Missing libgvplugin_pango

[johanneskoester]

I get the following error when using the dot command:

Warning: Could not load "/home/johannes/.local/opt/miniconda3/envs/snakemake-tutorial/lib/graphviz/libgvplugin_pango.so.6" - file not found
Warning: Could not load "/home/johannes/.local/opt/miniconda3/envs/snakemake-tutorial/lib/graphviz/libgvplugin_pango.so.6" - file not found
Format: "jpg" not recognized. Use one of: bmp canon cmap cmapx cmapx_np dot eps fig gv ico imap imap_np ismap jpe jpeg jpg pdf pic plain plain-ext png pov ps ps2 svg svgz tif tiff tk vml vmlz xdot xdot1.2 xdot1.4

This is on fedora linux 26.

[johanneskoester]

@ocefpaf, since you are one of the maintainers, any insight on this?

[ocefpaf]

No idea. I kind don't really use graphviz a lot. Ping @conda-forge/graphviz team.

[ocefpaf]

BTW, if you can create a test and send it as a PR we can check if a re-build fixes this.

[ccordoba12]

@johanneskoester, what were you doing when you got that error?

[rasmusagren]

I have the same error on Ubuntu. Here is a Dockerfile to reproduce it.

FROM ubuntu:latest

RUN apt-get update && apt-get -y dist-upgrade
RUN apt-get install -y --no-install-recommends bzip2 wget

RUN wget --no-check-certificate https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
    bash Miniconda3-latest-Linux-x86_64.sh -bf && \
    rm Miniconda3-latest-Linux-x86_64.sh
ENV PATH="/root/miniconda3/bin:${PATH}"

RUN conda install -c conda-forge graphviz=2.38.0

CMD dot

This gives:

$ docker run --rm docker_graphviz
Warning: Could not load "/root/miniconda3/lib/graphviz/libgvplugin_pango.so.6" - file not found

Seems like an X libraries thing..

root@e87e82132286:/home# ldd /root/miniconda3/lib/graphviz/libgvplugin_pango.so.6
        linux-vdso.so.1 =>  (0x00007ffec4fe2000)
        libgvc.so.6 => /root/miniconda3/lib/graphviz/../libgvc.so.6 (0x00007fba3fcc6000)
        libltdl.so.7 => /root/miniconda3/lib/graphviz/../libltdl.so.7 (0x00007fba3fabd000)
        libxdot.so.4 => /root/miniconda3/lib/graphviz/../libxdot.so.4 (0x00007fba3f8b8000)
        libcgraph.so.6 => /root/miniconda3/lib/graphviz/../libcgraph.so.6 (0x00007fba3f6a2000)
        libcdt.so.5 => /root/miniconda3/lib/graphviz/../libcdt.so.5 (0x00007fba3f49c000)
        libpathplan.so.4 => /root/miniconda3/lib/graphviz/../libpathplan.so.4 (0x00007fba3f294000)
        libexpat.so.1 => /root/miniconda3/lib/graphviz/../libexpat.so.1 (0x00007fba3f06a000)
        libpangocairo-1.0.so.0 => /root/miniconda3/lib/graphviz/../libpangocairo-1.0.so.0 (0x00007fba3ee5e000)
        libcairo.so.2 => /root/miniconda3/lib/graphviz/../libcairo.so.2 (0x00007fba3eb19000)
        libpixman-1.so.0 => /root/miniconda3/lib/graphviz/../libpixman-1.so.0 (0x00007fba3e873000)
        libXrender.so.1 => not found
        libSM.so.6 => not found
        libICE.so.6 => not found
        libX11.so.6 => not found
        libXext.so.6 => not found
        libpangoft2-1.0.so.0 => /root/miniconda3/lib/graphviz/../libpangoft2-1.0.so.0 (0x00007fba3e65e000)
        libharfbuzz.so.0 => /root/miniconda3/lib/graphviz/../libharfbuzz.so.0 (0x00007fba3e3d0000)
        libgraphite2.so.3 => /root/miniconda3/lib/graphviz/../libgraphite2.so.3 (0x00007fba3e19c000)
        libpango-1.0.so.0 => /root/miniconda3/lib/graphviz/../libpango-1.0.so.0 (0x00007fba3df52000)
        libgthread-2.0.so.0 => /root/miniconda3/lib/graphviz/../libgthread-2.0.so.0 (0x00007fba3dd51000)
        libfontconfig.so.1 => /root/miniconda3/lib/graphviz/../libfontconfig.so.1 (0x00007fba3db0f000)
        libxml2.so.2 => /root/miniconda3/lib/graphviz/../libxml2.so.2 (0x00007fba3d7a9000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fba3d5a5000)
        libicui18n.so.58 => /root/miniconda3/lib/graphviz/../libicui18n.so.58 (0x00007fba3d0a5000)
        libicuuc.so.58 => /root/miniconda3/lib/graphviz/../libicuuc.so.58 (0x00007fba3cca6000)
        libicudata.so.58 => /root/miniconda3/lib/graphviz/../libicudata.so.58 (0x00007fba3b1a6000)
        liblzma.so.5 => /root/miniconda3/lib/graphviz/../liblzma.so.5 (0x00007fba3af80000)
        libgobject-2.0.so.0 => /root/miniconda3/lib/graphviz/../libgobject-2.0.so.0 (0x00007fba3ad2b000)
        libffi.so.6 => /root/miniconda3/lib/graphviz/../libffi.so.6 (0x00007fba3ab22000)
        libglib-2.0.so.0 => /root/miniconda3/lib/graphviz/../libglib-2.0.so.0 (0x00007fba3a7f7000)
        libiconv.so.2 => /root/miniconda3/lib/graphviz/../libiconv.so.2 (0x00007fba3a509000)
        libpcre.so.1 => /root/miniconda3/lib/graphviz/../libpcre.so.1 (0x00007fba3a2c7000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fba3a0aa000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fba39ea2000)
        libfreetype.so.6 => /root/miniconda3/lib/graphviz/../libfreetype.so.6 (0x00007fba39c0a000)
        libpng16.so.16 => /root/miniconda3/lib/graphviz/../libpng16.so.16 (0x00007fba399ca000)
        libz.so.1 => /root/miniconda3/lib/graphviz/../libz.so.1 (0x00007fba397b3000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fba394aa000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fba390e0000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fba4016c000)
        libXrender.so.1 => not found
        libSM.so.6 => not found
        libICE.so.6 => not found
        libX11.so.6 => not found
        libXext.so.6 => not found
        libXrender.so.1 => not found
        libSM.so.6 => not found
        libICE.so.6 => not found
        libX11.so.6 => not found
        libXext.so.6 => not found
        libstdc++.so.6 => /root/miniconda3/lib/graphviz/.././libstdc++.so.6 (0x00007fba38da6000)
        libgcc_s.so.1 => /root/miniconda3/lib/graphviz/.././libgcc_s.so.1 (0x00007fba38b94000)

If I install them from conda-forge it works.

FROM ubuntu:latest

RUN apt-get update && apt-get -y dist-upgrade
RUN apt-get install -y --no-install-recommends bzip2 wget

RUN wget --no-check-certificate https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
    bash Miniconda3-latest-Linux-x86_64.sh -bf && \
    rm Miniconda3-latest-Linux-x86_64.sh
ENV PATH="/root/miniconda3/bin:${PATH}"

RUN conda install -c conda-forge graphviz=2.38.0 xorg-libxrender xorg-libxpm

CMD dot

I don't know if they should be added as dependencies or if a fancier solution is required?

[jakirkham]

Did you install the yum requirements from the recipe? Note the names may be different for apt-get.

[rasmusagren]

No, I have never encountered that for a recipe before. How is it intended to be used? Would it not be more self contained to include the conda-forge packages as dependencies when they exist?

[jakirkham]

Just install everything listed in yum_requirements.txt. There is currently no gtk2 package. Using X11 condapackages as dependencies is an ongoing discussion.

[rasmusagren]

I understand. May I ask why you're reluctant to add it as a dependency? Is it because conda-forge doesn't want large dependencies that the majority of the users would already have installed? If so, is there a list somewhere of these programs that are considered "outside of conda"? Thanks!

[ccordoba12]

@rasmusagren, the simplest way for you to solve this for now is to install an X server in your server.

[rasmusagren]

Thanks, but the solution with xorg-libxrender xorg-libxpm works for me right now. I still think that all dependencies should be included in the recipes, in particular as docker and singularity are becoming so popular and there people often use slimmed down distributions.

[jakirkham]

May I ask why you're reluctant to add it as a dependency?

We have discussed this. Unfortunately the issue is complicated and we haven't found the right solution.

xref: conda-forge/cfep#7

[jakirkham]

Should add put up PR ( conda-forge/staged-recipes#3920 ) for gtk2 some time ago, which is the only package we are getting from yum here. Not sure if that is enough to make this installable from conda alone or if there are more issues hidden.

[johanneskoester]

I can confirm that running conda install -c conda-forge xorg-libxrender xorg-libxpm fixes the issue. So, no gtk needed.

[jakirkham]

So, no gtk needed.

Ha! No wonder. :)

[ccordoba12]

Fixed by #23.