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GraphViz.layout! command causes Malt.TerminatedWorkerException() #3128

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danvinci opened this issue Dec 25, 2024 · 4 comments
Closed

GraphViz.layout! command causes Malt.TerminatedWorkerException() #3128

danvinci opened this issue Dec 25, 2024 · 4 comments

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@danvinci
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Reproducible example:

using GraphViz

g_dot_spec = dot"""digraph G {
rankdir="LR"
    1 [label="{b | data -3.0 | grad -4.0 }"][shape="record"];
    2 [label="{c | data 10.0 | grad -2.0 }"][shape="record"];
    3 [label="{L | data -8.0 | grad 0.0 }"][shape="record"];
    4 [label="*"];
    5 [label="{f | data -2.0 | grad 4.0 }"][shape="record"];
    6 [label="{a | data 2.0 | grad 6.0 }"][shape="record"];
    7 [label="{e | data -6.0 | grad -2.0 }"][shape="record"];
    8 [label="*"];
    9 [label="{d | data 4.0 | grad -2.0 }"][shape="record"];
    10 [label="+"];
    1 -> 8;
    2 -> 10;
    4 -> 3;
    5 -> 4;
    6 -> 8;
    7 -> 10;
    8 -> 7;
    9 -> 4;
    10 -> 9;
}"""

above will work (although output is broken, JuliaGraphs/GraphViz.jl#38)

GraphViz.layout!(g_dot_spec, engine = "dot")
this causes the exception

also reported in GraphViz repo: JuliaGraphs/GraphViz.jl#38 (comment)
@danvinci danvinci mentioned this issue Dec 25, 2024
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@danvinci
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Edit: was just necessary to suppress output of cell defining the graph in DOT with a ";" 😅

@fonsp
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fonsp commented Dec 31, 2024

Okay! But is it still expected that the worker crashes?

@danvinci
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danvinci commented Jan 5, 2025

No, that was unexpected - I think it should maybe result in a simple error for that cell if any 👌🏻

@fonsp
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fonsp commented Jan 10, 2025

For me it works:

image

Details 

### A Pluto.jl notebook ###
# v0.20.4

using Markdown
using InteractiveUtils

# ╔═╡ 9459ad7f-2116-4b3e-8532-61d540da4777
using GraphViz

# ╔═╡ c2365610-cf4e-11ef-1745-b5c9dbfdc56b
g_dot_spec = dot"""digraph G {
rankdir="LR"
    1 [label="{b | data -3.0 | grad -4.0 }"][shape="record"];
    2 [label="{c | data 10.0 | grad -2.0 }"][shape="record"];
    3 [label="{L | data -8.0 | grad 0.0 }"][shape="record"];
    4 [label="*"];
    5 [label="{f | data -2.0 | grad 4.0 }"][shape="record"];
    6 [label="{a | data 2.0 | grad 6.0 }"][shape="record"];
    7 [label="{e | data -6.0 | grad -2.0 }"][shape="record"];
    8 [label="*"];
    9 [label="{d | data 4.0 | grad -2.0 }"][shape="record"];
    10 [label="+"];
    1 -> 8;
    2 -> 10;
    4 -> 3;
    5 -> 4;
    6 -> 8;
    7 -> 10;
    8 -> 7;
    9 -> 4;
    10 -> 9;
}"""

# ╔═╡ 00000000-0000-0000-0000-000000000001
PLUTO_PROJECT_TOML_CONTENTS = """
[deps]
GraphViz = "f526b714-d49f-11e8-06ff-31ed36ee7ee0"

[compat]
GraphViz = "~0.2.0"
"""

# ╔═╡ 00000000-0000-0000-0000-000000000002
PLUTO_MANIFEST_TOML_CONTENTS = """
# This file is machine-generated - editing it directly is not advised

julia_version = "1.11.2"
manifest_format = "2.0"
project_hash = "f74c2b9db31b9c550d12da2dd3578ad2e146dd59"

[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
version = "1.1.2"

[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
version = "1.11.0"

[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
version = "1.11.0"

[[deps.Bzip2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1"
uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
version = "1.0.8+4"

[[deps.Cairo_jll]]
deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642"
uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
version = "1.18.2+1"

[[deps.CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "1.1.1+0"

[[deps.Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
version = "1.11.0"

[[deps.Downloads]]
deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
version = "1.6.0"

[[deps.Expat_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99"
uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
version = "2.6.4+3"

[[deps.FileIO]]
deps = ["Pkg", "Requires", "UUIDs"]
git-tree-sha1 = "2dd20384bf8c6d411b5c7370865b1e9b26cb2ea3"
uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
version = "1.16.6"

    [deps.FileIO.extensions]
    HTTPExt = "HTTP"

    [deps.FileIO.weakdeps]
    HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"

[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
version = "1.11.0"

[[deps.Fontconfig_jll]]
deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b"
uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
version = "2.15.0+0"

[[deps.FreeType2_jll]]
deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
git-tree-sha1 = "786e968a8d2fb167f2e4880baba62e0e26bd8e4e"
uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
version = "2.13.3+1"

[[deps.FriBidi_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "846f7026a9decf3679419122b49f8a1fdb48d2d5"
uuid = "559328eb-81f9-559d-9380-de523a88c83c"
version = "1.0.16+0"

[[deps.Gettext_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"]
git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046"
uuid = "78b55507-aeef-58d4-861c-77aaff3498b1"
version = "0.21.0+0"

[[deps.Glib_jll]]
deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
git-tree-sha1 = "b0036b392358c80d2d2124746c2bf3d48d457938"
uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
version = "2.82.4+0"

[[deps.GraphViz]]
deps = ["FileIO", "Graphviz_jll", "Requires"]
git-tree-sha1 = "da5580b236c5b6bb634e96ca35dcd7eaeeac1bd1"
uuid = "f526b714-d49f-11e8-06ff-31ed36ee7ee0"
version = "0.2.0"

[[deps.Graphite2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "01979f9b37367603e2848ea225918a3b3861b606"
uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472"
version = "1.3.14+1"

[[deps.Graphviz_jll]]
deps = ["Artifacts", "Cairo_jll", "Expat_jll", "JLLWrappers", "Libdl", "Pango_jll", "Pkg"]
git-tree-sha1 = "a5d45833dda71048117e8a9828bef75c03b18b1c"
uuid = "3c863552-8265-54e4-a6dc-903eb78fde85"
version = "2.50.0+1"

[[deps.HarfBuzz_jll]]
deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"]
git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3"
uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566"
version = "8.5.0+0"

[[deps.JLLWrappers]]
deps = ["Artifacts", "Preferences"]
git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
version = "1.7.0"

[[deps.LLVMOpenMP_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929"
uuid = "1d63c593-3942-5779-bab2-d838dc0a180e"
version = "18.1.7+0"

[[deps.LZO_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731"
uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac"
version = "2.10.2+3"

[[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
version = "0.6.4"

[[deps.LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
version = "8.6.0+0"

[[deps.LibGit2]]
deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
version = "1.11.0"

[[deps.LibGit2_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
version = "1.7.2+0"

[[deps.LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
version = "1.11.0+1"

[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
version = "1.11.0"

[[deps.Libffi_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e"
uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490"
version = "3.2.2+2"

[[deps.Libgcrypt_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"]
git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b"
uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4"
version = "1.11.0+0"

[[deps.Libgpg_error_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "df37206100d39f79b3376afb6b9cee4970041c61"
uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8"
version = "1.51.1+0"

[[deps.Libiconv_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269"
uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
version = "1.17.0+1"

[[deps.Libmount_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "84eef7acd508ee5b3e956a2ae51b05024181dee0"
uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
version = "2.40.2+2"

[[deps.Libuuid_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "edbf5309f9ddf1cab25afc344b1e8150b7c832f9"
uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
version = "2.40.2+2"

[[deps.Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
version = "1.11.0"

[[deps.Markdown]]
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
version = "1.11.0"

[[deps.MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.28.6+0"

[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
version = "2023.12.12"

[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"

[[deps.PCRE2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15"
version = "10.42.0+1"

[[deps.Pango_jll]]
deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"]
git-tree-sha1 = "ed6834e95bd326c52d5675b4181386dfbe885afb"
uuid = "36c8627f-9965-5494-a995-c6b170f724f3"
version = "1.55.5+0"

[[deps.Pixman_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"]
git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b"
uuid = "30392449-352a-5448-841d-b1acce4e97dc"
version = "0.43.4+0"

[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.11.0"

    [deps.Pkg.extensions]
    REPLExt = "REPL"

    [deps.Pkg.weakdeps]
    REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[deps.Preferences]]
deps = ["TOML"]
git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.4.3"

[[deps.Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
version = "1.11.0"

[[deps.Random]]
deps = ["SHA"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
version = "1.11.0"

[[deps.Requires]]
deps = ["UUIDs"]
git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7"
uuid = "ae029012-a4dd-5104-9daa-d747884805df"
version = "1.3.0"

[[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"

[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
version = "1.0.3"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.0"

[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
version = "1.11.0"

[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
version = "1.11.0"

[[deps.XML2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6"
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
version = "2.13.5+0"

[[deps.XSLT_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"]
git-tree-sha1 = "7d1671acbe47ac88e981868a078bd6b4e27c5191"
uuid = "aed1982a-8fda-507f-9586-7b0439959a61"
version = "1.1.42+0"

[[deps.Xorg_libX11_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
git-tree-sha1 = "9dafcee1d24c4f024e7edc92603cedba72118283"
uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc"
version = "1.8.6+3"

[[deps.Xorg_libXau_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "2b0e27d52ec9d8d483e2ca0b72b3cb1a8df5c27a"
uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec"
version = "1.0.11+3"

[[deps.Xorg_libXdmcp_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "02054ee01980c90297412e4c809c8694d7323af3"
uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05"
version = "1.1.4+3"

[[deps.Xorg_libXext_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
git-tree-sha1 = "d7155fea91a4123ef59f42c4afb5ab3b4ca95058"
uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3"
version = "1.3.6+3"

[[deps.Xorg_libXrender_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
git-tree-sha1 = "a490c6212a0e90d2d55111ac956f7c4fa9c277a6"
uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa"
version = "0.9.11+1"

[[deps.Xorg_libpthread_stubs_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "fee57a273563e273f0f53275101cd41a8153517a"
uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74"
version = "0.1.1+3"

[[deps.Xorg_libxcb_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"]
git-tree-sha1 = "1a74296303b6524a0472a8cb12d3d87a78eb3612"
uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b"
version = "1.17.0+3"

[[deps.Xorg_xtrans_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "b9ead2d2bdb27330545eb14234a2e300da61232e"
uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10"
version = "1.5.0+3"

[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.13+1"

[[deps.libpng_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
git-tree-sha1 = "b7bfd3ab9d2c58c3829684142f5804e4c6499abc"
uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
version = "1.6.45+0"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.59.0+0"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+2"
"""

# ╔═╡ Cell order:
# ╠═9459ad7f-2116-4b3e-8532-61d540da4777
# ╠═c2365610-cf4e-11ef-1745-b5c9dbfdc56b
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002

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@fonsp @danvinci