- using R Under development (unstable) (2025-02-26 r87830)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.7 (1+b1)
Debian flang-new version 19.1.7 (1+b1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘OmopSketch/DESCRIPTION’ ... OK
- this is package ‘OmopSketch’ version ‘0.2.2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘OmopSketch’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
- checking loading without being on the library search path ... [1s/2s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [12s/18s] OK
- checking Rd files ... [0s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking R/sysdata.rda ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [1s/2s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [11s/9s] OK
Running ‘testthat.R’ [10s/9s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [292s/403s] 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
- checking PDF version of manual ... [5s/7s] OK
- checking HTML version of manual ... [1s/1s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR