2025-12-26T04:21:31.143173Z 00O Running with gitlab-runner 18.7.0~pre.433.g3a5f2314 (3a5f2314)
2025-12-26T04:21:31.143186Z 00O   on blue-2.saas-linux-medium-amd64.runners-manager.gitlab.com/default ZQ74L_riD, system ID: s_805fb2e5035f
2025-12-26T04:21:31.143206Z 00O Resolving secrets
2025-12-26T04:21:31.143315Z 00O section_start:1766722891:prepare_executor
2025-12-26T04:21:31.143316Z 00O+Preparing the "docker+machine" executor
2025-12-26T04:21:31.273727Z 00O Using Docker executor with image registry.gitlab.com/rdatatable/dockerfiles/r-base ...
2025-12-26T04:21:35.626556Z 00O Using effective pull policy of [always] for container registry.gitlab.com/rdatatable/dockerfiles/r-base
2025-12-26T04:21:35.627186Z 00O Authenticating with credentials from job payload (GitLab Registry)
2025-12-26T04:21:35.627198Z 00O Pulling docker image registry.gitlab.com/rdatatable/dockerfiles/r-base ...
2025-12-26T04:21:47.206399Z 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 ...
2025-12-26T04:21:47.206479Z 00O section_end:1766722907:prepare_executor
2025-12-26T04:21:47.206481Z 00O+section_start:1766722907:prepare_script
2025-12-26T04:21:47.206562Z 00O+Preparing environment
2025-12-26T04:21:47.207327Z 00O Using effective pull policy of [always] for container sha256:419c86b3902baf5faa516c0fcf5dccdab1c04dd977d5c220871ba142fe2120c8
2025-12-26T04:21:58.251733Z 01O Running on runner-zq74lrid-project-3622566-concurrent-0 via runner-zq74lrid-s-l-m-amd64-1766722652-58174b7b...
2025-12-26T04:21:58.439670Z 00O section_end:1766722918:prepare_script
2025-12-26T04:21:58.439676Z 00O+section_start:1766722918:get_sources
2025-12-26T04:21:58.440180Z 00O+Getting source from Git repository
2025-12-26T04:21:58.856518Z 01O Gitaly correlation ID: e7f793f821494ed4881e429147be339e
2025-12-26T04:21:58.862856Z 01O Fetching changes...
2025-12-26T04:21:58.866233Z 01O Initialized empty Git repository in /builds/Rdatatable/data.table/.git/
2025-12-26T04:21:58.869214Z 01O Created fresh repository.
2025-12-26T04:22:04.511186Z 01O Checking out a29c209b as detached HEAD (ref is master)...
2025-12-26T04:22:04.696830Z 01O 
2025-12-26T04:22:04.696840Z 01O Skipping Git submodules setup
2025-12-26T04:22:04.696841Z 01O $ git remote set-url origin "${CI_REPOSITORY_URL}" || echo 'Not a git repository; skipping'
2025-12-26T04:22:04.933943Z 00O section_end:1766722924:get_sources
2025-12-26T04:22:04.933950Z 00O+section_start:1766722924:download_artifacts
2025-12-26T04:22:04.934593Z 00O+Downloading artifacts
2025-12-26T04:22:05.368227Z 01O Downloading artifacts for mirror-packages (12544376784)...
2025-12-26T04:22:06.229857Z 01E Downloading artifacts from coordinator... ok        correlation_id=284e43d103ec407bb83911efff97f2de host=storage.googleapis.com id=12544376784 responseStatus=200 OK token=6b_ADzk31
2025-12-26T04:22:06.453786Z 01O Downloading artifacts for build (12544376788)...
2025-12-26T04:22:06.820910Z 01E Downloading artifacts from coordinator... ok        correlation_id=4343098ce6e34c36a0abc040919fa787 host=storage.googleapis.com id=12544376788 responseStatus=200 OK token=6b_ADzk31
2025-12-26T04:22:07.527991Z 00O section_end:1766722927:download_artifacts
2025-12-26T04:22:07.527996Z 00O+section_start:1766722927:step_script
2025-12-26T04:22:07.528376Z 00O+Executing "step_script" stage of the job script
2025-12-26T04:22:07.528395Z 00O Using effective pull policy of [always] for container registry.gitlab.com/rdatatable/dockerfiles/r-base
2025-12-26T04:22:07.529355Z 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 ...
2025-12-26T04:22:07.911427Z 01O $ cp $(ls -1t bus/build/data.table_*.tar.gz | head -n 1) .
2025-12-26T04:22:07.921623Z 01O $ mkdir -p ~/.R
2025-12-26T04:22:07.923256Z 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)'
2025-12-26T04:22:08.157032Z 01E also installing the dependencies ‘commonmark’, ‘R.oo’, ‘R.methodsS3’, ‘evaluate’, ‘highr’, ‘xfun’, ‘litedown’
2025-12-26T04:22:08.157036Z 01E 
2025-12-26T04:23:15.678172Z 01O $ echo 'CFLAGS=-g -O2 -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' > ~/.R/Makevars
2025-12-26T04:23:15.678179Z 01O $ echo 'CXXFLAGS=-g -O2 -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' >> ~/.R/Makevars
2025-12-26T04:23:15.678187Z 01O $ res1=0; R CMD check --as-cran $(ls -1t data.table_*.tar.gz | head -n 1) || res1=$? # collapsed multi-line command
2025-12-26T04:23:15.853405Z 01O * using log directory ‘/builds/Rdatatable/data.table/data.table.Rcheck’
2025-12-26T04:23:15.853575Z 01O * using R version 4.5.0 (2025-04-11)
2025-12-26T04:23:15.853751Z 01O * using platform: x86_64-pc-linux-gnu
2025-12-26T04:23:15.854006Z 01O * R was compiled by
2025-12-26T04:23:15.854140Z 01O     gcc (Debian 14.2.0-19) 14.2.0
2025-12-26T04:23:15.854141Z 01O     GNU Fortran (Debian 14.2.0-19) 14.2.0
2025-12-26T04:23:15.854415Z 01O * running under: Debian GNU/Linux 13 (trixie)
2025-12-26T04:23:15.854652Z 01O * using session charset: UTF-8
2025-12-26T04:23:16.582375Z 01O * using option ‘--as-cran’
2025-12-26T04:23:16.582638Z 01O * checking for file ‘data.table/DESCRIPTION’ ... OK
2025-12-26T04:23:16.585209Z 01O * this is package ‘data.table’ version ‘1.18.99’
2025-12-26T04:23:16.585432Z 01O * package encoding: UTF-8
2025-12-26T04:23:16.585715Z 01O * checking CRAN incoming feasibility ... OK
2025-12-26T04:23:17.147604Z 01O * checking package namespace information ... OK
2025-12-26T04:23:17.156236Z 01O * checking package dependencies ... OK
2025-12-26T04:23:18.264218Z 01O * checking if this is a source package ... OK
2025-12-26T04:23:18.267230Z 01O * checking if there is a namespace ... OK
2025-12-26T04:23:18.272127Z 01O * checking for .dll and .exe files ... OK
2025-12-26T04:23:18.272611Z 01O * checking for hidden files and directories ... OK
2025-12-26T04:23:18.275754Z 01O * checking for portable file names ... OK
2025-12-26T04:23:18.280338Z 01O * checking for sufficient/correct file permissions ... OK
2025-12-26T04:23:18.284535Z 01O * checking serialization versions ... OK
2025-12-26T04:23:18.295342Z 01O * checking whether package ‘data.table’ can be installed ... [24s/24s] OK
2025-12-26T04:23:42.694676Z 01O * used C compiler: ‘gcc (Debian 14.2.0-19) 14.2.0’
2025-12-26T04:23:42.695004Z 01O * checking installed package size ... OK
2025-12-26T04:23:42.712900Z 01O * checking package directory ... OK
2025-12-26T04:23:42.713301Z 01O * checking for future file timestamps ... OK
2025-12-26T04:23:42.713864Z 01O * checking ‘build’ directory ... OK
2025-12-26T04:23:42.714757Z 01O * checking DESCRIPTION meta-information ... OK
2025-12-26T04:23:43.568476Z 01O * checking top-level files ... OK
2025-12-26T04:23:45.124828Z 01O * checking for left-over files ... OK
2025-12-26T04:23:45.128050Z 01O * checking index information ... OK
2025-12-26T04:23:45.425419Z 01O * checking package subdirectories ... OK
2025-12-26T04:23:46.029783Z 01O * checking code files for non-ASCII characters ... OK
2025-12-26T04:23:46.081910Z 01O * checking R files for syntax errors ... OK
2025-12-26T04:23:46.164710Z 01O * checking whether the package can be loaded ... OK
2025-12-26T04:23:46.364558Z 01O * checking whether the package can be loaded with stated dependencies ... OK
2025-12-26T04:23:46.520684Z 01O * checking whether the package can be unloaded cleanly ... OK
2025-12-26T04:23:46.678240Z 01O * checking whether the namespace can be loaded with stated dependencies ... OK
2025-12-26T04:23:46.838577Z 01O * checking whether the namespace can be unloaded cleanly ... OK
2025-12-26T04:23:47.045748Z 01O * checking loading without being on the library search path ... OK
2025-12-26T04:23:47.450621Z 01O * checking whether startup messages can be suppressed ... OK
2025-12-26T04:23:47.656446Z 01O * checking use of S3 registration ... OK
2025-12-26T04:23:48.652372Z 01O * checking dependencies in R code ... OK
2025-12-26T04:23:49.501911Z 01O * checking S3 generic/method consistency ... OK
2025-12-26T04:23:49.851519Z 01O * checking replacement functions ... OK
2025-12-26T04:23:50.065692Z 01O * checking foreign function calls ... OK
2025-12-26T04:23:50.818278Z 01O * checking R code for possible problems ... [16s/16s] OK
2025-12-26T04:24:07.114080Z 01O * checking Rd files ... OK
2025-12-26T04:24:07.698635Z 01O * checking Rd metadata ... OK
2025-12-26T04:24:07.744293Z 01O * checking Rd line widths ... OK
2025-12-26T04:24:08.041045Z 01O * checking Rd cross-references ... OK
2025-12-26T04:24:08.711988Z 01O * checking for missing documentation entries ... OK
2025-12-26T04:24:08.937642Z 01O * checking for code/documentation mismatches ... OK
2025-12-26T04:24:09.905797Z 01O * checking Rd \usage sections ... OK
2025-12-26T04:24:10.781759Z 01O * checking Rd contents ... OK
2025-12-26T04:24:11.231061Z 01O * checking for unstated dependencies in examples ... OK
2025-12-26T04:24:11.726237Z 01O * checking line endings in shell scripts ... OK
2025-12-26T04:24:11.726782Z 01O * checking line endings in C/C++/Fortran sources/headers ... OK
2025-12-26T04:24:11.744461Z 01O * checking line endings in Makefiles ... OK
2025-12-26T04:24:11.745016Z 01O * checking compilation flags in Makevars ... OK
2025-12-26T04:24:11.802183Z 01O * checking for GNU extensions in Makefiles ... OK
2025-12-26T04:24:11.802971Z 01O * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
2025-12-26T04:24:11.804165Z 01O * checking use of PKG_*FLAGS in Makefiles ... OK
2025-12-26T04:24:11.808220Z 01O * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
2025-12-26T04:24:11.814968Z 01O * checking pragmas in C/C++ headers and code ... OK
2025-12-26T04:24:11.836309Z 01O * checking compilation flags used ... OK
2025-12-26T04:24:11.837844Z 01O * checking compiled code ... NOTE
2025-12-26T04:24:11.914670Z 01O File ‘data.table/libs/data_table.so’:
2025-12-26T04:24:11.914673Z 01O   Found non-API calls to R: ‘IS_GROWABLE’, ‘LEVELS’, ‘SETLENGTH’,
2025-12-26T04:24:11.914674Z 01O     ‘SET_GROWABLE_BIT’, ‘SET_TRUELENGTH’, ‘TRUELENGTH’, ‘XTRUELENGTH’
2025-12-26T04:24:11.915220Z 01O 
2025-12-26T04:24:11.915220Z 01O Compiled code should not call non-API entry points in R.
2025-12-26T04:24:11.915244Z 01O 
2025-12-26T04:24:11.915245Z 01O See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
2025-12-26T04:24:11.915246Z 01O and section ‘Moving into C API compliance’ for issues with the use of
2025-12-26T04:24:11.915246Z 01O non-API entry points.
2025-12-26T04:24:11.916411Z 01O * checking installed files from ‘inst/doc’ ... OK
2025-12-26T04:24:12.195367Z 01O * checking files in ‘vignettes’ ... OK
2025-12-26T04:24:12.477770Z 01O * checking examples ... OK
2025-12-26T04:24:19.989843Z 01O * checking examples with --run-donttest ... OK
2025-12-26T04:24:29.828797Z 01O * checking for unstated dependencies in ‘tests’ ... OK
2025-12-26T04:24:29.894382Z 01O * checking tests ...
2025-12-26T04:24:30.041259Z 01E   Running ‘autoprint.R’
2025-12-26T04:24:30.286312Z 01E   Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ... OK
2025-12-26T04:24:30.293793Z 01E   Running ‘froll.R’ [441s/421s]
2025-12-26T04:31:31.149810Z 01E   Running ‘knitr.R’
2025-12-26T04:31:31.449929Z 01E   Comparing ‘knitr.Rout’ to ‘knitr.Rout.save’ ... OK
2025-12-26T04:31:31.455364Z 01E   Running ‘main.R’ [48s/43s]
2025-12-26T04:32:14.841959Z 01E   Running ‘mergelist.R’
2025-12-26T04:32:16.452452Z 01E   Running ‘nafill.R’
2025-12-26T04:32:16.898448Z 01E   Running ‘other.R’
2025-12-26T04:32:17.107451Z 01E   Running ‘programming.R’
2025-12-26T04:32:17.738432Z 01E   Running ‘S4.R’
2025-12-26T04:32:18.056573Z 01E   Running ‘types.R’
2025-12-26T04:32:18.324214Z 01O  [493s/468s] OK
2025-12-26T04:32:18.448502Z 01O * checking for unstated dependencies in vignettes ... OK
2025-12-26T04:32:18.833969Z 01O * checking package vignettes ... OK
2025-12-26T04:32:19.218580Z 01O * checking re-building of vignette outputs ... [24s/25s] OK
2025-12-26T04:32:44.600342Z 01O * checking PDF version of manual ... OK
2025-12-26T04:32:50.611176Z 01O * checking HTML version of manual ... OK
2025-12-26T04:32:53.785706Z 01O * checking for non-standard things in the check directory ... OK
2025-12-26T04:32:53.786221Z 01O * checking for detritus in the temp directory ... OK
2025-12-26T04:32:53.786881Z 01O * DONE
2025-12-26T04:32:53.787219Z 01E 
2025-12-26T04:32:53.787354Z 01O Status: 1 NOTE
2025-12-26T04:32:53.787513Z 01E See
2025-12-26T04:32:53.787514Z 01E   ‘/builds/Rdatatable/data.table/data.table.Rcheck/00check.log’
2025-12-26T04:32:53.787515Z 01E for details.
2025-12-26T04:32:53.787601Z 01E 
2025-12-26T04:32:54.146292Z 00O section_end:1766723574:step_script
2025-12-26T04:32:54.146301Z 00O+section_start:1766723574:after_script
2025-12-26T04:32:54.146674Z 00O+Running after_script
2025-12-26T04:32:54.515111Z 01O Running after script...
2025-12-26T04:32:54.515136Z 01O $ mkdir -p bus/$CI_JOB_NAME
2025-12-26T04:32:54.516333Z 01O $ echo $CI_JOB_ID > bus/$CI_JOB_NAME/id
2025-12-26T04:32:54.516377Z 01O $ echo $CI_JOB_STATUS > bus/$CI_JOB_NAME/status
2025-12-26T04:32:54.516493Z 01O $ echo $CI_JOB_IMAGE > bus/$CI_JOB_NAME/image
2025-12-26T04:32:54.516505Z 01O $ [ -d data.table.Rcheck ] && mv data.table.Rcheck bus/$CI_JOB_NAME/
2025-12-26T04:32:54.699451Z 00O section_end:1766723574:after_script
2025-12-26T04:32:54.699459Z 00O+section_start:1766723574:upload_artifacts_on_success
2025-12-26T04:32:54.700153Z 00O+Uploading artifacts for successful job
2025-12-26T04:32:55.105214Z 01O Uploading artifacts...
2025-12-26T04:32:55.174635Z 01E bus/test-lin-rel-cran: found 679 matching artifact files and directories 
2025-12-26T04:32:58.429792Z 01E Uploading artifacts as "archive" to coordinator... 201 Created  correlation_id=0bc7dd4be9cc477ca90bbd8cd27e2ad4 id=12544376795 responseStatus=201 Created token=6b_ADzk31
2025-12-26T04:32:58.620535Z 00O section_end:1766723578:upload_artifacts_on_success
2025-12-26T04:32:58.620543Z 00O+section_start:1766723578:cleanup_file_variables
2025-12-26T04:32:58.620631Z 00O+Cleaning up project directory and file based variables
2025-12-26T04:32:59.156277Z 00O section_end:1766723579:cleanup_file_variables
2025-12-26T04:32:59.156285Z 00O+
2025-12-26T04:32:59.197069Z 00O Job succeeded