segfaults with patchwork inside rmarkdown inside shiny inside shinytest #278

bersbersbers · 2021-10-04T20:38:08Z

I have a problem that is very delicate to reproduce. The only way I can reproduce it, though with varying success, is by plotting a some patchwork inside an Rmd file which is rendered using rmarkdown::render() in a shiny app tested using shinytest. However, running the Shiny app itself works fine, and so far, I have not found a way to remove anything meaningful from the Shiny app, or the problem stops to show.

The problem started after I changed a bunch of code before the patchwork calls - but the output of this changed piece of code is not used in the patchwork at all, and is identical to the output before the change. I can go back in time using version control to a point where the problem never shows, and then gradually change my code again to make the problem appear more and more often.

I collected some 10 stack traces, all of which hint at patchwork, so I wonder if my seemingly unrelated code change may have unearthed a bug in patchwork. It may also be that this is a bug in shiny, shinytest, rmarkdown, grid or one of countless other packages - if anyone has an idea how I could find this out, I would be glad.

Here's the tops of the stacktraces:

C/E -----------  1: modify_list(element_gp, gp)
C/E -----------  2: grob(label = label, x = x, y = y, just = just, hjust = hjust,     vjust = vjust, rot = rot, check.overlap = check.overlap,     name = name, gp = gp, vp = vp, cl = "text")
C/E -----------  3: textGrob(label, x, y, hjust = hjust, vjust = vjust, rot = angle,     gp = gp, check.overlap = check.overlap)
C/E -----------  4: title_spec(label, x = x, y = y, hjust = hjust, vjust = vjust,     angle = angle, gp = gp, debug = debug, check.overlap = check.overlap)
C/E -----------  5: titleGrob(label, x, y, hjust = hj, vjust = vj, angle = angle,     gp = modify_list(element_gp, gp), margin = margin, margin_x = margin_x,     margin_y = margin_y, debug = element$debug, ...)
C/E -----------  6: element_grob.element_text(title.theme, label = guide$title, hjust = title.hjust,     vjust = title.vjust, margin_x = TRUE, margin_y = TRUE)
C/E -----------  7: element_grob(title.theme, label = guide$title, hjust = title.hjust,     vjust = title.vjust, margin_x = TRUE, margin_y = TRUE)
C/E -----------  8: grobName(grob, prefix)
C/E -----------  9: ggname("guide.title", element_grob(title.theme, label = guide$title,     hjust = title.hjust, vjust = title.vjust, margin_x = TRUE,     margin_y = TRUE))
C/E ----------- 10: guide_gengrob.colorbar(X[[i]], ...)
C/E ----------- 11: FUN(X[[i]], ...)
C/E ----------- 12: lapply(gdefs, guide_gengrob, theme)
C/E ----------- 13: guides_gengrob(gdefs, theme)
C/E ----------- 14: build_guides(plot$scales, plot$layers, plot$mapping, position,     theme, plot$guides, plot$labels)
C/E ----------- 15: ggplot_gtable.ggplot_built(ggplot_build(x))
C/E ----------- 16: ggplot_gtable(ggplot_build(x))
C/E ----------- 17: ggplotGrob(x)
C/E ----------- 18: plot_table.ggplot(X[[i]], ...)
C/E ----------- 19: FUN(X[[i]], ...)
C/E ----------- 20: lapply(x$plots, plot_table, guides = guides)
C/E ----------- 21: build_patchwork(plot, plot$layout$guides %||% "auto")
C/E ----------- 22: print.patchwork(x)
C/E ----------- 23: print(x)
C/E ----------- 24: normal_print(x)
C/E ----------- 25: knit_print.default(x, ...)
C/E ----------- 26: knit_print(x, ...)

C/E -----------  1: validGP(list(...))
C/E -----------  2: gpar()
C/E -----------  3: is.gpar(gp)
C/E -----------  4: valid.viewport(x, y, width, height, just, gp, clip, mask, xscale,     yscale, angle, layout, layout.pos.row, layout.pos.col, name)
C/E -----------  5: viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,     clip = clip)
C/E -----------  6: (function (vp_name, t, r, b, l, clip) {    viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,         clip = clip)})(vp_name = dots[[1L]][[1L]], t = dots[[2L]][[1L]], r = dots[[3L]][[1L]],     b = dots[[4L]][[1L]], l = dots[[5L]][[1L]], clip = dots[[6L]][[1L]])
C/E -----------  7: mapply(child_vp, vp_name = vpname(x$layout), t = .subset2(x$layout,     "t"), r = .subset2(x$layout, "r"), b = .subset2(x$layout,     "b"), l = .subset2(x$layout, "l"), clip = x$layout$clip,     SIMPLIFY = FALSE)
C/E -----------  8: makeContent.gtable(x)
C/E -----------  9: makeContent(x)
C/E ----------- 10: drawGTree(x)
C/E ----------- 11: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
C/E ----------- 12: grid.draw.gTree(x$children[[i]], recording = FALSE)
C/E ----------- 13: grid.draw(x$children[[i]], recording = FALSE)
C/E ----------- 14: drawGTree(x)
C/E ----------- 15: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
C/E ----------- 16: grid.draw.gTree(gtable)
C/E ----------- 17: grid.draw(gtable)
C/E ----------- 18: print.patchwork(x)
C/E ----------- 19: print(x)
C/E ----------- 20: normal_print(x)
C/E ----------- 21: knit_print.default(x, ...)
C/E ----------- 22: knit_print(x, ...)

C/E ----------- �[35m 1: mapply(child_vp, vp_name = vpname(x$layout), t = .subset2(x$layout,     "t"), r = .subset2(x$layout, "r"), b = .subset2(x$layout,     "b"), l = .subset2(x$layout, "l"), clip = x$layout$clip,     SIMPLIFY = FALSE)�[39m
C/E ----------- �[35m 2: makeContent.gtable(x)�[39m
C/E ----------- �[35m 3: makeContent(x)�[39m
C/E ----------- �[35m 4: drawGTree(x)�[39m
C/E ----------- �[35m 5: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m 6: grid.draw.gTree(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m 7: grid.draw(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m 8: drawGTree(x)�[39m
C/E ----------- �[35m 9: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m10: grid.draw.gTree(gtable)�[39m
C/E ----------- �[35m11: grid.draw(gtable)�[39m
C/E ----------- �[35m12: print.patchwork(x)�[39m
C/E ----------- �[35m13: print(x)�[39m
C/E ----------- �[35m14: normal_print(x)�[39m
C/E ----------- �[35m15: knit_print.default(x, ...)�[39m
C/E ----------- �[35m16: knit_print(x, ...)�[39m

C/E ----------- �[35m 1: numnotnull("alpha")�[39m
C/E ----------- �[35m 2: validGP(list(...))�[39m
C/E ----------- �[35m 3: gpar()�[39m
C/E ----------- �[35m 4: is.gpar(gp)�[39m
C/E ----------- �[35m 5: valid.viewport(x, y, width, height, just, gp, clip, mask, xscale,     yscale, angle, layout, layout.pos.row, layout.pos.col, name)�[39m
C/E ----------- �[35m 6: viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,     clip = clip)�[39m
C/E ----------- �[35m 7: (function (vp_name, t, r, b, l, clip) {    viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,         clip = clip)})(vp_name = dots[[1L]][[1L]], t = dots[[2L]][[1L]], r = dots[[3L]][[1L]],     b = dots[[4L]][[1L]], l = dots[[5L]][[1L]], clip = dots[[6L]][[1L]])�[39m
C/E ----------- �[35m 8: mapply(child_vp, vp_name = vpname(x$layout), t = .subset2(x$layout,     "t"), r = .subset2(x$layout, "r"), b = .subset2(x$layout,     "b"), l = .subset2(x$layout, "l"), clip = x$layout$clip,     SIMPLIFY = FALSE)�[39m
C/E ----------- �[35m 9: makeContent.gtable(x)�[39m
C/E ----------- �[35m10: makeContent(x)�[39m
C/E ----------- �[35m11: drawGTree(x)�[39m
C/E ----------- �[35m12: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m13: grid.draw.gTree(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m14: grid.draw(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m15: drawGTree(x)�[39m
C/E ----------- �[35m16: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m17: grid.draw.gTree(gtable)�[39m
C/E ----------- �[35m18: grid.draw(gtable)�[39m
C/E ----------- �[35m19: print.patchwork(x)�[39m
C/E ----------- �[35m20: print(x)�[39m
C/E ----------- �[35m21: normal_print(x)�[39m
C/E ----------- �[35m22: knit_print.default(x, ...)�[39m
C/E ----------- �[35m23: knit_print(x, ...)�[39m

C/E ----------- �[35m 1: numnotnull("lex")�[39m
C/E ----------- �[35m 2: validGP(list(...))�[39m
C/E ----------- �[35m 3: gpar()�[39m
C/E ----------- �[35m 4: is.gpar(gp)�[39m
C/E ----------- �[35m 5: valid.viewport(x, y, width, height, just, gp, clip, mask, xscale,     yscale, angle, layout, layout.pos.row, layout.pos.col, name)�[39m
C/E ----------- �[35m 6: viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,     clip = clip)�[39m
C/E ----------- �[35m 7: (function (vp_name, t, r, b, l, clip) {    viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,         clip = clip)})(vp_name = dots[[1L]][[1L]], t = dots[[2L]][[1L]], r = dots[[3L]][[1L]],     b = dots[[4L]][[1L]], l = dots[[5L]][[1L]], clip = dots[[6L]][[1L]])�[39m
C/E ----------- �[35m 8: mapply(child_vp, vp_name = vpname(x$layout), t = .subset2(x$layout,     "t"), r = .subset2(x$layout, "r"), b = .subset2(x$layout,     "b"), l = .subset2(x$layout, "l"), clip = x$layout$clip,     SIMPLIFY = FALSE)�[39m
C/E ----------- �[35m 9: makeContent.gtable(x)�[39m
C/E ----------- �[35m10: makeContent(x)�[39m
C/E ----------- �[35m11: drawGTree(x)�[39m
C/E ----------- �[35m12: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m13: grid.draw.gTree(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m14: grid.draw(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m15: drawGTree(x)�[39m
C/E ----------- �[35m16: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m17: grid.draw.gTree(gtable)�[39m
C/E ----------- �[35m18: grid.draw(gtable)�[39m
C/E ----------- �[35m19: print.patchwork(x)�[39m
C/E ----------- �[35m20: print(x)�[39m
C/E ----------- �[35m21: normal_print(x)�[39m
C/E ----------- �[35m22: knit_print.default(x, ...)�[39m
C/E ----------- �[35m23: knit_print(x, ...)�[39m

C/E ----------- �[35m 1: checkNA("cex")�[39m
C/E ----------- �[35m 2: validGP(list(...))�[39m
C/E ----------- �[35m 3: gpar()�[39m
C/E ----------- �[35m 4: is.gpar(gp)�[39m
C/E ----------- �[35m 5: valid.viewport(x, y, width, height, just, gp, clip, mask, xscale,     yscale, angle, layout, layout.pos.row, layout.pos.col, name)�[39m
C/E ----------- �[35m 6: viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,     clip = clip)�[39m
C/E ----------- �[35m 7: (function (vp_name, t, r, b, l, clip) {    viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,         clip = clip)})(vp_name = dots[[1L]][[2L]], t = dots[[2L]][[2L]], r = dots[[3L]][[2L]],     b = dots[[4L]][[2L]], l = dots[[5L]][[2L]], clip = dots[[6L]][[2L]])�[39m
C/E ----------- �[35m 8: mapply(child_vp, vp_name = vpname(x$layout), t = .subset2(x$layout,     "t"), r = .subset2(x$layout, "r"), b = .subset2(x$layout,     "b"), l = .subset2(x$layout, "l"), clip = x$layout$clip,     SIMPLIFY = FALSE)�[39m
C/E ----------- �[35m 9: makeContent.gtable(x)�[39m
C/E ----------- �[35m10: makeContent(x)�[39m
C/E ----------- �[35m11: drawGTree(x)�[39m
C/E ----------- �[35m12: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m13: grid.draw.gTree(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m14: grid.draw(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m15: drawGTree(x)�[39m
C/E ----------- �[35m16: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m17: grid.draw.gTree(gtable)�[39m
C/E ----------- �[35m18: grid.draw(gtable)�[39m
C/E ----------- �[35m19: print.patchwork(x)�[39m
C/E ----------- �[35m20: print(x)�[39m
C/E ----------- �[35m21: normal_print(x)�[39m
C/E ----------- �[35m22: knit_print.default(x, ...)�[39m
C/E ----------- �[35m23: knit_print(x, ...)�[39m

C/E ----------- �[35m 1: validGP(list(...))�[39m
C/E ----------- �[35m 2: gpar()�[39m
C/E ----------- �[35m 3: is.gpar(gp)�[39m
C/E ----------- �[35m 4: valid.viewport(x, y, width, height, just, gp, clip, mask, xscale,     yscale, angle, layout, layout.pos.row, layout.pos.col, name)�[39m
C/E ----------- �[35m 5: viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,     clip = clip)�[39m
C/E ----------- �[35m 6: (function (vp_name, t, r, b, l, clip) {    viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,         clip = clip)})(vp_name = dots[[1L]][[2L]], t = dots[[2L]][[2L]], r = dots[[3L]][[2L]],     b = dots[[4L]][[2L]], l = dots[[5L]][[2L]], clip = dots[[6L]][[2L]])�[39m
C/E ----------- �[35m 7: mapply(child_vp, vp_name = vpname(x$layout), t = .subset2(x$layout,     "t"), r = .subset2(x$layout, "r"), b = .subset2(x$layout,     "b"), l = .subset2(x$layout, "l"), clip = x$layout$clip,     SIMPLIFY = FALSE)�[39m
C/E ----------- �[35m 8: makeContent.gtable(x)�[39m
C/E ----------- �[35m 9: makeContent(x)�[39m
C/E ----------- �[35m10: drawGTree(x)�[39m
C/E ----------- �[35m11: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m12: grid.draw.gTree(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m13: grid.draw(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m14: drawGTree(x)�[39m
C/E ----------- �[35m15: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m16: grid.draw.gTree(gtable)�[39m
C/E ----------- �[35m17: grid.draw(gtable)�[39m
C/E ----------- �[35m18: print.patchwork(x)�[39m
C/E ----------- �[35m19: print(x)�[39m
C/E ----------- �[35m20: normal_print(x)�[39m
C/E ----------- �[35m21: knit_print.default(x, ...)�[39m
C/E ----------- �[35m22: knit_print(x, ...)�[39m

C/E ----------- �[35m 1: diff.default(yscale)�[39m
C/E ----------- �[35m 2: diff(yscale)�[39m
C/E ----------- �[35m 3: valid.viewport(x, y, width, height, just, gp, clip, mask, xscale,     yscale, angle, layout, layout.pos.row, layout.pos.col, name)�[39m
C/E ----------- �[35m 4: viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,     clip = clip)�[39m
C/E ----------- �[35m 5: (function (vp_name, t, r, b, l, clip) {    viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,         clip = clip)})(vp_name = dots[[1L]][[2L]], t = dots[[2L]][[2L]], r = dots[[3L]][[2L]],     b = dots[[4L]][[2L]], l = dots[[5L]][[2L]], clip = dots[[6L]][[2L]])�[39m
C/E ----------- �[35m 6: mapply(child_vp, vp_name = vpname(x$layout), t = .subset2(x$layout,     "t"), r = .subset2(x$layout, "r"), b = .subset2(x$layout,     "b"), l = .subset2(x$layout, "l"), clip = x$layout$clip,     SIMPLIFY = FALSE)�[39m
C/E ----------- �[35m 7: makeContent.gtable(x)�[39m
C/E ----------- �[35m 8: makeContent(x)�[39m
C/E ----------- �[35m 9: drawGTree(x)�[39m
C/E ----------- �[35m10: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m11: grid.draw.gTree(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m12: grid.draw(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m13: drawGTree(x)�[39m
C/E ----------- �[35m14: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m15: grid.draw.gTree(gtable)�[39m
C/E ----------- �[35m16: grid.draw(gtable)�[39m
C/E ----------- �[35m17: print.patchwork(x)�[39m
C/E ----------- �[35m18: print(x)�[39m
C/E ----------- �[35m19: normal_print(x)�[39m
C/E ----------- �[35m20: knit_print.default(x, ...)�[39m
C/E ----------- �[35m21: knit_print(x, ...)�[39m

C/E ----------- �[35m 1: diff.default(yscale)�[39m
C/E ----------- �[35m 2: diff(yscale)�[39m
C/E ----------- �[35m 3: valid.viewport(x, y, width, height, just, gp, clip, mask, xscale,     yscale, angle, layout, layout.pos.row, layout.pos.col, name)�[39m
C/E ----------- �[35m 4: viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,     clip = clip)�[39m
C/E ----------- �[35m 5: (function (vp_name, t, r, b, l, clip) {    viewport(name = vp_name, layout.pos.row = t:b, layout.pos.col = l:r,         clip = clip)})(vp_name = dots[[1L]][[2L]], t = dots[[2L]][[2L]], r = dots[[3L]][[2L]],     b = dots[[4L]][[2L]], l = dots[[5L]][[2L]], clip = dots[[6L]][[2L]])�[39m
C/E ----------- �[35m 6: mapply(child_vp, vp_name = vpname(x$layout), t = .subset2(x$layout,     "t"), r = .subset2(x$layout, "r"), b = .subset2(x$layout,     "b"), l = .subset2(x$layout, "l"), clip = x$layout$clip,     SIMPLIFY = FALSE)�[39m
C/E ----------- �[35m 7: makeContent.gtable(x)�[39m
C/E ----------- �[35m 8: makeContent(x)�[39m
C/E ----------- �[35m 9: drawGTree(x)�[39m
C/E ----------- �[35m10: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m11: grid.draw.gTree(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m12: grid.draw(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m13: drawGTree(x)�[39m
C/E ----------- �[35m14: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m15: grid.draw.gTree(gtable)�[39m
C/E ----------- �[35m16: grid.draw(gtable)�[39m
C/E ----------- �[35m17: print.patchwork(x)�[39m

C/E ----------- �[35m 1: unique(lengths(x))�[39m
C/E ----------- �[35m 2: simplify2array(answer, higher = (simplify == "array"))�[39m
C/E ----------- �[35m 3: sapply(gl, is.grob)�[39m
C/E ----------- �[35m 4: gList(list(name = "legend.box.background.2-4-4-2", gp = NULL,     vp = NULL, wrapvp = list(x = 0.5, y = 0.5, width = 1, height = 1,         justification = c(0.5, 0.5), gp = list(), clip = NA,         xscale = c(0, 1), yscale = c(0, 1), angle = 0, layout = NULL,         layout.pos.row = c(2L, 4L), layout.pos.col = c(2L, 4L        ), valid.just = c(0.5, 0.5), valid.pos.row = c(2L, 4L        ), valid.pos.col = c(2L, 4L), name = "legend.box.background.2-4-4-2",         parentgpar = NULL, gpar = NULL, trans = NULL, widths = NULL,         heights = NULL, width.cm = NULL, height.cm = NULL, rotation = NULL,         cliprect = NULL, parent = NULL, children = NULL, devwidth = NULL,         devheight = NULL, clippath = NULL, mask = TRUE, resolvedmask = NULL)),     `99_d3e6e6f4fc5b27ad2680d0b9b28b49b8` = list(grobs = list(        list(name = "legend.background..zeroGrob.5727", gp = NULL,             vp = NULL), list(name = "GRID.gTree.5728", gp = NULL,             vp = list(x = 0, y = 0.5, width = list(list(1, list(                widths = list(list(0, NULL, 8L), list(1, list(                  list(1, list(label = "factor(wellType)", x = 0,                     y = 0.5, just = "centre", hjust = 0, vjust = 0.5,                     rot = 0, check.overlap = FALSE, name = "GRID.text.5694",                     gp = list(fontsize = 11, col = "black", fontfamily = "",                       lineheight = 0.9, font = c(plain = 1L)),                     vp = NULL), 21L), list(0, NULL, 2L)), 201L),                   list(0, NULL, 8L)), heights = list(list(0,                   NULL, 8L), list(1, list(list(1, list(label = "factor(wellType)",                   x = 0, y = 0.5, just = "centre", hjust = 0,                   vjust = 0.5, rot = 0, check.overlap = FALSE,                   name = "GRID.text.5694", gp = list(fontsize = 11,                     col = "black", fontfamily = "", lineheight = 0.9,                     font = c(plain = 1L)), vp = NULL), 22L),       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= 1L)), vp = NULL)), childrenOrder = "GRID.text.5712"),                   22L)), justification = c(0, 0.5), gp = list(),                 clip = FALSE, xscale = c(0, 1), yscale = c(0,                 1), angle = 0, layout = NULL, layout.pos.row = NULL,                 layout.pos.col = NULL, valid.just = c(0, 0.5),                 valid.pos.row = NULL, valid.pos.col = NULL, name = "GRID.VP.1540",                 parentgpar = NULL, gpar = NULL, trans = NULL,                 widths = NULL, heights = NULL, width.cm = NULL,                 height.cm = NULL, rotation = NULL, cliprect = NULL,                 parent = NULL, children = NULL, devwidth = NULL,                 devheight = NULL, clippath = NULL, mask = TRUE,                 resolvedmask = NULL), children = list(guide.label.titleGrob.5714 = list(                widths = list(list(0, NULL, 8L), list(1, list(                  list(1, list(label = "untreated", x = 0, y = 0.5,                     just = "centre", hjust = 0, vjust = 0.5,                     rot = 0, check.overlap = FALSE, name = "GRID.text.5712",                     gp = list(fontsize = 8.8, col = "black",                       fontfamily = "", lineheight = 0.9, font = c(plain = 1L)),                     vp = NULL), 21L), list(0, NULL, 2L)), 201L),                   list(0, NULL, 8L)), heights = list(list(0,                   NULL, 8L), list(1, list(list(1, list(label = "untreated",                   x = 0, y = 0.5, just = "centre", hjust = 0,                   vjust = 0.5, rot = 0, check.overlap = FALSE,                   name = "GRID.text.5712", gp = list(fontsize = 8.8,                     col = "black", fontfamily = "", lineheight = 0.9,                     font = c(plain = 1L)), vp = NULL), 22L),                   list(0.0260416666666667, NULL, 2L)), 201L),                   list(0, NULL, 8L)), name = "guide.label.titleGrob.5714",                 gp = NULL, vp = list(parent = list(x = 0.5, y = 0.5,                   width = 1, height = 1, justification = c(0.5,                   0.5), gp = list(fontsize = 8.8, col = "black",                     fontfamily = "", lineheight = 0.9, font = c(plain = 1L)),                   clip = FALSE, xscale = c(0, 1), yscale = c(0,                   1), angle = 0, layout = list(nrow = 3L, ncol = 3L,                     widths = list(list(0, NULL, 8L), list(1,                       list(list(1, list(label = "untreated",                         x = 0, y = 0.5, just = "centre", hjust = 0,                         vjust = 0.5, rot = 0, check.overlap = FALSE,                         name = "GRID.text.5712", gp = list(fontsize = 8.8,                           col = "black", fontfamily = "", lineheight = 0.9,                           font = c(plain = 1L)), vp = NULL),                         21L), list(0, NULL, 2L)), 201L), list(                      0, NULL, 8L)), heights = list(list(0, NULL,                       8L), list(1, list(list(1, list(label = "untreated",                       x = 0, y = 0.5, just = "centre", hjust = 0,                       vjust = 0.5, rot = 0, check.overlap = FALSE,                       name = "GRID.text.5712", gp = list(fontsize = 8.8,                         col = "black", fontfamily = "", lineheight = 0.9,                         font = c(plain = 1L)), vp = NULL), 22L),                       list(0.0260416666666667, NULL, 2L)), 201L),                       list(0, NULL, 8L)), respect = FALSE, valid.respect = 0L,                     respect.mat = c(0L, 0L, 0L, 0L, 0L, 0L, 0L,                     0L, 0L), just = "centre", valid.just = c(0.5,                     0.5)), layout.pos.row = NULL, layout.pos.col = NULL,                   valid.just = c(0.5, 0.5), valid.pos.row = NULL,                   valid.pos.col = NULL, name = "GRID.VP.1532",                   parentgpar = NULL, gpar = NULL, trans = NULL,                   widths = NULL, heights = NULL, width.cm = NULL,                   height.cm = NULL, rotation = NULL, cliprect = NULL,                   parent = NULL, children = NULL, devwidth = NULL,                   devheight = NULL, clippath = NULL, mask = TRUE,                   resolvedmask = NULL), children = list(list(                  x = 0.5, y = 0.5, width = 1, height = 1, justification = c(0.5,                   0.5), gp = list(), clip = FALSE, xscale = c(0,                   1), yscale = c(0, 1), angle = 0, layout = NULL,                   layout.pos.row = c(2L, 2L), layout.pos.col = c(2L,                   2L), valid.just = c(0.5, 0.5), valid.pos.row = c(2L,                   2L), valid.pos.col = c(2L, 2L), name = "GRID.VP.1533",                   parentgpar = NULL, gpar = NULL, trans = NULL,                   widths = NULL, heights = NULL, width.cm = NULL,                   height.cm = NULL, rotation = NULL, cliprect = NULL,                   parent = NULL, children = NULL, devwidth = NULL,                   devheight = NULL, clippath = NULL, mask = TRUE,                   resolvedmask = NULL))), children = list(GRID.text.5712 = list(                  label = "untreated", x = 0, y = 0.5, just = "centre",                   hjust = 0, vjust = 0.5, rot = 0, check.overlap = FALSE,                   name = "GRID.text.5712", gp = list(fontsize = 8.8,                     col = "black", fontfamily = "", lineheight = 0.9,                     font = c(plain = 1L)), vp = NULL)), childrenOrder = "GRID.text.5712")),             childrenOrder = "guide.label.titleGrob.5714")), layout = list(        t = c(1, 2, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 4, 5,         6, 7, 8, 9), l = c(1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,         2, 2, 4, 4, 4, 4, 4, 4), b = c(10, 2, 4, 4, 5, 5, 6,         6, 7, 7, 8, 8, 9, 9, 4, 5, 6, 7, 8, 9), r = c(6, 5, 2,         2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4), z = c(1,         2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,         18, 19, 20), clip = c("off", "off", "off", "off", "off",         "off", "off", "off", "off", "off", "off", "off", "off",         "off", "off", "off", "off", "off", "off", "off"), name = c("background",         "title", "key-3-1-bg", "key-3-1-1", "key-4-1-bg", "key-4-1-1",         "key-5-1-bg", "key-5-1-1", "key-6-1-bg", "key-6-1-1",         "key-7-1-bg", "key-7-1-1", "key-8-1-bg", "key-8-1-1",         "label-3-3", "label-4-3", "label-5-3", "label-6-3", "label-7-3",         "label-8-3")), widths = c(0, 0.6096, 0.193302891933029,     1.32291666666667, 0.691992941400305, 0), heights = c(0, 0.370416666666667,     0.193302891933029, 0.6096, 0.6096, 0.6096, 0.6096, 0.6096,     0.6096, 0), respect = FALSE, rownames = NULL, colnames = NULL,         name = "guides.3-3-3-3", gp = NULL, vp = list(x = 0,             y = 1, width = 2.8178125, height = 1, justification = c(0,             1), gp = list(), clip = FALSE, xscale = c(0, 1),             yscale = c(0, 1), angle = 0, layout = NULL, layout.pos.row = NULL,             layout.pos.col = NULL, valid.just = c(0, 1), valid.pos.row = NULL,             valid.pos.col = NULL, name = "GRID.VP.1541", parentgpar = NULL,             gpar = NULL, trans = NULL, widths = NULL, heights = NULL,             width.cm = NULL, height.cm = NULL, rotation = NULL,             cliprect = NULL, parent = NULL, children = NULL,             devwidth = NULL, devheight = NULL, clippath = NULL,             mask = TRUE, resolvedmask = NULL), children = list(),         childrenOrder = character(0), wrapvp = list(x = 0.5,             y = 0.5, width = 1, height = 1, justification = c(0.5,             0.5), gp = list(), clip = NA, xscale = c(0, 1), yscale = c(0,             1), angle = 0, layout = NULL, layout.pos.row = c(3L,             3L), layout.pos.col = c(3L, 3L), valid.just = c(0.5,             0.5), valid.pos.row = c(3L, 3L), valid.pos.col = c(3L,             3L), name = "guides.3-3-3-3", parentgpar = NULL,             gpar = NULL, trans = NULL, widths = NULL, heights = NULL,             width.cm = NULL, height.cm = NULL, rotation = NULL,             cliprect = NULL, parent = NULL, children = NULL,             devwidth = NULL, devheight = NULL, clippath = NULL,             mask = TRUE, resolvedmask = NULL)))�[39m
C/E ----------- �[35m 5: do.call("gList", x$grobs[order(.subset2(x$layout, "z"))])�[39m
C/E ----------- �[35m 6: setChildren(x, do.call("gList", x$grobs[order(.subset2(x$layout,     "z"))]))�[39m
C/E ----------- �[35m 7: makeContent.gtable(x)�[39m
C/E ----------- �[35m 8: makeContent(x)�[39m
C/E ----------- �[35m 9: drawGTree(x)�[39m
C/E ----------- �[35m10: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m11: grid.draw.gTree(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m12: grid.draw(x$children[[i]], recording = FALSE)�[39m
C/E ----------- �[35m13: drawGTree(x)�[39m
C/E ----------- �[35m14: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))�[39m
C/E ----------- �[35m15: grid.draw.gTree(gtable)�[39m
C/E ----------- �[35m16: grid.draw(gtable)�[39m
C/E ----------- �[35m17: print.patchwork(x)�[39m
C/E ----------- �[35m18: print(x)�[39m
C/E ----------- �[35m19: normal_print(x)�[39m
C/E ----------- �[35m20: knit_print.default(x, ...)�[39m
C/E ----------- �[35m21: knit_print(x, ...)�[39m

The text was updated successfully, but these errors were encountered:

bersbersbers · 2021-10-04T21:26:22Z

I was able to find a repro example without using patchwork at all, narrowing down the list of potentially problematic packages by one :)

bersbersbers · 2021-10-27T07:38:47Z

Fyi, apparently fixed in r-lib/cpp11#245.

bersbersbers mentioned this issue Oct 4, 2021

segfaults inside shiny inside shinytest when rmarkdown is involved rstudio/rmarkdown#2229

Closed

bersbersbers closed this as completed Oct 4, 2021

This was referenced Oct 8, 2021

Segmentation fault involving code using simplifyPieces (and openxlsx) when tidyr is installed from CRAN tidyverse/tidyr#1163

Closed

Segmentation fault involving code using write.xlsx (and tidyr) ycphs/openxlsx#267

Closed

bersbersbers mentioned this issue Oct 18, 2021

Reproducible segmentation fault (with tidyr and openxlsx), bisect included r-lib/cpp11#244

Closed

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segfaults with patchwork inside rmarkdown inside shiny inside shinytest #278

segfaults with patchwork inside rmarkdown inside shiny inside shinytest #278

bersbersbers commented Oct 4, 2021

bersbersbers commented Oct 4, 2021

bersbersbers commented Oct 27, 2021

segfaults with patchwork inside rmarkdown inside shiny inside shinytest #278

segfaults with patchwork inside rmarkdown inside shiny inside shinytest #278

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bersbersbers commented Oct 4, 2021

bersbersbers commented Oct 4, 2021

bersbersbers commented Oct 27, 2021