Last updated on 2025-03-03 01:50:52 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 | 4.13 | 246.61 | 250.74 | 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 | 284.00 | 292.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.2 | 7.11 | 337.46 | 344.57 | ERROR | |
| r-release-linux-x86_64 | 0.2.2 | 5.86 | 320.72 | 326.58 | 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 |
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_fpo) AS counts_number_subjects
FROM (
SELECT q01.*, 1.0 AS id_fpo
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_1740919255
) 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_fpo) 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 = 19878 bytes
Input file size = 20760 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14898
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 = 12374
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 12313
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 = 12313
Output IDAT size = 12313 bytes (7565 bytes decrease)
Output file size = 12391 bytes (8369 bytes = 40.31% 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 = 40392 bytes
Input file size = 40518 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 = 36533
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 = 36533
Output IDAT size = 36533 bytes (3859 bytes decrease)
Output file size = 36611 bytes (3907 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 = 41765 bytes
Input file size = 42683 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37588
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 37146
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 = 37146
Output IDAT size = 37146 bytes (4619 bytes decrease)
Output file size = 37224 bytes (5459 bytes = 12.79% 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 = 182946 bytes
Input file size = 183288 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 145015
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 = 145015
Output IDAT size = 145015 bytes (37931 bytes decrease)
Output file size = 145093 bytes (38195 bytes = 20.84% 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
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_pbx) AS counts_number_subjects
FROM (
SELECT q01.*, 1.0 AS id_pbx
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_1740760480
) 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_pbx) 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-devel-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_gwk) AS counts_number_subjects
FROM (
SELECT q01.*, 1.0 AS id_gwk
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_1740763374
) 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_gwk) 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-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 = 19281 bytes
Input file size = 20163 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14264
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 = 11607
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11553
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 = 11553
Output IDAT size = 11553 bytes (7728 bytes decrease)
Output file size = 11631 bytes (8532 bytes = 42.32% 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 = 39870 bytes
Input file size = 39996 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 = 36055
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 = 36055
Output IDAT size = 36055 bytes (3815 bytes decrease)
Output file size = 36133 bytes (3863 bytes = 9.66% 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 = 41068 bytes
Input file size = 41986 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36532
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 36000
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 = 36000
Output IDAT size = 36000 bytes (5068 bytes decrease)
Output file size = 36078 bytes (5908 bytes = 14.07% 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 = 185380 bytes
Input file size = 185722 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 147327
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 = 147327
Output IDAT size = 147327 bytes (38053 bytes decrease)
Output file size = 147405 bytes (38317 bytes = 20.63% 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-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
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_sbb) AS counts_number_subjects
FROM (
SELECT q01.*, 1.0 AS id_sbb
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_1740848942
) 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_sbb) 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-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 = 20006 bytes
Input file size = 20888 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14924
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 = 12289
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 12231
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 = 12231
Output IDAT size = 12231 bytes (7775 bytes decrease)
Output file size = 12309 bytes (8579 bytes = 41.07% 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 = 40481 bytes
Input file size = 40607 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 = 36611
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 = 36611
Output IDAT size = 36611 bytes (3870 bytes decrease)
Output file size = 36689 bytes (3918 bytes = 9.65% 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 = 42243 bytes
Input file size = 43161 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37614
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 37209
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 = 37209
Output IDAT size = 37209 bytes (5034 bytes decrease)
Output file size = 37287 bytes (5874 bytes = 13.61% 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 = 186711 bytes
Input file size = 187053 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 147910
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 = 147910
Output IDAT size = 147910 bytes (38801 bytes decrease)
Output file size = 147988 bytes (39065 bytes = 20.88% 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-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