CRAN Package Check Results for Package deeptime

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

Check Details

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&timescale=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&timescale=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&timescale=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$render_axis_v(range, theme)
     14. └─deeptime:::f(..., self = self)
     15. └─deeptime:::render_geo_scale(self, panel_params, theme, "left")
     16. └─base::mapply(...)
     17. └─(function (self, dat, fill, color, alpha, pos, lab, rot, abbrv, ...
     18. └─deeptime::getScaleData(dat)
     19. └─utils::read.csv(URL, header = TRUE, stringsAsFactors = FALSE)
     20. └─utils::read.table(...)
     21. ├─base::open(file, "rt")
     22. └─base::open.connection(file, "rt")
     ── Error (test-coord_geo.R:53:3): scales on different sides works ──────────────
     Error in `open.connection(file, "rt")`: cannot open the connection to 'https://macrostrat.org/api/v2/defs/intervals?format=csv&timescale=Geomagnetic%20Polarity%20Chron'
     Backtrace:
     █
     1. └─vdiffr::expect_doppelganger("scales on different sides", gg) test-coord_geo.R:53:2
     2. └─vdiffr:::writer(fig, testcase, title)
     3. ├─vdiffr:::print_plot(plot, title)
     4. └─vdiffr:::print_plot.ggplot(plot, title)
     5. ├─base::print(p)
     6. └─ggplot2:::print.ggplot(p)
     7. ├─ggplot2::ggplot_gtable(data)
     8. └─ggplot2:::ggplot_gtable.ggplot_built(data)
     9. └─layout$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&timescale=Geomagnetic%20Polarity%20Chron)
     2: In for (j in seq_along(x)) { :
     closing unused connection 4 (https://macrostrat.org/api/v2/defs/intervals?format=csv&timescale=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&timescale=Geomagnetic%20Polarity%20Chron)
     2: In .subset2(x, name) :
     closing unused connection 4 (https://macrostrat.org/api/v2/defs/intervals?format=csv&timescale=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&timescale=Geomagnetic%20Polarity%20Chron)
     2: In for (j in seq_along(x)) { :
     closing unused connection 4 (https://macrostrat.org/api/v2/defs/intervals?format=csv&timescale=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