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1Running with gitlab-runner 17.5.3 (12030cf4)
2 on shared-runner 3bec7447, system ID: r_kwcfy97npBfq
3 feature flags: FF_USE_ADVANCED_POD_SPEC_CONFIGURATION:true
4Resolving secrets
5 Preparing the "kubernetes" executor 00:00
6Using Kubernetes namespace: gitlab-dynprov
7Using Kubernetes executor with image rocker/rstudio ...
8Using attach strategy to execute scripts...
9 Preparing environment 00:03
10Using FF_USE_POD_ACTIVE_DEADLINE_SECONDS, the Pod activeDeadlineSeconds will be set to the job timeout: 1h0m0s...
11WARNING: Advanced Pod Spec configuration enabled, merging the provided PodSpec to the generated one. This is a beta feature and is subject to change. Feedback is collected in this issue: https://gitlab.com/gitlab-org/gitlab-runner/-/issues/29659 ...
12Waiting for pod gitlab-dynprov/runner-3bec7447-project-45400-concurrent-0-y7ebtrsu to be running, status is Pending
13Running on runner-3bec7447-project-45400-concurrent-0-y7ebtrsu via shared-ci-gitlab-runner-776c85dbb4-dz6l9...
14 Getting source from Git repository 00:02
15Fetching changes with git depth set to 20...
16Initialized empty Git repository in /builds/liume102/Advanced_R_Group_Cooperation/.git/
17Created fresh repository.
18Checking out 13cf53bd as detached HEAD (ref is master)...
19Skipping Git submodules setup
20 Executing "step_script" stage of the job script 03:39
21$ Rscript -e 'install.packages("remotes")'
22Installing package into ‘/usr/local/lib/R/site-library’
23(as ‘lib’ is unspecified)
24trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/remotes_2.5.0.tar.gz'
25Content type 'binary/octet-stream' length 436043 bytes (425 KB)
26==================================================
27downloaded 425 KB
28* installing *binary* package ‘remotes’ ...
29* DONE (remotes)
30The downloaded source packages are in
31 ‘/tmp/RtmpfVaZYZ/downloaded_packages’
32$ Rscript -e 'install.packages("devtools")'
33Installing package into ‘/usr/local/lib/R/site-library’
34(as ‘lib’ is unspecified)
35also installing the dependencies ‘Rcpp’, ‘utf8’, ‘askpass’, ‘credentials’, ‘sys’, ‘zip’, ‘gitcreds’, ‘ini’, ‘fastmap’, ‘httpuv’, ‘mime’, ‘xtable’, ‘sourcetools’, ‘later’, ‘promises’, ‘base64enc’, ‘jquerylib’, ‘sass’, ‘fansi’, ‘systemfonts’, ‘textshaping’, ‘tinytex’, ‘xfun’, ‘pillar’, ‘pkgconfig’, ‘highr’, ‘diffobj’, ‘clipr’, ‘crayon’, ‘curl’, ‘gert’, ‘gh’, ‘glue’, ‘jsonlite’, ‘purrr’, ‘rappdirs’, ‘rprojroot’, ‘rstudioapi’, ‘whisker’, ‘yaml’, ‘R6’, ‘cachem’, ‘shiny’, ‘htmltools’, ‘callr’, ‘processx’, ‘bslib’, ‘digest’, ‘downlit’, ‘fontawesome’, ‘httr2’, ‘openssl’, ‘ragg’, ‘rmarkdown’, ‘tibble’, ‘xml2’, ‘htmlwidgets’, ‘vctrs’, ‘prettyunits’, ‘xopen’, ‘brew’, ‘commonmark’, ‘knitr’, ‘stringi’, ‘stringr’, ‘cpp11’, ‘brio’, ‘evaluate’, ‘magrittr’, ‘praise’, ‘ps’, ‘waldo’, ‘usethis’, ‘cli’, ‘desc’, ‘ellipsis’, ‘fs’, ‘lifecycle’, ‘memoise’, ‘miniUI’, ‘pkgbuild’, ‘pkgdown’, ‘pkgload’, ‘profvis’, ‘rcmdcheck’, ‘rlang’, ‘roxygen2’, ‘rversions’, ‘sessioninfo’, ‘testthat’, ‘urlchecker’, ‘withr’
36trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/Rcpp_1.0.13-1.tar.gz'
37Content type 'binary/octet-stream' length 2164251 bytes (2.1 MB)
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40trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/utf8_1.2.4.tar.gz'
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44trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/askpass_1.2.1.tar.gz'
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48trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/credentials_2.0.2.tar.gz'
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52trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/sys_3.4.3.tar.gz'
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56trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/zip_2.3.1.tar.gz'
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60trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/gitcreds_0.1.2.tar.gz'
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64trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/ini_0.3.1.tar.gz'
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68trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/fastmap_1.2.0.tar.gz'
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72trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/httpuv_1.6.15.tar.gz'
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76trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/mime_0.12.tar.gz'
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80trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/xtable_1.8-4.tar.gz'
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84trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/sourcetools_0.1.7-1.tar.gz'
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88trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/later_1.3.2.tar.gz'
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92trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/promises_1.3.0.tar.gz'
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96trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/base64enc_0.1-3.tar.gz'
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100trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/jquerylib_0.1.4.tar.gz'
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104trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/sass_0.4.9.tar.gz'
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108trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/fansi_1.0.6.tar.gz'
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112trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/systemfonts_1.1.0.tar.gz'
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116trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/textshaping_0.4.0.tar.gz'
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128trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/pillar_1.9.0.tar.gz'
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132trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/pkgconfig_2.0.3.tar.gz'
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140trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/diffobj_0.3.5.tar.gz'
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144trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/clipr_0.8.0.tar.gz'
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148trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/crayon_1.5.3.tar.gz'
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152trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/curl_6.0.0.tar.gz'
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156trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/gert_2.1.4.tar.gz'
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160trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/gh_1.4.1.tar.gz'
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164trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/glue_1.8.0.tar.gz'
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168trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/jsonlite_1.8.9.tar.gz'
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172trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/purrr_1.0.2.tar.gz'
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176trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/rappdirs_0.3.3.tar.gz'
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180trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/rprojroot_2.0.4.tar.gz'
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184trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/rstudioapi_0.17.1.tar.gz'
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188trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/whisker_0.4.1.tar.gz'
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192trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/yaml_2.3.10.tar.gz'
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196trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/R6_2.5.1.tar.gz'
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200trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/cachem_1.1.0.tar.gz'
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204trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/shiny_1.9.1.tar.gz'
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208trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/htmltools_0.5.8.1.tar.gz'
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232trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/fontawesome_0.5.2.tar.gz'
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397Content type 'binary/octet-stream' length 34030 bytes (33 KB)
398==================================================
399downloaded 33 KB
400trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/withr_3.0.2.tar.gz'
401Content type 'binary/octet-stream' length 223690 bytes (218 KB)
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403downloaded 218 KB
404trying URL 'https://p3m.dev/cran/__linux__/jammy/latest/src/contrib/devtools_2.4.5.tar.gz'
405Content type 'binary/octet-stream' length 435688 bytes (425 KB)
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407downloaded 425 KB
408* installing *binary* package ‘Rcpp’ ...
409* DONE (Rcpp)
410* installing *binary* package ‘utf8’ ...
411* DONE (utf8)
412* installing *binary* package ‘sys’ ...
413* DONE (sys)
414* installing *binary* package ‘zip’ ...
415* DONE (zip)
416* installing *binary* package ‘gitcreds’ ...
417* DONE (gitcreds)
418* installing *binary* package ‘ini’ ...
419* DONE (ini)
420* installing *binary* package ‘fastmap’ ...
421* DONE (fastmap)
422* installing *binary* package ‘mime’ ...
423* DONE (mime)
424* installing *binary* package ‘xtable’ ...
425* DONE (xtable)
426* installing *binary* package ‘sourcetools’ ...
427* DONE (sourcetools)
428* installing *binary* package ‘base64enc’ ...
429* DONE (base64enc)
430* installing *binary* package ‘fansi’ ...
431* DONE (fansi)
432* installing *binary* package ‘xfun’ ...
433* DONE (xfun)
434* installing *binary* package ‘pkgconfig’ ...
435* DONE (pkgconfig)
436* installing *binary* package ‘clipr’ ...
437* DONE (clipr)
438* installing *binary* package ‘crayon’ ...
439* DONE (crayon)
440* installing *binary* package ‘curl’ ...
441* DONE (curl)
442* installing *binary* package ‘glue’ ...
443* DONE (glue)
444* installing *binary* package ‘jsonlite’ ...
445* DONE (jsonlite)
446* installing *binary* package ‘rappdirs’ ...
447* DONE (rappdirs)
448* installing *binary* package ‘rprojroot’ ...
449* DONE (rprojroot)
450* installing *binary* package ‘rstudioapi’ ...
451* DONE (rstudioapi)
452* installing *binary* package ‘whisker’ ...
453* DONE (whisker)
454* installing *binary* package ‘yaml’ ...
455* DONE (yaml)
456* installing *binary* package ‘R6’ ...
457* DONE (R6)
458* installing *binary* package ‘digest’ ...
459* DONE (digest)
460* installing *binary* package ‘prettyunits’ ...
461* DONE (prettyunits)
462* installing *binary* package ‘brew’ ...
463* DONE (brew)
464* installing *binary* package ‘commonmark’ ...
465* DONE (commonmark)
466* installing *binary* package ‘stringi’ ...
467* DONE (stringi)
468* installing *binary* package ‘cpp11’ ...
469* DONE (cpp11)
470* installing *binary* package ‘brio’ ...
471* DONE (brio)
472* installing *binary* package ‘evaluate’ ...
473* DONE (evaluate)
474* installing *binary* package ‘magrittr’ ...
475* DONE (magrittr)
476* installing *binary* package ‘praise’ ...
477* DONE (praise)
478* installing *binary* package ‘ps’ ...
479* DONE (ps)
480* installing *binary* package ‘cli’ ...
481* DONE (cli)
482* installing *binary* package ‘fs’ ...
483* DONE (fs)
484* installing *binary* package ‘rlang’ ...
485* DONE (rlang)
486* installing *binary* package ‘withr’ ...
487* DONE (withr)
488* installing *binary* package ‘askpass’ ...
489* DONE (askpass)
490* installing *binary* package ‘later’ ...
491* DONE (later)
492* installing *binary* package ‘tinytex’ ...
493* DONE (tinytex)
494* installing *binary* package ‘highr’ ...
495* DONE (highr)
496* installing *binary* package ‘diffobj’ ...
497* DONE (diffobj)
498* installing *binary* package ‘cachem’ ...
499* DONE (cachem)
500* installing *binary* package ‘htmltools’ ...
501* DONE (htmltools)
502* installing *binary* package ‘processx’ ...
503* DONE (processx)
504* installing *binary* package ‘xml2’ ...
505* DONE (xml2)
506* installing *binary* package ‘desc’ ...
507* DONE (desc)
508* installing *binary* package ‘ellipsis’ ...
509* DONE (ellipsis)
510* installing *binary* package ‘lifecycle’ ...
511* DONE (lifecycle)
512* installing *binary* package ‘sessioninfo’ ...
513* DONE (sessioninfo)
514* installing *binary* package ‘promises’ ...
515* DONE (promises)
516* installing *binary* package ‘jquerylib’ ...
517* DONE (jquerylib)
518* installing *binary* package ‘sass’ ...
519* DONE (sass)
520* installing *binary* package ‘systemfonts’ ...
521* DONE (systemfonts)
522* installing *binary* package ‘callr’ ...
523* DONE (callr)
524* installing *binary* package ‘fontawesome’ ...
525* DONE (fontawesome)
526* installing *binary* package ‘openssl’ ...
527* DONE (openssl)
528* installing *binary* package ‘vctrs’ ...
529* DONE (vctrs)
530* installing *binary* package ‘xopen’ ...
531* DONE (xopen)
532* installing *binary* package ‘knitr’ ...
533* DONE (knitr)
534* installing *binary* package ‘waldo’ ...
535* DONE (waldo)
536* installing *binary* package ‘memoise’ ...
537* DONE (memoise)
538* installing *binary* package ‘rversions’ ...
539* DONE (rversions)
540* installing *binary* package ‘urlchecker’ ...
541* DONE (urlchecker)
542* installing *binary* package ‘credentials’ ...
543* DONE (credentials)
544* installing *binary* package ‘httpuv’ ...
545* DONE (httpuv)
546* installing *binary* package ‘textshaping’ ...
547* DONE (textshaping)
548* installing *binary* package ‘pillar’ ...
549* DONE (pillar)
550* installing *binary* package ‘purrr’ ...
551* DONE (purrr)
552* installing *binary* package ‘bslib’ ...
553* DONE (bslib)
554* installing *binary* package ‘downlit’ ...
555* DONE (downlit)
556* installing *binary* package ‘httr2’ ...
557* DONE (httr2)
558* installing *binary* package ‘stringr’ ...
559* DONE (stringr)
560* installing *binary* package ‘pkgbuild’ ...
561* DONE (pkgbuild)
562* installing *binary* package ‘gert’ ...
563* DONE (gert)
564* installing *binary* package ‘gh’ ...
565* DONE (gh)
566* installing *binary* package ‘shiny’ ...
567* DONE (shiny)
568* installing *binary* package ‘ragg’ ...
569* DONE (ragg)
570* installing *binary* package ‘rmarkdown’ ...
571* DONE (rmarkdown)
572* installing *binary* package ‘tibble’ ...
573* DONE (tibble)
574* installing *binary* package ‘pkgload’ ...
575* DONE (pkgload)
576* installing *binary* package ‘rcmdcheck’ ...
577* DONE (rcmdcheck)
578* installing *binary* package ‘htmlwidgets’ ...
579* DONE (htmlwidgets)
580* installing *binary* package ‘usethis’ ...
581* DONE (usethis)
582* installing *binary* package ‘miniUI’ ...
583* DONE (miniUI)
584* installing *binary* package ‘pkgdown’ ...
585* DONE (pkgdown)
586* installing *binary* package ‘roxygen2’ ...
587* DONE (roxygen2)
588* installing *binary* package ‘testthat’ ...
589* DONE (testthat)
590* installing *binary* package ‘profvis’ ...
591* DONE (profvis)
592* installing *binary* package ‘devtools’ ...
593* DONE (devtools)
594The downloaded source packages are in
595 ‘/tmp/RtmpMgO6UI/downloaded_packages’
596$ R -e "remotes::install_deps(dependencies = TRUE)"
597R version 4.4.1 (2024-06-14) -- "Race for Your Life"
598Copyright (C) 2024 The R Foundation for Statistical Computing
599Platform: x86_64-pc-linux-gnu
600R is free software and comes with ABSOLUTELY NO WARRANTY.
601You are welcome to redistribute it under certain conditions.
602Type 'license()' or 'licence()' for distribution details.
603 Natural language support but running in an English locale
604R is a collaborative project with many contributors.
605Type 'contributors()' for more information and
606'citation()' on how to cite R or R packages in publications.
607Type 'demo()' for some demos, 'help()' for on-line help, or
608'help.start()' for an HTML browser interface to help.
609Type 'q()' to quit R.
610> remotes::install_deps(dependencies = TRUE)
611>
612>
613$ R -e 'devtools::check()'
614R version 4.4.1 (2024-06-14) -- "Race for Your Life"
615Copyright (C) 2024 The R Foundation for Statistical Computing
616Platform: x86_64-pc-linux-gnu
617R is free software and comes with ABSOLUTELY NO WARRANTY.
618You are welcome to redistribute it under certain conditions.
619Type 'license()' or 'licence()' for distribution details.
620 Natural language support but running in an English locale
621R is a collaborative project with many contributors.
622Type 'contributors()' for more information and
623'citation()' on how to cite R or R packages in publications.
624Type 'demo()' for some demos, 'help()' for on-line help, or
625'help.start()' for an HTML browser interface to help.
626Type 'q()' to quit R.
627> devtools::check()
628══ Documenting ═════════════════════════════════════════════════════════════════
629ℹ Updating lab documentation
630ℹ Loading lab
631══ Building ════════════════════════════════════════════════════════════════════
632Setting env vars:
633• CFLAGS : -Wall -pedantic
634• CXXFLAGS : -Wall -pedantic
635• CXX11FLAGS: -Wall -pedantic
636• CXX14FLAGS: -Wall -pedantic
637• CXX17FLAGS: -Wall -pedantic
638• CXX20FLAGS: -Wall -pedantic
639── R CMD build ─────────────────────────────────────────────────────────────────
640* checking for file ‘/builds/liume102/Advanced_R_Group_Cooperation/DESCRIPTION’ ... OK
641* preparing ‘lab’:
642* checking DESCRIPTION meta-information ... OK
643* checking for LF line-endings in source and make files and shell scripts
644* checking for empty or unneeded directories
645Removed empty directory ‘lab/data-raw’
646* building ‘lab_1.0.tar.gz’
647══ Checking ════════════════════════════════════════════════════════════════════
648Setting env vars:
649• _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
650• _R_CHECK_CRAN_INCOMING_ : FALSE
651• _R_CHECK_FORCE_SUGGESTS_ : FALSE
652• _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
653• NOT_CRAN : true
654── R CMD check ─────────────────────────────────────────────────────────────────
655* using log directory ‘/tmp/RtmpZfXcJg/file124370dedaa8/lab.Rcheck’
656* using R version 4.4.1 (2024-06-14)
657* using platform: x86_64-pc-linux-gnu
658* R was compiled by
659 gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
660 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
661* running under: Ubuntu 22.04.4 LTS
662* using session charset: UTF-8
663* using options ‘--no-manual --as-cran’
664* checking for file ‘lab/DESCRIPTION’ ... OK
665* checking extension type ... Package
666* this is package ‘lab’ version ‘1.0’
667* package encoding: UTF-8
668* checking package namespace information ... OK
669* checking package dependencies ... OK
670* checking if this is a source package ... OK
671* checking if there is a namespace ... OK
672* checking for executable files ... OK
673* checking for hidden files and directories ... NOTE
674Found the following hidden files and directories:
675 .gitlab-ci.yml
676These were most likely included in error. See section ‘Package
677structure’ in the ‘Writing R Extensions’ manual.
678* checking for portable file names ... OK
679* checking for sufficient/correct file permissions ... OK
680* checking serialization versions ... OK
681* checking whether package ‘lab’ can be installed ... OK
682* checking installed package size ... OK
683* checking package directory ... OK
684* checking for future file timestamps ... NOTE
685unable to verify current time
686* checking DESCRIPTION meta-information ... OK
687* checking top-level files ... NOTE
688Non-standard file/directory found at top level:
689 ‘READMD.Rmd’
690* checking for left-over files ... OK
691* checking index information ... OK
692* checking package subdirectories ... OK
693* checking code files for non-ASCII characters ... OK
694* checking R files for syntax errors ... OK
695* checking whether the package can be loaded ... OK
696* checking whether the package can be loaded with stated dependencies ... OK
697* checking whether the package can be unloaded cleanly ... OK
698* checking whether the namespace can be loaded with stated dependencies ... OK
699* checking whether the namespace can be unloaded cleanly ... OK
700* checking loading without being on the library search path ... OK
701* checking dependencies in R code ... OK
702* checking S3 generic/method consistency ... OK
703* checking replacement functions ... OK
704* checking foreign function calls ... OK
705* checking R code for possible problems ... OK
706* checking Rd files ... OK
707* checking Rd metadata ... OK
708* checking Rd line widths ... OK
709* checking Rd cross-references ... OK
710* checking for missing documentation entries ... OK
711* checking for code/documentation mismatches ... OK
712* checking Rd \usage sections ... OK
713* checking Rd contents ... OK
714* checking for unstated dependencies in examples ... OK
715* checking contents of ‘data’ directory ... OK
716* checking data for non-ASCII characters ... OK
717* checking LazyData ... OK
718* checking data for ASCII and uncompressed saves ... OK
719* checking examples ... OK
720* checking for unstated dependencies in ‘tests’ ... OK
721* checking tests ...
722 Running ‘testthat.R’
723 OK
724* checking for non-standard things in the check directory ... OK
725* checking for detritus in the temp directory ... OK
726* DONE
727Status: 3 NOTEs
728See
729 ‘/tmp/RtmpZfXcJg/file124370dedaa8/lab.Rcheck/00check.log’
730for details.
731── R CMD check results ──────────────────────────────────────────── lab 1.0 ────
732Duration: 32s
733❯ checking for hidden files and directories ... NOTE
734 Found the following hidden files and directories:
735 .gitlab-ci.yml
736 These were most likely included in error. See section ‘Package
737 structure’ in the ‘Writing R Extensions’ manual.
738❯ checking for future file timestamps ... NOTE
739 unable to verify current time
740❯ checking top-level files ... NOTE
741 Non-standard file/directory found at top level:
742 ‘READMD.Rmd’
7430 errors ✔ | 0 warnings ✔ | 3 notes ✖
744>
745>
746 Cleaning up project directory and file based variables 00:01
747Job succeeded