new casac fails to find libicuuc.so.54 #3
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There may have been a dependency resolution failure here. You should have an "icu" package at version 54.1 that provides that library. But there's an annoying thing where Anaconda's "boost" packages require a newer version of icu that they don't actually provide! So your broken tree might be wedged in a state where ICU is not installed. Can you see if icu and/or boost are installed, and what versions they're at? (See anaconda-issues#700). |
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Yes, that seems to be the issue. My working casac environment has: The most up to date one has icu 56.1. |
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Has this issue been resolved? I ran 'conda update --all' and have gotten myself into dependency hell. but importing casac gives: From our earlier discussion, I would have thought that would be adequate. Downgrading 'casa-python' to 4.5.2, then leads to a series of other errors, such as: and then downgrading 'casa-tools' to 4.5.2: Any thoughts? |
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It seems that something in casa-python is still looking for icu-56? Not clear how, but when I make my own symlinks into my conda environment, the import works. Here's the nominal set of versions (with icu-56 linked in by hand beside the icu-54 libraries): |
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Sorry, I never really worked on addressing this. I highly suspect that |
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Your channel and conda-forge are my two extra channels and I have not had a problem before. I see that boost and icu are currently being picked up from anaconda directly at the moment, so maybe there is a way to set priorities on what channel is used first? |
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I believe there are mechanisms to affect priorities between channels, but based on my understanding of the situation it will make a lot of sense for me to work towards basing things on conda-forge. (And, eventually, submitting my packages directly there.) OK, basic question: you were able to get things into a working state, right? There are other things that I ought to prioritize these days, but if this is really making you stuck, I want to fix that. |
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I am up and running after linking in some icu libraries by hand. Not pretty, but your job applications definitely take priority! |
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I wanted to raise this again, in case there was an easy solution. I am about to release new data that will be a great demonstration of my rtpipe and your pwkit code. Unfortunately, I am still having trouble with a simple install to get access to casac in Python. But the first line grabs icu v56, which is too high and the dependency is not properly handled to downgrade for the second line. |
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As it happens, just today I took a look at porting my packages over to conda-forge. I don't think I can switch everything over as quickly as I'd like, but I have some ideas about making my stuff more compatible. I appreciate your persistence! Updates soon, I hope. |
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Casey, for your demos and needs, do you absolutely need conda-forge as a dependency? For the time being, it is going to be easiest to avoid mixing and matching their repo and mine. I have started the work of importing my projects into conda-forge, which is clearly the sensible long-term solution. They have been quite helpful so far but it will take some time to bring everything in. |
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I should add that I might be able to create a channel that builds my stuff aiming for compatibility with conda-forge. At a minimum it will take a fair amount of effort, though, and if there are disagreeing choices with certain core packages it might not be possible to make them compatible. |
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I don't think conda-forge is a requirement. I thought it was good practice, but I'll back that change out for now. |
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Well, I'm taking a look and I think I can make and distribute a subset of packages that are based on conda-forge. Let me get back to you in a few hours. |
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Try installing from the I've only made builds for linux-64 but this was straightforward enough that OSX should also be doable. |
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I didn't see that boost warning (it installed boost 1.61). I did see a
conda warning after the successful installation ("dbus post-link ::
/etc/machine-id not found.."), so something funny going on there.
Then, when running 'python -c "import casac"', I get:
ImportError: No module named _atmosphere
Not quite there yet, but I can force the icu=54.0 for now and/or avoid
conda-forge.
On Fri, Dec 16, 2016 at 10:01 AM Peter Williams <notifications@github.com> wrote:
Try installing from the pkgw-forge channel rather than just pkgw. It should
provide casa-python and pwkit in a way that is compatible with — and, in
fact, requires — conda-forge. When I tested it, something strange happened
where I had to explicitly tell it to upgrade to boost version 1.62.0 in
order for everything to get synched up, though.
I've only made builds for linux-64 but this was straightforward enough that
OSX should also be doable.
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So, that dbus warning is fine and can be ignored. The message about "no module named _atmosphere" is actually indicating that some of the dependent libraries aren't aligned. You should have boost = 1.62.0 and icu = 1.56.1, so try |
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Ok, that's got it. First install bulk of dependencies from channel
'pkgw-forge'. Then boost from 'conda-forge'.
On Sat, Dec 17, 2016 at 8:08 AM Peter Williams <notifications@github.com> wrote:
So, that dbus warning is fine and can be ignored.
The message about "no module named _atmosphere" is actually indicating that
some of the dependent libraries aren't aligned. You should have boost =
1.62.0 and icu = 1.56.1, so try conda install boost=1.62.0 (plus any flags
to get the custom channels you need).
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Well, if you start with a fresh installation and add Casey, if your cool data demonstration is going to include instructions to get the requisite software stack installed, I would like to help make them as easy as possible. I am happy to do a test-run in a test environment, and if there are any problems I will see if there are ways to update the packaging to make things more robust. By the way, I uploaded OSX builds of casa-python and friends to |
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Oh yeah also we're getting kind of far afield from what this issue was originally about. I'm going to close it; you know how to reach me if there's more to discuss! |
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First, @pkgw thanks so much for developing the Python 3.6.7 | packaged by conda-forge | (default, Nov 21 2018, 03:09:43)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import casac
Traceback (most recent call last):
File "/opt/conda/lib/python3.6/site-packages/__casac__/atmosphere.py", line 14, in swig_import_helper
return importlib.import_module(mname)
File "/opt/conda/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 994, in _gcd_import
File "<frozen importlib._bootstrap>", line 971, in _find_and_load
File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 658, in _load_unlocked
File "<frozen importlib._bootstrap>", line 571, in module_from_spec
File "<frozen importlib._bootstrap_external>", line 922, in create_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
ImportError: /opt/conda/lib/python3.6/site-packages/__casac__/../../../libcasadbus.so.54.0.0: undefined symbol: _ZN4DBus14InterfaceProxyC2ERKSs
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/conda/lib/python3.6/site-packages/casac.py", line 1, in <module>
import __casac__
File "/opt/conda/lib/python3.6/site-packages/__casac__/__init__.py", line 54, in <module>
from . import atmosphere
File "/opt/conda/lib/python3.6/site-packages/__casac__/atmosphere.py", line 17, in <module>
_atmosphere = swig_import_helper()
File "/opt/conda/lib/python3.6/site-packages/__casac__/atmosphere.py", line 16, in swig_import_helper
return importlib.import_module('_atmosphere')
File "/opt/conda/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
ModuleNotFoundError: No module named '_atmosphere'This is the problematic configuration: $ conda list | egrep 'boost|icu|casa|pwkit'
boost 1.68.0 py36h8619c78_1001 conda-forge
boost-cpp 1.68.0 h11c811c_1000 conda-forge
casa-data r20180919 0 pkgw-forge
casa-python 5.4.1 py36hc5275ef_0 pkgw-forge
casa-tools 5.4.1 h6c11689_1 pkgw-forge
casacore 2.4.2a0 py36he20af57_1 conda-forge
icu 58.2 hf484d3e_1000 conda-forgeIt appears to me as well that the issue comes from the builds of $ conda list | egrep 'boost|icu|casa|pwkit'
boost 1.68.0 py36h3e44d54_1 conda-forge
boost-cpp 1.68.0 h3a22d5f_0 conda-forge
casa-data r20180919 0 pkgw-forge
casa-python 5.4.1 py36hc5275ef_0 pkgw-forge
casa-tools 5.4.1 h6c11689_1 pkgw-forge
casacore 2.4.2a0 py36he20af57_1 conda-forge
icu 58.2 hfc679d8_0 conda-forgeI think it would be a huge contribution to have |
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@mtazzari Thanks for the detailed report! Are you able to upgrade to Python 3.7? I just recently released new versions of the packages to add support for 3.7, and part of that update process involved synchronizing them with the latest conda-forge dependencies. I suspect that updating everything might fix your problem. For reference, here are the versions for my install: If you're stuck on 3.6, I should be able to make a new build for that version too. It will just take a while to compile everything. Relatedly, the main reason these packages aren't in conda-forge is that they take too long to build in the CI systems. However, the project is right now looking into migrating some builds onto the Azure Pipelines system, which supports much longer build timeouts. So we might be able to make more of these packages official in the near future! |
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Fantastic! I have been able to upgrade my stack to Python 3.7 and it all works again! Thank you! I see the complication with getting the packages in conda-forge. I have GALARIO on conda-forge and the latest conda-smithy updates moved most if not all the builds on Azure. See the tests of the last commit in the galario feedstock, https://github.com/conda-forge/galario-feedstock |
I am working with conda at the AOC. There, I have two environments for using pwkit to get access to casac. The newly-updated one how produces this error when importing casac:
After some fiddling with version numbers of casa/pwkit, it seems that a recent update to casa is the problem. Here are the casa/pwkit versions that fail:
And a test in my still-working casac environment:
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