c collocations.cpp -o collocations.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c matrix_utils.cpp -o matrix_utils.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c memory_tools.cpp -o memory_tools.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/Rcpp/include' -I'/opt/R/4.0.3/lib/R/library/digest/include' -I/usr/local/include -DRCPP_NO_MODULES -fpic -g -O2 -c warplda.cpp -o warplda.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o text2vec.so HashCorpus.o RcppExports.o VocabCorpus.o Vocabulary.o collocations.o matrix_utils.o memory_tools.o utils.o warplda.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-text2vec/00new/text2vec/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'text2vec' done BNS html finding level-2 HTML links ... done Collocations html GloVe html LatentDirichletAllocation html LatentSemanticAnalysis html RelaxedWordMoversDistance html TfIdf html as.lda_c html check_analogy_accuracy html coherence html combine_vocabularies html create_dtm html create_tcm html create_vocabulary html distances html ifiles html itoken html jsPCA_robust html movie_review html normalize html perplexity html prepare_analogy_questions html prune_vocabulary html reexports html similarities html split_into html text2vec html tokenizers html vectorizers html ** building package indices ** installing vignettes ** 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 (text2vec) Making 'packages.html' ... done * installing *source* package 'tibble' ... ** package 'tibble' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c attributes.c -o attributes.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coerce.c -o coerce.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c matrixToDataFrame.c -o matrixToDataFrame.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o tibble.so attributes.o coerce.o init.o matrixToDataFrame.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-tibble/00new/tibble/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'tibble' done add_column html add_row html as_tibble html char html deprecated html finding level-2 HTML links ... done enframe html formatting html frame_matrix html is.tibble html is_tibble html knit_print.trunc_mat html lst html name-repair-superseded html name-repair html new_tibble html num html reexports html rownames html subsetting html tbl_df-class html tibble-package html tibble html tibble_options html tribble html trunc_mat html view html *** copying figures ** building package indices ** installing vignettes ** 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 (tibble) Making 'packages.html' ... done * installing *source* package 'ggplot2' ... ** package 'ggplot2' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'ggplot2' done absoluteGrob html add_theme html aes html aes_ html aes_all html aes_auto html aes_colour_fill_alpha html aes_eval html aes_group_order html aes_linetype_size_shape html aes_position html annotate html annotation_custom html annotation_logticks html annotation_map html annotation_raster html as.list.ggproto html as_labeller html autolayer html autoplot html benchplot html bidirection html binned_scale html borders html calc_element html combine_vars html continuous_scale html coord_cartesian html coord_fixed html coord_flip html coord_map html coord_munch html coord_polar html coord_trans html cut_interval html diamonds html discrete_scale html draw_key html economics html element html element_grob html element_render html expand_limits html expansion html facet_grid html facet_null html facet_wrap html faithfuld html find_panel html fortify-multcomp html fortify html fortify.lm html fortify.map html fortify.sp html geom_abline html geom_bar html geom_bin_2d html geom_blank html geom_boxplot html geom_contour html geom_count html geom_density html geom_density_2d html geom_dotplot html geom_errorbarh html geom_function html geom_hex html geom_histogram html geom_jitter html geom_linerange html geom_map html geom_path html geom_point html geom_polygon html geom_qq html geom_quantile html geom_ribbon html geom_rug html geom_segment html geom_smooth html geom_spoke html geom_text html geom_tile html geom_violin html get_alt_text html gg-add html gg_dep html ggplot html ggplot2-ggproto html finding level-2 HTML links ... done ggplot2-package html ggplotGrob html ggplot_add html ggplot_build html ggplot_gtable html ggproto html ggsave html ggsf html ggtheme html graphical-units html guide-exts html guide_axis html guide_bins html guide_colourbar html guide_coloursteps html guide_legend html guide_none html guides html hmisc html is.Coord html is.facet html is.ggplot html is.rel html is.theme html label_bquote html labeller html labellers html labs html last_plot html layer html layer_sf html limits html lims html luv_colours html map_data html max_height html mean_se html merge_element html midwest html mpg html msleep html position_dodge html position_identity html position_jitter html position_jitterdodge html position_nudge html position_stack html presidential html print.ggplot html print.ggproto html qplot html reexports html register_theme_elements html remove_missing html render_axes html render_strips html resolution html scale_alpha html scale_binned html scale_brewer html scale_colour_continuous html scale_colour_discrete html scale_continuous html scale_date html scale_discrete html scale_gradient html scale_grey html scale_hue html scale_identity html scale_linetype html scale_manual html scale_shape html scale_size html scale_steps html scale_type html scale_viridis html seals html sec_axis html set_last_plot html sf_transform_xy html should_stop html standardise_aes_names html stat_ecdf html stat_ellipse html stat_identity html stat_sf_coordinates html stat_summary html stat_summary_2d html stat_unique html summarise_plot html summary.ggplot html theme html theme_get html tidyeval html transform_position html translate_qplot_ggplot html translate_qplot_lattice html txhousing html update_defaults html update_labels html vars html waiver html wrap_dims html zeroGrob html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggplot2) Making 'packages.html' ... done * installing *source* package 'dplyr' ... ** package 'dplyr' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c chop.cpp -o chop.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c funs.cpp -o funs.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c group_by.cpp -o group_by.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c group_data.cpp -o group_data.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c imports.cpp -o imports.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mask.cpp -o mask.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mutate.cpp -o mutate.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c slice.cpp -o slice.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c summarise.cpp -o summarise.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-dplyr/00new/dplyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'dplyr' done across html add_rownames html all_equal html all_vars html arrange html arrange_all html auto_copy html backend_dbplyr html band_members html bench_compare html between html bind html c_across html case_when html check_dbplyr html coalesce html combine html common_by html compute html context html copy_to html count html cumall html defunct html desc html dim_desc html distinct html distinct_all html do html dplyr-package html dplyr_data_masking html dplyr_extending html dplyr_tidy_select html explain html filter-joins html filter html filter_all html funs html group_by html group_by_all html group_by_drop_default html group_by_prepare html group_cols html group_data html group_map html group_nest html group_split html group_trim html grouped_df html ident html if_else html lead-lag html location html make_tbl html mutate-joins html mutate html mutate_all html n_distinct html na_if html near html nest_by html nest_join html new_grouped_df html nth html order_by html progress_estimated html pull html ranking html recode html reexports html relocate html rename html rows html rowwise html same_src html sample_n html scoped html se-deprecated html select html select_all html select_vars html setops html slice html sql html src html src_dbi html src_local html src_tbls html starwars html storms html summarise html summarise_all html summarise_each html tbl html tbl_df html tbl_ptype html tbl_vars html tidyeval-compat html top_n html vars html with_groups html with_order html *** copying figures ** building package indices ** installing vignettes ** 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 (dplyr) Making 'packages.html' ... done * installing *source* package 'tidyr' ... ** package 'tidyr' successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/cpp11/include' -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/cpp11/include' -I/usr/local/include -fpic -g -O2 -c fill.cpp -o fill.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/cpp11/include' -I/usr/local/include -fpic -g -O2 -c melt.cpp -o melt.o g++ -std=gnu++11 -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I'/opt/R/4.0.3/lib/R/library/cpp11/include' -I/usr/local/include -fpic -g -O2 -c simplifyPieces.cpp -o simplifyPieces.o g++ -std=gnu++11 -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o tidyr.so cpp11.o fill.o melt.o simplifyPieces.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-tidyr/00new/tidyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices finding HTML links ... converting help for package 'tidyr' done billboard html chop html complete html construction html deprecated-se html drop_na html expand html expand_grid html extract html extract_numeric html fill html fish_encounters html full_seq html gather html hoist html nest html nest_legacy html pack html pipe html Rd warning: /tmp/RtmpICoEwY/R.INSTALL3e081c038987/tidyr/man/pipe.Rd:10: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic pivot_longer html pivot_longer_spec html pivot_wider html pivot_wider_spec html reexports html relig_income html replace_na html separate html separate_rows html smiths html spread html table1 html tidyr-package html tidyr_legacy html tidyr_tidy_select html uncount html unite html us_rent_income html who html world_bank_pop html *** copying figures ** building package indices ** installing vignettes ** 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 (tidyr) Making 'packages.html' ... done * installing *source* package 'recipes' ... ** package 'recipes' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help System has not been booted with systemd as init system (PID 1). Can't operate. Failed to create bus connection: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 *** installing help indices finding HTML links ... converting help for package 'recipes' done add_step html bake html finding level-2 HTML links ... done check_class html check_cols html check_missing html check_name html check_new_values html check_range html check_type html detect_step html discretize html fixed html format_ch_vec html formula.recipe html fully_trained html get_keep_original_cols html has_role html juice html names0 html prep html prepper html print.recipe html rand_id html recipe html recipes-internal html recipes html recipes_pkg_check html reexports html required_pkgs.step html roles html selections html step html step_BoxCox html step_YeoJohnson html step_arrange html step_bin2factor html step_bs html step_center html step_classdist html step_corr html step_count html step_cut html step_date html step_depth html step_discretize html step_downsample html step_dummy html step_factor2string html step_filter html step_geodist html step_holiday html step_hyperbolic html step_ica html step_impute_bag html step_impute_knn html step_impute_linear html step_impute_lower html step_impute_mean html step_impute_median html step_impute_mode html step_impute_roll html step_indicate_na html step_integer html step_interact html step_intercept html step_inverse html step_invlogit html step_isomap html step_kpca html step_kpca_poly html step_kpca_rbf html step_lag html step_lincomb html step_log html step_logit html step_mutate html step_mutate_at html step_naomit html step_nnmf html step_normalize html step_novel html step_ns html step_num2factor html step_nzv html step_ordinalscore html step_other html step_pca html step_pls html step_poly html step_profile html step_range html step_ratio html step_regex html step_relevel html step_relu html step_rename html step_rename_at html step_rm html step_sample html step_scale html step_select html step_shuffle html step_slice html step_spatialsign html step_sqrt html step_string2factor html step_unknown html step_unorder html step_upsample html step_window html step_zv html summary.recipe html terms_select html tidy.recipe html tunable.recipe html update.step html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location System has not been booted with systemd as init system (PID 1). Can't operate. Failed to create bus connection: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path System has not been booted with systemd as init system (PID 1). Can't operate. Failed to create bus connection: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 * DONE (recipes) Making 'packages.html' ... done ERROR: dependency 'httr' is not available for package 'oysteR' * removing '/opt/R/4.0.3/lib/R/library/oysteR' * installing *source* package 'caret' ... ** package 'caret' successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R/4.0.3/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c caret.c -o caret.o gcc -shared -L/opt/R/4.0.3/lib/R/lib -L/usr/local/lib -o caret.so caret.o -L/opt/R/4.0.3/lib/R/lib -lR installing to /opt/R/4.0.3/lib/R/library/00LOCK-caret/00new/caret/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help System has not been booted with systemd as init system (PID 1). Can't operate. Failed to create bus connection: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 *** installing help indices finding HTML links ... converting help for package 'caret' done BloodBrain html BoxCoxTrans html GermanCredit html Sacramento html as.matrix.confusionMatrix html avNNet html bag html bagEarth html bagFDA html calibration html caret-internal html caretFuncs html caretSBF html cars html classDist html confusionMatrix html confusionMatrix.train html cox2 html createDataPartition html densityplot.rfe html dhfr html diff.resamples html dotPlot html dotplot.diff.resamples html Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/dotplot.diff.resamples.Rd:23: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/dotplot.diff.resamples.Rd:66: file link 'bwplot' in package 'lattice' does not exist and so has been treated as a topic downSample html dummyVars html Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/dummyVars.Rd:83: file link 'contr.treatment' in package 'stats' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/dummyVars.Rd:86: file link 'contr.treatment' in package 'stats' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/dummyVars.Rd:173: file link 'contr.treatment' in package 'stats' does not exist and so has been treated as a topic featurePlot html filterVarImp html findCorrelation html findLinearCombos html format.bagEarth html gafs.default html gafs_initial html getSamplingInfo html histogram.train html icr.formula html index2vec html knn3 html knnreg html learning_curve_dat html lift html maxDissim html mdrr html modelLookup html Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/modelLookup.Rd:26: file link 'grepl' in package 'base' does not exist and so has been treated as a topic Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/modelLookup.Rd:78: file link 'grepl' in package 'base' does not exist and so has been treated as a topic models html nearZeroVar html nullModel html oil html oneSE html panel.lift2 html panel.needle html pcaNNet html plot.gafs html plot.rfe html plot.train html plot.varImp.train html plotClassProbs html Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/plotClassProbs.Rd:23: file link 'densityplot' in package 'lattice' does not exist and so has been treated as a topic plotObsVsPred html plsda html postResample html pottery html prcomp.resamples html preProcess html predict.bagEarth html predict.gafs html predict.knn3 html predict.knnreg html predict.train html predictors html print.confusionMatrix html print.train html recall html resampleHist html resampleSummary html resamples html rfe html rfeControl html safs html safsControl html safs_initial html sbf html sbfControl html scat html segmentationData html sensitivity html spatialSign html summary.bagEarth html tecator html thresholder html train html finding level-2 HTML links ... done trainControl html twoClassSim html update.safs html update.train html varImp html varImp.gafs html var_seq html xyplot.resamples html Rd warning: /tmp/RtmpcOnc5Q/R.INSTALL3f29c563ce0/caret/man/xyplot.resamples.Rd:162: file link 'bwplot' in package 'lattice' does not exist and so has been treated as a topic ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location System has not been booted with systemd as init system (PID 1). Can't operate. Failed to create bus connection: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 ** 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 System has not been booted with systemd as init system (PID 1). Can't operate. Failed to create bus connection: Host is down Warning in system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 * DONE (caret) Making 'packages.html' ... done Updating HTML index of packages in '.Library' Making 'packages.html' ...> > done Warning messages: 1: In install.packages(c("ggplot2", "data.table", "dplyr", "tidyr", : installation of package 'openssl' had non-zero exit status 2: In install.packages(c("ggplot2", "data.table", "dplyr", "tidyr", : installation of package 'httr' had non-zero exit status 3: In install.packages(c("ggplot2", "data.table", "dplyr", "tidyr", : installation of package 'oysteR' had non-zero exit status 25 files removed STEP 9: ENV LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8 LANGUAGE=en_US.UTF-8 STEP 10: USER ${USER} STEP 11: HEALTHCHECK --start-period=60s CMD rstudio-server status | grep -e "running" STEP 12: EXPOSE 8787 STEP 13: ENTRYPOINT ["rstudio-server", "start"] STEP 14: COMMIT registry1.dso.mil/ironbank-staging/opensource/r/r-studio Getting image source signatures Copying blob sha256:98469092e6042f8c9cc81dcb1a710957fb5ef27817c9b178f7b71c4f242cb2ed Copying blob sha256:bfb9caafb0fc0d8496a27709f1698ac90d1a306556387a75b92a86063544f4c8 Copying blob sha256:f221949c4d4c872ec15a3aece5a3367c1730ec2c25d8d3a1173c8d8f4f630adb Copying blob sha256:279b6f39b2d0a5abfe8271ed710bad4011d2b168e6d2ff598f281aeb2c905e0e Copying blob sha256:aeef7d6b86b3eaf8704d625029c65edfdf2ce13eca888783bb31c756a26c26dc Copying config sha256:7b662def6dcf3555b9bfe47da258f940f701ece6338a48134f635ccb57c3a826 Writing manifest to image destination Storing signatures --> 7b662def6dc Successfully tagged registry1.dso.mil/ironbank-staging/opensource/r/r-studio:latest 7b662def6dcf3555b9bfe47da258f940f701ece6338a48134f635ccb57c3a826 + buildah tag --storage-driver=vfs registry1.dso.mil/ironbank-staging/opensource/r/r-studio registry1.dso.mil/ironbank-staging/opensource/r/r-studio:ibci-453155 + buildah push --storage-driver=vfs --authfile staging_auth.json --digestfile=ci-artifacts/build/digest registry1.dso.mil/ironbank-staging/opensource/r/r-studio:ibci-453155 Getting image source signatures Copying blob sha256:bfb9caafb0fc0d8496a27709f1698ac90d1a306556387a75b92a86063544f4c8 Copying blob sha256:f221949c4d4c872ec15a3aece5a3367c1730ec2c25d8d3a1173c8d8f4f630adb Copying blob sha256:98469092e6042f8c9cc81dcb1a710957fb5ef27817c9b178f7b71c4f242cb2ed Copying blob sha256:279b6f39b2d0a5abfe8271ed710bad4011d2b168e6d2ff598f281aeb2c905e0e Copying blob sha256:aeef7d6b86b3eaf8704d625029c65edfdf2ce13eca888783bb31c756a26c26dc Copying config sha256:7b662def6dcf3555b9bfe47da258f940f701ece6338a48134f635ccb57c3a826 Writing manifest to image destination Storing signatures Read the tags + echo 'Read the tags' + tags_file=ci-artifacts/preflight/tags.txt + test -f ci-artifacts/preflight/tags.txt + IFS= + read -r tag + buildah tag --storage-driver=vfs registry1.dso.mil/ironbank-staging/opensource/r/r-studio registry1.dso.mil/ironbank-staging/opensource/r/r-studio:1.4.1717 + buildah push --storage-driver=vfs --authfile staging_auth.json registry1.dso.mil/ironbank-staging/opensource/r/r-studio:1.4.1717 Getting image source signatures Copying blob sha256:98469092e6042f8c9cc81dcb1a710957fb5ef27817c9b178f7b71c4f242cb2ed Copying blob sha256:f221949c4d4c872ec15a3aece5a3367c1730ec2c25d8d3a1173c8d8f4f630adb Copying blob sha256:279b6f39b2d0a5abfe8271ed710bad4011d2b168e6d2ff598f281aeb2c905e0e Copying blob sha256:aeef7d6b86b3eaf8704d625029c65edfdf2ce13eca888783bb31c756a26c26dc Copying blob sha256:bfb9caafb0fc0d8496a27709f1698ac90d1a306556387a75b92a86063544f4c8 Copying config sha256:7b662def6dcf3555b9bfe47da258f940f701ece6338a48134f635ccb57c3a826 Writing manifest to image destination Storing signatures + IFS= + read -r tag + buildah tag --storage-driver=vfs registry1.dso.mil/ironbank-staging/opensource/r/r-studio registry1.dso.mil/ironbank-staging/opensource/r/r-studio:latest + buildah push --storage-driver=vfs --authfile staging_auth.json registry1.dso.mil/ironbank-staging/opensource/r/r-studio:latest Getting image source signatures Copying blob sha256:98469092e6042f8c9cc81dcb1a710957fb5ef27817c9b178f7b71c4f242cb2ed Copying blob sha256:aeef7d6b86b3eaf8704d625029c65edfdf2ce13eca888783bb31c756a26c26dc Copying blob sha256:279b6f39b2d0a5abfe8271ed710bad4011d2b168e6d2ff598f281aeb2c905e0e Copying blob sha256:f221949c4d4c872ec15a3aece5a3367c1730ec2c25d8d3a1173c8d8f4f630adb Copying blob sha256:bfb9caafb0fc0d8496a27709f1698ac90d1a306556387a75b92a86063544f4c8 Copying config sha256:7b662def6dcf3555b9bfe47da258f940f701ece6338a48134f635ccb57c3a826 Writing manifest to image destination Storing signatures + IFS= + read -r tag ++ podman inspect --storage-driver=vfs registry1.dso.mil/ironbank-staging/opensource/r/r-studio --format '{{.Id}}' + IMAGE_ID=sha256:7b662def6dcf3555b9bfe47da258f940f701ece6338a48134f635ccb57c3a826 + echo IMAGE_ID=sha256:7b662def6dcf3555b9bfe47da258f940f701ece6338a48134f635ccb57c3a826 + IMAGE_PODMAN_SHA=sha256:0992fb2484faef5510f0e906896317de39a3f995b66fd9f4e617eda8ddf5b757 + echo IMAGE_PODMAN_SHA=sha256:0992fb2484faef5510f0e906896317de39a3f995b66fd9f4e617eda8ddf5b757 + echo IMAGE_FULLTAG=registry1.dso.mil/ironbank-staging/opensource/r/r-studio:ibci-453155 + echo IMAGE_NAME=opensource/r/r-studio + branches=("master" "development") + [[ master development =~ master ]] A tarball of the built image can be retrieved from the documentation job artifacts. + msg='A tarball of the built image can be retrieved from the documentation job artifacts.' + echo 'A tarball of the built image can be retrieved from the documentation job artifacts.' section_end:1630432760:step_script section_start:1630432760:upload_artifacts_on_success Uploading artifacts for successful job Uploading artifacts... ci-artifacts/build/: found 2 matching files and directories Uploading artifacts as "archive" to coordinator... ok id=6111637 responseStatus=201 Created token=18z_Y9Ts Uploading artifacts... build.env: found 1 matching files and directories  Uploading artifacts as "dotenv" to coordinator... ok id=6111637 responseStatus=201 Created token=18z_Y9Ts section_end:1630432762:upload_artifacts_on_success section_start:1630432762:cleanup_file_variables Cleaning up file based variables section_end:1630432762:cleanup_file_variables Job succeeded