circos missing modules #9830
Comments
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@mcornwell1957 can you install circos into its own env and provide us with the detailed log, especially which packages gets installed from which channel. Thanks! |
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Hi @bgruening thanks for getting back to me, and I very much appreciate your help. |
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Hi @bgruening - is there anything else you want me to provide to help solve this problem? Thanks for your help! |
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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. |
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Hi @rvalieris - thank you very much for your input. And it looks like you are already doing the rebuild! I will try again when the rebuild is done, thanks again! |
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new package is up, please test it on osx ! |
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Tested and working - thank you so much!! (hope it wasnt too much trouble) |
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I'm having the same issue on Linux systems too. On one of the systems, I fixed it by changing into 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 The environment on Travis: Vlad |
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I had the same problem on Ubuntu 18.04 LTS. The solution gave by @vladsaveliev with linking libwebp.so.6 and libwebp.so.7 solved the problem. What is interesting on my other system (Ubuntu Mate 18.04 LTS) circos works just fine. |
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I had the same issue under several Ubuntu installations. I also tested in a docker image made with the following Dockerfile: When running a container using this image, and issuing the commands: I obtain the same problem with GD: |
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I have the same issue here, on osx Mojave 10.14 ''' Package Plan environment location: /anaconda3/envs/circos added / updated specs: The following packages will be downloaded: The following NEW packages will be INSTALLED: So I checked the modules, Any help is welcome :) |
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I am having the same problem as described by JihedC. |
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@telatin |
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I confirm that the issue still exists and linking suggested by @vladsaveliev fixes it, Should/can we patch this in the recipe? |
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Not sure what's changed, but it's no longer an issue for me since just recently. |
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Thanks @bgruening the issue seems to be resolved now. This commit is reverted back, and with build-n2 the correct .so file is getting installed. |
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Hi all, Please note I have installed all the required modules, However, when I ran the given example, I still met error as following Any advice is appreciated. Thank you very much! Xiao |
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Seems that original issue resolved so closing. |
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how to solve this error I INSTALL the software all afternoon |
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A very similar issue cropped up again for me - Installed circos into a fresh environment, and received the error that GD and GD::polyline could not be found in my @inc, so then I checked what is installed:
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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 circosit installs everything it needs to, but the installed version of circos can't find the GD package:If you just run circos to see what the problem is - you get the following
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
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