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When I try to update all packages in my Anaconda3 virtualenv using the conda update --all command, instead of upgrading all packages, some packages Anaconda tells me would be downgraded.

This is the output of the conda update --all command:

Fetching package metadata: ....
Solving package specifications: ......................................................................................................................................................................................................................................................................................
Package plan for installation in environment /home/xiaolong/development/anaconda3/envs/jupyter:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    mkl-rt-11.1                |               p0       100.1 MB
    numpy-1.10.2               |          py35_p0         5.8 MB
    pillow-3.1.1               |           py35_0         812 KB
    werkzeug-0.11.4            |           py35_0         420 KB
    clyent-1.2.1               |           py35_0          13 KB
    numexpr-2.4.4              |     np110py35_p0         334 KB
    scipy-0.16.1               |     np110py35_p0        23.2 MB
    bokeh-0.11.1               |           py35_0         3.1 MB
    datashape-0.5.1            |           py35_0          91 KB
    scikit-learn-0.17          |     np110py35_p1         8.8 MB
    odo-0.4.2                  |           py35_0         176 KB
    ------------------------------------------------------------
                                           Total:       142.8 MB

The following NEW packages will be INSTALLED:

    mkl-rt:       11.1-p0            

The following packages will be UPDATED:

    bokeh:        0.11.0-py35_0      --> 0.11.1-py35_0      
    clyent:       1.2.0-py35_0       --> 1.2.1-py35_0       
    datashape:    0.5.0-py35_0       --> 0.5.1-py35_0       
    odo:          0.4.0-py35_0       --> 0.4.2-py35_0       
    pillow:       3.1.0-py35_0       --> 3.1.1-py35_0       
    werkzeug:     0.11.3-py35_0      --> 0.11.4-py35_0      

The following packages will be DOWNGRADED:

    numexpr:      2.4.6-np110py35_1  --> 2.4.4-np110py35_p0  [mkl]
    numpy:        1.10.4-py35_0      --> 1.10.2-py35_p0      [mkl]
    scikit-learn: 0.17-np110py35_2   --> 0.17-np110py35_p1   [mkl]
    scipy:        0.17.0-np110py35_1 --> 0.16.1-np110py35_p0 [mkl]

Proceed ([y]/n)?

I'd like to know why this is happening. Why would some packages be downgraded? Maybe a better question is:

What changed in those downgrading versions of the packages, so that now when I update other packages, they need to be reverted to an earlier version?

From this I hope to conclude, whether I need any property of the current version of for example scipy, or if I can let it be downgraded.

Zelphir Kaltstahl
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    Probably a Bug in Conda (see also https://github.com/conda/conda/issues/2052) or the newer packages are not built against MKL. If you used python2.7 numpy wants to downgrade even further :-) – MSeifert Feb 19 '16 at 23:27
  • @MSeifert I read about MKL being faster and stuff, so I thought it might have to do with scipy now using that as well, but I don't understand why they should go back to not using MKL in a newer version then. – Zelphir Kaltstahl Feb 20 '16 at 00:19
  • It's about which packages are avaiable in the conda repository. It may be possible that newer packages are not yet built against MKL there. But on the other hand it may also be just a bug. – MSeifert Feb 20 '16 at 00:21

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