Open alimanfoo opened 7 years ago
OK, travis build is erroring with same problem:
ImportError: libicuuc.so.54: cannot open shared object file: No such file or directory
@hardingnj any chance you could investigate? Looks like either a missing dependency or dependency conflict?
Yes-can have a look tomorrow
Potentially relevant: https://github.com/pkgw/pwkit/issues/3
Using R
in the docker image doesn't work either.
This workaround fixes: https://github.com/ContinuumIO/anaconda-issues/issues/152#issuecomment-225214743
But we still have the issue with libicuuc
I wonder if the icu issue is to do with the fact that some r packages are coming from conda-forge and some from the r channel, e.g.:
r 3.3.2 r3.3.2_0 r r-base 3.3.2 2 conda-forge
I'm trying again with the channel priorities changed so r takes precendence, will see if that's better...
On Wednesday, February 1, 2017, Nick Harding notifications@github.com wrote:
Using R in the docker image doesn't work either.
This workaround fixes: ContinuumIO/anaconda-issues#152 (comment) https://github.com/ContinuumIO/anaconda-issues/issues/152#issuecomment-225214743
But we still have the issue with libicuuc
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-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health http://cggh.org The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: alimanfoo@googlemail.com Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721
Seems to be with icu. We can go up to 58.1, but mpl require 56.*
Although that may not explain missing lib error
Yeah missing lib error suggests some package has a dependency on icu 54 which hasn't been properly declared, but icu 56 gets installed because that's what r-base, matplotlib, qt etc. explicitly declare.
On Wednesday, February 1, 2017, Nick Harding notifications@github.com wrote:
Seems to be with icu. We can go up to 58.1, but mpl require 56.*
Although that may not explain missing lib error
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Changing channel priority does not fix the problem, r-base still ends up getting installed from conda-forge.
I tried manually installing r-base from the r channel, it looks like the dependencies are different from conda-forge. r-base=3.3.2 from r channel depends on icu 54, wherease r-base=3.3.2 from conda-forge depends on icu 56. I wonder if some other parts of r just assume icu 54 because that's where the current r-base package is at on the r channel, but then if r-base gets installed from conda-forge then icu 54 is obviously missing.
I can't see any easy way to resolve this, other than waiting for the r channel to upgrade it's icu dependency. If we force r-base to install from r channel then currently it will downgrade icu to 54 which will force downgrade of matplotlib etc.
Some people have reported a workaround by symlinking 56 > 54, but not a good fix.
Sounds like a bad idea to me!
On Wednesday, February 1, 2017, Nick Harding notifications@github.com wrote:
Some people have reported a workaround by symlinking 56 > 54, but not a good fix.
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-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health http://cggh.org The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: alimanfoo@googlemail.com Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721
Seems like we've stumbled into a bit of a rat's nest: https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/myBjZaaAoDI
Doesn't look like there's an easy solution for the moment.
Symlinking ICU is actually not very risky. IMHO ICU shouldn't bother with versioned shared libraries since their interface doesn't change in incompatible ways.
Thanks Ray, very useful to know.
On Monday, February 6, 2017, Ray Donnelly notifications@github.com wrote:
Symlinking ICU is actually not very risky. IMHO ICU shouldn't bother with versioned shared libraries since their interface doesn't change in incompatible ways.
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-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health http://cggh.org The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: alimanfoo@googlemail.com Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721
Resolve rpy2 installation/dependency issues, xref #38.