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OK, travis build is erroring with same problem: @hardingnj any chance you could investigate? Looks like either a missing dependency or dependency conflict? |
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Yes-can have a look tomorrow
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Potentially relevant: |
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Using This workaround fixes: But we still have the issue with libicuuc |
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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 ***@***.***> wrote:
Using R in the docker image doesn't work either.
This workaround fixes:
ContinuumIO/anaconda-issues#152 (comment)
<ContinuumIO/anaconda-issues#152 (comment)>
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
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Email: alimanfoo@googlemail.com
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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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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 ***@***.***> 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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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
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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. |
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Some people have reported a workaround by symlinking 56 > 54, but not a good fix. |
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Sounds like a bad idea to me!
…On Wednesday, February 1, 2017, Nick Harding ***@***.***> 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
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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. |
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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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Thanks Ray, very useful to know.
…On Monday, February 6, 2017, Ray Donnelly ***@***.***> 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
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Tel: +44 (0)1865 287721
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3 participants
Resolve rpy2 installation/dependency issues, xref #38.