Last updated on 2026-10-29 23:00:18 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.4 | 13.75 | 215.45 | 229.20 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.4 | 10.70 | 148.78 | 159.48 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.4 | 11.00 | 174.19 | 185.19 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.4 | 10.00 | 166.68 | 176.68 | OK | |
| r-devel-windows-x86_64 | 0.3.4 | 18.00 | 260.00 | 278.00 | OK | |
| r-patched-linux-x86_64 | 0.3.4 | 16.44 | 203.61 | 220.05 | OK | |
| r-release-linux-x86_64 | 0.3.4 | 14.30 | 204.25 | 218.55 | OK | |
| r-release-macos-arm64 | 0.3.4 | 4.00 | 51.00 | 55.00 | OK | |
| r-release-macos-x86_64 | 0.3.4 | 10.00 | 221.00 | 231.00 | OK | |
| r-release-windows-x86_64 | 0.3.4 | 16.00 | 218.00 | 234.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.4 | 3.00 | 52.00 | 55.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.4 | 10.00 | 221.00 | 231.00 | OK | |
| r-oldrel-windows-x86_64 | 0.3.4 | 23.00 | 280.00 | 303.00 | OK |
Version: 0.3.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [1m/80m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ukbflow)
>
> test_check("ukbflow")
v Logged in to DNAnexus as: "TestUser"
v Logged out from DNAnexus.
v Project selected: "project-XXXXXXXXXXXX"
v Renamed 1 column.
* date_of_attending_assessment_centre_i0
v derive_hes (t2d): 26 cases, 26 with date.
v derive_icd10 (t2d): 26 cases across 1 source, 26 with date.
v derive_age: 1 event processed.
Read '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c73e2c910.csv': 3 rows, 2 columns.
Read '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c2e66ca30.csv': 5 rows, 3 columns.
Read '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c61f7dad3.csv': 5 rows, 3 columns.
v No NA values.
Read '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c40dfebdf.csv': 3 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
v All effect alleles are A/T/C/G.
Read '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c65b49328.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All effect alleles are A/T/C/G.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c1af935bd.txt'
Read '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c87cca26.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c52e2c6e.txt'
Read '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c41e6fd13.csv': 5 rows, 3 columns.
v No NA values.
v No duplicate SNPs.
v All SNP IDs match rs[0-9]+ format.
v All effect alleles are A/T/C/G.
Beta summary:
Range : -0.2 to 0.3
Mean |beta|: 0.16
Positive : 3 (60%)
Negative : 2 (40%)
Zero : 0
v Weights file passed checks: 5 SNPs ready for UKB RAP.
v Saved: '/tmp/RtmpMbkWg8/working_dir/Rtmp0jgj7N/file30757c3b4c18f9.txt'
Auto-detected 1 GRS column(s): "GRS_flat"
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_b_z -> GRS_b_z_z [mean=-0.0275, sd=0.9886]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
v GRS_a_z -> GRS_a_z_z [mean=-0.0218, sd=0.9873]
Auto-detected 2 GRS column(s): "GRS_a_z" and "GRS_b_z"
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_quad ----------------------------------------------------
GRS_b_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_tri -----------------------------------------------------
GRS_b_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
-- GRS_b_z --
v Unadjusted | GRS_b_z: OR 0.86 (0.63-1.17), p = 0.328
v Done: 2 result rows across 2 exposures and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
-- GRS_b_z_tri --
v Unadjusted | GRS_b_z_triMid: OR 0.51 (0.25-1.04), p = 0.063
v Unadjusted | GRS_b_z_triHigh: OR 0.67 (0.28-1.62), p = 0.377
v Done: 4 result rows across 2 exposures and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposures GRS_a_z_quad and GRS_b_z_quad are not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 2 exposures x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
-- GRS_b_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_b_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_b_z_quadQ2: OR 0.49 (0.21-1.14), p = 0.0976
v Unadjusted | GRS_b_z_quadQ3: OR 0.66 (0.30-1.48), p = 0.315
v Unadjusted | GRS_b_z_quadQ4: OR 0.54 (0.24-1.25), p = 0.151
i Unadjusted | trend: OR_per_score = 0.84 (0.65-1.11), p_trend = 0.221
v Done: 8 result rows across 2 exposures and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_quad ----------------------------------------------------
GRS_b_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_b_z -------------------------------------------------------------
GRS_b_z: mean=-0.03, median=-0.06, sd=0.99, Q1=-0.64, Q3=0.67, NA=0% (n=0)
-- New column: GRS_b_z_tri -----------------------------------------------------
GRS_b_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
-- GRS_b_z --
v Unadjusted | GRS_b_z: OR 0.86 (0.63-1.17), p = 0.328
v Done: 2 result rows across 2 exposures and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 2 exposures x 1 model = 2 logistic regressions
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
-- GRS_b_z_tri --
v Unadjusted | GRS_b_z_triMid: OR 0.51 (0.25-1.04), p = 0.063
v Unadjusted | GRS_b_z_triHigh: OR 0.67 (0.28-1.62), p = 0.377
v Done: 4 result rows across 2 exposures and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposures GRS_a_z_quad and GRS_b_z_quad are not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 2 exposures x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
-- GRS_b_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_b_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_b_z_quadQ2: OR 0.49 (0.21-1.14), p = 0.0976
v Unadjusted | GRS_b_z_quadQ3: OR 0.66 (0.30-1.48), p = 0.315
v Unadjusted | GRS_b_z_quadQ4: OR 0.54 (0.24-1.25), p = 0.151
i Unadjusted | trend: OR_per_score = 0.84 (0.65-1.11), p_trend = 0.221
v Done: 8 result rows across 2 exposures and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
v Done: 4 result rows across 1 exposure and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (HR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_coxph -----------------------------------------------------------------
i 1 exposure x 1 model = 1 Cox regression
i Input cohort: 300 participants (n/n_events/person_years reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: HR 1.12 (0.83-1.51), p = 0.465
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_coxph -----------------------------------------------------------------
i 1 exposure x 1 model = 1 Cox regression
i Input cohort: 300 participants (n/n_events/person_years reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: HR 0.82 (0.40-1.68), p = 0.585
v Unadjusted | GRS_a_z_triHigh: HR 1.19 (0.51-2.76), p = 0.685
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: HR 0.64 (0.28-1.47), p = 0.294
v Unadjusted | GRS_a_z_quadQ3: HR 1.10 (0.52-2.31), p = 0.805
v Unadjusted | GRS_a_z_quadQ4: HR 1.05 (0.47-2.34), p = 0.905
i Unadjusted | trend: HR_per_score = 1.08 (0.83-1.41), p_trend = 0.546
v Done: 4 result rows across 1 exposure and 1 model.
-- C-index ---------------------------------------------------------------------
v Validation complete.
-- Creating GRS groups ---------------------------------------------------------
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_quad ----------------------------------------------------
GRS_a_z_quad [4 levels]
Q1: n=75 (25%)
Q2: n=75 (25%)
Q3: n=75 (25%)
Q4: n=75 (25%)
<NA>: n=0 (0%)
-- Source: GRS_a_z -------------------------------------------------------------
GRS_a_z: mean=-0.02, median=-0.02, sd=0.99, Q1=-0.66, Q3=0.64, NA=0% (n=0)
-- New column: GRS_a_z_tri -----------------------------------------------------
GRS_a_z_tri [3 levels]
Low: n=60 (20%)
Mid: n=180 (60%)
High: n=60 (20%)
<NA>: n=0 (0%)
-- Effect per SD (OR) ----------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z --
v Unadjusted | GRS_a_z: OR 1.10 (0.81-1.49), p = 0.556
v Done: 1 result row across 1 exposure and 1 model.
-- High vs Low -----------------------------------------------------------------
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_logistic --------------------------------------------------------------
i 1 exposure x 1 model = 1 logistic regression
i Input cohort: 300 participants | CI method: wald (n/n_cases reflect each model's actual analysis set)
-- GRS_a_z_tri --
v Unadjusted | GRS_a_z_triMid: OR 1.00 (0.46-2.19), p = 1
v Unadjusted | GRS_a_z_triHigh: OR 1.25 (0.49-3.16), p = 0.637
v Done: 2 result rows across 1 exposure and 1 model.
-- Trend test ------------------------------------------------------------------
! Exposure GRS_a_z_quad is not an ordered factor -- levels will be scored 0, 1, 2, ... (equal spacing assumed).
! Age and sex adjusted model skipped: age column (UKB field 21022) not found and sex column (UKB field 31) not found.
-- assoc_trend -----------------------------------------------------------------
i 1 exposure x 1 model (categorical + trend model per combination)
-- GRS_a_z_quad --
i Levels: Q1 -> Q2 -> Q3 -> Q4 | Scores: 0, 1, 2, 3
i Unadjusted | GRS_a_z_quadQ1: 1.00 (ref)
v Unadjusted | GRS_a_z_quadQ2: OR 0.90 (0.37-2.20), p = 0.821
v Unadjusted | GRS_a_z_quadQ3: OR 1.54 (0.68-3.50), p = 0.303
v Unadjusted | GRS_a_z_quadQ4: OR 1.00 (0.42-2.39), p = 1
i Unadjusted | trend: OR_per_score = 1.06 (0.81-1.38), p_trend = 0.682
v Done: 4 result rows across 1 exposure and 1 model.
-- AUC -------------------------------------------------------------------------
v Validation complete.
xlim, ticks_at will be deprecated, use set_xaxis() instead.
arrow_lab will be deprecated, use set_labs() instead.
theme will be deprecated, use style of forest() instead.
Saving _problems/test-plot-126.R
[ FAIL 1 | WARN 1 | SKIP 11 | PASS 1022 ]
══ Skipped tests (11) ══════════════════════════════════════════════════════════
• On CRAN (11): 'test-integration-assoc.R:11:1', 'test-integration-auth.R:7:1',
'test-integration-decode.R:8:1', 'test-integration-derive.R:13:1',
'test-integration-extract.R:7:1', 'test-integration-fetch.R:7:1',
'test-integration-grs.R:12:1', 'test-integration-job.R:7:1',
'test-integration-plot.R:12:1', 'test-plot.R:337:3', 'test-plot.R:347:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plot.R:119:3'): plot_forest() aborts when save=TRUE and dest=NULL ──
Error in `(function (file = if (onefile) "Rplots.pdf" else "Rplot%03d.pdf", width, height, onefile, family, title, fonts, version, paper, encoding, bg, fg, pointsize, pagecentre, colormodel, useDingbats, useKerning, fillOddEven, compress, timestamp, producer, author) { initPSandPDFfonts() new <- list() if (!missing(width)) new$width <- width if (!missing(height)) new$height <- height if (!missing(onefile)) new$onefile <- onefile if (!missing(title)) new$title <- title if (!missing(fonts)) new$fonts <- fonts if (!missing(version)) new$version <- version if (!missing(paper)) new$paper <- paper if (!missing(encoding)) new$encoding <- encoding if (!missing(bg)) new$bg <- bg if (!missing(fg)) new$fg <- fg if (!missing(pointsize)) new$pointsize <- pointsize if (!missing(pagecentre)) new$pagecentre <- pagecentre if (!missing(colormodel)) new$colormodel <- colormodel if (!missing(useDingbats)) new$useDingbats <- useDingbats if (!missing(useKerning)) new$useKerning <- useKerning if (!missing(fillOddEven)) new$fillOddEven <- fillOddEven if (!missing(compress)) new$compress <- compress if (!missing(timestamp)) new$timestamp <- timestamp if (!missing(producer)) new$producer <- producer if (!missing(author)) new$author <- author old <- check.options(new, name.opt = ".PDF.Options", envir = .PSenv) if (!missing(family) && (inherits(family, "Type1Font") || inherits(family, "CIDFont"))) { enc <- family$encoding if (inherits(family, "Type1Font") && !is.null(enc) && enc != "default" && (is.null(old$encoding) || old$encoding == "default")) old$encoding <- enc family <- family$metrics } if (is.null(old$encoding) || old$encoding == "default") old$encoding <- guessEncoding() if (!missing(family)) { if (length(family) == 4L) { family <- c(family, "Symbol.afm") } else if (length(family) == 5L) { } else if (length(family) == 1L) { pf <- pdfFonts(family)[[1L]] if (is.null(pf)) stop(gettextf("unknown family '%s'", family), domain = NA) matchFont(pf, old$encoding) } else stop("invalid 'family' argument") old$family <- family } version <- old$version versions <- c("1.1", "1.2", "1.3", "1.4", "1.5", "1.6", "1.7", "2.0") if (version %in% versions) version <- as.integer(strsplit(version, "[.]")[[1L]]) else stop("invalid PDF version") onefile <- old$onefile if (!checkIntFormat(file)) stop(gettextf("invalid 'file' argument '%s'", file), domain = NA) .External(C_PDF, file, old$paper, old$family, old$encoding, old$bg, old$fg, old$width, old$height, old$pointsize, onefile, old$pagecentre, old$title, old$fonts, version[1L], version[2L], old$colormodel, old$useDingbats, old$useKerning, old$fillOddEven, old$compress, old$timestamp, old$producer, old$author) invisible() })()`: lazy-load database '/data/localhost/ripley/R/R-clang/library/grDevices/R/grDevices.rdb' is corrupt
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-plot.R:119:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─ukbflow::plot_forest(...)
8. │ └─forestploter::forest(...)
9. │ └─forestploter:::build_plot(recipe)
10. │ ├─base::withCallingHandlers(...)
11. │ └─forestploter:::draw_forest(recipe)
12. │ └─forestploter:::add_axis_grobs(...)
13. │ └─base::sapply(...)
14. │ └─base::lapply(X = X, FUN = FUN, ...)
15. │ └─forestploter (local) FUN(X[[i]], ...)
16. │ └─grid::convertHeight(ht, unitTo = "mm", valueOnly = TRUE)
17. │ └─grid::convertUnit(...)
18. │ └─grid:::grid.Call(...)
19. └─grDevices (local) `<fn>`()
[ FAIL 1 | WARN 1 | SKIP 11 | PASS 1022 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang