Last updated on 2025-02-16 10:50:43 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.4 | 8.30 | 759.46 | 767.76 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.4 | 5.51 | 512.37 | 517.88 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3.4 | 1190.73 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.4 | 1101.50 | OK | |||
| r-devel-macos-arm64 | 0.3.4 | 323.00 | OK | |||
| r-devel-macos-x86_64 | 0.3.4 | 584.00 | OK | |||
| r-devel-windows-x86_64 | 0.3.4 | 11.00 | 536.00 | 547.00 | ERROR | |
| r-patched-linux-x86_64 | 0.3.4 | 9.43 | 680.98 | 690.41 | ERROR | |
| r-release-linux-x86_64 | 0.3.4 | 8.00 | 675.95 | 683.95 | ERROR | |
| r-release-macos-arm64 | 0.3.4 | 307.00 | NOTE | |||
| r-release-macos-x86_64 | 0.3.4 | 695.00 | NOTE | |||
| r-release-windows-x86_64 | 0.3.4 | 11.00 | 555.00 | 566.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.3.3 | 270.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.3.4 | 562.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.3.4 | 14.00 | 759.00 | 773.00 | NOTE |
Version: 0.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a00_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a00_introduction.Rmd’
--- re-building ‘a01_building_base_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a01_building_base_cohorts.Rmd’
--- re-building ‘a02_cohort_table_requirements.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-15-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3779 bytes
Input file size = 4634 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3377
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 = 3377
Output IDAT size = 3377 bytes (402 bytes decrease)
Output file size = 3455 bytes (1179 bytes = 25.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-16-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3614 bytes
Input file size = 4460 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3284
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 = 3284
Output IDAT size = 3284 bytes (330 bytes decrease)
Output file size = 3362 bytes (1098 bytes = 24.62% decrease)
--- finished re-building ‘a02_cohort_table_requirements.Rmd’
--- re-building ‘a03_require_demographics.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a03_require_demographics.Rmd’
--- re-building ‘a04_require_intersections.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a04_require_intersections.Rmd’
--- re-building ‘a05_update_cohort_start_end.Rmd’ using rmarkdown
--- finished re-building ‘a05_update_cohort_start_end.Rmd’
--- re-building ‘a06_concatanate_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a06_concatanate_cohorts.Rmd’
--- re-building ‘a07_filter_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a07_filter_cohorts.Rmd’
--- re-building ‘a08_split_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a08_split_cohorts.Rmd’
--- re-building ‘a09_combine_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 96-102 [unnamed-chunk-8] (a09_combine_cohorts.Rmd)
Error: processing vignette 'a09_combine_cohorts.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT *
FROM main.my_study_og_033_1739620919_attrition
Error: Catalog Error: Table with name my_study_og_033_1739620919_attrition does not exist!
Did you mean "my_study_medintersect_attrition"?
LINE 2: FROM main.my_study_og_033_173962091...
^
--- failed re-building ‘a09_combine_cohorts.Rmd’
--- re-building ‘a10_match_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a10_match_cohorts.Rmd’
--- re-building ‘a11_benchmark.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-5-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 133789 bytes
Input file size = 134059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 98903
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 = 98903
Output IDAT size = 98903 bytes (34886 bytes decrease)
Output file size = 98981 bytes (35078 bytes = 26.17% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-7-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76134 bytes
Input file size = 76320 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59778
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 = 59778
Output IDAT size = 59778 bytes (16356 bytes decrease)
Output file size = 59856 bytes (16464 bytes = 21.57% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-10-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 42145 bytes
Input file size = 42283 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36072
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 = 36072
Output IDAT size = 36072 bytes (6073 bytes decrease)
Output file size = 36150 bytes (6133 bytes = 14.50% decrease)
--- finished re-building ‘a11_benchmark.Rmd’
SUMMARY: processing the following file failed:
‘a09_combine_cohorts.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a00_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a00_introduction.Rmd’
--- re-building ‘a01_building_base_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a01_building_base_cohorts.Rmd’
--- re-building ‘a02_cohort_table_requirements.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-15-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3797 bytes
Input file size = 4652 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3381
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 = 3381
Output IDAT size = 3381 bytes (416 bytes decrease)
Output file size = 3459 bytes (1193 bytes = 25.64% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-16-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3656 bytes
Input file size = 4502 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3291
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 = 3291
Output IDAT size = 3291 bytes (365 bytes decrease)
Output file size = 3369 bytes (1133 bytes = 25.17% decrease)
--- finished re-building ‘a02_cohort_table_requirements.Rmd’
--- re-building ‘a03_require_demographics.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a03_require_demographics.Rmd’
--- re-building ‘a04_require_intersections.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a04_require_intersections.Rmd’
--- re-building ‘a05_update_cohort_start_end.Rmd’ using rmarkdown
--- finished re-building ‘a05_update_cohort_start_end.Rmd’
--- re-building ‘a06_concatanate_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a06_concatanate_cohorts.Rmd’
--- re-building ‘a07_filter_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a07_filter_cohorts.Rmd’
--- re-building ‘a08_split_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a08_split_cohorts.Rmd’
--- re-building ‘a09_combine_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 96-102 [unnamed-chunk-8] (a09_combine_cohorts.Rmd)
Error: processing vignette 'a09_combine_cohorts.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT *
FROM main.my_study_og_033_1739520120_attrition
Error: Catalog Error: Table with name my_study_og_033_1739520120_attrition does not exist!
Did you mean "my_study_medintersect_attrition"?
LINE 2: FROM main.my_study_og_033_173952012...
^
--- failed re-building ‘a09_combine_cohorts.Rmd’
--- re-building ‘a10_match_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a10_match_cohorts.Rmd’
--- re-building ‘a11_benchmark.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-5-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 132673 bytes
Input file size = 132943 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 91279
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 = 91279
Output IDAT size = 91279 bytes (41394 bytes decrease)
Output file size = 91357 bytes (41586 bytes = 31.28% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-7-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 75627 bytes
Input file size = 75813 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 57967
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 = 57967
Output IDAT size = 57967 bytes (17660 bytes decrease)
Output file size = 58045 bytes (17768 bytes = 23.44% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-10-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 41797 bytes
Input file size = 41935 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 34662
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 = 34662
Output IDAT size = 34662 bytes (7135 bytes decrease)
Output file size = 34740 bytes (7195 bytes = 17.16% decrease)
--- finished re-building ‘a11_benchmark.Rmd’
SUMMARY: processing the following file failed:
‘a09_combine_cohorts.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'a00_introduction.Rmd' using rmarkdown
--- finished re-building 'a00_introduction.Rmd'
--- re-building 'a01_building_base_cohorts.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'a01_building_base_cohorts.Rmd'
--- re-building 'a02_cohort_table_requirements.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'a02_cohort_table_requirements.Rmd'
--- re-building 'a03_require_demographics.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'a03_require_demographics.Rmd'
--- re-building 'a04_require_intersections.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'a04_require_intersections.Rmd'
--- re-building 'a05_update_cohort_start_end.Rmd' using rmarkdown
--- finished re-building 'a05_update_cohort_start_end.Rmd'
--- re-building 'a06_concatanate_cohorts.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'a06_concatanate_cohorts.Rmd'
--- re-building 'a07_filter_cohorts.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'a07_filter_cohorts.Rmd'
--- re-building 'a08_split_cohorts.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building 'a08_split_cohorts.Rmd'
--- re-building 'a09_combine_cohorts.Rmd' using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 96-102 [unnamed-chunk-8] (a09_combine_cohorts.Rmd)
Error: processing vignette 'a09_combine_cohorts.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT *
FROM main.my_study_og_033_1739594347_attrition
Error: Catalog Error: Table with name my_study_og_033_1739594347_attrition does not exist!
Did you mean "my_study_medintersect_attrition"?
LINE 2: FROM main.my_study_og_033_173959434...
^
--- failed re-building 'a09_combine_cohorts.Rmd'
--- re-building 'a10_match_cohorts.Rmd' using rmarkdown
--- finished re-building 'a10_match_cohorts.Rmd'
--- re-building 'a11_benchmark.Rmd' using rmarkdown
--- finished re-building 'a11_benchmark.Rmd'
SUMMARY: processing the following file failed:
'a09_combine_cohorts.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a00_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a00_introduction.Rmd’
--- re-building ‘a01_building_base_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a01_building_base_cohorts.Rmd’
--- re-building ‘a02_cohort_table_requirements.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-15-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3779 bytes
Input file size = 4634 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3377
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 = 3377
Output IDAT size = 3377 bytes (402 bytes decrease)
Output file size = 3455 bytes (1179 bytes = 25.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-16-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3614 bytes
Input file size = 4460 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3284
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 = 3284
Output IDAT size = 3284 bytes (330 bytes decrease)
Output file size = 3362 bytes (1098 bytes = 24.62% decrease)
--- finished re-building ‘a02_cohort_table_requirements.Rmd’
--- re-building ‘a03_require_demographics.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a03_require_demographics.Rmd’
--- re-building ‘a04_require_intersections.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a04_require_intersections.Rmd’
--- re-building ‘a05_update_cohort_start_end.Rmd’ using rmarkdown
--- finished re-building ‘a05_update_cohort_start_end.Rmd’
--- re-building ‘a06_concatanate_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a06_concatanate_cohorts.Rmd’
--- re-building ‘a07_filter_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a07_filter_cohorts.Rmd’
--- re-building ‘a08_split_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a08_split_cohorts.Rmd’
--- re-building ‘a09_combine_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 96-102 [unnamed-chunk-8] (a09_combine_cohorts.Rmd)
Error: processing vignette 'a09_combine_cohorts.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT *
FROM main.my_study_og_033_1739547148_attrition
Error: Catalog Error: Table with name my_study_og_033_1739547148_attrition does not exist!
Did you mean "my_study_medintersect_attrition"?
LINE 2: FROM main.my_study_og_033_173954714...
^
--- failed re-building ‘a09_combine_cohorts.Rmd’
--- re-building ‘a10_match_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a10_match_cohorts.Rmd’
--- re-building ‘a11_benchmark.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-5-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 133789 bytes
Input file size = 134059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 98903
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 = 98903
Output IDAT size = 98903 bytes (34886 bytes decrease)
Output file size = 98981 bytes (35078 bytes = 26.17% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-7-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76134 bytes
Input file size = 76320 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59778
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 = 59778
Output IDAT size = 59778 bytes (16356 bytes decrease)
Output file size = 59856 bytes (16464 bytes = 21.57% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-10-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 42145 bytes
Input file size = 42283 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36072
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 = 36072
Output IDAT size = 36072 bytes (6073 bytes decrease)
Output file size = 36150 bytes (6133 bytes = 14.50% decrease)
--- finished re-building ‘a11_benchmark.Rmd’
SUMMARY: processing the following file failed:
‘a09_combine_cohorts.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a00_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a00_introduction.Rmd’
--- re-building ‘a01_building_base_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a01_building_base_cohorts.Rmd’
--- re-building ‘a02_cohort_table_requirements.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-15-1.png
288x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3779 bytes
Input file size = 4634 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3377
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 = 3377
Output IDAT size = 3377 bytes (402 bytes decrease)
Output file size = 3455 bytes (1179 bytes = 25.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a02_cohort_table_requirements_files/figure-html/unnamed-chunk-16-1.png
288x288 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3614 bytes
Input file size = 4460 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3284
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 = 3284
Output IDAT size = 3284 bytes (330 bytes decrease)
Output file size = 3362 bytes (1098 bytes = 24.62% decrease)
--- finished re-building ‘a02_cohort_table_requirements.Rmd’
--- re-building ‘a03_require_demographics.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a03_require_demographics.Rmd’
--- re-building ‘a04_require_intersections.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a04_require_intersections.Rmd’
--- re-building ‘a05_update_cohort_start_end.Rmd’ using rmarkdown
--- finished re-building ‘a05_update_cohort_start_end.Rmd’
--- re-building ‘a06_concatanate_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a06_concatanate_cohorts.Rmd’
--- re-building ‘a07_filter_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a07_filter_cohorts.Rmd’
--- re-building ‘a08_split_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a08_split_cohorts.Rmd’
--- re-building ‘a09_combine_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 96-102 [unnamed-chunk-8] (a09_combine_cohorts.Rmd)
Error: processing vignette 'a09_combine_cohorts.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT *
FROM main.my_study_og_033_1739632787_attrition
Error: Catalog Error: Table with name my_study_og_033_1739632787_attrition does not exist!
Did you mean "my_study_medintersect_attrition"?
LINE 2: FROM main.my_study_og_033_173963278...
^
--- failed re-building ‘a09_combine_cohorts.Rmd’
--- re-building ‘a10_match_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a10_match_cohorts.Rmd’
--- re-building ‘a11_benchmark.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-5-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 133789 bytes
Input file size = 134059 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 98903
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 = 98903
Output IDAT size = 98903 bytes (34886 bytes decrease)
Output file size = 98981 bytes (35078 bytes = 26.17% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-7-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76134 bytes
Input file size = 76320 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 59778
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 = 59778
Output IDAT size = 59778 bytes (16356 bytes decrease)
Output file size = 59856 bytes (16464 bytes = 21.57% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortConstructor.Rcheck/vign_test/CohortConstructor/vignettes/a11_benchmark_files/figure-html/unnamed-chunk-10-1.png
960x672 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 42145 bytes
Input file size = 42283 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36072
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 = 36072
Output IDAT size = 36072 bytes (6073 bytes decrease)
Output file size = 36150 bytes (6133 bytes = 14.50% decrease)
--- finished re-building ‘a11_benchmark.Rmd’
SUMMARY: processing the following file failed:
‘a09_combine_cohorts.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.3.4
Check: installed package size
Result: NOTE
installed size is 10.1Mb
sub-directories of 1Mb or more:
doc 9.4Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.3.3
Check: installed package size
Result: NOTE
installed size is 10.1Mb
sub-directories of 1Mb or more:
doc 9.4Mb
Flavor: r-oldrel-macos-arm64
Version: 0.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a00_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a00_introduction.Rmd’
--- re-building ‘a01_building_base_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a01_building_base_cohorts.Rmd’
--- re-building ‘a02_cohort_table_requirements.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a02_cohort_table_requirements.Rmd’
--- re-building ‘a03_require_demographics.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a03_require_demographics.Rmd’
--- re-building ‘a04_require_intersections.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a04_require_intersections.Rmd’
--- re-building ‘a05_update_cohort_start_end.Rmd’ using rmarkdown
--- finished re-building ‘a05_update_cohort_start_end.Rmd’
--- re-building ‘a06_concatanate_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a06_concatanate_cohorts.Rmd’
--- re-building ‘a07_filter_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a07_filter_cohorts.Rmd’
--- re-building ‘a08_split_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
--- finished re-building ‘a08_split_cohorts.Rmd’
--- re-building ‘a09_combine_cohorts.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 96-102 [unnamed-chunk-8] (a09_combine_cohorts.Rmd)
Error: processing vignette 'a09_combine_cohorts.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT *
FROM main.my_study_og_033_1739694057_attrition
Error: Catalog Error: Table with name my_study_og_033_1739694057_attrition does not exist!
Did you mean "my_study_medintersect_attrition"?
LINE 2: FROM main.my_study_og_033_173969405...
^
--- failed re-building ‘a09_combine_cohorts.Rmd’
--- re-building ‘a10_match_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a10_match_cohorts.Rmd’
--- re-building ‘a11_benchmark.Rmd’ using rmarkdown
--- finished re-building ‘a11_benchmark.Rmd’
SUMMARY: processing the following file failed:
‘a09_combine_cohorts.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.