Different behavior between versions and links not working in pdf

elysch · November 24, 2024, 12:28am

I’m trying to get this graph working.

With version 12, 11, 10, Graphviz just generates pdf with zero size, with 9, 8, it generates the pdf but there are no links

Any help making it work will be really appreciated

digraph WT_Graph {
ranksep="0.27 equally"
nodesep="0.15"
dpi="72"
mclimit="1"
rankdir="LR"
pagedir="LT"
bgcolor="#eeeeee"
splines="spline"
edge [ style=solid, arrowhead=normal, arrowtail=none];
node [ shape=plaintext font_size="10" fontname="Arial"];
I57 [ label=<<TABLE COLOR="#606060" BORDER="1" CELLBORDER="0" CELLPADDING="2" CELLSPACING="0" BGCOLOR="#fefefe" TARGET="_blank" HREF="https://genealogy.someplace.com/webtrees/tree/familia/individual/I57/Baruj-Palacci"><TR><TD COLSPAN="6" CELLPADDING="2" BGCOLOR="#add8e6" PORT="nam" ></TD></TR><TR><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ALIGN="LEFT" BALIGN="LEFT"  TARGET="_BLANK" CELLPADDING="4" PORT="dat"><FONT COLOR="#333333" POINT-SIZE="12">Baruj Palacci (I57)</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">Male</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">↑ 1865 </FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">↓ &gt; July 20, 1914 &lt; October 15, 1918 </FONT> </TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD CELLPADDING="10"></TD></TR></TABLE>>];
I19 [ label=<<TABLE COLOR="#606060" BORDER="1" CELLBORDER="0" CELLPADDING="2" CELLSPACING="0" BGCOLOR="#fefefe" TARGET="_blank" HREF="https://genealogy.someplace.com/webtrees/tree/familia/individual/I19/Caden-Behora-Levy"><TR><TD COLSPAN="6" CELLPADDING="2" BGCOLOR="#ffb6c1" PORT="nam" ></TD></TR><TR><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ALIGN="LEFT" BALIGN="LEFT"  TARGET="_BLANK" CELLPADDING="4" PORT="dat"><FONT COLOR="#333333" POINT-SIZE="12">Caden Behora Levy (I19)</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">Female</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">↑ 1864 </FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">↓ November 22, 1951 (Distrito Federal, México)</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">_  (Sección Sefaradí, Panteón Jardín, Distrito Federal, México)</FONT></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="40" HEIGHT="40" FIXEDSIZE="true" ALIGN="CENTER" VALIGN="MIDDLE" HREF="https://genealogy.someplace.com/webtrees/tree/familia/media-download?xref=X244&amp;fact_id=6792575f3d13dfbdd756bd341b861621&amp;disposition=inline&amp;mark=0"><IMG SCALE="true" SRC="data/media/media/schoenfeld-liberman.ged/Levi-Assayas/I19-Levy-Assayas-CadenBehora-ActaDefuncion-1951.jpg" ALT="Acta de Defunción de Caden Behora Levy Assayas - 22 NOV 1951"  /></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="40" HEIGHT="40" FIXEDSIZE="true" ALIGN="CENTER" VALIGN="MIDDLE" HREF="https://genealogy.someplace.com/webtrees/tree/familia/media-download?xref=X291&amp;fact_id=897e93c6b72e91045fc315cf71888654&amp;disposition=inline&amp;mark=0"><IMG SCALE="true" SRC="data/media/media/schoenfeld-liberman.ged/Levi-Assayas/I19-Levy-Assayas-Behora-Lapida-2012.jpg" ALT="Lápida de Caden Behora Levy Assayas - 2012"  /></TD><TD CELLPADDING="10"></TD></TR></TABLE>>];
I63 [ label=<<TABLE COLOR="#606060" BORDER="1" CELLBORDER="0" CELLPADDING="2" CELLSPACING="0" BGCOLOR="#fefefe" TARGET="_blank" HREF="https://genealogy.someplace.com/webtrees/tree/familia/individual/I63/Abraham-Levi"><TR><TD COLSPAN="6" CELLPADDING="2" BGCOLOR="#add8e6" PORT="nam" ></TD></TR><TR><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ALIGN="LEFT" BALIGN="LEFT"  TARGET="_BLANK" CELLPADDING="4" PORT="dat"><FONT COLOR="#333333" POINT-SIZE="12">Abraham Levi (I63)</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">Male</FONT>  </TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD CELLPADDING="10"></TD></TR></TABLE>>];
I64 [ label=<<TABLE COLOR="#606060" BORDER="1" CELLBORDER="0" CELLPADDING="2" CELLSPACING="0" BGCOLOR="#fefefe" TARGET="_blank" HREF="https://genealogy.someplace.com/webtrees/tree/familia/individual/I64/Reyna-Babachi-Assayas-de-Levi"><TR><TD COLSPAN="6" CELLPADDING="2" BGCOLOR="#ffb6c1" PORT="nam" ></TD></TR><TR><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ALIGN="LEFT" BALIGN="LEFT"  TARGET="_BLANK" CELLPADDING="4" PORT="dat"><FONT COLOR="#333333" POINT-SIZE="12">Reyna "Babachi" Assayas de Levi (I64)</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">Female</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">↑ 1842 (Izmir, Turquia)</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">↓ 1939 (Distrito Federal, México)</FONT><BR /><FONT COLOR="#555555" POINT-SIZE="10">_  (Panteón del Monte Sinaí, Colonia Huichapan, Delegación Miguel Hidalgo, Distrito Federal, México)</FONT></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="0" HEIGHT="40" FIXEDSIZE="true"></TD><TD ROWSPAN="2" CELLPADDING="1" PORT="pic" WIDTH="40" HEIGHT="40" FIXEDSIZE="true" ALIGN="CENTER" VALIGN="MIDDLE" HREF="https://genealogy.someplace.com/webtrees/tree/familia/media-download?xref=X245&amp;fact_id=e2340ead4ce7cfc70e34799acc084731&amp;disposition=inline&amp;mark=0"><IMG SCALE="true" SRC="data/media/media/schoenfeld-liberman.ged/0-PanteonMonteSinaiLagoSaima/PanteonMonteSinaiLagoSaima-Nombres-Fila-31-2020-FindAGrave.JPG" ALT="Nombres Fila 31 en 2020, Panteón Monte Sinai en Lago Saima 78"  /></TD><TD CELLPADDING="10"></TD></TR></TABLE>>];
F7 [ color="#606060",fillcolor="#ffffee", target="_blank" href="https://genealogy.someplace.com/webtrees/tree/familia/family/F7/Baruj-Palacci-Caden-Behora-Levy", target="_blank",  shape=oval, style="filled", margin=0.01, label=<<TABLE border="0" CELLPADDING="5" CELLSPACING="0"><TR><TD><FONT COLOR="#555555" POINT-SIZE="10"> <BR /> (F7)</FONT></TD></TR></TABLE>>];
F23 [ color="#606060",fillcolor="#ffffee", target="_blank" href="https://genealogy.someplace.com/webtrees/tree/familia/family/F23/Abraham-Levi-Reyna-Babachi-Assayas-de-Levi", target="_blank",  shape=oval, style="filled", margin=0.01, label=<<TABLE border="0" CELLPADDING="5" CELLSPACING="0"><TR><TD><FONT COLOR="#555555" POINT-SIZE="10"> <BR /> (F23)</FONT></TD></TR></TABLE>>];
I57 -> F7 [color="#555555", style="dotted", arrowsize=0.3]
I19 -> F7 [color="#555555", style="bold", arrowsize=0.3]
I63 -> F23 [color="#555555", style="solid", arrowsize=0.3]
I64 -> F23 [color="#555555", style="dotted", arrowsize=0.3]
F23 -> I19 [color="#555555", style="solid", arrowsize=0.3]
}

steveroush · November 24, 2024, 5:22am

Your input has many non-ASCII characters. Please place it within triple back-quotes

place program here

elysch · November 24, 2024, 6:59pm

Done

Thank you steveroush

When I execute dot with “-v” option in version 12.2.0 it gives me the following:

dot.exe : dot - graphviz version 12.2.0 (20241103.1931)
En línea: 1 Carácter: 1
+ dot.exe -v -Tpdf -oC:\Users\XXXX ...
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : NotSpecified: (dot - graphviz ...(20241103.1931):String) [], RemoteException
    + FullyQualifiedErrorId : NativeCommandError
 
Using render: cairo:cairo
Using device: pdf:cairo:cairo
libdir = "C:\Program Files\Graphviz\bin"
Activated plugin library: gvplugin_dot_layout.dll
Using layout: dot:dot_layout
The plugin configuration file:
	C:\Program Files\Graphviz\bin\config6
		was successfully loaded.
    render	:  cairo dot dot_json fig gd gdiplus json json0 map pic pov ps svg svg_inline tk vrml xdot xdot_json
    layout	:  circo dot fdp neato nop nop1 nop2 osage patchwork sfdp twopi
    textlayout	:  textlayout
    device	:  bmp canon cmap cmapx cmapx_np dot dot_json emf emfplus eps fig gd gd2 gif gv imap imap_np ismap jpe jpeg 
jpg json json0 kitty kittyz metafile pdf pic plain plain-ext png pov ps ps2 svg svg_inline svgz tif tiff tk vrml vt 
vt-24bit vt-4up vt-6up vt-8up wbmp webp xdot xdot1.2 xdot1.4 xdot_json
    loadimage	:  (lib) bmp eps gd gd2 gif jpe jpeg jpg png ps svg webp
pack info:
  mode   undefined
  size   0
  flags  0
  margin 8
pack info:
  mode   node
  size   0
  flags  0
Warning: fixed cell size with unspecified width or height
fontname: "Arial" resolved to: (PangoCairoWin32Font) "Arial 12" 
Warning: fixed cell size with unspecified width or height
Warning: fixed cell size with unspecified width or height
Warning: fixed cell size with unspecified width or height
in label of node I57
Warning: Illegal attribute ALT in <IMG> - ignored
Warning: Illegal attribute ALT in <IMG> - ignored
Warning: fixed cell size with unspecified width or height
Warning: fixed cell size with unspecified width or height
Warning: "data/media/media/schoenfeld-liberman.ged/Levi-Assayas/I19-Levy-Assayas-Behora-Lapida-2012.jpg" was not found 
as a file or as a shape library member
Error: No or improper image 
file="data/media/media/schoenfeld-liberman.ged/Levi-Assayas/I19-Levy-Assayas-Behora-Lapida-2012.jpg"
in label of node I19
Warning: fixed cell size with unspecified width or height
Warning: fixed cell size with unspecified width or height
Warning: fixed cell size with unspecified width or height
Warning: fixed cell size with unspecified width or height
in label of node I63
Warning: Illegal attribute ALT in <IMG> - ignored
Warning: fixed cell size with unspecified width or height
Warning: fixed cell size with unspecified width or height
Warning: fixed cell size with unspecified width or height
in label of node I64
network simplex:  6 nodes 5 edges maxiter=2147483647 balance=1
network simplex: 6 nodes 5 edges 0 iter 0.00 sec
Maxrank = 3, minrank = 0
mincross: pass 0 iter 0 trying 0 cur_cross 0 best_cross 0
merge2: graph WT_Graph, rank 0 has only 2 < 3 nodes
merge2: graph WT_Graph, rank 1 has only 1 < 2 nodes
merge2: graph WT_Graph, rank 2 has only 2 < 3 nodes
merge2: graph WT_Graph, rank 3 has only 1 < 2 nodes
mincross WT_Graph: 0 crossings, 0.00 secs.
network simplex:  11 nodes 12 edges maxiter=2147483647 balance=2
network simplex: 11 nodes 12 edges 0 iter 0.00 sec
routesplines: 5 edges, 15 boxes 0.00 sec
Using render: cairo:cairo
Using device: pdf:cairo:cairo
Using render: cairo:cairo
Activated plugin library: gvplugin_gd.dll
Using loadimage: jpeg:cairo:gd

On versions lower than 10, it doesn’t complain about the images, it finds them.

steveroush · November 25, 2024, 4:47am

Just a guess, but you are running on a Windows OS while using Linux filenames. Try using backslashes instead of slashes in the filename.

Here are some other suggestions separate from the image problem

Unless 72 dpi is important to this effort, just use the default of 96 dpi
mclimit default is 1. Why explicitly set it to 1?
the documentation says that pagedir is ignored unless page is set.
the port names all see to be pic. For a given node, the port names must be unique.
some of the cells have width=“0”. Though undocumented, a positive integer seems to be required.

elysch · November 25, 2024, 3:59pm

Thank you for your answer.

I tried your suggestions even if I know where aesthetic ones mainly.

Do you have any other ideas on how to get a non zero size pdf file?

About images: Forgot to mention earlier I already tried forwardslash, backslash, double backslash and the whole path (no spaces in paths, in case you would ask )

gvexport-small-x.dot (6.8 KB)
mensajes-12_2_0-inst_small-forwardSlash.txt (6.4 KB)
mensajes-12_2_0-inst_small-backSlash.txt (6.4 KB)
mensajes-12_2_0-inst_small-doubleBackSlash.txt (6.4 KB)

steveroush · November 25, 2024, 4:47pm

try: dot gvexport.dot -o look.txt << no explicit output format.
- what does the output look like? An augmented version of the input?
try: dot gvexport.dot -Tpng -o look.png
- Is there a usable png result (with or without images?)

I should have noted that my Linux system produced usable pdf and png files using the original input (no images, of course). So my guess is that this is Windows-specific

elysch · November 25, 2024, 5:26pm

Thanks.

The png generated is also an empty file. Even tried deactivating the antivirus.

Here is the look.txt. It’s very similar to the original file.

look-small.txt (7.6 KB)

I should have noted that my Linux system produced usable pdf and png files using the original input (no images, of course). So my guess is that this is Windows-specific

What Linux flavor, version and kernel are you using with version 12?

The links worked ok when you tested it?

steveroush · November 26, 2024, 4:32pm

[ this may or may not be a real bug. But I encourage you to create an issue here]

so, not just a pdf problem
HREFs work on my Linux output
try neato -n2 look-small.txt -Tpdf -o o.pdf
- is o.pdf a usable pdf?
- do the HREFs work?
- (neato -n2 will take the dot output & produce a nearly identical result)
My setup
- dot - graphviz version 12.2.0~dev.20241020.1953 (20241020.1953) (out of habit, I build my own)
- Ubuntu - I can’t recommend, but it is what I use. Standard Graphviz package is old.
- lsb_release -d gives: Ubuntu 24.04.1 LTS

elysch · November 26, 2024, 10:27pm

Thank you for your answer.

Both the look-small.txt and the dot file generate an empty file when using neato -n2. It’s strange, I guess.

I’ll open the issue.

Thank you for the information of your environment.

elysch · November 26, 2024, 10:59pm

https://gitlab.com/graphviz/graphviz/-/issues/2619

Topic		Replies	Views
Rendering graphviz with python Help	2	1491	May 31, 2020
Could someone please try for me? Dev	3	319	April 24, 2023
Graphviz SVG for Obsidian Dev	31	2355	April 16, 2022
Graphviz in Jupyter notebook	7	4146	May 23, 2021
After upgrading graphviz to 9.0 y-coordinates are differently calculated	1	149	May 6, 2024

Different behavior between versions and links not working in pdf

Related topics