CRAN Package Check Results for Package OmopSketch

Last updated on 2025-03-01 06:51:16 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.2 6.83 349.75 356.58 ERROR
r-devel-linux-x86_64-debian-gcc 0.2.2 4.51 243.63 248.14 ERROR
r-devel-linux-x86_64-fedora-clang 0.2.2 555.12 ERROR
r-devel-linux-x86_64-fedora-gcc 0.2.2 595.81 ERROR
r-devel-macos-arm64 0.2.2 109.00 OK
r-devel-macos-x86_64 0.2.2 389.00 OK
r-devel-windows-x86_64 0.2.2 8.00 360.00 368.00 OK
r-patched-linux-x86_64 0.2.2 5.89 354.27 360.16 ERROR
r-release-linux-x86_64 0.2.2 6.00 360.70 366.70 ERROR
r-release-macos-arm64 0.2.2 181.00 OK
r-release-macos-x86_64 0.2.2 364.00 OK
r-release-windows-x86_64 0.2.2 8.00 301.00 309.00 ERROR
r-oldrel-macos-arm64 0.2.0 OK
r-oldrel-macos-x86_64 0.2.2 323.00 OK
r-oldrel-windows-x86_64 0.2.2 10.00 383.00 393.00 ERROR

Check Details

Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown Quitting from lines 108-120 [unnamed-chunk-7] (A-summarise_clinical_tables_records.Rmd) Error: processing vignette 'A-summarise_clinical_tables_records.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::collect()`: ! Failed to collect lazy table. Caused by error in `dbSendQuery()`: ! rapi_prepare: Failed to prepare query SELECT strata_id, SUM(number_subjects * ".data".id_bif) AS counts_number_subjects FROM ( SELECT q01.*, 1.0 AS id_bif FROM ( SELECT 1 AS strata_id, q01.* FROM ( SELECT CASE WHEN (n = 0.0) THEN 0 WHEN NOT (n = 0.0) THEN 1 END AS number_subjects, n FROM tmp_020_og_030_1740675936 ) q01 ) q01 ) q01 GROUP BY strata_id Error: Binder Error: Referenced table ".data" not found! Candidate tables: "q01" LINE 3: SUM(number_subjects * ".data".id_bif) AS counts_number_subjects ^ --- failed re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘B-summarise_concept_set_counts.Rmd’ --- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15522 bytes Input file size = 16389 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11819 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 10600 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 Output IDAT size = 10555 bytes (4967 bytes decrease) Output file size = 10633 bytes (5756 bytes = 35.12% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 19481 bytes Input file size = 20363 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14275 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 11608 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11568 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11568 Output IDAT size = 11568 bytes (7913 bytes decrease) Output file size = 11646 bytes (8717 bytes = 42.81% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40535 bytes Input file size = 40661 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36645 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36645 Output IDAT size = 36645 bytes (3890 bytes decrease) Output file size = 36723 bytes (3938 bytes = 9.68% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 36472 bytes Input file size = 37378 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32786 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 32462 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 32462 Output IDAT size = 32462 bytes (4010 bytes decrease) Output file size = 32540 bytes (4838 bytes = 12.94% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 177737 bytes Input file size = 178067 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 142880 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 142880 Output IDAT size = 142880 bytes (34857 bytes decrease) Output file size = 142958 bytes (35109 bytes = 19.72% decrease) --- finished re-building ‘C-summarise_observation_period.Rmd’ SUMMARY: processing the following files failed: ‘A-summarise_clinical_tables_records.Rmd’ ‘B-summarise_concept_set_counts.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown Quitting from lines 108-120 [unnamed-chunk-7] (A-summarise_clinical_tables_records.Rmd) Error: processing vignette 'A-summarise_clinical_tables_records.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::collect()`: ! Failed to collect lazy table. Caused by error in `dbSendQuery()`: ! rapi_prepare: Failed to prepare query SELECT strata_id, SUM(number_subjects * ".data".id_wuz) AS counts_number_subjects FROM ( SELECT q01.*, 1.0 AS id_wuz FROM ( SELECT 1 AS strata_id, q01.* FROM ( SELECT CASE WHEN (n = 0.0) THEN 0 WHEN NOT (n = 0.0) THEN 1 END AS number_subjects, n FROM tmp_020_og_030_1740746387 ) q01 ) q01 ) q01 GROUP BY strata_id Error: Binder Error: Referenced table ".data" not found! Candidate tables: "q01" LINE 3: SUM(number_subjects * ".data".id_wuz) AS counts_number_subjects ^ --- failed re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘B-summarise_concept_set_counts.Rmd’ --- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15522 bytes Input file size = 16389 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11819 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 10600 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 Output IDAT size = 10555 bytes (4967 bytes decrease) Output file size = 10633 bytes (5756 bytes = 35.12% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 19411 bytes Input file size = 20293 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14405 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 11755 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11702 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11702 Output IDAT size = 11702 bytes (7709 bytes decrease) Output file size = 11780 bytes (8513 bytes = 41.95% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40443 bytes Input file size = 40569 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36582 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36582 Output IDAT size = 36582 bytes (3861 bytes decrease) Output file size = 36660 bytes (3909 bytes = 9.64% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 40721 bytes Input file size = 41627 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35717 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 35277 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 35277 Output IDAT size = 35277 bytes (5444 bytes decrease) Output file size = 35355 bytes (6272 bytes = 15.07% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 179706 bytes Input file size = 180036 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 142467 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 142467 Output IDAT size = 142467 bytes (37239 bytes decrease) Output file size = 142545 bytes (37491 bytes = 20.82% decrease) --- finished re-building ‘C-summarise_observation_period.Rmd’ SUMMARY: processing the following files failed: ‘A-summarise_clinical_tables_records.Rmd’ ‘B-summarise_concept_set_counts.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown Quitting from lines 108-120 [unnamed-chunk-7] (A-summarise_clinical_tables_records.Rmd) Error: processing vignette 'A-summarise_clinical_tables_records.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::collect()`: ! Failed to collect lazy table. Caused by error in `dbSendQuery()`: ! rapi_prepare: Failed to prepare query SELECT strata_id, SUM(number_subjects * ".data".id_txc) AS counts_number_subjects FROM ( SELECT q01.*, 1.0 AS id_txc FROM ( SELECT 1 AS strata_id, q01.* FROM ( SELECT CASE WHEN (n = 0.0) THEN 0 WHEN NOT (n = 0.0) THEN 1 END AS number_subjects, n FROM tmp_020_og_030_1740783801 ) q01 ) q01 ) q01 GROUP BY strata_id Error: Binder Error: Referenced table ".data" not found! Candidate tables: "q01" LINE 3: SUM(number_subjects * ".data".id_txc) AS counts_number_subjects ^ --- failed re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘B-summarise_concept_set_counts.Rmd’ --- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15443 bytes Input file size = 16310 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11852 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11816 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 10566 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10475 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10475 Output IDAT size = 10475 bytes (4968 bytes decrease) Output file size = 10553 bytes (5757 bytes = 35.30% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 18516 bytes Input file size = 19398 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14778 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 12230 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 12128 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 12128 Output IDAT size = 12128 bytes (6388 bytes decrease) Output file size = 12206 bytes (7192 bytes = 37.08% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40010 bytes Input file size = 40136 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 34980 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 34980 Output IDAT size = 34980 bytes (5030 bytes decrease) Output file size = 35058 bytes (5078 bytes = 12.65% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 41503 bytes Input file size = 42421 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36155 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 35623 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 35623 Output IDAT size = 35623 bytes (5880 bytes decrease) Output file size = 35701 bytes (6720 bytes = 15.84% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 183043 bytes Input file size = 183385 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 139576 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 139576 Output IDAT size = 139576 bytes (43467 bytes decrease) Output file size = 139654 bytes (43731 bytes = 23.85% decrease) --- finished re-building ‘C-summarise_observation_period.Rmd’ SUMMARY: processing the following files failed: ‘A-summarise_clinical_tables_records.Rmd’ ‘B-summarise_concept_set_counts.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown Quitting from lines 108-120 [unnamed-chunk-7] (A-summarise_clinical_tables_records.Rmd) Error: processing vignette 'A-summarise_clinical_tables_records.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::collect()`: ! Failed to collect lazy table. Caused by error in `dbSendQuery()`: ! rapi_prepare: Failed to prepare query SELECT strata_id, SUM(number_subjects * ".data".id_hnv) AS counts_number_subjects FROM ( SELECT q01.*, 1.0 AS id_hnv FROM ( SELECT 1 AS strata_id, q01.* FROM ( SELECT CASE WHEN (n = 0.0) THEN 0 WHEN NOT (n = 0.0) THEN 1 END AS number_subjects, n FROM tmp_020_og_030_1740777062 ) q01 ) q01 ) q01 GROUP BY strata_id Error: Binder Error: Referenced table ".data" not found! Candidate tables: "q01" LINE 3: SUM(number_subjects * ".data".id_hnv) AS counts_number_subjects ^ --- failed re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘B-summarise_concept_set_counts.Rmd’ --- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15443 bytes Input file size = 16310 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11852 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11816 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 10566 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10475 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10475 Output IDAT size = 10475 bytes (4968 bytes decrease) Output file size = 10553 bytes (5757 bytes = 35.30% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 18078 bytes Input file size = 18960 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14224 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 11430 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11347 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11347 Output IDAT size = 11347 bytes (6731 bytes decrease) Output file size = 11425 bytes (7535 bytes = 39.74% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40170 bytes Input file size = 40296 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 35109 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 35109 Output IDAT size = 35109 bytes (5061 bytes decrease) Output file size = 35187 bytes (5109 bytes = 12.68% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 40543 bytes Input file size = 41449 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35240 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 34630 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 34630 Output IDAT size = 34630 bytes (5913 bytes decrease) Output file size = 34708 bytes (6741 bytes = 16.26% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 189584 bytes Input file size = 189938 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 146029 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 146029 Output IDAT size = 146029 bytes (43555 bytes decrease) Output file size = 146107 bytes (43831 bytes = 23.08% decrease) --- finished re-building ‘C-summarise_observation_period.Rmd’ SUMMARY: processing the following files failed: ‘A-summarise_clinical_tables_records.Rmd’ ‘B-summarise_concept_set_counts.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-9-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 57390 bytes Input file size = 58332 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 50421 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 50220 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 50220 Output IDAT size = 50220 bytes (7170 bytes decrease) Output file size = 50298 bytes (8034 bytes = 13.77% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-10-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 55613 bytes Input file size = 56543 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 49845 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 49845 Output IDAT size = 49845 bytes (5768 bytes decrease) Output file size = 49923 bytes (6620 bytes = 11.71% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-11-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 50298 bytes Input file size = 51228 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 45168 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 45117 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 45117 Output IDAT size = 45117 bytes (5181 bytes decrease) Output file size = 45195 bytes (6033 bytes = 11.78% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 206665 bytes Input file size = 207043 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 170695 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 170695 Output IDAT size = 170695 bytes (35970 bytes decrease) Output file size = 170773 bytes (36270 bytes = 17.52% decrease) --- finished re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘B-summarise_concept_set_counts.Rmd’ --- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15522 bytes Input file size = 16389 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11819 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 10600 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 Output IDAT size = 10555 bytes (4967 bytes decrease) Output file size = 10633 bytes (5756 bytes = 35.12% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 19186 bytes Input file size = 20068 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14238 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 11560 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11530 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11530 Output IDAT size = 11530 bytes (7656 bytes decrease) Output file size = 11608 bytes (8460 bytes = 42.16% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 39936 bytes Input file size = 40062 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36085 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36085 Output IDAT size = 36085 bytes (3851 bytes decrease) Output file size = 36163 bytes (3899 bytes = 9.73% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 42390 bytes Input file size = 43308 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37519 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 37148 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 37148 Output IDAT size = 37148 bytes (5242 bytes decrease) Output file size = 37226 bytes (6082 bytes = 14.04% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 199439 bytes Input file size = 199805 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 155404 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 155404 Output IDAT size = 155404 bytes (44035 bytes decrease) Output file size = 155482 bytes (44323 bytes = 22.18% decrease) --- finished re-building ‘C-summarise_observation_period.Rmd’ SUMMARY: processing the following file failed: ‘B-summarise_concept_set_counts.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-patched-linux-x86_64

Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-9-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 56620 bytes Input file size = 57550 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48343 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 48210 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 48210 Output IDAT size = 48210 bytes (8410 bytes decrease) Output file size = 48288 bytes (9262 bytes = 16.09% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-10-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 76529 bytes Input file size = 77495 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 69211 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 68676 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 67722 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 66868 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 66868 Output IDAT size = 66868 bytes (9661 bytes decrease) Output file size = 66946 bytes (10549 bytes = 13.61% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-11-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 62469 bytes Input file size = 63411 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55505 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 55505 Output IDAT size = 55505 bytes (6964 bytes decrease) Output file size = 55583 bytes (7828 bytes = 12.34% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 257353 bytes Input file size = 257803 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 212295 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 212295 Output IDAT size = 212295 bytes (45058 bytes decrease) Output file size = 212373 bytes (45430 bytes = 17.62% decrease) --- finished re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building ‘B-summarise_concept_set_counts.Rmd’ --- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png 1344x960 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15522 bytes Input file size = 16389 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11819 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 10600 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555 Output IDAT size = 10555 bytes (4967 bytes decrease) Output file size = 10633 bytes (5756 bytes = 35.12% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 18814 bytes Input file size = 19696 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13807 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 11002 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10956 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10956 Output IDAT size = 10956 bytes (7858 bytes decrease) Output file size = 11034 bytes (8662 bytes = 43.98% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40512 bytes Input file size = 40638 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36644 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 36644 Output IDAT size = 36644 bytes (3868 bytes decrease) Output file size = 36722 bytes (3916 bytes = 9.64% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 43439 bytes Input file size = 44357 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38942 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 38529 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 38529 Output IDAT size = 38529 bytes (4910 bytes decrease) Output file size = 38607 bytes (5750 bytes = 12.96% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 188188 bytes Input file size = 188530 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 149140 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 149140 Output IDAT size = 149140 bytes (39048 bytes decrease) Output file size = 149218 bytes (39312 bytes = 20.85% decrease) --- finished re-building ‘C-summarise_observation_period.Rmd’ SUMMARY: processing the following file failed: ‘B-summarise_concept_set_counts.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64

Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'A-summarise_clinical_tables_records.Rmd' using rmarkdown --- finished re-building 'A-summarise_clinical_tables_records.Rmd' --- re-building 'B-summarise_concept_set_counts.Rmd' using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building 'B-summarise_concept_set_counts.Rmd' --- re-building 'C-summarise_observation_period.Rmd' using rmarkdown --- finished re-building 'C-summarise_observation_period.Rmd' SUMMARY: processing the following file failed: 'B-summarise_concept_set_counts.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-release-windows-x86_64

Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'A-summarise_clinical_tables_records.Rmd' using rmarkdown Quitting from lines 108-120 [unnamed-chunk-7] (A-summarise_clinical_tables_records.Rmd) Error: processing vignette 'A-summarise_clinical_tables_records.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::collect()`: ! Failed to collect lazy table. Caused by error in `dbSendQuery()`: ! rapi_prepare: Failed to prepare query SELECT strata_id, SUM(number_subjects * ".data".id_tqk) AS counts_number_subjects FROM ( SELECT q01.*, 1.0 AS id_tqk FROM ( SELECT 1 AS strata_id, q01.* FROM ( SELECT CASE WHEN (n = 0.0) THEN 0 WHEN NOT (n = 0.0) THEN 1 END AS number_subjects, n FROM tmp_020_og_030_1740721928 ) q01 ) q01 ) q01 GROUP BY strata_id Error: Binder Error: Referenced table ".data" not found! Candidate tables: "q01" LINE 3: SUM(number_subjects * ".data".id_tqk) AS counts_number_subjects ^ --- failed re-building 'A-summarise_clinical_tables_records.Rmd' --- re-building 'B-summarise_concept_set_counts.Rmd' using rmarkdown Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd) Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics: could not find function "eunomia_is_available" --- failed re-building 'B-summarise_concept_set_counts.Rmd' --- re-building 'C-summarise_observation_period.Rmd' using rmarkdown --- finished re-building 'C-summarise_observation_period.Rmd' SUMMARY: processing the following files failed: 'A-summarise_clinical_tables_records.Rmd' 'B-summarise_concept_set_counts.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-windows-x86_64