Running with gitlab-runner 17.10.0~pre.41.g5c23fd8e (5c23fd8e)  on green-4.saas-linux-medium-amd64.runners-manager.gitlab.com/default Yy-Tzs3Q, system ID: s_57a32fe7e1c1 Resolving secrets section_start:1742530736:prepare_executor Preparing the "docker+machine" executor Using Docker executor with image registry.gitlab.com/rdatatable/dockerfiles/r-3.3.0 ... Authenticating with credentials from job payload (GitLab Registry) Pulling docker image registry.gitlab.com/rdatatable/dockerfiles/r-3.3.0 ... Using docker image sha256:c24bfe2f3c8a7897d8f61c459b3baa9ff7f1d3b6fe37751afa1ea7a3147b055d for registry.gitlab.com/rdatatable/dockerfiles/r-3.3.0 with digest registry.gitlab.com/rdatatable/dockerfiles/r-3.3.0@sha256:6c3a4201737aa9bc6ad0d12b1e3682a0807dfd371ccff82f4eb3258590eaecce ... section_end:1742530770:prepare_executor section_start:1742530770:prepare_script Preparing environment Running on runner-yy-tzs3q-project-3622566-concurrent-0 via runner-yy-tzs3q-s-l-m-amd64-1742530653-65e9ad6c... section_end:1742530779:prepare_script section_start:1742530779:get_sources Getting source from Git repository Fetching changes... Initialized empty Git repository in /builds/Rdatatable/data.table/.git/ Created fresh repository. Checking out 09090480 as detached HEAD (ref is master)... Skipping Git submodules setup $ git remote set-url origin "${CI_REPOSITORY_URL}" section_end:1742530785:get_sources section_start:1742530785:download_artifacts Downloading artifacts Downloading artifacts for build (9478998722)... Downloading artifacts from coordinator... ok  host=storage.googleapis.com id=9478998722 responseStatus=200 OK token=66_y-TTBx Downloading artifacts for mirror-packages (9478998713)... Downloading artifacts from coordinator... ok  host=storage.googleapis.com id=9478998713 responseStatus=200 OK token=66_y-TTBx section_end:1742530787:download_artifacts section_start:1742530787:step_script Executing "step_script" stage of the job script Using docker image sha256:c24bfe2f3c8a7897d8f61c459b3baa9ff7f1d3b6fe37751afa1ea7a3147b055d for registry.gitlab.com/rdatatable/dockerfiles/r-3.3.0 with digest registry.gitlab.com/rdatatable/dockerfiles/r-3.3.0@sha256:6c3a4201737aa9bc6ad0d12b1e3682a0807dfd371ccff82f4eb3258590eaecce ... $ cp $(ls -1t bus/build/data.table_*.tar.gz | head -n 1) . $ mkdir -p ~/.R $ 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’, ‘commonmark’, ‘xfun’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: packages ‘bit64’, ‘bit’, ‘xts’, ‘knitr’ are not available (for R version 3.3.0) $ R CMD check --no-manual --no-build-vignettes --ignore-vignettes $(ls -1t data.table_*.tar.gz | head -n 1) * using log directory ‘/builds/Rdatatable/data.table/data.table.Rcheck’ * using R version 3.3.0 (2016-05-03) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-manual --ignore-vignettes’ * checking for file ‘data.table/DESCRIPTION’ ... OK * this is package ‘data.table’ version ‘1.17.99’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Packages suggested but not available for checking: ‘bit64’ ‘bit’ ‘xts’ ‘knitr’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘data.table’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: libs 2.0Mb po 1.6Mb tests 1.9Mb * checking package 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 R 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 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 cross-references ... WARNING Unknown package ‘bit64’ in Rd xrefs * 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 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 compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... SKIPPED * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘autoprint.R’ Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ...17,20d16 < a < < 1: 1 < 2: 3 27,30d22 < a < < 1: 1 < 2: 3 32,36d23 < Index: < a < < 1: 1 < 2: 3 38,42d24 < Index: < a < < 1: 1 < 2: 3 60,63d41 < a < < 1: 1 < 2: 5 65,68d42 < a < < 1: 1 < 2: 6 72,75d45 < a < < 1: 1 < 2: 5 142,144d111 < a < < 1: 9 150,153d116 < a < < 1: 10 < 2: 10 155,158d117 < a < < 1: 10 < 2: 10 160,163d118 < a < < 1: 10 < 2: 10 209,214d163 < x y < < 1: 1 1 < Warning message: < In `[.data.table`(dt, , `:=`(y, 1)) : < A shallow copy of this data.table was taken so that := can add or remove 1 columns by reference. At an earlier point, this data.table was copied by R (or was created manually using structure() or similar). Avoid names<- and attr<- which in R currently (and oddly) may copy the whole data.table. Use set* syntax instead to avoid copying: ?set, ?setnames and ?setattr. It's also not unusual for data.table-agnostic packages to produce tables affected by this issue. If this message doesn't help, please report your use case to the data.table issue tracker so the root cause can be fixed or this message improved. 219a169,184 > > if (TRUE) withAutoprint({ > + DT # yes > + DT[1L, 1L] # yes > + DT[2L, a := 10L] # no > + }) > > DT > a > > 1: 10 > 2: 10 > > DT[1L, 1L] > a > > 1: 10 > > DT[2L, `:=`(a, 10L)] > > Running ‘froll.R’ Running ‘knitr.R’ Comparing ‘knitr.Rout’ to ‘knitr.Rout.save’ ... OK Running ‘main.R’ Running ‘nafill.R’ Running ‘other.R’ Running ‘programming.R’ Running ‘S4.R’ Running ‘types.R’ OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/builds/Rdatatable/data.table/data.table.Rcheck/00check.log’ for details. section_end:1742530887:step_script section_start:1742530887: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:1742530887:after_script section_start:1742530887:upload_artifacts_on_success Uploading artifacts for successful job Uploading artifacts... bus/test-lin-ancient-cran: found 635 matching artifact files and directories Uploading artifacts as "archive" to coordinator... 201 Created id=9478998902 responseStatus=201 Created token=66_y-TTBx section_end:1742530891:upload_artifacts_on_success section_start:1742530891:cleanup_file_variables Cleaning up project directory and file based variables section_end:1742530891:cleanup_file_variables Job succeeded