Last updated on 2021-10-21 05:50:55 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 7.98 | 105.58 | 113.56 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 5.88 | 77.30 | 83.18 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 137.95 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 125.61 | OK | |||
| r-devel-windows-x86_64 | 0.2.0 | 17.00 | 137.00 | 154.00 | OK | |
| r-devel-windows-x86_64-gcc10-UCRT | 0.2.0 | ERROR | ||||
| r-patched-linux-x86_64 | 0.2.0 | 8.16 | 98.45 | 106.61 | OK | |
| r-patched-solaris-x86 | 0.2.0 | 143.10 | ERROR | |||
| r-release-linux-x86_64 | 0.2.0 | 7.39 | 97.43 | 104.82 | OK | |
| r-release-macos-arm64 | 0.2.0 | OK | ||||
| r-release-macos-x86_64 | 0.2.0 | ERROR | ||||
| r-release-windows-ix86+x86_64 | 0.2.0 | 25.00 | 138.00 | 163.00 | OK | |
| r-oldrel-macos-x86_64 | 0.2.0 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 0.2.0 | 19.00 | 132.00 | 151.00 | ERROR |
Version: 0.2.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'phytools', 'paleotree', 'dispRity'
Flavor: r-devel-windows-x86_64-gcc10-UCRT
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in 'deeptime-Ex.R' failed
The error most likely occurred in:
> ### Name: gggeo_scale_old
> ### Title: Add a geologic scale to ggplots (old version)
> ### Aliases: gggeo_scale_old
>
> ### ** Examples
>
> library(ggplot2)
> # bottom scale by default
> p <- ggplot() +
+ geom_point(aes(y = runif(1000, .5, 8), x = runif(1000, 0, 1000))) +
+ scale_x_reverse() +
+ coord_cartesian(xlim = c(0, 1000), ylim = c(0,8), expand = FALSE) +
+ theme_classic()
> gggeo_scale_old(p)
>
> # can specify any side of the plot
> p <- ggplot() +
+ geom_point(aes(x = runif(1000, .5, 8), y = runif(1000, 0, 1000))) +
+ scale_y_reverse() +
+ coord_cartesian(xlim = c(0, 8), ylim = c(0,1000), expand = FALSE) +
+ theme_classic()
> gggeo_scale_old(p, pos = "left", rot = 90)
>
> # can add multiple scales
> p <- ggplot() +
+ geom_point(aes(y = runif(1000, 1, 8), x = runif(1000, 0, 1000))) +
+ scale_x_reverse() +
+ coord_cartesian(xlim = c(0, 100), ylim = c(0,8), expand = FALSE) +
+ theme_classic()
> p <- gggeo_scale_old(p, height = .03, abbrv = FALSE)
> p <- gggeo_scale_old(p, dat = "epochs", gap = .03, height = .1, rot = 90, size = 2.5, abbrv = FALSE)
>
> # intervals on both sides for different timescales (ICS stages vs North American Land Mammal Ages)
> p <- ggplot() +
+ geom_point(aes(x = runif(1000, 1, 9), y = runif(1000, 0, 65))) +
+ scale_y_reverse() +
+ coord_cartesian(xlim = c(0, 10), ylim = c(0,65), expand = FALSE) +
+ theme_classic()
> p <- gggeo_scale_old(p, dat = "stages", pos = "left", height = .1, size = 2.5, abbrv = FALSE)
> gggeo_scale_old(p, dat = "North American Land Mammal Ages", pos = "right", height = .1, size = 2.5,
+ abbrv = FALSE)
>
> #can add scales to a faceted plot
> df <- data.frame(x = runif(1000,0,541), y = runif(1000,.5,8), z = sample(c(1,2,3,4), 1000, TRUE))
> p <- ggplot(df) +
+ geom_point(aes(x, y)) +
+ scale_x_reverse() +
+ coord_cartesian(xlim = c(0, 541), ylim = c(0,8), expand = FALSE) +
+ theme_classic() +
+ facet_wrap(~z, nrow = 2)
> gggeo_scale_old(p)
>
> #can even add a scale to a phylogeny (using ggtree)
> library(phytools)
Error in library(phytools) : there is no package called 'phytools'
Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT
Version: 0.2.0
Check: tests
Result: ERROR
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(deeptime)
>
> test_check("deeptime")
Error in library(paleotree, quietly = TRUE) :
there is no package called 'paleotree'
Calls: test_check ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘deeptime-Ex.R’ failed
The error most likely occurred in:
> ### Name: gggeo_scale
> ### Title: Add a geologic scale to ggplots
> ### Aliases: gggeo_scale gggeo_scale.gtable gggeo_scale.ggplot
> ### gggeo_scale.geo_scale print.geo_scale
>
> ### ** Examples
>
> library(ggplot2)
> # bottom scale by default
> p <- ggplot() +
+ geom_point(aes(y = runif(1000, 0, 8), x = runif(1000, 0, 1000))) +
+ scale_x_reverse() +
+ coord_cartesian(xlim = c(1000, 0), ylim = c(0, 8), expand = FALSE) +
+ theme_classic()
> gggeo_scale(p)
>
> # can specify any side of the plot
> p <- ggplot() +
+ geom_point(aes(x = runif(1000, 0, 8), y = runif(1000, 0, 1000))) +
+ scale_y_reverse() +
+ coord_cartesian(xlim = c(0, 8), ylim = c(1000, 0), expand = FALSE) +
+ theme_classic()
> gggeo_scale(p, pos = "left", rot = 90)
>
> # can add multiple scales
> p <- ggplot() +
+ geom_point(aes(y = runif(1000, 0, 8), x = runif(1000, 0, 100))) +
+ scale_x_reverse() +
+ coord_cartesian(xlim = c(100, 0), ylim = c(0, 8), expand = FALSE) +
+ theme_classic()
> p <- gggeo_scale(p, abbrv = FALSE)
> p <- gggeo_scale(p, dat = "epochs", height = unit(4, "lines"), rot = 90, size = 2.5, abbrv = FALSE)
> gggeo_scale(p, dat = "stages", height = unit(4, "lines"), rot = 90, size = 2.5, abbrv = FALSE)
>
> # intervals on both sides for different timescales (ICS stages vs North American Land Mammal Ages)
> p <- ggplot() +
+ geom_point(aes(x = runif(1000, 0, 10), y = runif(1000, 0, 65))) +
+ scale_y_reverse() +
+ coord_cartesian(xlim = c(0, 10), ylim = c(65, 0), expand = FALSE) +
+ theme_classic()
> p <- gggeo_scale(p, dat = "stages", pos = "left", height = unit(4, "lines"), size = 2.5,
+ abbrv = FALSE)
> gggeo_scale(p, dat = "North American Land Mammal Ages", pos = "right", height = unit(4, "lines"),
+ size = 2.5, abbrv = FALSE)
Warning in open.connection(file, "rt") :
URL 'https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=North%20American%20Land%20Mammal%20Ages': status was 'Peer certificate cannot be authenticated with given CA certificates'
Error in open.connection(file, "rt") :
cannot open the connection to 'https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=North%20American%20Land%20Mammal%20Ages'
Calls: gggeo_scale ... <Anonymous> -> read.table -> open -> open.connection
Execution halted
Flavors: r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/60s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(deeptime)
>
> test_check("deeptime")
NULL
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (13)
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-coord_geo.R:42:3): scales on different sides works ──────────────
Error in `open.connection(file, "rt")`: cannot open the connection to 'https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=Geomagnetic%20Polarity%20Chron'
Backtrace:
█
1. └─vdiffr::expect_doppelganger("scales on different sides", gg) test-coord_geo.R:42:2
2. └─vdiffr:::writer(fig, testcase, title)
3. ├─vdiffr:::print_plot(plot, title)
4. └─vdiffr:::print_plot.ggplot(plot, title)
5. ├─base::print(p)
6. └─ggplot2:::print.ggplot(p)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2:::ggplot_gtable.ggplot_built(data)
9. └─layout$render(geom_grobs, data, theme, plot$labels)
10. └─ggplot2:::f(..., self = self)
11. └─self$facet$draw_panels(...)
12. └─ggplot2:::f(...)
13. └─coord$render_axis_v(range, theme)
14. └─deeptime:::f(..., self = self)
15. └─deeptime:::render_geo_scale(self, panel_params, theme, "left")
16. └─base::mapply(...)
17. └─(function (self, dat, fill, color, alpha, pos, lab, rot, abbrv, ...
18. └─deeptime::getScaleData(dat)
19. └─utils::read.csv(URL, header = TRUE, stringsAsFactors = FALSE)
20. └─utils::read.table(...)
21. ├─base::open(file, "rt")
22. └─base::open.connection(file, "rt")
── Error (test-coord_geo.R:53:3): scales on different sides works ──────────────
Error in `open.connection(file, "rt")`: cannot open the connection to 'https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=Geomagnetic%20Polarity%20Chron'
Backtrace:
█
1. └─vdiffr::expect_doppelganger("scales on different sides", gg) test-coord_geo.R:53:2
2. └─vdiffr:::writer(fig, testcase, title)
3. ├─vdiffr:::print_plot(plot, title)
4. └─vdiffr:::print_plot.ggplot(plot, title)
5. ├─base::print(p)
6. └─ggplot2:::print.ggplot(p)
7. ├─ggplot2::ggplot_gtable(data)
8. └─ggplot2:::ggplot_gtable.ggplot_built(data)
9. └─layout$render(geom_grobs, data, theme, plot$labels)
10. └─ggplot2:::f(..., self = self)
11. └─self$facet$draw_panels(...)
12. └─ggplot2:::f(...)
13. └─coord$render_axis_v(range, theme)
14. └─deeptime:::f(..., self = self)
15. └─deeptime:::render_geo_scale(self, panel_params, theme, "left")
16. └─base::mapply(...)
17. └─(function (self, dat, fill, color, alpha, pos, lab, rot, abbrv, ...
18. └─deeptime::getScaleData(dat)
19. └─utils::read.csv(URL, header = TRUE, stringsAsFactors = FALSE)
20. └─utils::read.table(...)
21. ├─base::open(file, "rt")
22. └─base::open.connection(file, "rt")
[ FAIL 2 | WARN 2 | SKIP 13 | PASS 15 ]
Deleting unused snapshots:
* coord_geo/scale-on-all-facets.svg
* coord_trans_xy/coord-trans-xy-with-expansion.svg
* ggarrange2/double-ggarrange2-layout.svg
* ggarrange2/double-ggarrange2.svg
* ggarrange2/ggarrange2-layout.svg
* ggarrange2/ggarrange2-with-layout-layout.svg
* ggarrange2/ggarrange2-with-layout.svg
* gggeo_scale/gggeo-scale-left-and-right.svg
* gggeo_scale/gggeo-scale-top.svg
Error: Test failures
In addition: Warning messages:
1: In for (j in seq_along(x)) { :
closing unused connection 5 (https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=Geomagnetic%20Polarity%20Chron)
2: In for (j in seq_along(x)) { :
closing unused connection 4 (https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=Geomagnetic%20Polarity%20Chron)
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.2.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ggtree’
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
* coord_geo/scale-on-ggtree.svg
* coord_trans_xy/coord-trans-xy-with-expansion.svg
* ggarrange2/double-ggarrange2-layout.svg
* ggarrange2/double-ggarrange2.svg
* ggarrange2/ggarrange2-layout.svg
* ggarrange2/ggarrange2-with-layout-layout.svg
* ggarrange2/ggarrange2-with-layout.svg
* gggeo_scale/gggeo-scale-left-and-right.svg
* gggeo_scale/gggeo-scale-top.svg
Error: Test failures
In addition: Warning messages:
1: closing unused connection 4 (https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=Geomagnetic%20Polarity%20Chron)
2: In .subset2(x, name) :
closing unused connection 4 (https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=Geomagnetic%20Polarity%20Chron)
Execution halted
Flavor: r-release-macos-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
* coord_geo/scale-on-ggtree.svg
* coord_trans_xy/coord-trans-xy-with-expansion.svg
* ggarrange2/double-ggarrange2-layout.svg
* ggarrange2/double-ggarrange2.svg
* ggarrange2/ggarrange2-layout.svg
* ggarrange2/ggarrange2-with-layout-layout.svg
* ggarrange2/ggarrange2-with-layout.svg
* gggeo_scale/gggeo-scale-left-and-right.svg
* gggeo_scale/gggeo-scale-top.svg
Error: Test failures
In addition: Warning messages:
1: closing unused connection 4 (https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=Geomagnetic%20Polarity%20Chron)
2: In for (j in seq_along(x)) { :
closing unused connection 4 (https://macrostrat.org/api/v2/defs/intervals?format=csv×cale=Geomagnetic%20Polarity%20Chron)
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in 'deeptime-Ex.R' failed
The error most likely occurred in:
> ### Name: gggeo_scale_old
> ### Title: Add a geologic scale to ggplots (old version)
> ### Aliases: gggeo_scale_old
>
> ### ** Examples
>
> library(ggplot2)
> # bottom scale by default
> p <- ggplot() +
+ geom_point(aes(y = runif(1000, .5, 8), x = runif(1000, 0, 1000))) +
+ scale_x_reverse() +
+ coord_cartesian(xlim = c(0, 1000), ylim = c(0,8), expand = FALSE) +
+ theme_classic()
> gggeo_scale_old(p)
>
> # can specify any side of the plot
> p <- ggplot() +
+ geom_point(aes(x = runif(1000, .5, 8), y = runif(1000, 0, 1000))) +
+ scale_y_reverse() +
+ coord_cartesian(xlim = c(0, 8), ylim = c(0,1000), expand = FALSE) +
+ theme_classic()
> gggeo_scale_old(p, pos = "left", rot = 90)
>
> # can add multiple scales
> p <- ggplot() +
+ geom_point(aes(y = runif(1000, 1, 8), x = runif(1000, 0, 1000))) +
+ scale_x_reverse() +
+ coord_cartesian(xlim = c(0, 100), ylim = c(0,8), expand = FALSE) +
+ theme_classic()
> p <- gggeo_scale_old(p, height = .03, abbrv = FALSE)
> p <- gggeo_scale_old(p, dat = "epochs", gap = .03, height = .1, rot = 90, size = 2.5, abbrv = FALSE)
>
> # intervals on both sides for different timescales (ICS stages vs North American Land Mammal Ages)
> p <- ggplot() +
+ geom_point(aes(x = runif(1000, 1, 9), y = runif(1000, 0, 65))) +
+ scale_y_reverse() +
+ coord_cartesian(xlim = c(0, 10), ylim = c(0,65), expand = FALSE) +
+ theme_classic()
> p <- gggeo_scale_old(p, dat = "stages", pos = "left", height = .1, size = 2.5, abbrv = FALSE)
> gggeo_scale_old(p, dat = "North American Land Mammal Ages", pos = "right", height = .1, size = 2.5,
+ abbrv = FALSE)
>
> #can add scales to a faceted plot
> df <- data.frame(x = runif(1000,0,541), y = runif(1000,.5,8), z = sample(c(1,2,3,4), 1000, TRUE))
> p <- ggplot(df) +
+ geom_point(aes(x, y)) +
+ scale_x_reverse() +
+ coord_cartesian(xlim = c(0, 541), ylim = c(0,8), expand = FALSE) +
+ theme_classic() +
+ facet_wrap(~z, nrow = 2)
> gggeo_scale_old(p)
>
> #can even add a scale to a phylogeny (using ggtree)
> library(phytools)
Loading required package: ape
Loading required package: maps
> library(ggtree)
Error: package or namespace load failed for 'ggtree':
object 'get_aes_var' is not exported by 'namespace:rvcheck'
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(deeptime)
>
> test_check("deeptime")
NULL
== Skipped tests ===============================================================
* The R graphics engine is too old. (13)
== Failed tests ================================================================
-- Error (test-coord_geo.R:107:1): (code run outside of `test_that()`) ---------
Error: package or namespace load failed for 'ggtree':
object 'get_aes_var' is not exported by 'namespace:rvcheck'
Backtrace:
x
1. +-base::suppressPackageStartupMessages(library(ggtree, quietly = TRUE)) test-coord_geo.R:107:0
2. | \-base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
3. \-base::library(ggtree, quietly = TRUE)
4. \-base::tryCatch(...)
5. \-base:::tryCatchList(expr, classes, parentenv, handlers)
6. \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. \-value[[3L]](cond)
[ FAIL 1 | WARN 0 | SKIP 13 | PASS 15 ]
Deleting unused snapshots:
* coord_geo/scale-on-all-facets.svg
* coord_geo/scale-on-fossil-ggtree.svg
* coord_geo/scale-on-ggtree.svg
* coord_trans_xy/coord-trans-xy-with-expansion.svg
* ggarrange2/double-ggarrange2-layout.svg
* ggarrange2/double-ggarrange2.svg
* ggarrange2/ggarrange2-layout.svg
* ggarrange2/ggarrange2-with-layout-layout.svg
* ggarrange2/ggarrange2-with-layout.svg
* gggeo_scale/gggeo-scale-left-and-right.svg
* gggeo_scale/gggeo-scale-top.svg
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64