R Under development (unstable) (2024-06-07 r86704 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > test_check("geoflow") Loading required package: geoflow Loading ISO 19139 XML schemas... Loading ISO 19115 codelists... Session info ==================================================================================================== R Under development (unstable) (2024-06-07 r86704 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default locale: [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=C LC_NUMERIC=C [5] LC_TIME=C time zone: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] geoflow_1.0.0 testthat_3.2.1.1 loaded via a namespace (and not attached): [1] ocs4R_0.2-3 xfun_0.44 dotenv_1.0.3 [4] rdflib_0.2.8 gargle_1.5.2 tzdb_0.4.0 [7] vctrs_0.6.5 tools_4.5.0 generics_0.1.3 [10] curl_5.2.1 parallel_4.5.0 tibble_3.2.1 [13] proxy_0.4-27 geometa_0.8-0 fansi_1.0.6 [16] geonapi_0.7-2 pkgconfig_2.0.3 KernSmooth_2.23-24 [19] desc_1.4.3 redland_1.0.17-18 assertthat_0.2.1 [22] uuid_1.2-0 lifecycle_1.0.4 compiler_4.5.0 [25] atom4R_0.3-3 stringr_1.5.1 brio_1.1.5 [28] terra_1.7-78 datapack_1.4.1 keyring_1.3.2 [31] codetools_0.2-20 class_7.3-22 tidyr_1.3.1 [34] pillar_1.9.0 crayon_1.5.2 whisker_0.4.1 [37] openssl_2.2.0 classInt_0.4-10 zen4R_0.10 [40] mime_0.12 digest_0.6.35 tidyselect_1.2.1 [43] zip_2.3.1 stringi_1.8.4 geonode4R_0.1-1 [46] sf_1.0-16 dplyr_1.1.4 purrr_1.0.2 [49] grid_4.5.0 cli_3.6.2 geosapi_0.7-1 [52] magrittr_2.0.3 base64enc_0.1-3 XML_3.99-0.16.1 [55] utf8_1.2.4 e1071_1.7-14 withr_3.0.0 [58] readr_2.1.5 waldo_0.5.2 bit64_4.0.5 [61] googledrive_2.1.1 roxygen2_7.3.1 httr_1.4.7 [64] bit_4.0.5 askpass_1.2.0 png_0.1-8 [67] hms_1.1.3 parsedate_1.3.1 knitr_1.47 [70] thredds_0.1-4 dataone_2.2.2 rlang_1.1.4 [73] Rcpp_1.0.12 glue_1.7.0 DBI_1.2.3 [76] ows4R_0.3-6 xml2_1.3.6 vroom_1.6.5 [79] jsonlite_1.8.8 d4storagehub4R_0.4-4 R6_2.5.1 [82] plyr_1.8.9 fs_1.6.4 units_0.8-5 ==================================================================================================== Workflow initialization ==================================================================================================== [geoflow][my-workflow][INFO] Init Workflow configuration [geoflow][my-workflow][INFO] Workflow job directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171052 [geoflow][my-workflow][INFO] Creating workflow profile... [geoflow][my-workflow][INFO] Workflow ID: my-workflow [geoflow][my-workflow][INFO] Workflow name: My workflow [geoflow][my-workflow][INFO] Workflow project: Test geoflow project [geoflow][my-workflow][INFO] Workflow organization: My organization [geoflow][my-workflow][INFO] Setting geoflow global options... [geoflow][my-workflow][INFO] Loading metadata elements... [geoflow][my-workflow][INFO] Loading metadata contacts... [geoflow][my-workflow][INFO] Loading metadata contacts from 'https://docs.google.com/spreadsheets/d/1BqlXwA2fKiRuozNAQhBb_PbQVSPTCfl8_Q9rfM8E2ws/edit?usp=sharing' [with 'gsheet' handler]... [geoflow][my-workflow][INFO] Try to use embedded contacts handler [geoflow][my-workflow][INFO] Execute contact handler to load contacts... [geoflow][my-workflow][INFO] Validating contacts [geoflow][my-workflow][INFO] No validation issue detected! [geoflow][my-workflow][INFO] Parsing 4 contacts from tabular source [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][INFO] Successfuly fetched 4 contacts! [geoflow][my-workflow][INFO] Successfuly loaded 4 contacts! [geoflow][my-workflow][INFO] Loading metadata entities... [geoflow][my-workflow][INFO] Loading metadata entities from 'https://docs.google.com/spreadsheets/d/1KSc_IrM86GrNpUASCIVfq6L9cmML77iwpcSbliynYZk/edit?usp=sharing' [with 'gsheet' handler]... [geoflow][my-workflow][INFO] Try to use embedded entities handler [geoflow][my-workflow][INFO] Execute handler to load entities... [geoflow][my-workflow][INFO] Validating entities [geoflow][my-workflow][INFO] Validation issues --> row col type 1 1 Identifier WARNING 2 1 Subject WARNING 3 1 Date WARNING 4 2 Identifier WARNING 5 2 Subject WARNING 6 2 Date WARNING 7 2 Type WARNING message 1 Key is omitted, default key 'id' will be applied 2 Keyword topic's 'taxonomy' is not a recognized ISO keyword topic. 3 key 'edition' is not a recognized ISO date key. 4 Key is omitted, default key 'id' will be applied 5 Keyword topic's 'taxonomy' is not a recognized ISO keyword topic. 6 key 'edition' is not a recognized ISO date key. 7 Key is omitted, default key 'generic' will be applied [geoflow][my-workflow][INFO] Parsing 2 entities from tabular source [geoflow][my-workflow][INFO] Parsing entity 1 [geoflow][my-workflow][INFO] Parsing entity 2 [geoflow][my-workflow][INFO] Successfuly fetched 2 entities! [geoflow][my-workflow][INFO] Enrich metadata entities from directory of contacts [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] geoflow [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] geoflow [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] Successfuly loaded 2 entities! Session info ==================================================================================================== R Under development (unstable) (2024-06-07 r86704 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default locale: [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=C LC_NUMERIC=C [5] LC_TIME=C time zone: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] geoflow_1.0.0 testthat_3.2.1.1 loaded via a namespace (and not attached): [1] ocs4R_0.2-3 xfun_0.44 dotenv_1.0.3 [4] rdflib_0.2.8 gargle_1.5.2 tzdb_0.4.0 [7] vctrs_0.6.5 tools_4.5.0 generics_0.1.3 [10] curl_5.2.1 parallel_4.5.0 tibble_3.2.1 [13] proxy_0.4-27 geometa_0.8-0 fansi_1.0.6 [16] geonapi_0.7-2 pkgconfig_2.0.3 KernSmooth_2.23-24 [19] desc_1.4.3 redland_1.0.17-18 assertthat_0.2.1 [22] uuid_1.2-0 lifecycle_1.0.4 compiler_4.5.0 [25] atom4R_0.3-3 stringr_1.5.1 brio_1.1.5 [28] terra_1.7-78 datapack_1.4.1 keyring_1.3.2 [31] codetools_0.2-20 class_7.3-22 tidyr_1.3.1 [34] pillar_1.9.0 crayon_1.5.2 whisker_0.4.1 [37] openssl_2.2.0 classInt_0.4-10 zen4R_0.10 [40] mime_0.12 digest_0.6.35 tidyselect_1.2.1 [43] zip_2.3.1 stringi_1.8.4 geonode4R_0.1-1 [46] sf_1.0-16 dplyr_1.1.4 purrr_1.0.2 [49] grid_4.5.0 cli_3.6.2 geosapi_0.7-1 [52] magrittr_2.0.3 base64enc_0.1-3 XML_3.99-0.16.1 [55] utf8_1.2.4 e1071_1.7-14 withr_3.0.0 [58] readr_2.1.5 waldo_0.5.2 bit64_4.0.5 [61] googledrive_2.1.1 roxygen2_7.3.1 httr_1.4.7 [64] bit_4.0.5 askpass_1.2.0 png_0.1-8 [67] hms_1.1.3 gsheet_0.4.5 parsedate_1.3.1 [70] knitr_1.47 thredds_0.1-4 dataone_2.2.2 [73] rlang_1.1.4 Rcpp_1.0.12 glue_1.7.0 [76] DBI_1.2.3 ows4R_0.3-6 xml2_1.3.6 [79] vroom_1.6.5 jsonlite_1.8.8 d4storagehub4R_0.4-4 [82] R6_2.5.1 plyr_1.8.9 fs_1.6.4 [85] units_0.8-5 ==================================================================================================== Workflow initialization ==================================================================================================== [geoflow][my-workflow][INFO] Init Workflow configuration [geoflow][my-workflow][INFO] Workflow job directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171108 [geoflow][my-workflow][INFO] Creating workflow profile... [geoflow][my-workflow][INFO] Workflow ID: my-workflow [geoflow][my-workflow][INFO] Workflow name: My workflow [geoflow][my-workflow][INFO] Workflow project: Test geoflow project [geoflow][my-workflow][INFO] Workflow organization: My organization [geoflow][my-workflow][INFO] Setting geoflow global options... [geoflow][my-workflow][INFO] Loading metadata elements... [geoflow][my-workflow][INFO] Loading metadata contacts... [geoflow][my-workflow][INFO] Loading metadata contacts from 'https://docs.google.com/spreadsheets/d/1BqlXwA2fKiRuozNAQhBb_PbQVSPTCfl8_Q9rfM8E2ws/edit?usp=sharing' [with 'gsheet' handler]... [geoflow][my-workflow][INFO] Try to use embedded contacts handler [geoflow][my-workflow][INFO] Execute contact handler to load contacts... [geoflow][my-workflow][INFO] Validating contacts [geoflow][my-workflow][INFO] No validation issue detected! [geoflow][my-workflow][INFO] Parsing 4 contacts from tabular source [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][INFO] Successfuly fetched 4 contacts! [geoflow][my-workflow][INFO] Successfuly loaded 4 contacts! [geoflow][my-workflow][INFO] Loading metadata entities... [geoflow][my-workflow][INFO] Loading metadata entities from 'https://docs.google.com/spreadsheets/d/1KSc_IrM86GrNpUASCIVfq6L9cmML77iwpcSbliynYZk/edit?usp=sharing' [with 'gsheet' handler]... [geoflow][my-workflow][INFO] Try to use embedded entities handler [geoflow][my-workflow][INFO] Execute handler to load entities... [geoflow][my-workflow][INFO] Validating entities [geoflow][my-workflow][INFO] Validation issues --> row col type 1 1 Identifier WARNING 2 1 Subject WARNING 3 1 Date WARNING 4 2 Identifier WARNING 5 2 Subject WARNING 6 2 Date WARNING 7 2 Type WARNING message 1 Key is omitted, default key 'id' will be applied 2 Keyword topic's 'taxonomy' is not a recognized ISO keyword topic. 3 key 'edition' is not a recognized ISO date key. 4 Key is omitted, default key 'id' will be applied 5 Keyword topic's 'taxonomy' is not a recognized ISO keyword topic. 6 key 'edition' is not a recognized ISO date key. 7 Key is omitted, default key 'generic' will be applied [geoflow][my-workflow][INFO] Parsing 2 entities from tabular source [geoflow][my-workflow][INFO] Parsing entity 1 [geoflow][my-workflow][INFO] Parsing entity 2 [geoflow][my-workflow][INFO] Successfuly fetched 2 entities! [geoflow][my-workflow][INFO] Enrich metadata entities from directory of contacts [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] geoflow [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] geoflow [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] Successfuly loaded 2 entities! [geoflow][my-workflow][INFO] Create entity job dir at 'D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171108/entities/my-geoflow-record' [geoflow][my-workflow][INFO] Creating 'data' directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171108/entities/my-geoflow-record/data [geoflow][my-workflow][INFO] Creating 'metadata' directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171108/entities/my-geoflow-record/metadata [geoflow][my-workflow][INFO] Entity working directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171108/entities/my-geoflow-record [geoflow][my-workflow][INFO] SkipDataDownload is false: copying and fetching data... [geoflow][my-workflow][INFO] Copying data to entity job data directory 'D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171108/entities/my-geoflow-record/data' [geoflow][my-workflow][INFO] Copying data source 1 'README.md' (https://raw.githubusercontent.com/eblondel/zen4R/master/README.md) to entity job data directory 'D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171108/entities/my-geoflow-record/data' [geoflow][my-workflow][INFO] Copying data to job data directory from remote file(s) using accessor 'default' [geoflow][INFO] Default HTTP(S) data accessor: Download data 'README.md' from 'https://raw.githubusercontent.com/eblondel/zen4R/master/README.md' to 'D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171108/entities/my-geoflow-record/data/README.md' trying URL 'https://raw.githubusercontent.com/eblondel/zen4R/master/README.md' Content type 'text/plain; charset=utf-8' length 2134 bytes ================================================== downloaded 2134 bytes trying URL 'https://raw.githubusercontent.com/eblondel/zen4R/master/README.md' Content type 'text/plain; charset=utf-8' length 2134 bytes ================================================== downloaded 2134 bytes trying URL 'https://raw.githubusercontent.com/eblondel/zen4R/master/README.md' Content type 'text/plain; charset=utf-8' length 2134 bytes ================================================== downloaded 2134 bytes Session info ==================================================================================================== R Under development (unstable) (2024-06-07 r86704 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default locale: [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=C LC_NUMERIC=C [5] LC_TIME=C time zone: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] geoflow_1.0.0 testthat_3.2.1.1 loaded via a namespace (and not attached): [1] ocs4R_0.2-3 xfun_0.44 dotenv_1.0.3 [4] rdflib_0.2.8 gargle_1.5.2 tzdb_0.4.0 [7] vctrs_0.6.5 tools_4.5.0 generics_0.1.3 [10] curl_5.2.1 parallel_4.5.0 tibble_3.2.1 [13] proxy_0.4-27 geometa_0.8-0 fansi_1.0.6 [16] geonapi_0.7-2 pkgconfig_2.0.3 KernSmooth_2.23-24 [19] desc_1.4.3 redland_1.0.17-18 assertthat_0.2.1 [22] uuid_1.2-0 lifecycle_1.0.4 compiler_4.5.0 [25] atom4R_0.3-3 stringr_1.5.1 brio_1.1.5 [28] terra_1.7-78 datapack_1.4.1 keyring_1.3.2 [31] codetools_0.2-20 class_7.3-22 tidyr_1.3.1 [34] pillar_1.9.0 crayon_1.5.2 whisker_0.4.1 [37] openssl_2.2.0 classInt_0.4-10 zen4R_0.10 [40] mime_0.12 digest_0.6.35 tidyselect_1.2.1 [43] zip_2.3.1 stringi_1.8.4 geonode4R_0.1-1 [46] sf_1.0-16 dplyr_1.1.4 purrr_1.0.2 [49] grid_4.5.0 cli_3.6.2 geosapi_0.7-1 [52] magrittr_2.0.3 base64enc_0.1-3 XML_3.99-0.16.1 [55] utf8_1.2.4 e1071_1.7-14 withr_3.0.0 [58] readr_2.1.5 waldo_0.5.2 bit64_4.0.5 [61] googledrive_2.1.1 roxygen2_7.3.1 httr_1.4.7 [64] bit_4.0.5 askpass_1.2.0 png_0.1-8 [67] hms_1.1.3 gsheet_0.4.5 parsedate_1.3.1 [70] knitr_1.47 thredds_0.1-4 dataone_2.2.2 [73] rlang_1.1.4 Rcpp_1.0.12 glue_1.7.0 [76] DBI_1.2.3 ows4R_0.3-6 xml2_1.3.6 [79] vroom_1.6.5 jsonlite_1.8.8 d4storagehub4R_0.4-4 [82] R6_2.5.1 plyr_1.8.9 fs_1.6.4 [85] units_0.8-5 ==================================================================================================== Workflow initialization ==================================================================================================== [geoflow][my-workflow][INFO] Init Workflow configuration [geoflow][my-workflow][INFO] Workflow job directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171146 [geoflow][my-workflow][INFO] Creating workflow profile... [geoflow][my-workflow][INFO] Workflow ID: my-workflow [geoflow][my-workflow][INFO] Workflow name: My workflow [geoflow][my-workflow][INFO] Workflow project: Test geoflow project [geoflow][my-workflow][INFO] Workflow organization: My organization [geoflow][my-workflow][WARN] Configuration file TO UPDATE: 'options' should be defined in profile! [geoflow][my-workflow][INFO] Setting geoflow global options... [geoflow][my-workflow][INFO] Loading metadata elements... [geoflow][my-workflow][INFO] Loading metadata contacts... [geoflow][my-workflow][INFO] Loading metadata contacts from 'https://docs.google.com/spreadsheets/d/1BqlXwA2fKiRuozNAQhBb_PbQVSPTCfl8_Q9rfM8E2ws/edit?usp=sharing' [with 'gsheet' handler]... [geoflow][my-workflow][INFO] Try to use embedded contacts handler [geoflow][my-workflow][INFO] Execute contact handler to load contacts... [geoflow][my-workflow][INFO] Validating contacts [geoflow][my-workflow][INFO] No validation issue detected! [geoflow][my-workflow][INFO] Parsing 4 contacts from tabular source [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][INFO] Successfuly fetched 4 contacts! [geoflow][my-workflow][INFO] Successfuly loaded 4 contacts! [geoflow][my-workflow][INFO] Loading metadata entities... [geoflow][my-workflow][INFO] Loading metadata entities from 'https://docs.google.com/spreadsheets/d/1KSc_IrM86GrNpUASCIVfq6L9cmML77iwpcSbliynYZk/edit?usp=sharing' [with 'gsheet' handler]... [geoflow][my-workflow][INFO] Try to use embedded entities handler [geoflow][my-workflow][INFO] Execute handler to load entities... [geoflow][my-workflow][INFO] Validating entities [geoflow][my-workflow][INFO] Validation issues --> row col type 1 1 Identifier WARNING 2 1 Subject WARNING 3 1 Date WARNING 4 2 Identifier WARNING 5 2 Subject WARNING 6 2 Date WARNING 7 2 Type WARNING message 1 Key is omitted, default key 'id' will be applied 2 Keyword topic's 'taxonomy' is not a recognized ISO keyword topic. 3 key 'edition' is not a recognized ISO date key. 4 Key is omitted, default key 'id' will be applied 5 Keyword topic's 'taxonomy' is not a recognized ISO keyword topic. 6 key 'edition' is not a recognized ISO date key. 7 Key is omitted, default key 'generic' will be applied [geoflow][my-workflow][INFO] Parsing 2 entities from tabular source [geoflow][my-workflow][INFO] Parsing entity 1 [geoflow][my-workflow][INFO] Parsing entity 2 [geoflow][my-workflow][INFO] Successfuly fetched 2 entities! [geoflow][my-workflow][INFO] Enrich metadata entities from directory of contacts [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] geoflow [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] geoflow [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] Successfuly loaded 2 entities! [geoflow][INFO] Check package dependencies for action 'eml-create-eml' [geoflow][INFO] The following packages have been imported for action 'eml-create-eml': package installed version 1 EML TRUE 2.0.6.1 2 emld TRUE 0.5.1 Session info ==================================================================================================== R Under development (unstable) (2024-06-07 r86704 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default locale: [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=C LC_NUMERIC=C [5] LC_TIME=C time zone: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] emld_0.5.1 EML_2.0.6.1 geoflow_1.0.0 testthat_3.2.1.1 loaded via a namespace (and not attached): [1] tidyselect_1.2.1 dplyr_1.1.4 fastmap_1.2.0 [4] lazyeval_0.2.2 XML_3.99-0.16.1 digest_0.6.35 [7] mime_0.12 lifecycle_1.0.4 sf_1.0-16 [10] dotenv_1.0.3 waldo_0.5.2 terra_1.7-78 [13] magrittr_2.0.3 zen4R_0.10 compiler_4.5.0 [16] rlang_1.1.4 tools_4.5.0 utf8_1.2.4 [19] yaml_2.3.8 d4storagehub4R_0.4-4 knitr_1.47 [22] ocs4R_0.2-3 askpass_1.2.0 bit_4.0.5 [25] classInt_0.4-10 curl_5.2.1 plyr_1.8.9 [28] xml2_1.3.6 redland_1.0.17-18 KernSmooth_2.23-24 [31] withr_3.0.0 purrr_1.0.2 rdflib_0.2.8 [34] desc_1.4.3 grid_4.5.0 googledrive_2.1.1 [37] fansi_1.0.6 roxygen2_7.3.1 atom4R_0.3-3 [40] datapack_1.4.1 gsheet_0.4.5 e1071_1.7-14 [43] thredds_0.1-4 cli_3.6.2 rmarkdown_2.27 [46] crayon_1.5.2 generics_0.1.3 parsedate_1.3.1 [49] httr_1.4.7 tzdb_0.4.0 DBI_1.2.3 [52] geosapi_0.7-1 geometa_0.8-0 proxy_0.4-27 [55] stringr_1.5.1 assertthat_0.2.1 parallel_4.5.0 [58] base64enc_0.1-3 vctrs_0.6.5 V8_4.4.2 [61] jsonlite_1.8.8 hms_1.1.3 bit64_4.0.5 [64] ows4R_0.3-6 tidyr_1.3.1 units_0.8-5 [67] keyring_1.3.2 glue_1.7.0 dataone_2.2.2 [70] codetools_0.2-20 stringi_1.8.4 jsonld_2.2 [73] tibble_3.2.1 pillar_1.9.0 htmltools_0.5.8.1 [76] brio_1.1.5 openssl_2.2.0 jqr_1.3.3 [79] R6_2.5.1 evaluate_0.24.0 vroom_1.6.5 [82] geonapi_0.7-2 readr_2.1.5 geonode4R_0.1-1 [85] png_0.1-8 gargle_1.5.2 class_7.3-22 [88] Rcpp_1.0.12 zip_2.3.1 uuid_1.2-0 [91] whisker_0.4.1 xfun_0.44 fs_1.6.4 [94] pkgconfig_2.0.3 ==================================================================================================== Workflow initialization ==================================================================================================== [geoflow][my-workflow][INFO] Init Workflow configuration [geoflow][my-workflow][INFO] Workflow job directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171208 [geoflow][my-workflow][INFO] Creating workflow profile... [geoflow][my-workflow][INFO] Workflow ID: my-workflow [geoflow][my-workflow][INFO] Workflow name: My workflow [geoflow][my-workflow][INFO] Workflow project: Test geoflow project [geoflow][my-workflow][INFO] Workflow organization: My organization [geoflow][my-workflow][WARN] Configuration file TO UPDATE: 'options' should be defined in profile! [geoflow][my-workflow][INFO] Setting geoflow global options... [geoflow][my-workflow][INFO] Loading metadata elements... [geoflow][my-workflow][INFO] Loading metadata contacts... [geoflow][my-workflow][INFO] Loading metadata contacts from 'https://docs.google.com/spreadsheets/d/1BqlXwA2fKiRuozNAQhBb_PbQVSPTCfl8_Q9rfM8E2ws/edit?usp=sharing' [with 'gsheet' handler]... [geoflow][my-workflow][INFO] Try to use embedded contacts handler [geoflow][my-workflow][INFO] Execute contact handler to load contacts... [geoflow][my-workflow][INFO] Validating contacts [geoflow][my-workflow][INFO] No validation issue detected! [geoflow][my-workflow][INFO] Parsing 4 contacts from tabular source [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][WARN] Use 'Identifier' column as contact Ids. Make sure to use these identifiers in your dataset contact references [geoflow][my-workflow][INFO] Successfuly fetched 4 contacts! [geoflow][my-workflow][INFO] Successfuly loaded 4 contacts! [geoflow][my-workflow][INFO] Loading metadata entities... [geoflow][my-workflow][INFO] Loading metadata entities from 'https://docs.google.com/spreadsheets/d/1KSc_IrM86GrNpUASCIVfq6L9cmML77iwpcSbliynYZk/edit?usp=sharing' [with 'gsheet' handler]... [geoflow][my-workflow][INFO] Try to use embedded entities handler [geoflow][my-workflow][INFO] Execute handler to load entities... [geoflow][my-workflow][INFO] Validating entities [geoflow][my-workflow][INFO] Validation issues --> row col type 1 1 Identifier WARNING 2 1 Subject WARNING 3 1 Date WARNING 4 2 Identifier WARNING 5 2 Subject WARNING 6 2 Date WARNING 7 2 Type WARNING message 1 Key is omitted, default key 'id' will be applied 2 Keyword topic's 'taxonomy' is not a recognized ISO keyword topic. 3 key 'edition' is not a recognized ISO date key. 4 Key is omitted, default key 'id' will be applied 5 Keyword topic's 'taxonomy' is not a recognized ISO keyword topic. 6 key 'edition' is not a recognized ISO date key. 7 Key is omitted, default key 'generic' will be applied [geoflow][my-workflow][INFO] Parsing 2 entities from tabular source [geoflow][my-workflow][INFO] Parsing entity 1 [geoflow][my-workflow][INFO] Parsing entity 2 [geoflow][my-workflow][INFO] Successfuly fetched 2 entities! [geoflow][my-workflow][INFO] Enrich metadata entities from directory of contacts [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] geoflow [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] 0000-0002-5870-5762 [geoflow][my-workflow][INFO] geoflow [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] emmanuel.blondel1@gmail.com [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] julien.barde@ird.fr [geoflow][my-workflow][INFO] wilfried.heintz@inrae.fr [geoflow][my-workflow][INFO] Successfuly loaded 2 entities! [geoflow][INFO] Check package dependencies for action 'eml-create-eml' [geoflow][INFO] The following packages have been imported for action 'eml-create-eml': package installed version 1 EML TRUE 2.0.6.1 2 emld TRUE 0.5.1 [geoflow][my-workflow][INFO] Create entity job dir at 'D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171208/entities/my-geoflow-record' [geoflow][my-workflow][INFO] Creating 'data' directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171208/entities/my-geoflow-record/data [geoflow][my-workflow][INFO] Creating 'metadata' directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171208/entities/my-geoflow-record/metadata [geoflow][my-workflow][INFO] Entity working directory: D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171208/entities/my-geoflow-record [geoflow][my-workflow][INFO] SkipDataDownload is false: copying and fetching data... [geoflow][my-workflow][INFO] Copying data to entity job data directory 'D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171208/entities/my-geoflow-record/data' [geoflow][my-workflow][INFO] Copying data source 1 'README.md' (https://raw.githubusercontent.com/eblondel/zen4R/master/README.md) to entity job data directory 'D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171208/entities/my-geoflow-record/data' [geoflow][my-workflow][INFO] Copying data to job data directory from remote file(s) using accessor 'default' [geoflow][INFO] Default HTTP(S) data accessor: Download data 'README.md' from 'https://raw.githubusercontent.com/eblondel/zen4R/master/README.md' to 'D:/RCompile/CRANincoming/R-devel/geoflow.Rcheck/tests/testthat/jobs/20240610171208/entities/my-geoflow-record/data/README.md' trying URL 'https://raw.githubusercontent.com/eblondel/zen4R/master/README.md' Content type 'text/plain; charset=utf-8' length 2134 bytes ================================================== downloaded 2134 bytes [geoflow][my-workflow][WARN] Metadata dynamic handling based on 'data' not implemented for source type 'other' [geoflow][my-workflow][WARN] Metadata dynamic handling based on 'data' not implemented for source type 'other' [geoflow][my-workflow][WARN] Metadata dynamic handling based on 'data' not implemented for type 'other' trying URL 'https://raw.githubusercontent.com/eblondel/zen4R/master/README.md' Content type 'text/plain; charset=utf-8' length 2134 bytes ================================================== downloaded 2134 bytes trying URL 'https://raw.githubusercontent.com/eblondel/zen4R/master/README.md' Content type 'text/plain; charset=utf-8' length 2134 bytes ================================================== downloaded 2134 bytes [ FAIL 0 | WARN 0 | SKIP 43 | PASS 43 ] ══ Skipped tests (43) ══════════════════════════════════════════════════════════ • On CRAN (37): 'test_config_metadata_csw.R:14:5', 'test_config_metadata_csw.R:30:5', 'test_config_metadata_csw.R:40:5', 'test_config_metadata_dataverse.R:11:3', 'test_config_metadata_dataverse.R:29:3', 'test_config_metadata_gsheets_iso19115_inspire.R:13:3', 'test_config_metadata_gsheets_iso19115_inspire.R:31:3', 'test_config_metadata_gsheets_iso19115_inspire.R:40:3', 'test_config_metadata_gsheets_iso19115_inspire_geonetwork.R:14:3', 'test_config_metadata_gsheets_iso19115_inspire_geonetwork.R:32:3', 'test_config_metadata_gsheets_iso19115_inspire_geonetwork.R:41:3', 'test_config_metadata_gsheets_iso19115_inspire_geonetwork_with_uuid.R:14:3', 'test_config_metadata_gsheets_iso19115_inspire_geonetwork_with_uuid.R:32:3', 'test_config_metadata_gsheets_iso19115_inspire_geonetwork_with_uuid.R:41:3', 'test_config_metadata_gsheets_sdi_geoserver_geotiff.R:13:3', 'test_config_metadata_gsheets_sdi_geoserver_geotiff.R:31:3', 'test_config_metadata_gsheets_sdi_geoserver_geotiff.R:40:3', 'test_config_metadata_gsheets_sdi_geoserver_geotiff_view.R:13:3', 'test_config_metadata_gsheets_sdi_geoserver_geotiff_view.R:31:3', 'test_config_metadata_gsheets_sdi_geoserver_geotiff_view.R:40:3', 'test_config_metadata_gsheets_sdi_geoserver_shp.R:13:3', 'test_config_metadata_gsheets_sdi_geoserver_shp.R:31:3', 'test_config_metadata_gsheets_sdi_geoserver_shp.R:40:3', 'test_config_metadata_gsheets_zenodo.R:11:3', 'test_config_metadata_gsheets_zenodo.R:31:3', 'test_config_metadata_gsheets_zenodo.R:42:3', 'test_config_metadata_gsheets_zenodo_full.R:11:4', 'test_config_metadata_ncml.R:11:3', 'test_config_metadata_ncml.R:24:3', 'test_config_metadata_thredds_noaa.R:11:3', 'test_config_metadata_thredds_noaa.R:24:3', 'test_config_metadata_zenodo.R:13:3', 'test_config_metadata_zenodo.R:30:3', 'test_config_metadata_zenodo.R:39:3', 'test_config_metadata_zenodo_with_options.R:13:3', 'test_config_metadata_zenodo_with_options.R:30:3', 'test_config_metadata_zenodo_with_options.R:40:3' • empty test (6): 'test_config_metadata_dataverse.R:38:1', 'test_config_metadata_gsheets_sdi_geonode_shp.R:12:1', 'test_config_metadata_gsheets_sdi_geonode_shp.R:29:1', 'test_config_metadata_gsheets_sdi_geonode_shp.R:37:1', 'test_config_metadata_ncml.R:33:1', 'test_config_metadata_thredds_noaa.R:33:1' [ FAIL 0 | WARN 0 | SKIP 43 | PASS 43 ] > > proc.time() user system elapsed 11.25 0.98 118.56