Searching for fonts is cluttering the debug output!

[Dirk Krienbühl]

First I want to say thanks for that wonderful piece of software !

Well, I’m just a beginner, made some progress and creating some nice SVG’s 

Actually, I was trying to debug another small issue I’ve got, as my custom link.conf is was found, but is included in my custom circus.conf but that I could resolve by myself.

Nevertheless, circos -debug shows many entries while it’s searching for fonts but finally after trying various locations they are found :-)

I would like to know on how I can fix this, so that the fonts are found on the first try and does not clutter the debug output?

Many thanks in advance for any hint!

NB: Unfortunately Pastebin.com is in maintenance mode, so I post a small part of the message in the debug log,  with the repeating and desperate search for fonts :-)

debuggroup summary 0.34s applying global and local scaling
debuggroup image 0.36s creating image template for circle 1500 px diameter
debuggroup summary 0.36s allocating image, colors and brushes
debuggroup io 1.50s locating file fonts/modern/cmunbmr.ttf role _undef_
debuggroup io 1.50s trying path /usr/local/Cellar/circos/0.69-9/bin/. /usr/local/Cellar/circos/0.69-9/bin/etc /usr/local/Cellar/circos/0.69-9/bin/data /usr/local/Cellar/circos/0.69-9/bin/../. /usr/local/Cellar/circos/0.69-9/bin/../etc /usr/local/Cellar/circos/0.69-9/bin/../data /usr/local/Cellar/circos/0.69-9/bin/../../. /usr/local/Cellar/circos/0.69-9/bin/../../etc /usr/local/Cellar/circos/0.69-9/bin/../../data /usr/local/Cellar/circos/0.69-9/bin/../../../. /usr/local/Cellar/circos/0.69-9/bin/../../../etc /usr/local/Cellar/circos/0.69-9/bin/../../../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../data /usr/local/Cellar/circos/0.69-9/libexec/bin/. /usr/local/Cellar/circos/0.69-9/libexec/bin/etc /usr/local/Cellar/circos/0.69-9/libexec/bin/data /usr/local/Cellar/circos/0.69-9/libexec/bin/../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../data /usr/local/Cellar/circos/0.69-9/libexec/bin/../../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../../data /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../data
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../../fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../../etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../../data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../../../fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../../../etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/bin/../../../data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/libexec/bin/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/libexec/bin/etc/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/libexec/bin/data/fonts/modern/cmunbmr.ttf
debuggroup io 1.50s trying /usr/local/Cellar/circos/0.69-9/libexec/bin/../fonts/modern/cmunbmr.ttf
debuggroup io 1.50s fonts/modern/cmunbmr.ttf found in /usr/local/Cellar/circos/0.69-9/libexec/bin/../fonts/modern/cmunbmr.ttf
debuggroup io 1.55s locating file fonts/symbols/circossymbols.otf role _undef_
debuggroup io 1.55s trying path /usr/local/Cellar/circos/0.69-9/bin/. /usr/local/Cellar/circos/0.69-9/bin/etc /usr/local/Cellar/circos/0.69-9/bin/data /usr/local/Cellar/circos/0.69-9/bin/../. /usr/local/Cellar/circos/0.69-9/bin/../etc /usr/local/Cellar/circos/0.69-9/bin/../data /usr/local/Cellar/circos/0.69-9/bin/../../. /usr/local/Cellar/circos/0.69-9/bin/../../etc /usr/local/Cellar/circos/0.69-9/bin/../../data /usr/local/Cellar/circos/0.69-9/bin/../../../. /usr/local/Cellar/circos/0.69-9/bin/../../../etc /usr/local/Cellar/circos/0.69-9/bin/../../../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../data /usr/local/Cellar/circos/0.69-9/libexec/bin/. /usr/local/Cellar/circos/0.69-9/libexec/bin/etc /usr/local/Cellar/circos/0.69-9/libexec/bin/data /usr/local/Cellar/circos/0.69-9/libexec/bin/../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../data /usr/local/Cellar/circos/0.69-9/libexec/bin/../../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../../data /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../data
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../../fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../../etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../../data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../../../fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../../../etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/bin/../../../data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/libexec/bin/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/libexec/bin/etc/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/libexec/bin/data/fonts/symbols/circossymbols.otf
debuggroup io 1.55s trying /usr/local/Cellar/circos/0.69-9/libexec/bin/../fonts/symbols/circossymbols.otf
debuggroup io 1.55s fonts/symbols/circossymbols.otf found in /usr/local/Cellar/circos/0.69-9/libexec/bin/../fonts/symbols/circossymbols.otf
debuggroup io 1.56s locating file fonts/modern/cmunrm.otf role _undef_
debuggroup io 1.56s trying path /usr/local/Cellar/circos/0.69-9/bin/. /usr/local/Cellar/circos/0.69-9/bin/etc /usr/local/Cellar/circos/0.69-9/bin/data /usr/local/Cellar/circos/0.69-9/bin/../. /usr/local/Cellar/circos/0.69-9/bin/../etc /usr/local/Cellar/circos/0.69-9/bin/../data /usr/local/Cellar/circos/0.69-9/bin/../../. /usr/local/Cellar/circos/0.69-9/bin/../../etc /usr/local/Cellar/circos/0.69-9/bin/../../data /usr/local/Cellar/circos/0.69-9/bin/../../../. /usr/local/Cellar/circos/0.69-9/bin/../../../etc /usr/local/Cellar/circos/0.69-9/bin/../../../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../data /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../. /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../etc /Users/dirk/Desktop/2020_PYTHON/lnd/circos/../../../data /usr/local/Cellar/circos/0.69-9/libexec/bin/. /usr/local/Cellar/circos/0.69-9/libexec/bin/etc /usr/local/Cellar/circos/0.69-9/libexec/bin/data /usr/local/Cellar/circos/0.69-9/libexec/bin/../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../data /usr/local/Cellar/circos/0.69-9/libexec/bin/../../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../../data /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../. /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../etc /usr/local/Cellar/circos/0.69-9/libexec/bin/../../../data
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/etc/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/data/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../etc/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../data/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../../fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../../etc/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../../data/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../../../fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../../../etc/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /usr/local/Cellar/circos/0.69-9/bin/../../../data/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/etc/fonts/modern/cmunrm.otf
debuggroup io 1.56s trying /Users/dirk/Desktop/2020_PYTHON/lnd/circos/data/fonts/modern/cmunrm.otf

[Martin Krzywinski]

You can explicitly set which debug groups are being reported. The font messages are part of the "io" group.

To exclude it, you can call only on some basic groups:

../bin/circos -debug_group summary,image,karyotype,layer

and to see the full list of groups

../bin/circos -debug_group

and you'll see the ones that are on by default with "*".

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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