autotest parses examples incorrectly #79
Description
The main function dosearch of the dosearch package has 7 examples that are not wrapped in \dontrun, but if understand the output correctly, autotest thinks that there is only 1 example. This is what I get from examples_to_yaml
#> [1] "package: dosearch"
#> [2] "functions:"
#> [3] " - dosearch:"
#> [4] " - preprocess:"
#> [5] " - 'data1 <- \"P(x,y,z)\"'"
#> [6] " - 'query1 <- \"P(y|do(x))\"'"
#> [7] " - 'graph1 <- \" x -> y z -> x z -> y \"'"
#> [8] " - 'data2 <- \"P(x,y,z)\"'"
#> [9] " - 'query2 <- \"P(y|do(x))\"'"
#> [10] " - 'graph2 <- \" x -> z z -> y x <-> y \"'"
#> [11] " - 'data <- \" p(x,z,y|s) p(y,z|t,do(x)) \"'"
#> [12] " - 'query <- \"p(y|do(x))\"'"
#> [13] " - 'graph <- \" x -> z z -> y x -> s t -> z x <-> y \"'"
#> [14] " - 'data <- \" p(x*,y*,r_x,r_y) p(y) \"'"
#> [15] " - 'graph <- \" x -> y y -> r_y r_y -> r_x \"'"
#> [16] " - 'md <- \"r_x : x, r_y : y\"'"
#> [17] " - 'if (requireNamespace(\"igraph\", quietly = TRUE)) { g_igraph <- igraph::graph.formula( x -+ z, z -+ y, x -+ y, y -+ x, simplify = FALSE ); g_igraph <- igraph::set.edge.attribute(g_igraph, \"description\", 3:4, \"U\"); dosearch(data2, query2, g_igraph) }'"
#> [18] " - 'if (requireNamespace(\"dagitty\", quietly = TRUE)) { g_dagitty <- dagitty::dagitty(\"dag{x -> z -> y; x <-> y}\"); dosearch(data2, query2, g_dagitty) }'"
#> [19] " - parameters:"
#> [20] " - data: data2"
#> [21] " - query: query2"
#> [22] " - graph: g_igraph"
#> [23] " - control: list()"
#> [24] " - classes:"
#> [25] " - control: function"
#> [26] " - control: function"
#> [27] " - class:"
#> [28] " - data: character"
#> [29] " - query: character"
#> [30] " - graph: dagitty"
#> [31] " - dosearch:"
#> [32] " - preprocess:"
#> [33] " - 'data1 <- \"P(x,y,z)\"'"
#> [34] " - 'query1 <- \"P(y|do(x))\"'"
#> [35] " - 'graph1 <- \" x -> y z -> x z -> y \"'"
#> [36] " - 'data2 <- \"P(x,y,z)\"'"
#> [37] " - 'query2 <- \"P(y|do(x))\"'"
#> [38] " - 'graph2 <- \" x -> z z -> y x <-> y \"'"
#> [39] " - 'data <- \" p(x,z,y|s) p(y,z|t,do(x)) \"'"
#> [40] " - 'query <- \"p(y|do(x))\"'"
#> [41] " - 'graph <- \" x -> z z -> y x -> s t -> z x <-> y \"'"
#> [42] " - 'data <- \" p(x*,y*,r_x,r_y) p(y) \"'"
#> [43] " - 'graph <- \" x -> y y -> r_y r_y -> r_x \"'"
#> [44] " - 'md <- \"r_x : x, r_y : y\"'"
#> [45] " - 'if (requireNamespace(\"igraph\", quietly = TRUE)) { g_igraph <- igraph::graph.formula( x -+ z, z -+ y, x -+ y, y -+ x, simplify = FALSE ); g_igraph <- igraph::set.edge.attribute(g_igraph, \"description\", 3:4, \"U\"); dosearch(data2, query2, g_igraph) }'"
#> [46] " - 'if (requireNamespace(\"dagitty\", quietly = TRUE)) { g_dagitty <- dagitty::dagitty(\"dag{x -> z -> y; x <-> y}\"); dosearch(data2, query2, g_dagitty) }'"
#> [47] " - parameters:"
#> [48] " - data: data2"
#> [49] " - query: query2"
#> [50] " - graph: g_dagitty"
#> [51] " - control: list()"
#> [52] " - classes:"
#> [53] " - control: function"
#> [54] " - control: function"
#> [55] " - class:"
#> [56] " - data: character"
#> [57] " - query: character"
#> [58] " - graph: dagitty" It seems that for some reason the examples are combined together and the preprocess-elements contain setup variables from different examples. For example, the first example in the package documentation only uses data1, query1 and graph1.
Session info
library(autotest)
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23 ucrt)
#> os Windows 10 x64 (build 19044)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate Finnish_Finland.utf8
#> ctype Finnish_Finland.utf8
#> tz Europe/Helsinki
#> date 2022-08-26
#> pandoc 2.17.1.1 @ C:/Program Files/RStudio/bin/quarto/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> autotest * 0.0.2.196 2022-08-26 [1] Github (ropensci-review-tools/autotest@382e92f)
#> cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.3)
#> cli 3.3.0 2022-04-25 [1] CRAN (R 4.1.3)
#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.3)
#> evaluate 0.16 2022-08-09 [1] CRAN (R 4.1.3)
#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.3)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.3)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.3)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.3)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.1.3)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.1.3)
#> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
#> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.3)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.3)
#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.3)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.3)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.3)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.1.3)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.1.3)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.1.3)
#> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.1.3)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.1.3)
#> rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.1)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.3)
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.2)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)
#> styler 1.7.0 2022-03-13 [1] CRAN (R 4.1.3)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.1.3)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.3)
#> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.3)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.3)
#> xfun 0.32 2022-08-10 [1] CRAN (R 4.1.3)
#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.1.2)
#>
#> [1] C:/devel/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────