gratia
gratia copied to clipboard
Published
20 hours ago •
gavinsimpson
gavinsimpson
JOSS review: failing tests
Running tests for the package on a Debian sid system (details at the bottom), I get failures on visual diffs of the plots.
I'm not familiar with vdiffr so not sure if this is expected or not?
Looking at these, I don't see any differences in some plots (see below also). I thought it was an mgcv/scam/ggplot2 version issue but re-installed from CRAN and got the following:
✔ | F W S OK | Context
✔ | 82 | add-functions [2.4s]
✔ | 4 | bam-ar
✔ | 4 | basis-size
✖ | 2 1 29 | basis [6.1s]
────────────────────────────────────────────────────────────────────────────────
Failure (test-basis.R:83:3): basis() works with bivariate tprs smooths
Snapshot of `testcase` to 'basis/draw-basis-works-with-a-bivariate-tprs-contour.svg' has changed
Run `testthat::snapshot_review('basis/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-basis.R:83:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-basis.R:104:3): basis() works with bivariate te smooths
Snapshot of `testcase` to 'basis/draw-basis-works-with-a-bivariate-te-contour.svg' has changed
Run `testthat::snapshot_review('basis/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-basis.R:104:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
────────────────────────────────────────────────────────────────────────────────
✔ | 14 | by-variables
✖ | 3 29 | compare-smooths [3.1s]
────────────────────────────────────────────────────────────────────────────────
Failure (test-compare-smooths.R:37:3): draw.compare_smooths() can plot a comparison of smooths
Snapshot of `testcase` to 'compare-smooths/compare-smooths-all-smooths.svg' has changed
Run `testthat::snapshot_review('compare-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-compare-smooths.R:37:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-compare-smooths.R:38:3): draw.compare_smooths() can plot a comparison of smooths
Snapshot of `testcase` to 'compare-smooths/compare-smooths-set-nrow-ncol.svg' has changed
Run `testthat::snapshot_review('compare-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-compare-smooths.R:38:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-compare-smooths.R:39:3): draw.compare_smooths() can plot a comparison of smooths
Snapshot of `testcase` to 'compare-smooths/compare-smooths-bottom-legend.svg' has changed
Run `testthat::snapshot_review('compare-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-compare-smooths.R:39:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
────────────────────────────────────────────────────────────────────────────────
✔ | 20 | concurvity
✔ | 1 44 | confint-methods [1.1s]
✔ | 100 | data-sim
✔ | 99 | data-slice
✔ | 36 | datagen
✖ | 2 222 | derivatives [7.1s]
────────────────────────────────────────────────────────────────────────────────
Failure (test-derivatives.R:441:3): derivatives() works for factor by smooths issue 47
Snapshot of `testcase` to 'derivatives/draw-issue-47-derivatives-for-gamm-factor-by.svg' has changed
Run `testthat::snapshot_review('derivatives/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-derivatives.R:441:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-derivatives.R:477:3): derivatives() works for fs smooths issue 57 and 301
Snapshot of `testcase` to 'derivatives/draw-issue-57-derivatives-for-factor-by.svg' has changed
Run `testthat::snapshot_review('derivatives/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-derivatives.R:477:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
────────────────────────────────────────────────────────────────────────────────
✔ | 40 | diagnostic-plots [3.3s]
✖ | 2 30 | difference-smooths [5.9s]
────────────────────────────────────────────────────────────────────────────────
Failure (test-difference-smooths.R:76:3): difference_smooths() works for a gamm model
Snapshot of `testcase` to 'difference-smooths/draw-difference-smooths-gamm.svg' has changed
Run `testthat::snapshot_review('difference-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-difference-smooths.R:76:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-difference-smooths.R:129:3): difference_smooths() works for a bivariate gam
Snapshot of `testcase` to 'difference-smooths/draw-difference-smooths-bivariate-gam-contours.svg' has changed
Run `testthat::snapshot_review('difference-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-difference-smooths.R:129:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
────────────────────────────────────────────────────────────────────────────────
✔ | 12 | distribution-helpers
✖ | 3 66 | draw-gam [15.8s]
────────────────────────────────────────────────────────────────────────────────
Failure (test-draw-gam.R:47:3): draw.gam works for m_gamm4
Snapshot of `testcase` to 'draw-gam/draw-gam-m-gamm4.svg' has changed
Run `testthat::snapshot_review('draw-gam/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger("draw_gam m_gamm4", plt) at test-draw-gam.R:47:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-draw-gam.R:91:3): draw.gam works for dlnm_m
Snapshot of `testcase` to 'draw-gam/draw-gam-dlnm-m.svg' has changed
Run `testthat::snapshot_review('draw-gam/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger("draw_gam dlnm_m", plt) at test-draw-gam.R:91:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-draw-gam.R:201:3): draw.gam works for a quadvariate smooth
Snapshot of `testcase` to 'draw-gam/draw-gam-quadvar-te.svg' has changed
Run `testthat::snapshot_review('draw-gam/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger("draw_gam quadvar te", plt) at test-draw-gam.R:201:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
────────────────────────────────────────────────────────────────────────────────
Maximum number of failures exceeded; quitting at end of file.
ℹ Increase this number with (e.g.) `testthat::set_max_fails(Inf)`
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 48.7 s
── Skipped tests (2) ───────────────────────────────────────────────────────────
• On Linux (1): test-confint-methods.R:199:3
• This needs fixing as something in scam changed (1): test-basis.R:53:3
── Failed tests ────────────────────────────────────────────────────────────────
Failure (test-basis.R:83:3): basis() works with bivariate tprs smooths
Snapshot of `testcase` to 'basis/draw-basis-works-with-a-bivariate-tprs-contour.svg' has changed
Run `testthat::snapshot_review('basis/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-basis.R:83:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-basis.R:104:3): basis() works with bivariate te smooths
Snapshot of `testcase` to 'basis/draw-basis-works-with-a-bivariate-te-contour.svg' has changed
Run `testthat::snapshot_review('basis/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-basis.R:104:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-compare-smooths.R:37:3): draw.compare_smooths() can plot a comparison of smooths
Snapshot of `testcase` to 'compare-smooths/compare-smooths-all-smooths.svg' has changed
Run `testthat::snapshot_review('compare-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-compare-smooths.R:37:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-compare-smooths.R:38:3): draw.compare_smooths() can plot a comparison of smooths
Snapshot of `testcase` to 'compare-smooths/compare-smooths-set-nrow-ncol.svg' has changed
Run `testthat::snapshot_review('compare-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-compare-smooths.R:38:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-compare-smooths.R:39:3): draw.compare_smooths() can plot a comparison of smooths
Snapshot of `testcase` to 'compare-smooths/compare-smooths-bottom-legend.svg' has changed
Run `testthat::snapshot_review('compare-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-compare-smooths.R:39:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-derivatives.R:441:3): derivatives() works for factor by smooths issue 47
Snapshot of `testcase` to 'derivatives/draw-issue-47-derivatives-for-gamm-factor-by.svg' has changed
Run `testthat::snapshot_review('derivatives/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-derivatives.R:441:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-derivatives.R:477:3): derivatives() works for fs smooths issue 57 and 301
Snapshot of `testcase` to 'derivatives/draw-issue-57-derivatives-for-factor-by.svg' has changed
Run `testthat::snapshot_review('derivatives/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-derivatives.R:477:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-difference-smooths.R:76:3): difference_smooths() works for a gamm model
Snapshot of `testcase` to 'difference-smooths/draw-difference-smooths-gamm.svg' has changed
Run `testthat::snapshot_review('difference-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-difference-smooths.R:76:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-difference-smooths.R:129:3): difference_smooths() works for a bivariate gam
Snapshot of `testcase` to 'difference-smooths/draw-difference-smooths-bivariate-gam-contours.svg' has changed
Run `testthat::snapshot_review('difference-smooths/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger(...) at test-difference-smooths.R:129:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-draw-gam.R:47:3): draw.gam works for m_gamm4
Snapshot of `testcase` to 'draw-gam/draw-gam-m-gamm4.svg' has changed
Run `testthat::snapshot_review('draw-gam/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger("draw_gam m_gamm4", plt) at test-draw-gam.R:47:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-draw-gam.R:91:3): draw.gam works for dlnm_m
Snapshot of `testcase` to 'draw-gam/draw-gam-dlnm-m.svg' has changed
Run `testthat::snapshot_review('draw-gam/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger("draw_gam dlnm_m", plt) at test-draw-gam.R:91:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
Failure (test-draw-gam.R:201:3): draw.gam works for a quadvariate smooth
Snapshot of `testcase` to 'draw-gam/draw-gam-quadvar-te.svg' has changed
Run `testthat::snapshot_review('draw-gam/')` to review changes
Backtrace:
▆
1. └─gratia:::expect_doppelganger("draw_gam quadvar te", plt) at test-draw-gam.R:201:3
2. └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:39:5
3. ├─base::withCallingHandlers(...)
4. └─testthat::expect_snapshot_file(...)
[ FAIL 12 | WARN 0 | SKIP 2 | PASS 831 ]
══ Terminated early ════════════════════════════════════════════════════════════
>
Example "bad" plots:
old:
new:
another with an actual difference
old:
new:
Finally, some information, about my session (post-running devtools::test()):
> session_info()
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.4.1 (2024-06-14)
os Debian GNU/Linux 12 (bookworm)
system x86_64, linux-gnu
ui X11
language en_GB:en
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/London
date 2024-07-29
pandoc 2.17.1.1 @ /usr/bin/pandoc
─ Packages ───────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
boot 1.3-30 2024-02-26 [1] CRAN (R 4.4.0)
brio 1.1.5 2024-04-24 [1] CRAN (R 4.4.0)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.4.0)
cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.1)
colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.4.1)
desc 1.4.3 2023-12-10 [1] CRAN (R 4.4.0)
devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.4.0)
digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.0)
evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0)
farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.4.0)
fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0)
gamm4 * 0.2-6 2020-04-03 [1] CRAN (R 4.4.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
ggokabeito 0.1.0 2021-10-18 [1] CRAN (R 4.4.0)
ggplot2 * 3.5.1 2024-04-23 [1] CRAN (R 4.4.1)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
P gratia * 0.9.2.9005 2024-07-29 [?] Github (gavinsimpson/gratia@d7c32c3)
gtable 0.3.5 2024-04-22 [1] CRAN (R 4.4.0)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0)
isoband 0.2.7 2022-12-20 [1] CRAN (R 4.4.0)
labeling 0.4.3 2023-08-29 [1] CRAN (R 4.4.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0)
lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.0)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
lme4 * 1.1-35.3 2024-04-16 [1] CRAN (R 4.4.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
MASS 7.3-60.2 2024-04-26 [1] CRAN (R 4.4.0)
Matrix * 1.7-0 2024-04-26 [1] CRAN (R 4.4.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0)
mgcv * 1.9-1 2023-12-21 [1] CRAN (R 4.4.1)
mime 0.12 2021-09-28 [1] CRAN (R 4.4.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0)
minqa 1.2.6 2023-09-11 [1] CRAN (R 4.4.0)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0)
mvnfast 0.2.8 2023-02-23 [1] CRAN (R 4.4.0)
nlme * 3.1-164 2023-11-27 [1] CRAN (R 4.4.0)
nloptr 2.0.3 2022-05-26 [1] CRAN (R 4.4.0)
patchwork 1.2.0 2024-01-08 [1] CRAN (R 4.4.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.4.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.4.0)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0)
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.4.0)
Rcpp 1.0.13 2024-07-17 [1] CRAN (R 4.4.1)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0)
rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.0)
rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.4.0)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0)
scam * 1.2-17 2024-06-19 [1] CRAN (R 4.4.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
testthat * 3.2.1.1 2024-04-14 [1] CRAN (R 4.4.0)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.0)
usethis * 2.2.3 2024-02-19 [1] CRAN (R 4.4.0)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
vdiffr 1.0.7 2023-09-22 [1] CRAN (R 4.4.0)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.4.0)
waldo 0.5.2 2023-11-02 [1] CRAN (R 4.4.0)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
[1] /home/dill/R/x86_64-pc-linux-gnu-library/4.4
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
P ── Loaded and on-disk path mismatch.
──────────────────────────────────────────────────────────────────────────────
>
