bioconda-recipes: circos missing modules
Hi all - I have been trying to load up the circos package (which I know is notorious for its problems) and am running into some problems that I can’t fix.
Simply enough - after doing a standard conda install circos it installs everything it needs to, but the installed version of circos can’t find the GD package:
macintoshs-mbp:~ tosh$ circos -modules
ok 1.38 Carp
ok 0.38 Clone
ok 2.61 Config::General
ok 3.73 Cwd
ok 2.158 Data::Dumper
ok 2.54 Digest::MD5
ok 2.85 File::Basename
ok 3.73 File::Spec::Functions
ok 0.2304 File::Temp
ok 1.51 FindBin
ok 0.39 Font::TTF::Font
missing GD
missing GD::Polyline
ok 2.45 Getopt::Long
ok 1.16 IO::File
ok 0.428 List::MoreUtils
ok 1.45 List::Util
ok 0.01 Math::Bezier
ok 1.9997 Math::BigFloat
ok 0.07 Math::Round
ok 0.08 Math::VecStat
ok 1.03 Memoize
ok 1.53 POSIX
ok 1.26 Params::Validate
ok 1.64 Pod::Usage
ok 1.04 Readonly
ok 2016060801 Regexp::Common
ok 2.64 SVG
ok 1.19 Set::IntSpan
ok 1.6611 Statistics::Basic
ok 2.53 Storable
ok 1.20 Sys::Hostname
ok 2.03 Text::Balanced
ok 0.59 Text::Format
ok 1.9728 Time::HiRes
If you just run circos to see what the problem is - you get the following
macintoshs-mbp:~ tosh$ circos
*** REQUIRED MODULE(S) MISSING OR OUT-OF-DATE ***
You are missing one or more Perl modules, require newer versions, or some modules failed to load. Use CPAN to install it as described in this tutorial
http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules
missing GD
error Can't load '/Users/tosh/miniconda3/lib/perl5/site_perl/5.22.0/darwin-thread-multi-2level/auto/GD/GD.bundle' for module GD: dlopen(/Users/tosh/miniconda3/lib/perl5/site_perl/5.22.0/darwin-thread-multi-2level/auto/GD/GD.bundle, 1): Library not loaded: /usr/local/opt/libpng/lib/libpng16.16.dylib Referenced from: /Users/tosh/miniconda3/lib/perl5/site_perl/5.22.0/darwin-thread-multi-2level/auto/GD/GD.bundle Reason: image not found at /Users/tosh/miniconda3/lib/perl5/5.22.0/darwin-thread-multi-2level/DynaLoader.pm line 197. at (eval 25) line 1.Compilation failed in require at (eval 25) line 1.
missing GD::Polyline
error Attempt to reload GD.pm aborted.Compilation failed in require at /Users/tosh/miniconda3/lib/perl5/site_perl/5.22.0/darwin-thread-multi-2level/GD/Polyline.pm line 45.
I believe the issue occurs due to the fact that there is a line in there that still tries to search for a global element (/usr/local/opt/libpng/lib/libpng16.16.dylib) that is (correctly) not there.
Bioconda has been such a good tool - and I’m sure I could install circos from scratch and go from there, but it would be great if I could continue to have all of my packages in this pipeline come from bioconda.
Any ideas of how to fix this? Thanks a lot for your help
About this issue
- Original URL
- State: closed
- Created 6 years ago
- Comments: 19 (13 by maintainers)
I’m having the same issue on Linux systems too.
On one of the systems, I fixed it by changing into
$CONDA_PREFIX/liband linking libwebp as follows:For some reason libgd was expecting version 7 if this lib instead of 6.
Another linux system with this issue is Travis: https://travis-ci.org/umccr/umccrise/builds/453904242 Getting the same error output there:
The environment on Travis:
Vlad
its working on linux, I am guess you are on osx. osx builds of perl-gd are currently set to skip, so I am guessing the need to be re-built to pick up the new libs.