dyld[74537]: missing symbol called error

[Nikki Ni]

Hello Everyone, 

I am using the Apple M1 Pro. I installed the circos-0.69.tgz version from this page:

https://circos.ca/software/download/circos/

I have the perl pre-installed:

% perl -v

This is perl 5, version 34, subversion 1 (v5.34.1) built for darwin-thread-multi-2level

I follow the tutorial and installed all the modules expect the GD. so I Installed libpng 1.6.26, freetype 2.4.0, libgd 2.2.3 following this page:

https://circos.ca/tutorials/lessons/configuration/perl_and_modules/

and then I installed GD 2.53 version 

All my modules are installed ok:

% circos -modules

ok       1.52 Carp

ok       0.45 Clone

ok       2.67 Config::General

ok       3.80 Cwd

ok      2.179 Data::Dumper

ok       2.58 Digest::MD5

ok       2.85 File::Basename

ok       3.80 File::Spec::Functions

ok     0.2311 File::Temp

ok       1.52 FindBin

ok       0.39 Font::TTF::Font

ok       2.51 GD

ok        0.2 GD::Polyline

ok       2.52 Getopt::Long

ok       1.46 IO::File

ok      0.430 List::MoreUtils

ok       1.55 List::Util

ok       0.01 Math::Bezier

ok   1.999818 Math::BigFloat

ok       0.08 Math::Round

ok       0.08 Math::VecStat

ok    1.03_01 Memoize

ok       1.97 POSIX

ok       1.31 Params::Validate

ok       2.01 Pod::Usage

ok       2.05 Readonly

ok 2024080801 Regexp::Common

ok       2.87 SVG

ok       1.19 Set::IntSpan

ok     1.6611 Statistics::Basic

ok       3.23 Storable

ok       1.23 Sys::Hostname

ok       2.04 Text::Balanced

ok       0.63 Text::Format

ok     1.9767 Time::HiRes

Finally I cd example/ and 

./run

what I get is:

% ./run
Creating image circos.png and writing report to run.out.
Example takes ~45-60 seconds to generate.
dyld[75039]: missing symbol called
./run: line 7: 75039 Abort trap: 6           ../bin/circos -conf etc/circos.conf -debug_group summary,timer > run.out

There is no default circos.conf file in the circos/etc directory but there is one in the example.

 % ../bin/circos -conf etc/circos.conf

debuggroup summary 0.09s welcome to circos v0.69 6 Dec 2015 on Perl 5.034001

debuggroup summary 0.10s current working directory /Users/qinyunikki/circos/circos-0.69/example

debuggroup summary 0.10s command ../bin/circos -conf etc/circos.conf

debuggroup summary 0.10s loading configuration from file etc/circos.conf

debuggroup summary 0.10s found conf file etc/circos.conf

debuggroup summary 0.20s debug will appear for these features: output,summary

debuggroup summary 0.20s bitmap output image ./circos.png

debuggroup summary 0.20s SVG output image ./circos.svg

debuggroup summary 0.20s parsing karyotype and organizing ideograms

debuggroup summary 0.26s karyotype has 66 chromosomes of total size 8,540,079,869

debuggroup summary 0.26s applying global and local scaling

debuggroup summary 0.29s allocating image, colors and brushes

dyld[75053]: missing symbol called

zsh: abort      ../bin/circos -conf etc/circos.conf

When I specify the .conf to example/etc/.circos.conf, it still gave the same fault.
and the ouptput svg only has one line: This XML file does not appear to have any style information associated with it. The document tree is shown below.

[Martin Krzywinski]

With a dyld error, it looks like a library linking issue on the Mac. But from the error, it's impossible to tell where.

If it happens right after "allocating image, colors, and brushes" it's probably related to gdlib and GD. Even though Circos shows that GD is installed correctly, it doesn't actually mean that the library is functioning correctly. In Perl, you can check whether a module (GD, which interfaces to libgd) is installed, but this check is shallow.

You should check whether the libgd/GD installation is intact -- both libgd and GD should have some test suites that you can run.

Martin Krzywinski

science + art

https://mk.bcgsc.ca

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