Trouble installing pypath

[Taylor M Sorenson]

Hello,

I just attempted to install pypath using the Anaconda distribution, but received the message below. It appears that cairo, igraph, pymysql, pygraphviz, and of course pypath failed to install. Do you have any recommendations on what I should do next to ensure they're properly installed?

Thanks,

Taylor Sorenson

Research Intern

Massachusetts General Hospital

===[ Testing installation ]===

[ !! ] Module `cairo` for Python 3 failed to install.

[ !! ] Module `igraph` for Python 3 failed to install.

[ OK ] Module `future` for Python 3 is available.

[ OK ] Module `numpy` for Python 3 is available.

[ OK ] Module `scipy` for Python 3 is available.

[ OK ] Module `pandas` for Python 3 is available.

[ OK ] Module `suds` for Python 3 is available.

[ OK ] Module `bioservices` for Python 3 is available.

[ !! ] Module `pymysql` for Python 3 failed to install.

[ !! ] Module `pygraphviz` for Python 3 failed to install.

[ OK ] Module `fisher` for Python 3 is available.

[ OK ] Module `pysftp` for Python 3 is available.

[ OK ] Module `fabric` for Python 3 is available.

[ OK ] Module `tqdm` for Python 3 is available.

[ !! ] Module `pypath` for Python 3 failed to install.

[ !! ] You have no pypath installed or some issue avoids the module to load.

          Please check the list above for failed items.

[Dénes Türei]

Dear Taylor,

Apologies for late reply, I was on holidays in the past weeks.

As I see the modules installed directly by conda are ones which the failed.
Did you have already Anaconda installed or the script installed it?
What was the root of your Anaconda installation? Did you provide it to
the script as a parameter? E.g,

mac-install-conda.sh -p 3 -a /home/me/anaconda3/

What is the output if you try to install manually these modules?

/your/anaconda/installation/bin/conda install -y -c vgauthier cairo=1.12.18
/your/anaconda/installation/bin/conda install -y -c richlewis pycairo=1.10.0
/your/anaconda/installation/bin/conda install -y graphviz
/your/anaconda/installation/bin/conda install -y -c omnia pygraphviz
/your/anaconda/installation/bin/conda install -y -c bioconda python-igraph

Some of these repositories might have changed or there might be
permission problems or there might be some confusion around the
location of the Anaconda distribution. But I expect the output of the
lines above will clarify this.

Thank you for using pypath, sorry again for the delay and from now you
can expect me to reply more promptly.

Best wishes,

Denes

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--
Denes Turei, Ph.D.

postdoc @ EMBL
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--
Denes Turei, Ph.D.

postdoc @ EMBL
+4915166299976 Germany
+447442970610 UK
de...@ebi.ac.uk
http://www.ebi.ac.uk/~denes
public key: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x5706A4B609DD65A6