Running with gitlab-runner 17.7.0~pre.103.g896916a8 (896916a8)  on blue-5.saas-linux-medium-amd64.runners-manager.gitlab.com/default nEW2M-oD, system ID: s_fe9b8d77dc4b Resolving secrets section_start:1737346722:prepare_executor Preparing the "docker+machine" executor Using Docker executor with image registry.gitlab.com/jangorecki/dockerfiles/r-devel-gcc-strict ... Authenticating with credentials from job payload (GitLab Registry) Pulling docker image registry.gitlab.com/jangorecki/dockerfiles/r-devel-gcc-strict ... Using docker image sha256:f5f3841aaf82913611640c10bf929fb9888694a5f71377a2777ce9bdf3819dc7 for registry.gitlab.com/jangorecki/dockerfiles/r-devel-gcc-strict with digest registry.gitlab.com/jangorecki/dockerfiles/r-devel-gcc-strict@sha256:dad69f421b4e48ec4b0d5b825640498449d535c2131983a34530fe790767e26d ... section_end:1737346740:prepare_executor section_start:1737346740:prepare_script Preparing environment Running on runner-new2m-od-project-3622566-concurrent-0 via runner-new2m-od-s-l-m-amd64-1737346513-943d1a29... section_end:1737346751:prepare_script section_start:1737346751:get_sources Getting source from Git repository Fetching changes... Initialized empty Git repository in /builds/Rdatatable/data.table/.git/ Created fresh repository. Checking out 3a7ec2db as detached HEAD (ref is master)... Skipping Git submodules setup $ git remote set-url origin "${CI_REPOSITORY_URL}" section_end:1737346756:get_sources section_start:1737346756:download_artifacts Downloading artifacts Downloading artifacts for build (8893843115)... Downloading artifacts from coordinator... ok  host=storage.googleapis.com id=8893843115 responseStatus=200 OK token=glcbt-66 Downloading artifacts for mirror-packages (8893843111)... Downloading artifacts from coordinator... ok  host=storage.googleapis.com id=8893843111 responseStatus=200 OK token=glcbt-66 section_end:1737346759:download_artifacts section_start:1737346759:step_script Executing "step_script" stage of the job script Using docker image sha256:f5f3841aaf82913611640c10bf929fb9888694a5f71377a2777ce9bdf3819dc7 for registry.gitlab.com/jangorecki/dockerfiles/r-devel-gcc-strict with digest registry.gitlab.com/jangorecki/dockerfiles/r-devel-gcc-strict@sha256:dad69f421b4e48ec4b0d5b825640498449d535c2131983a34530fe790767e26d ... $ cp $(ls -1t bus/build/data.table_*.tar.gz | head -n 1) . $ mkdir -p ~/.R $ echo 'CFLAGS=-g -O2 -flto=auto -fno-common -fopenmp -Wall -Wvla -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' > ~/.R/Makevars $ echo 'CXXFLAGS=-g -O2 -flto=auto -fno-common -fopenmp -Wall -Wvla -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' >> ~/.R/Makevars $ 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)' also installing the dependencies ‘R.oo’, ‘R.methodsS3’, ‘lattice’, ‘evaluate’, ‘highr’, ‘xfun’, ‘commonmark’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages(dcf.dependencies("DESCRIPTION", which = "all"), : installation of package ‘bit’ had non-zero exit status 2: In install.packages(dcf.dependencies("DESCRIPTION", which = "all"), : installation of package ‘bit64’ had non-zero exit status $ R CMD check --as-cran $(ls -1t data.table_*.tar.gz | head -n 1) * using log directory ‘/builds/Rdatatable/data.table/data.table.Rcheck’ * using R Under development (unstable) (2025-01-04 r87523) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Debian 14.2.0-8) 14.2.0 GNU Fortran (Debian 14.2.0-8) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * using option ‘--as-cran’ * checking for file ‘data.table/DESCRIPTION’ ... OK * this is package ‘data.table’ version ‘1.16.99’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: ‘Tyson Barrett ’ Size of tarball: 5628730 bytes * checking package namespace information ... OK * checking package dependencies ... INFO Packages suggested but not available for checking: 'bit64', 'bit' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for .dll and .exe files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘data.table’ can be installed ... [40s/27s] OK * used C compiler: ‘gcc (Debian 14.2.0-8) 14.2.0’ * checking installed package size ... INFO installed size is 7.3Mb sub-directories of 1Mb or more: libs 1.9Mb po 1.3Mb tests 1.9Mb * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... INFO Package unavailable to check Rd xrefs: ‘bit64’ * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... NOTE File ‘data.table/libs/data_table.so’: Found non-API calls to R: ‘LEVELS’, ‘SETLENGTH’, ‘SET_GROWABLE_BIT’, ‘SET_TRUELENGTH’, ‘TRUELENGTH’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘autoprint.R’ Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ... OK Running ‘froll.R’ [28s/28s] Running ‘knitr.R’ Comparing ‘knitr.Rout’ to ‘knitr.Rout.save’ ... OK Running ‘main.R’ [142s/137s] Running ‘nafill.R’ Running ‘other.R’ Running ‘programming.R’ Running ‘S4.R’ Running ‘types.R’ [174s/168s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [31s/31s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 NOTEs See ‘/builds/Rdatatable/data.table/data.table.Rcheck/00check.log’ for details. $ (! grep "warning:" data.table.Rcheck/00install.out) $ Rscript -e 'l=tail(readLines("data.table.Rcheck/00check.log"), 1L); notes<-"Status: 3 NOTEs"; if (!identical(l, notes)) stop("Last line of ", shQuote("00check.log"), " is not ", shQuote(notes), " (size of tarball, installed package size, non-API calls) but ", shQuote(l)) else q("no")' Error: Last line of '00check.log' is not 'Status: 3 NOTEs' (size of tarball, installed package size, non-API calls) but 'Status: 2 NOTEs' Execution halted section_end:1737347151:step_script section_start:1737347151:after_script Running after_script Running after script... $ mkdir -p bus/$CI_JOB_NAME $ echo $CI_JOB_ID > bus/$CI_JOB_NAME/id $ echo $CI_JOB_STATUS > bus/$CI_JOB_NAME/status $ echo $CI_JOB_IMAGE > bus/$CI_JOB_NAME/image $ [ -d data.table.Rcheck ] && mv data.table.Rcheck bus/$CI_JOB_NAME/ section_end:1737347151:after_script section_start:1737347151:upload_artifacts_on_failure Uploading artifacts for failed job Uploading artifacts... bus/test-lin-dev-gcc-strict-cran: found 626 matching artifact files and directories WARNING: Upload request redirected  location=https://gitlab.com/api/v4/jobs/8893843146/artifacts?artifact_format=zip&artifact_type=archive&expire_in=2+weeks new-url=https://gitlab.com WARNING: Retrying...  context=artifacts-uploader error=request redirected Uploading artifacts as "archive" to coordinator... 201 Created id=8893843146 responseStatus=201 Created token=glcbt-66 section_end:1737347155:upload_artifacts_on_failure section_start:1737347155:cleanup_file_variables Cleaning up project directory and file based variables section_end:1737347156:cleanup_file_variables ERROR: Job failed: exit code 1