Fix issue due to Conda-forge #45

licode · 2016-09-12T19:02:59Z

also corrected sha256 number, and remove unused tests.

licode · 2016-09-12T19:25:54Z

Now conda auto-build is back again after a quick fix.

tacaswell · 2016-09-13T02:48:46Z

scripts/nsls2-dev-build.sh

- conda-forge
- defaults" > $CONDARC_PATH
+- defaults
+- conda-forge" > $CONDARC_PATH


This seems a bit dangerous as we might get versions of things from conda-forge that have matching deps on conda-forge, but we will use the defaults version of the dep which may be older.

That's also one of my concerns. But this is a temporary solution after discussing with conda-forge team. We will move back when conda team fixed the bugs.

sounds good. Trust them over me here.

What are these bugs?

licode · 2016-09-19T17:32:48Z

Thanks for checking on this. Here is the error info

latest: Pulling from nsls2/debian-with-miniconda
Digest: sha256:362eb464ac1e3f283378dbce0384d1e37328cfdf64f7cc4da9307f55a7d1d1d7
Status: Image is up to date for nsls2/debian-with-miniconda:latest
Running the docker container
CONDARC_PATH=/root/.condarc
Exporting CONDARC=/root/.condarc
showing conda info
Current conda install:

             platform : linux-64
        conda version : 4.0.5
  conda-build version : not installed
       python version : 3.5.1.final.0
     requests version : 2.9.1
     root environment : /conda  (writable)
  default environment : /conda
     envs directories : /conda/envs
        package cache : /conda/pkgs
         channel URLs : https://conda.anaconda.org/lightsource2-tag/linux-64/
                        https://conda.anaconda.org/lightsource2-tag/noarch/
                        https://conda.anaconda.org/conda-forge/linux-64/
                        https://conda.anaconda.org/conda-forge/noarch/
                        https://repo.continuum.io/pkgs/free/linux-64/
                        https://repo.continuum.io/pkgs/free/noarch/
                        https://repo.continuum.io/pkgs/pro/linux-64/
                        https://repo.continuum.io/pkgs/pro/noarch/
          config file : /root/.condarc
    is foreign system : False

contents of condarc at /root/.condarc
binstar_upload: false
always_yes: true
show_channel_urls: true
channels:
- lightsource2-tag
- conda-forge
- defaults
Fetching package metadata: ........
Solving package specifications: .........

Package plan for installation in environment /conda:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ncurses-5.9                |                9         954 KB  conda-forge
    patchelf-0.9               |                1         349 KB  conda-forge
    sqlite-3.13.0              |                0         4.9 MB  conda-forge
    xz-5.2.2                   |                0         853 KB  conda-forge
    python-3.5.2               |                3        31.8 MB  conda-forge
    conda-env-2.5.1            |           py35_0          27 KB  defaults
    markupsafe-0.23            |           py35_2          32 KB  defaults
    psutil-4.3.1               |           py35_0         228 KB  defaults
    pytz-2016.6.1              |           py35_0         162 KB  conda-forge
    ruamel_yaml-0.11.14        |           py35_0         377 KB  defaults
    six-1.10.0                 |           py35_0          18 KB  conda-forge
    clyent-1.2.2               |           py35_0          15 KB  defaults
    conda-4.1.12               |           py35_0         204 KB  defaults
    jinja2-2.8                 |           py35_1         278 KB  conda-forge
    python-dateutil-2.5.3      |           py35_0         237 KB  conda-forge
    anaconda-client-1.4.0      |           py35_0         101 KB  defaults
    conda-build-1.21.3         |           py35_0         238 KB  defaults
    conda-execute-0.6.0        |           py35_0          14 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        40.7 MB

The following NEW packages will be INSTALLED:

    anaconda-client: 1.4.0-py35_0    defaults
    clyent:          1.2.2-py35_0    defaults
    conda-build:     1.21.3-py35_0   defaults
    conda-execute:   0.6.0-py35_0    conda-forge
    jinja2:          2.8-py35_1      conda-forge
    markupsafe:      0.23-py35_2     defaults
    ncurses:         5.9-9           conda-forge
    patchelf:        0.9-1           conda-forge
    psutil:          4.3.1-py35_0    defaults
    python-dateutil: 2.5.3-py35_0    conda-forge
    pytz:            2016.6.1-py35_0 conda-forge
    ruamel_yaml:     0.11.14-py35_0  defaults
    six:             1.10.0-py35_0   conda-forge

The following packages will be UPDATED:

    conda:           4.0.5-py35_0 defaults    --> 4.1.12-py35_0   defaults
    conda-env:       2.4.5-py35_0 defaults    --> 2.5.1-py35_0    defaults
    python:          3.5.1-0      conda-forge --> 3.5.2-3         conda-forge
    sqlite:          3.9.2-0      conda-forge --> 3.13.0-0        conda-forge
    xz:              5.0.5-1      conda-forge --> 5.2.2-0         conda-forge

...

   Building: linux-64/metadataclient-0.1.1-py34_0.tar.bz2
Build cmd: conda build /repo/recipes-tag/metadataclient --python 3.4 --numpy 1.11
BUILD START: metadataclient-0.1.1-py34_0
    (actual version deferred until further download or env creation)
updating index in: /conda/tmp_envs/55fc582f7dd397d3a5f0/pkgs
updating index in: /conda/tmp_envs/55fc582f7dd397d3a5f0/conda-bld/linux-64
updating index in: /conda/tmp_envs/55fc582f7dd397d3a5f0/conda-bld/noarch

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2016.8.31  |                0         163 KB  conda-forge
    ncurses-5.9                |                9         954 KB  conda-forge
    sqlite-3.13.0              |                1         4.9 MB  conda-forge
    tk-8.5.19                  |                0         1.9 MB  conda-forge
    xz-5.2.2                   |                0         853 KB  conda-forge
    zlib-1.2.8                 |                3          87 KB  conda-forge
    openssl-1.0.2h             |                2         3.4 MB  conda-forge
    readline-6.2               |                0         713 KB  conda-forge
    python-3.4.5               |                2        26.9 MB  conda-forge
    certifi-2016.8.31          |           py34_0         220 KB  conda-forge
    setuptools-26.1.1          |           py34_0         354 KB  conda-forge
    wheel-0.29.0               |           py34_0          82 KB  conda-forge
    pip-8.1.2                  |           py34_0         1.6 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        42.0 MB

The following NEW packages will be INSTALLED:

    ca-certificates: 2016.8.31-0      conda-forge
    certifi:         2016.8.31-py34_0 conda-forge
    ncurses:         5.9-9            conda-forge
    openssl:         1.0.2h-2         conda-forge
    pip:             8.1.2-py34_0     conda-forge
    python:          3.4.5-2          conda-forge
    readline:        6.2-0            conda-forge
                                                                                                               824,0-1       19%

os.uname(): posix.uname_result(sysname='Linux', nodename='763b6f905bd2', release='3.19.0-59-generic', version='#65-Ubuntu SMP Mon Apr 18 16:12:07 UTC 2016', machine='x86_64')

sys.version: 3.5.2 | packaged by conda-forge | (default, Sep  8 2016, 14:23:11)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]

log file: /root/auto-build-logs/09.12-02.51
Building: linux-64/metadataclient-0.1.1-py34_0.tar.bz2
Build cmd: conda build /repo/recipes-tag/metadataclient --python 3.4 --numpy 1.11
BUILD START: metadataclient-0.1.1-py34_0
    (actual version deferred until further download or env creation)
updating index in: /conda/tmp_envs/55fc582f7dd397d3a5f0/pkgs
updating index in: /conda/tmp_envs/55fc582f7dd397d3a5f0/conda-bld/linux-64
updating index in: /conda/tmp_envs/55fc582f7dd397d3a5f0/conda-bld/noarch

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2016.8.31  |                0         163 KB  conda-forge
    ncurses-5.9                |                9         954 KB  conda-forge
    sqlite-3.13.0              |                1         4.9 MB  conda-forge
    tk-8.5.19                  |                0         1.9 MB  conda-forge
    xz-5.2.2                   |                0         853 KB  conda-forge
    zlib-1.2.8                 |                3          87 KB  conda-forge
    openssl-1.0.2h             |                2         3.4 MB  conda-forge
    readline-6.2               |                0         713 KB  conda-forge
    python-3.4.5               |                2        26.9 MB  conda-forge
    certifi-2016.8.31          |           py34_0         220 KB  conda-forge
    setuptools-26.1.1          |           py34_0         354 KB  conda-forge
    wheel-0.29.0               |           py34_0          82 KB  conda-forge
    pip-8.1.2                  |           py34_0         1.6 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        42.0 MB

The following NEW packages will be INSTALLED:

    ca-certificates: 2016.8.31-0      conda-forge
    certifi:         2016.8.31-py34_0 conda-forge
    ncurses:         5.9-9            conda-forge
    openssl:         1.0.2h-2         conda-forge
    pip:             8.1.2-py34_0     conda-forge
    python:          3.4.5-2          conda-forge
    readline:        6.2-0            conda-forge
    setuptools:      26.1.1-py34_0    conda-forge
    sqlite:          3.13.0-1         conda-forge
    tk:              8.5.19-0         conda-forge
    wheel:           0.29.0-py34_0    conda-forge
                                                                                                                    824,0-1       19%
    certifi:         2016.8.31-py34_0 conda-forge
    ncurses:         5.9-9            conda-forge
    openssl:         1.0.2h-2         conda-forge
    pip:             8.1.2-py34_0     conda-forge
    python:          3.4.5-2          conda-forge
    readline:        6.2-0            conda-forge
    setuptools:      26.1.1-py34_0    conda-forge
    sqlite:          3.13.0-1         conda-forge
    tk:              8.5.19-0         conda-forge
    wheel:           0.29.0-py34_0    conda-forge
    xz:              5.2.2-0          conda-forge
    zlib:            1.2.8-3          conda-forge



========== STDOUT ==========

None

========== STDERR ==========

('Using Anaconda API: https://api.anaconda.org\n'
 'WARNING:/conda/tmp_envs/55fc582f7dd397d3a5f0/lib/python3.5/site-packages/conda_build/build.py:Build '
 'prefix failed with prefix length 255\n'
 'WARNING:/conda/tmp_envs/55fc582f7dd397d3a5f0/lib/python3.5/site-packages/conda_build/build.py:Error '
 'was: \n'
 'WARNING:/conda/tmp_envs/55fc582f7dd397d3a5f0/lib/python3.5/site-packages/conda_build/build.py:ERROR: '
 'placeholder '
 "'/opt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeho' "
 'too short in: conda-forge::ncurses-5.9-9\n'
 '\n'
 'WARNING:/conda/tmp_envs/55fc582f7dd397d3a5f0/lib/python3.5/site-packages/conda_build/build.py:One '
 'or more of your package dependencies needs to be rebuilt with a longer '
 'prefix length.\n'
 'WARNING:/conda/tmp_envs/55fc582f7dd397d3a5f0/lib/python3.5/site-packages/conda_build/build.py:Falling '
 'back to legacy prefix length of 80 characters.\n'
 'WARNING:/conda/tmp_envs/55fc582f7dd397d3a5f0/lib/python3.5/site-packages/conda_build/build.py:Your '
 'package will not install into prefixes > 80 characters.\n'
 'ERROR: placeholder '
 "'/opt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeho' "
 'too short in: conda-forge::ncurses-5.9-9\n'
 '\n')
Sending the following message to slack

licode · 2016-09-19T18:03:37Z

It looks that the issue has been resolved by conda team. We can move conda-forge in front of defaults now.

ericdill · 2016-09-22T02:19:43Z

I think that problem was coming from the conda 4.0.x binaries. Updating conda to 4.1.x or 4.2.x might fix it.

ericdill · 2016-09-22T02:24:02Z

Also there is a tremendously long issue where it is being discussed how to handle the change in the prefix length: conda-forge/conda-forge.github.io#171

licode · 2016-09-22T14:51:31Z

I was using conda 4.1.2, but still got the error. I think the issue came from pytz and sqlite, which need to be installed from default, instead of conda-forge, according to conda-forge team.

However, those two packages have been fixed for now at conda-forge. Thanks for the follow up!

jupyterhub 0.7 is released

add xf11id-ws4 to inventory

licode added 4 commits September 12, 2016 11:35

BUG: use defaults before conda-forge

41c38c8

BUG: corrected sha number

abe2de0

BUG: correction on mds tests

d89375a

BUG: unused tests on bluesky

a859c69

MNT: turn off some msg for slack, but keep them at log

be87436

tacaswell reviewed Sep 13, 2016
View reviewed changes

tacaswell merged commit 3cca774 into NSLS-II:master Sep 13, 2016

mrakitin pushed a commit to mrakitin/lightsource2-recipes that referenced this pull request Jun 28, 2019

Merge pull request NSLS-II#45 from minrk/07-rlease

b50259b

jupyterhub 0.7 is released

mrakitin pushed a commit to mrakitin/lightsource2-recipes that referenced this pull request Jun 28, 2019

Merge pull request NSLS-II#45 from NSLS-II/xf11idws4

1fb3a40

add xf11id-ws4 to inventory

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Fix issue due to Conda-forge #45

Fix issue due to Conda-forge #45

licode commented Sep 12, 2016

licode commented Sep 12, 2016

tacaswell Sep 13, 2016

licode Sep 13, 2016

tacaswell Sep 13, 2016

ericdill Sep 19, 2016

licode commented Sep 19, 2016

licode commented Sep 19, 2016

ericdill commented Sep 22, 2016

ericdill commented Sep 22, 2016 •

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licode commented Sep 22, 2016

Fix issue due to Conda-forge #45

Fix issue due to Conda-forge #45

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licode commented Sep 12, 2016

licode commented Sep 12, 2016

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