2026-10-12T04:21:04.748702Z 00O Running with gitlab-runner 19.5.0~pre.2272.g28a18501 (28a18501)
2026-10-12T04:21:04.748732Z 00O   on k8s.saas-linux-medium-amd64.runners-manager.gitlab.com/default j8vTLRhES, system ID: r_HSob3J6Ku4Mv
2026-10-12T04:21:04.748734Z 00O   UUID: 01a01aa6-2f91-7d2c-b24d-7e2d2752ac58
2026-10-12T04:21:04.748744Z 00O   feature flags: FF_USE_GIT_PROACTIVE_AUTH:true, FF_HASH_CACHE_KEYS:true, FF_USE_JOB_ROUTER:true, FF_MACHINE_OPTIONS_EXPAND_ENV:true, FF_DOCKER_MACHINE_JSON_OUTPUT:true
2026-10-12T04:21:04.748784Z 00O Resolving secrets
2026-10-12T04:21:04.749002Z 00O section_start:1791778864:prepare_executor

2026-10-12T04:21:04.749006Z 00O+Preparing the "docker+machine" executor
2026-10-12T04:21:04.843702Z 00O Using Docker executor with image registry.gitlab.com/rdatatable/dockerfiles/r-base ...
2026-10-12T04:21:04.843762Z 00O Using helper image:  registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501  (overridden, default would be  registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-v19.5.0 )
2026-10-12T04:21:04.843773Z 00O Using effective pull policy of [always] for container registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501
2026-10-12T04:21:04.844472Z 00O Authenticating with credentials from job payload (GitLab Registry)
2026-10-12T04:21:04.844486Z 00O Pulling docker image registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501 ...
2026-10-12T04:21:06.308084Z 00O Using docker image sha256:08749606eabcea842cbd189a80b2f3d7670b949f70dfc654d45d8b81554bd837 for registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501 with digest registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper@sha256:eea1152121f06d47f94871fef69559be0a87c75212f227e34e7617d1a3bbe6c3 ...
2026-10-12T04:21:07.964787Z 00O Using helper image:  registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501  (overridden, default would be  registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-v19.5.0 )
2026-10-12T04:21:07.964815Z 00O Using effective pull policy of [always] for container registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501
2026-10-12T04:21:07.966095Z 00O Using docker image sha256:08749606eabcea842cbd189a80b2f3d7670b949f70dfc654d45d8b81554bd837 for registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501 with digest registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper@sha256:eea1152121f06d47f94871fef69559be0a87c75212f227e34e7617d1a3bbe6c3 ...
2026-10-12T04:21:07.966116Z 00O Using effective pull policy of [always] for container registry.gitlab.com/rdatatable/dockerfiles/r-base
2026-10-12T04:21:07.966947Z 00O Authenticating with credentials from job payload (GitLab Registry)
2026-10-12T04:21:07.966958Z 00O Pulling docker image registry.gitlab.com/rdatatable/dockerfiles/r-base ...
2026-10-12T04:21:18.262003Z 00O Using docker image sha256:02effb957528a82923993d0dfe5945c03a2f9e25844af0e8471caad307239e23 for registry.gitlab.com/rdatatable/dockerfiles/r-base with digest registry.gitlab.com/rdatatable/dockerfiles/r-base@sha256:f5668901f25070b6a9c52510da0995a41a22acf73417481b293f7de9255902c6 ...
2026-10-12T04:21:18.262116Z 00O section_end:1791778878:prepare_executor

2026-10-12T04:21:18.262286Z 00O+section_start:1791778878:prepare_script

2026-10-12T04:21:18.262294Z 00O+Preparing environment
2026-10-12T04:21:18.262342Z 00O Using helper image:  registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501  (overridden, default would be  registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-v19.5.0 )
2026-10-12T04:21:18.262353Z 00O Using effective pull policy of [always] for container registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501
2026-10-12T04:21:18.263273Z 00O Using docker image sha256:08749606eabcea842cbd189a80b2f3d7670b949f70dfc654d45d8b81554bd837 for registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper:x86_64-28a18501 with digest registry.gitlab.com/gitlab-org/gitlab-runner/gitlab-runner-helper@sha256:eea1152121f06d47f94871fef69559be0a87c75212f227e34e7617d1a3bbe6c3 ...
2026-10-12T04:21:18.263286Z 00O Using effective pull policy of [always] for container sha256:08749606eabcea842cbd189a80b2f3d7670b949f70dfc654d45d8b81554bd837
2026-10-12T04:21:27.401883Z 01O Running on runner-j8vtlrhes-project-3622566-concurrent-0 via runner-j8vtlrhes-s-l-m-amd64-1791778832-9f9d0c65...
2026-10-12T04:21:27.404784Z 01O Running on CPU: INTEL(R) XEON(R) PLATINUM 8581C CPU @ 2.10GHz (avx, avx2, avx512f)
2026-10-12T04:21:27.553416Z 00O section_end:1791778887:prepare_script

2026-10-12T04:21:27.554363Z 00O+section_start:1791778887:get_sources

2026-10-12T04:21:27.554379Z 00O+Getting source from Git repository
2026-10-12T04:21:27.873965Z 01O Gitaly correlation ID: e15c4183bce74905a93a98d4f1d51b52
2026-10-12T04:21:27.879238Z 01O Fetching changes...
2026-10-12T04:21:27.881747Z 01O Initialized empty Git repository in /builds/Rdatatable/data.table/.git/
2026-10-12T04:21:27.883803Z 01O Created fresh repository.
2026-10-12T04:21:33.415169Z 01O Checking out df59dd63 as detached HEAD (ref is master)...
2026-10-12T04:21:33.593908Z 01O 
2026-10-12T04:21:33.593923Z 01O Skipping Git submodules setup
2026-10-12T04:21:33.593926Z 01O $ git remote set-url origin "${CI_REPOSITORY_URL}" || echo 'Not a git repository; skipping'
2026-10-12T04:21:33.778056Z 00O section_end:1791778893:get_sources

2026-10-12T04:21:33.779179Z 00O+section_start:1791778893:download_artifacts

2026-10-12T04:21:33.779188Z 00O+Downloading artifacts
2026-10-12T04:21:34.136229Z 01O Downloading artifacts for build (17100991411)...
2026-10-12T04:21:34.327471Z 01E Direct download from storage.googleapis.com         correlation_id=fef94bbd257b41018d4505da78ee7611 id=17100991411 status=302 token=74_AtTxyn
2026-10-12T04:21:34.549843Z 01E Downloading artifacts from coordinator... ok        correlation_id=fef94bbd257b41018d4505da78ee7611 id=17100991411 status=302 token=74_AtTxyn
2026-10-12T04:21:34.558502Z 01O Downloading artifacts for mirror-packages (17100991410)...
2026-10-12T04:21:34.847593Z 01E Direct download from storage.googleapis.com         correlation_id=4c5a74d8c79b41dead76b5c43e28a66c id=17100991410 status=302 token=74_AtTxyn
2026-10-12T04:21:35.346107Z 01E Downloading artifacts from coordinator... ok        correlation_id=4c5a74d8c79b41dead76b5c43e28a66c id=17100991410 status=302 token=74_AtTxyn
2026-10-12T04:21:36.425815Z 00O section_end:1791778896:download_artifacts

2026-10-12T04:21:36.426301Z 00O+section_start:1791778896:step_script

2026-10-12T04:21:36.426310Z 00O+Executing "step_script" stage of the job script
2026-10-12T04:21:36.426325Z 00O Using effective pull policy of [always] for container registry.gitlab.com/rdatatable/dockerfiles/r-base
2026-10-12T04:21:36.427558Z 00O Using docker image sha256:02effb957528a82923993d0dfe5945c03a2f9e25844af0e8471caad307239e23 for registry.gitlab.com/rdatatable/dockerfiles/r-base with digest registry.gitlab.com/rdatatable/dockerfiles/r-base@sha256:f5668901f25070b6a9c52510da0995a41a22acf73417481b293f7de9255902c6 ...
2026-10-12T04:21:36.749868Z 01O $ cp $(ls -1t bus/build/data.table_*.tar.gz | head -n 1) .
2026-10-12T04:21:36.756372Z 01O $ mkdir -p ~/.R
2026-10-12T04:21:36.757502Z 01O $ Rscript -e 'source(".ci/ci.R"); install.packages(dcf.dependencies("DESCRIPTION", which="all"), repos=file.path("file:", normalizePath("bus/mirror-packages/cran", mustWork=FALSE)), quiet=TRUE)'
2026-10-12T04:21:36.966348Z 01E also installing the dependencies ‘bit’, ‘R.oo’, ‘R.methodsS3’, ‘commonmark’, ‘evaluate’, ‘highr’
2026-10-12T04:21:36.966364Z 01E 
2026-10-12T04:22:39.404914Z 01O $ echo 'CFLAGS=-g -O2 -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' > ~/.R/Makevars
2026-10-12T04:22:39.405052Z 01O $ echo 'CXXFLAGS=-g -O2 -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' >> ~/.R/Makevars
2026-10-12T04:22:39.405055Z 01O $ res1=0; R CMD check --as-cran $(ls -1t data.table_*.tar.gz | head -n 1) || res1=$? # collapsed multi-line command
2026-10-12T04:22:39.576509Z 01O * using log directory ‘/builds/Rdatatable/data.table/data.table.Rcheck’
2026-10-12T04:22:39.576526Z 01O * using R version 4.5.0 (2025-04-11)
2026-10-12T04:22:39.576677Z 01O * using platform: x86_64-pc-linux-gnu
2026-10-12T04:22:39.576855Z 01O * R was compiled by
2026-10-12T04:22:39.576950Z 01O     gcc (Debian 14.2.0-19) 14.2.0
2026-10-12T04:22:39.576952Z 01O     GNU Fortran (Debian 14.2.0-19) 14.2.0
2026-10-12T04:22:39.577214Z 01O * running under: Debian GNU/Linux 13 (trixie)
2026-10-12T04:22:39.577309Z 01O * using session charset: UTF-8
2026-10-12T04:22:40.241683Z 01O * using option ‘--as-cran’
2026-10-12T04:22:40.241814Z 01O * checking for file ‘data.table/DESCRIPTION’ ... OK
2026-10-12T04:22:40.244366Z 01O * this is package ‘data.table’ version ‘1.18.99’
2026-10-12T04:22:40.244522Z 01O * package encoding: UTF-8
2026-10-12T04:22:40.244745Z 01O * checking CRAN incoming feasibility ... OK
2026-10-12T04:22:40.792192Z 01O * checking package namespace information ... OK
2026-10-12T04:22:40.800065Z 01O * checking package dependencies ... OK
2026-10-12T04:22:41.837856Z 01O * checking if this is a source package ... OK
2026-10-12T04:22:41.840196Z 01O * checking if there is a namespace ... OK
2026-10-12T04:22:41.844018Z 01O * checking for .dll and .exe files ... OK
2026-10-12T04:22:41.844381Z 01O * checking for hidden files and directories ... OK
2026-10-12T04:22:41.846156Z 01O * checking for portable file names ... OK
2026-10-12T04:22:41.850004Z 01O * checking for sufficient/correct file permissions ... OK
2026-10-12T04:22:41.853935Z 01O * checking whether package ‘data.table’ can be installed ... [24s/24s] OK
2026-10-12T04:23:05.795723Z 01O * used C compiler: ‘gcc (Debian 14.2.0-19) 14.2.0’
2026-10-12T04:23:05.796057Z 01O * checking installed package size ... OK
2026-10-12T04:23:05.809965Z 01O * checking package directory ... OK
2026-10-12T04:23:05.810227Z 01O * checking for future file timestamps ... OK
2026-10-12T04:23:05.810757Z 01O * checking ‘build’ directory ... OK
2026-10-12T04:23:05.811467Z 01O * checking DESCRIPTION meta-information ... OK
2026-10-12T04:23:06.636955Z 01O * checking top-level files ... OK
2026-10-12T04:23:08.068126Z 01O * checking for left-over files ... OK
2026-10-12T04:23:08.070687Z 01O * checking index information ... OK
2026-10-12T04:23:08.227349Z 01O * checking package subdirectories ... OK
2026-10-12T04:23:08.567876Z 01O * checking code files for non-ASCII characters ... OK
2026-10-12T04:23:08.613098Z 01O * checking R files for syntax errors ... OK
2026-10-12T04:23:08.685818Z 01O * checking whether the package can be loaded ... OK
2026-10-12T04:23:08.874868Z 01O * checking whether the package can be loaded with stated dependencies ... OK
2026-10-12T04:23:09.024409Z 01O * checking whether the package can be unloaded cleanly ... OK
2026-10-12T04:23:09.175334Z 01O * checking whether the namespace can be loaded with stated dependencies ... OK
2026-10-12T04:23:09.329710Z 01O * checking whether the namespace can be unloaded cleanly ... OK
2026-10-12T04:23:09.524252Z 01O * checking loading without being on the library search path ... OK
2026-10-12T04:23:09.906684Z 01O * checking whether startup messages can be suppressed ... OK
2026-10-12T04:23:10.092586Z 01O * checking use of S3 registration ... OK
2026-10-12T04:23:11.073704Z 01O * checking dependencies in R code ... OK
2026-10-12T04:23:11.852195Z 01O * checking S3 generic/method consistency ... OK
2026-10-12T04:23:12.197807Z 01O * checking replacement functions ... OK
2026-10-12T04:23:12.392680Z 01O * checking foreign function calls ... OK
2026-10-12T04:23:13.134648Z 01O * checking R code for possible problems ... [15s/15s] OK
2026-10-12T04:23:28.145949Z 01O * checking Rd files ... OK
2026-10-12T04:23:28.698648Z 01O * checking Rd metadata ... OK
2026-10-12T04:23:28.737160Z 01O * checking Rd line widths ... OK
2026-10-12T04:23:29.019155Z 01O * checking Rd cross-references ... OK
2026-10-12T04:23:29.664888Z 01O * checking for missing documentation entries ... OK
2026-10-12T04:23:29.881021Z 01O * checking for code/documentation mismatches ... OK
2026-10-12T04:23:30.832330Z 01O * checking Rd \usage sections ... OK
2026-10-12T04:23:31.740059Z 01O * checking Rd contents ... OK
2026-10-12T04:23:32.155822Z 01O * checking for unstated dependencies in examples ... OK
2026-10-12T04:23:32.580991Z 01O * checking line endings in shell scripts ... OK
2026-10-12T04:23:32.581465Z 01O * checking line endings in C/C++/Fortran sources/headers ... OK
2026-10-12T04:23:32.600915Z 01O * checking line endings in Makefiles ... OK
2026-10-12T04:23:32.601336Z 01O * checking compilation flags in Makevars ... OK
2026-10-12T04:23:32.649864Z 01O * checking for GNU extensions in Makefiles ... OK
2026-10-12T04:23:32.650463Z 01O * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
2026-10-12T04:23:32.651468Z 01O * checking use of PKG_*FLAGS in Makefiles ... OK
2026-10-12T04:23:32.653946Z 01O * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
2026-10-12T04:23:32.658224Z 01O * checking pragmas in C/C++ headers and code ... OK
2026-10-12T04:23:32.677937Z 01O * checking compilation flags used ... OK
2026-10-12T04:23:32.679515Z 01O * checking compiled code ... NOTE
2026-10-12T04:23:32.747468Z 01O File ‘data.table/libs/data.table.so’:
2026-10-12T04:23:32.747470Z 01O   Found non-API calls to R: ‘IS_GROWABLE’, ‘LEVELS’, ‘R_GetConnection’,
2026-10-12T04:23:32.747471Z 01O     ‘R_ReadConnection’, ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
2026-10-12T04:23:32.747472Z 01O     ‘SET_TRUELENGTH’, ‘TRUELENGTH’, ‘XTRUELENGTH’
2026-10-12T04:23:32.747939Z 01O 
2026-10-12T04:23:32.747940Z 01O Compiled code should not call non-API entry points in R.
2026-10-12T04:23:32.747941Z 01O 
2026-10-12T04:23:32.747941Z 01O See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
2026-10-12T04:23:32.747942Z 01O and section ‘Moving into C API compliance’ for issues with the use of
2026-10-12T04:23:32.747943Z 01O non-API entry points.
2026-10-12T04:23:32.748923Z 01O * checking installed files from ‘inst/doc’ ... OK
2026-10-12T04:23:32.936584Z 01O * checking files in ‘vignettes’ ... OK
2026-10-12T04:23:33.121916Z 01O * checking examples ... OK
2026-10-12T04:23:39.647270Z 01O * checking examples with --run-donttest ... OK
2026-10-12T04:23:48.933253Z 01O * checking for unstated dependencies in ‘tests’ ... OK
2026-10-12T04:23:48.993976Z 01O * checking tests ...
2026-10-12T04:23:49.132712Z 01E   Running ‘autoprint.R’
2026-10-12T04:23:49.360670Z 01E   Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ... OK
2026-10-12T04:23:49.366655Z 01E   Running ‘froll.R’ [445s/428s]
2026-10-12T04:30:57.348735Z 01E   Running ‘litedown.R’
2026-10-12T04:30:57.641273Z 01E   Running ‘main.R’ [47s/43s]
2026-10-12T04:31:40.942436Z 01E   Running ‘mergelist.R’
2026-10-12T04:31:42.571768Z 01E   Running ‘nafill.R’
2026-10-12T04:31:43.083477Z 01E   Running ‘optimize.R’
2026-10-12T04:31:44.503250Z 01E   Running ‘other.R’
2026-10-12T04:31:44.714700Z 01E   Running ‘programming.R’
2026-10-12T04:31:45.325058Z 01E   Running ‘S4.R’
2026-10-12T04:31:45.641000Z 01E   Running ‘self.R’
2026-10-12T04:31:45.869772Z 01E   Running ‘types.R’
2026-10-12T04:31:46.111132Z 01O  [498s/477s] OK
2026-10-12T04:31:46.187455Z 01O * checking for unstated dependencies in vignettes ... OK
2026-10-12T04:31:46.451391Z 01O * checking package vignettes ... OK
2026-10-12T04:31:47.126124Z 01O * checking re-building of vignette outputs ... [29s/30s] OK
2026-10-12T04:32:16.859822Z 01O * checking PDF version of manual ... OK
2026-10-12T04:32:22.811256Z 01O * checking HTML version of manual ... OK
2026-10-12T04:32:25.722544Z 01O * checking for non-standard things in the check directory ... OK
2026-10-12T04:32:25.722938Z 01O * checking for detritus in the temp directory ... OK
2026-10-12T04:32:25.723529Z 01O * DONE
2026-10-12T04:32:25.723887Z 01E 
2026-10-12T04:32:25.723893Z 01O Status: 1 NOTE
2026-10-12T04:32:25.724035Z 01E See
2026-10-12T04:32:25.724037Z 01E   ‘/builds/Rdatatable/data.table/data.table.Rcheck/00check.log’
2026-10-12T04:32:25.724039Z 01E for details.
2026-10-12T04:32:25.724116Z 01E 
2026-10-12T04:32:26.055013Z 00O section_end:1791779546:step_script

2026-10-12T04:32:26.055493Z 00O+section_start:1791779546:after_script

2026-10-12T04:32:26.055499Z 00O+Running after_script
2026-10-12T04:32:26.378909Z 01O Running after script...
2026-10-12T04:32:26.378934Z 01O $ mkdir -p bus/$CI_JOB_NAME
2026-10-12T04:32:26.379446Z 01O $ echo $CI_JOB_ID > bus/$CI_JOB_NAME/id
2026-10-12T04:32:26.379459Z 01O $ echo $CI_JOB_STATUS > bus/$CI_JOB_NAME/status
2026-10-12T04:32:26.379461Z 01O $ echo $CI_JOB_IMAGE > bus/$CI_JOB_NAME/image
2026-10-12T04:32:26.379511Z 01O $ [ -d data.table.Rcheck ] && mv data.table.Rcheck bus/$CI_JOB_NAME/
2026-10-12T04:32:26.536758Z 00O section_end:1791779546:after_script

2026-10-12T04:32:26.537568Z 00O+section_start:1791779546:upload_artifacts_on_success

2026-10-12T04:32:26.537575Z 00O+Uploading artifacts for successful job
2026-10-12T04:32:26.905285Z 01O Uploading artifacts...
2026-10-12T04:32:26.961462Z 01E bus/test-lin-rel-cran: found 720 matching artifact files and directories 
2026-10-12T04:32:28.410596Z 01E Uploading artifacts as "archive" to coordinator... 201 Created  correlation_id=0d69ccbbbea74999b2fb7c88cfc66a28 id=17100991414 status=201 token=74_AtTxyn
2026-10-12T04:32:28.570433Z 00O section_end:1791779548:upload_artifacts_on_success

2026-10-12T04:32:28.571197Z 00O+section_start:1791779548:cleanup_file_variables

2026-10-12T04:32:28.571207Z 00O+Cleaning up project directory and file based variables
2026-10-12T04:32:29.074349Z 00O section_end:1791779549:cleanup_file_variables

2026-10-12T04:32:29.102846Z 00O Job succeeded