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Some fixes ( <-- most original/descriptive title... ) #593

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merged 3 commits into from
Jul 26, 2019
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mbargull
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Couple of small fixes.
Update to conda-build=3.18.9 to get conda/conda-build#3621 in. (run_exports-related, see conda/conda-build#3617 and linked issues for details)

@@ -1017,7 +1017,7 @@ def check_recipe_skippable(recipe, check_channels):
# No packages with same version + build num in channels: no need to skip
return False
num_new_pkg_builds = Counter(
(meta.name(), meta.version(), int(meta.build_number()) or 0, _meta_subdir(meta))
(meta.name(), meta.version(), int(meta.build_number() or 0), _meta_subdir(meta))
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fixes error in https://circleci.com/gh/bioconda/bioconda-recipes/65938:

...
  File "/Users/distiller/project/miniconda/lib/python3.6/site-packages/bioconda_utils/utils.py", line 1021, in <genexpr>
    for meta in metas
ValueError: invalid literal for int() with base 10: ''
Exited with code 1

@@ -261,7 +261,7 @@ def build_recipes(recipe_folder: str, config_path: str, recipes: List[str],

# setup linting
if do_lint:
always_exclude = ('build_number_needs_bump')
always_exclude = ('build_number_needs_bump',)
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Fixes error in https://circleci.com/gh/bioconda/bioconda-recipes/65883:

13:32:21 BIOCONDA INFO Linting recipe recipes/pylibseq
13:32:21 BIOCONDA ERROR Skipping unknown check s
13:32:21 BIOCONDA ERROR Skipping unknown check m
13:32:21 BIOCONDA ERROR Skipping unknown check n
13:32:21 BIOCONDA ERROR Skipping unknown check e
13:32:21 BIOCONDA ERROR Skipping unknown check p
13:32:21 BIOCONDA ERROR Skipping unknown check d
13:32:21 BIOCONDA ERROR Skipping unknown check _
13:32:21 BIOCONDA ERROR Skipping unknown check i
13:32:21 BIOCONDA ERROR Skipping unknown check b
13:32:21 BIOCONDA ERROR Skipping unknown check u
13:32:21 BIOCONDA ERROR Skipping unknown check l
13:32:21 BIOCONDA ERROR Skipping unknown check r
13:32:21 BIOCONDA ERROR 

set("build_number_needs_bump") == set("smnepd_ibulr") ;)

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thanks... that was my bug I think

@mbargull
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test-linux (long_running) failed with

==> WARNING: A newer version of conda exists. <==
  current version: 4.6.14
  latest version: 4.7.10

Please update conda by running

    $ conda update -n base conda


ERROR conda.core.link:_execute(568): An error occurred while installing package 'defaults::libgfortran-ng-7.3.0-hdf63c60_0'.
AssertionError()
Attempting to roll back.

Rolling back transaction: ...working... done

AssertionError()
Step 6/9 : RUN export PATH="/opt/conda/bin:${PATH}" &&     : 'Make sure we get the (working) conda we want before installing the rest.' &&     sed -nE         -e 's/\s*#.*$//'         -e 's/^(conda([><!=~ ].+)?)$/\1/p'         /tmp/repo/bioconda_utils/bioconda_utils-requirements.txt         | xargs -r conda install -y &&     conda install -y --file /tmp/repo/bioconda_utils/bioconda_utils-requirements.txt &&     conda clean -y -it
 ---> Running in 941ec5d13468
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - conda=4.6.14


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    conda-4.6.14               |           py37_0         2.1 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.1 MB

The following packages will be DOWNGRADED:

  conda                                       4.7.10-py37_0 --> 4.6.14-py37_0



Downloading and Extracting Packages

conda-4.6.14         | 2.1 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs:
    - aiofiles=0.4
    - aioftp=0.12
    - aiohttp-jinja2=1.1
    - aiohttp-security=0.4
    - aiohttp-session=2.7
    - aiohttp=3.4
    - aioredis=1.2
    - alabaster=0.7
    - anaconda-client=1.6
    - argh=0.26
    - backoff=1.6
    - beautifulsoup4=4.6
    - boltons=18
    - cachetools=3.0
    - celery=4.2
    - colorlog=3.1
    - conda-build==3.18.9
    - conda-forge-pinning==2019.07.11
    - conda-verify=3.1
    - conda==4.6.14
    - cryptography=2
    - docutils
    - galaxy-lib[version='>=18.9.1']
    - gidgethub=3.0
    - git=2.14
    - gitpython=2.1
    - gunicorn=19.9
    - involucro=1.1
    - jinja2[version='>=2.10.1,<2.11.a0']
    - jsonschema=2.6
    - libblas=[build=*openblas]
    - markdown=3.1
    - networkx==1.11
    - pandas=0.23
    - pyaml=17.12
    - pygithub=1.34
    - pyjwt=1.7
    - python[version='>=3.6']
    - regex==2018.08.29
    - requests=2.20
    - ruamel_yaml=0.15
    - six=1.11
    - skopeo==0.1.35
    - sphinx
    - sphinx-autodoc-typehints
    - tqdm[version='>=4.26']


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    aiofiles-0.4.0             |          py_1001          11 KB  conda-forge
    aioftp-0.12.0              |             py_0          30 KB  conda-forge
    aiohttp-3.4.4              |py36h14c3975_1000         581 KB  conda-forge
    aiohttp-jinja2-1.1.1       |             py_0          13 KB  conda-forge
    aiohttp-security-0.4.0     |             py_0          13 KB  conda-forge
    aiohttp-session-2.7.0      |             py_0          15 KB  conda-forge
    aioredis-1.2.0             |             py_0          48 KB  conda-forge
    alabaster-0.7.12           |             py_0          15 KB  conda-forge
    amqp-2.5.0                 |             py_1          41 KB  conda-forge
    anaconda-client-1.6.14     |             py_0          67 KB  conda-forge
    argh-0.26.2                |        py36_1001          33 KB  conda-forge
    asn1crypto-0.24.0          |        py36_1003         154 KB  conda-forge
    async-timeout-3.0.1        |          py_1000          11 KB  conda-forge
    babel-2.7.0                |             py_0         5.9 MB  conda-forge
    backoff-1.6.0              |             py_1          13 KB  conda-forge
    beautifulsoup4-4.6.3       |        py36_1000         141 KB  conda-forge
    billiard-3.6.0.0           |   py36h516909a_0         141 KB  conda-forge
    boltons-18.0.1             |             py_0         181 KB  conda-forge
    cachetools-3.0.0           |             py_0          11 KB  conda-forge
    celery-4.2.2               |             py_0         415 KB  conda-forge
    certifi-2019.6.16          |           py36_1         149 KB  conda-forge
    cffi-1.12.3                |   py36h8022711_0         218 KB  conda-forge
    chardet-3.0.4              |        py36_1003         190 KB  conda-forge
    click-7.0                  |             py_0          61 KB  conda-forge
    colorlog-3.1.4             |        py36_1000          19 KB  conda-forge
    conda-4.6.14               |           py36_0         2.1 MB  conda-forge
    conda-build-3.18.9         |           py36_0         516 KB  conda-forge
    conda-forge-pinning-2019.07.11|                0           6 KB  conda-forge
    conda-package-handling-1.3.11|           py36_0         257 KB  conda-forge
    conda-verify-3.1.1         |        py36_1000          32 KB  conda-forge
    cryptography-2.5           |   py36hb7f436b_1         645 KB  conda-forge
    curl-7.64.0                |       h646f8bb_0         143 KB  conda-forge
    docutils-0.15              |           py36_0         734 KB  conda-forge
    future-0.17.1              |        py36_1000         701 KB  conda-forge
    galaxy-lib-19.5.2          |             py_0         255 KB  bioconda
    gidgethub-3.0.0            |             py_0          71 KB  conda-forge
    git-2.14.2                 |                3        15.4 MB  conda-forge
    gitdb2-2.0.5               |             py_0          46 KB  conda-forge
    gitpython-2.1.12           |             py_0         337 KB  conda-forge
    gunicorn-19.9.0            |        py36_1000         171 KB  conda-forge
    hiredis-1.0.0              |   py36h516909a_1          23 KB  conda-forge
    idna-2.7                   |        py36_1002         131 KB  conda-forge
    idna_ssl-1.1.0             |        py36_1000           6 KB  conda-forge
    imagesize-1.1.0            |             py_0           6 KB  conda-forge
    involucro-1.1.2            |                1         2.1 MB  bioconda
    jsonschema-2.6.0           |        py36_1002          62 KB  conda-forge
    kombu-4.6.1                |             py_0         120 KB  conda-forge
    krb5-1.16.3                |    hc83ff2d_1000         1.4 MB  conda-forge
    libarchive-3.3.3           |    ha149a29_1000         1.4 MB  conda-forge
    libblas-3.8.0              |      10_openblas           6 KB  conda-forge
    libcblas-3.8.0             |      10_openblas           6 KB  conda-forge
    libcurl-7.64.0             |       h01ee5af_0         586 KB  conda-forge
    liblapack-3.8.0            |      10_openblas           6 KB  conda-forge
    libopenblas-0.3.6          |       h6e990d7_5         7.7 MB  conda-forge
    libssh2-1.8.0              |    h1ad7b7a_1003         246 KB  conda-forge
    markdown-3.1.1             |             py_0          60 KB  conda-forge
    markupsafe-1.1.1           |   py36h14c3975_0          26 KB  conda-forge
    multidict-4.5.2            |py36h14c3975_1000         142 KB  conda-forge
    networkx-1.11              |           py36_0         1.4 MB  conda-forge
    numpy-1.16.4               |   py36h95a1406_0         4.3 MB  conda-forge
    openblas-0.3.6             |       h6e990d7_5         8.2 MB  conda-forge
    openssl-1.0.2r             |       h14c3975_0         3.1 MB  conda-forge
    packaging-19.0             |             py_0          23 KB  conda-forge
    pandas-0.23.4              |py36h637b7d7_1000         9.8 MB  conda-forge
    pip-19.2.1                 |           py36_0         1.9 MB  conda-forge
    psutil-5.6.3               |   py36h516909a_0         322 KB  conda-forge
    py-lief-0.9.0              |   py36he1b5a44_1         1.4 MB  conda-forge
    pyaml-17.12.1              |             py_0          17 KB  conda-forge
    pycosat-0.6.3              |py36h14c3975_1001         104 KB  conda-forge
    pycparser-2.19             |           py36_1         173 KB  conda-forge
    pygithub-1.34              |           py36_0         1.9 MB  conda-forge
    pygments-2.4.2             |             py_0         661 KB  conda-forge
    pyjwt-1.7.1                |             py_0          17 KB  conda-forge
    pyopenssl-19.0.0           |           py36_0          81 KB  conda-forge
    pyparsing-2.4.1            |             py_0          57 KB  conda-forge
    pyrsistent-0.15.3          |   py36h516909a_0          89 KB  conda-forge
    pysocks-1.7.0              |           py36_0          26 KB  conda-forge
    python-3.6.7               |    hd21baee_1002        34.6 MB  conda-forge
    python-libarchive-c-2.8    |        py36_1004          21 KB  conda-forge
    pyyaml-5.1.1               |   py36h516909a_0         184 KB  conda-forge
    readline-7.0               |    hf8c457e_1001         391 KB  conda-forge
    regex-2018.08.29           |py36h14c3975_1000         347 KB  conda-forge
    requests-2.20.1            |        py36_1000          84 KB  conda-forge
    ruamel_yaml-0.15.71        |py36h14c3975_1000         257 KB  conda-forge
    setuptools-41.0.1          |           py36_0         612 KB  conda-forge
    simplejson-3.16.1          |   py36h470a237_0         147 KB  conda-forge
    six-1.11.0                 |        py36_1001          21 KB  conda-forge
    skopeo-0.1.35              |       haa36a5b_1         8.1 MB  conda-forge
    smmap2-2.0.5               |             py_0          21 KB  conda-forge
    snowballstemmer-1.9.0      |             py_0          51 KB  conda-forge
    soupsieve-1.9.2            |           py36_0          59 KB  conda-forge
    sphinx-2.1.2               |             py_0         1.4 MB  conda-forge
    sphinx-autodoc-typehints-1.6.0|             py_0           9 KB  conda-forge
    sphinxcontrib-applehelp-1.0.1|             py_0          28 KB  conda-forge
    sphinxcontrib-devhelp-1.0.1|             py_0          22 KB  conda-forge
    sphinxcontrib-htmlhelp-1.0.2|             py_0          27 KB  conda-forge
    sphinxcontrib-jsmath-1.0.1 |             py_0           7 KB  conda-forge
    sphinxcontrib-qthelp-1.0.2 |             py_0          25 KB  conda-forge
    sphinxcontrib-serializinghtml-1.1.1|             py_0          24 KB  conda-forge
    sqlalchemy-1.3.6           |   py36h516909a_0         1.7 MB  conda-forge
    sqlite-3.28.0              |       h8b20d00_0         1.9 MB  conda-forge
    traitlets-4.3.2            |        py36_1000         131 KB  conda-forge
    uritemplate-3.0.0          |             py_1           9 KB  conda-forge
    urllib3-1.23               |        py36_1001         152 KB  conda-forge
    vine-1.3.0                 |             py_0          15 KB  conda-forge
    wheel-0.33.4               |           py36_0          34 KB  conda-forge
    yarl-1.3.0                 |py36h14c3975_1000         133 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       127.7 MB

The following NEW packages will be INSTALLED:

  aiofiles           conda-forge/noarch::aiofiles-0.4.0-py_1001
  aioftp             conda-forge/noarch::aioftp-0.12.0-py_0
  aiohttp            conda-forge/linux-64::aiohttp-3.4.4-py36h14c3975_1000
  aiohttp-jinja2     conda-forge/noarch::aiohttp-jinja2-1.1.1-py_0
  aiohttp-security   conda-forge/noarch::aiohttp-security-0.4.0-py_0
  aiohttp-session    conda-forge/noarch::aiohttp-session-2.7.0-py_0
  aioredis           conda-forge/noarch::aioredis-1.2.0-py_0
  alabaster          conda-forge/noarch::alabaster-0.7.12-py_0
  amqp               conda-forge/noarch::amqp-2.5.0-py_1
  argh               conda-forge/linux-64::argh-0.26.2-py36_1001
  async-timeout      conda-forge/noarch::async-timeout-3.0.1-py_1000
  babel              conda-forge/noarch::babel-2.7.0-py_0
  backoff            conda-forge/noarch::backoff-1.6.0-py_1
  billiard           conda-forge/linux-64::billiard-3.6.0.0-py36h516909a_0
  boltons            conda-forge/noarch::boltons-18.0.1-py_0
  cachetools         conda-forge/noarch::cachetools-3.0.0-py_0
  celery             conda-forge/noarch::celery-4.2.2-py_0
  click              conda-forge/noarch::click-7.0-py_0
  colorlog           conda-forge/linux-64::colorlog-3.1.4-py36_1000
  conda-forge-pinni~ conda-forge/noarch::conda-forge-pinning-2019.07.11-0
  conda-verify       conda-forge/linux-64::conda-verify-3.1.1-py36_1000
  docutils           conda-forge/linux-64::docutils-0.15-py36_0
  future             conda-forge/linux-64::future-0.17.1-py36_1000
  galaxy-lib         bioconda/noarch::galaxy-lib-19.5.2-py_0
  gidgethub          conda-forge/noarch::gidgethub-3.0.0-py_0
  gitdb2             conda-forge/noarch::gitdb2-2.0.5-py_0
  gitpython          conda-forge/noarch::gitpython-2.1.12-py_0
  gunicorn           conda-forge/linux-64::gunicorn-19.9.0-py36_1000
  hiredis            conda-forge/linux-64::hiredis-1.0.0-py36h516909a_1
  idna_ssl           conda-forge/linux-64::idna_ssl-1.1.0-py36_1000
  imagesize          conda-forge/noarch::imagesize-1.1.0-py_0
  involucro          bioconda/linux-64::involucro-1.1.2-1
  kombu              conda-forge/noarch::kombu-4.6.1-py_0
  libblas            conda-forge/linux-64::libblas-3.8.0-10_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-10_openblas
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
  liblapack          conda-forge/linux-64::liblapack-3.8.0-10_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.6-h6e990d7_5
  markdown           conda-forge/noarch::markdown-3.1.1-py_0
  multidict          conda-forge/linux-64::multidict-4.5.2-py36h14c3975_1000
  networkx           conda-forge/linux-64::networkx-1.11-py36_0
  numpy              conda-forge/linux-64::numpy-1.16.4-py36h95a1406_0
  openblas           conda-forge/linux-64::openblas-0.3.6-h6e990d7_5
  packaging          conda-forge/noarch::packaging-19.0-py_0
  pandas             conda-forge/linux-64::pandas-0.23.4-py36h637b7d7_1000
  pyaml              conda-forge/noarch::pyaml-17.12.1-py_0
  pygithub           conda-forge/linux-64::pygithub-1.34-py36_0
  pygments           conda-forge/noarch::pygments-2.4.2-py_0
  pyjwt              conda-forge/noarch::pyjwt-1.7.1-py_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.1-py_0
  regex              conda-forge/linux-64::regex-2018.08.29-py36h14c3975_1000
  simplejson         conda-forge/linux-64::simplejson-3.16.1-py36h470a237_0
  skopeo             conda-forge/linux-64::skopeo-0.1.35-haa36a5b_1
  smmap2             conda-forge/noarch::smmap2-2.0.5-py_0
  snowballstemmer    conda-forge/noarch::snowballstemmer-1.9.0-py_0
  sphinx             conda-forge/noarch::sphinx-2.1.2-py_0
  sphinx-autodoc-ty~ conda-forge/noarch::sphinx-autodoc-typehints-1.6.0-py_0
  sphinxcontrib-app~ conda-forge/noarch::sphinxcontrib-applehelp-1.0.1-py_0
  sphinxcontrib-dev~ conda-forge/noarch::sphinxcontrib-devhelp-1.0.1-py_0
  sphinxcontrib-htm~ conda-forge/noarch::sphinxcontrib-htmlhelp-1.0.2-py_0
  sphinxcontrib-jsm~ conda-forge/noarch::sphinxcontrib-jsmath-1.0.1-py_0
  sphinxcontrib-qth~ conda-forge/noarch::sphinxcontrib-qthelp-1.0.2-py_0
  sphinxcontrib-ser~ conda-forge/noarch::sphinxcontrib-serializinghtml-1.1.1-py_0
  sqlalchemy         conda-forge/linux-64::sqlalchemy-1.3.6-py36h516909a_0
  uritemplate        conda-forge/noarch::uritemplate-3.0.0-py_1
  vine               conda-forge/noarch::vine-1.3.0-py_0
  yarl               conda-forge/linux-64::yarl-1.3.0-py36h14c3975_1000

The following packages will be DOWNGRADED:

  anaconda-client                                1.7.2-py_0 --> 1.6.14-py_0
  asn1crypto                               0.24.0-py37_1003 --> 0.24.0-py36_1003
  beautifulsoup4                               4.8.0-py37_0 --> 4.6.3-py36_1000
  certifi                                  2019.6.16-py37_1 --> 2019.6.16-py36_1
  cffi                                1.12.3-py37h8022711_0 --> 1.12.3-py36h8022711_0
  chardet                                   3.0.4-py37_1003 --> 3.0.4-py36_1003
  conda                                       4.6.14-py37_0 --> 4.6.14-py36_0
  conda-build                                 3.18.9-py37_0 --> 3.18.9-py36_0
  conda-package-han~                          1.3.11-py37_0 --> 1.3.11-py36_0
  cryptography                           2.7-py37h72c5cf5_0 --> 2.5-py36hb7f436b_1
  curl                                    7.65.3-hf8cf82a_0 --> 7.64.0-h646f8bb_0
  git                                2.22.0-pl526hce37bd2_0 --> 2.14.2-3
  idna                                        2.8-py37_1000 --> 2.7-py36_1002
  jsonschema                                   3.0.1-py37_0 --> 2.6.0-py36_1002
  krb5                                 1.16.3-h05b26f9_1001 --> 1.16.3-hc83ff2d_1000
  libarchive                            3.3.3-hb44662c_1005 --> 3.3.3-ha149a29_1000
  libcurl                                 7.65.3-hda55be3_0 --> 7.64.0-h01ee5af_0
  libssh2                                  1.8.2-h22169c7_2 --> 1.8.0-h1ad7b7a_1003
  markupsafe                           1.1.1-py37h14c3975_0 --> 1.1.1-py36h14c3975_0
  openssl                                 1.1.1c-h516909a_0 --> 1.0.2r-h14c3975_0
  pip                                         19.2.1-py37_0 --> 19.2.1-py36_0
  psutil                               5.6.3-py37h516909a_0 --> 5.6.3-py36h516909a_0
  py-lief                              0.9.0-py37he1b5a44_1 --> 0.9.0-py36he1b5a44_1
  pycosat                           0.6.3-py37h14c3975_1001 --> 0.6.3-py36h14c3975_1001
  pycparser                                     2.19-py37_1 --> 2.19-py36_1
  pyopenssl                                   19.0.0-py37_0 --> 19.0.0-py36_0
  pyrsistent                          0.15.3-py37h516909a_0 --> 0.15.3-py36h516909a_0
  pysocks                                      1.7.0-py37_0 --> 1.7.0-py36_0
  python                                   3.7.3-h33d41f4_1 --> 3.6.7-hd21baee_1002
  python-libarchive~                          2.8-py37_1004 --> 2.8-py36_1004
  pyyaml                               5.1.1-py37h516909a_0 --> 5.1.1-py36h516909a_0
  readline                                   8.0-hf8c457e_0 --> 7.0-hf8c457e_1001
  requests                                    2.22.0-py37_1 --> 2.20.1-py36_1000
  ruamel_yaml                     0.15.71-py37h14c3975_1000 --> 0.15.71-py36h14c3975_1000
  setuptools                                  41.0.1-py37_0 --> 41.0.1-py36_0
  six                                      1.12.0-py37_1000 --> 1.11.0-py36_1001
  soupsieve                                    1.9.2-py37_0 --> 1.9.2-py36_0
  sqlite                                  3.29.0-hcee41ef_0 --> 3.28.0-h8b20d00_0
  traitlets                                 4.3.2-py37_1000 --> 4.3.2-py36_1000
  urllib3                                     1.25.3-py37_0 --> 1.23-py36_1001
  wheel                                       0.33.4-py37_0 --> 0.33.4-py36_0



Downloading and Extracting Packages

billiard-3.6.0.0     | 141 KB    | ########## | 100% 

readline-7.0         | 391 KB    | ########## | 100% 

idna-2.7             | 131 KB    | ########## | 100% 

packaging-19.0       | 23 KB     | ########## | 100% 

git-2.14.2           | 15.4 MB   | ########## | 100% 

gidgethub-3.0.0      | 71 KB     | ########## | 100% 

numpy-1.16.4         | 4.3 MB    | ########## | 100% 

aiohttp-3.4.4        | 581 KB    | ########## | 100% 

backoff-1.6.0        | 13 KB     | ########## | 100% 

amqp-2.5.0           | 41 KB     | ########## | 100% 

jsonschema-2.6.0     | 62 KB     | ########## | 100% 

urllib3-1.23         | 152 KB    | ########## | 100% 

conda-build-3.18.9   | 516 KB    | ########## | 100% 

markupsafe-1.1.1     | 26 KB     | ########## | 100% 

babel-2.7.0          | 5.9 MB    | ########## | 100% 

simplejson-3.16.1    | 147 KB    | ########## | 100% 

cffi-1.12.3          | 218 KB    | ########## | 100% 

aiohttp-session-2.7. | 15 KB     | ########## | 100% 

asn1crypto-0.24.0    | 154 KB    | ########## | 100% 

sphinxcontrib-appleh | 28 KB     | ########## | 100% 

involucro-1.1.2      | 2.1 MB    | ########## | 100% 

certifi-2019.6.16    | 149 KB    | ########## | 100% 

sphinxcontrib-htmlhe | 27 KB     | ########## | 100% 

docutils-0.15        | 734 KB    | ########## | 100% 

six-1.11.0           | 21 KB     | ########## | 100% 

aiohttp-security-0.4 | 13 KB     | ########## | 100% 

pyopenssl-19.0.0     | 81 KB     | ########## | 100% 

multidict-4.5.2      | 142 KB    | ########## | 100% 

future-0.17.1        | 701 KB    | ########## | 100% 

chardet-3.0.4        | 190 KB    | ########## | 100% 

uritemplate-3.0.0    | 9 KB      | ########## | 100% 

setuptools-41.0.1    | 612 KB    | ########## | 100% 

colorlog-3.1.4       | 19 KB     | ########## | 100% 

libblas-3.8.0        | 6 KB      | ########## | 100% 

idna_ssl-1.1.0       | 6 KB      | ########## | 100% 

soupsieve-1.9.2      | 59 KB     | ########## | 100% 

libcurl-7.64.0       | 586 KB    | ########## | 100% 

openblas-0.3.6       | 8.2 MB    | ########## | 100% 

libssh2-1.8.0        | 246 KB    | ########## | 100% 

smmap2-2.0.5         | 21 KB     | ########## | 100% 

snowballstemmer-1.9. | 51 KB     | ########## | 100% 

sqlalchemy-1.3.6     | 1.7 MB    | ########## | 100% 

vine-1.3.0           | 15 KB     | ########## | 100% 

aioftp-0.12.0        | 30 KB     | ########## | 100% 

cryptography-2.5     | 645 KB    | ########## | 100% 

pyyaml-5.1.1         | 184 KB    | ########## | 100% 

py-lief-0.9.0        | 1.4 MB    | ########## | 100% 

hiredis-1.0.0        | 23 KB     | ########## | 100% 

pip-19.2.1           | 1.9 MB    | ########## | 100% 

pygithub-1.34        | 1.9 MB    | ########## | 100% 

curl-7.64.0          | 143 KB    | ########## | 100% 

conda-forge-pinning- | 6 KB      | ########## | 100% 

pysocks-1.7.0        | 26 KB     | ########## | 100% 

python-3.6.7         | 34.6 MB   | ########## | 100% 

click-7.0            | 61 KB     | ########## | 100% 

markdown-3.1.1       | 60 KB     | ########## | 100% 

python-libarchive-c- | 21 KB     | ########## | 100% 

krb5-1.16.3          | 1.4 MB    | ########## | 100% 

sphinxcontrib-devhel | 22 KB     | ########## | 100% 

libopenblas-0.3.6    | 7.7 MB    | ########## | 100% 

celery-4.2.2         | 415 KB    | ########## | 100% 

pyjwt-1.7.1          | 17 KB     | ########## | 100% 

aioredis-1.2.0       | 48 KB     | ########## | 100% 

sqlite-3.28.0        | 1.9 MB    | ########## | 100% 

cachetools-3.0.0     | 11 KB     | ########## | 100% 

gitdb2-2.0.5         | 46 KB     | ########## | 100% 

sphinx-2.1.2         | 1.4 MB    | ########## | 100% 

conda-verify-3.1.1   | 32 KB     | ########## | 100% 

alabaster-0.7.12     | 15 KB     | ########## | 100% 

yarl-1.3.0           | 133 KB    | ########## | 100% 

networkx-1.11        | 1.4 MB    | ########## | 100% 

boltons-18.0.1       | 181 KB    | ########## | 100% 

libarchive-3.3.3     | 1.4 MB    | ########## | 100% 

kombu-4.6.1          | 120 KB    | ########## | 100% 

ruamel_yaml-0.15.71  | 257 KB    | ########## | 100% 

imagesize-1.1.0      | 6 KB      | ########## | 100% 

argh-0.26.2          | 33 KB     | ########## | 100% 

sphinxcontrib-serial | 24 KB     | ########## | 100% 

liblapack-3.8.0      | 6 KB      | ########## | 100% 

openssl-1.0.2r       | 3.1 MB    | ########## | 100% 

async-timeout-3.0.1  | 11 KB     | ########## | 100% 

skopeo-0.1.35        | 8.1 MB    | ########## | 100% 

pyrsistent-0.15.3    | 89 KB     | ########## | 100% 

aiohttp-jinja2-1.1.1 | 13 KB     | ########## | 100% 

pycparser-2.19       | 173 KB    | ########## | 100% 

gitpython-2.1.12     | 337 KB    | ########## | 100% 

libcblas-3.8.0       | 6 KB      | ########## | 100% 

wheel-0.33.4         | 34 KB     | ########## | 100% 

conda-package-handli | 257 KB    | ########## | 100% 

conda-4.6.14         | 2.1 MB    | ########## | 100% 

regex-2018.08.29     | 347 KB    | ########## | 100% 

pygments-2.4.2       | 661 KB    | ########## | 100% 

traitlets-4.3.2      | 131 KB    | ########## | 100% 

pandas-0.23.4        | 9.8 MB    | ########## | 100% 

pycosat-0.6.3        | 104 KB    | ########## | 100% 

anaconda-client-1.6. | 67 KB     | ########## | 100% 

psutil-5.6.3         | 322 KB    | ########## | 100% 

sphinxcontrib-jsmath | 7 KB      | ########## | 100% 

sphinx-autodoc-typeh | 9 KB      | ########## | 100% 

pyaml-17.12.1        | 17 KB     | ########## | 100% 

aiofiles-0.4.0       | 11 KB     | ########## | 100% 

beautifulsoup4-4.6.3 | 141 KB    | ########## | 100% 

galaxy-lib-19.5.2    | 255 KB    | ########## | 100% 

sphinxcontrib-qthelp | 25 KB     | ########## | 100% 

pyparsing-2.4.1      | 57 KB     | ########## | 100% 

requests-2.20.1      | 84 KB     | ########## | 100% 

gunicorn-19.9.0      | 171 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... failed


==> WARNING: A newer version of conda exists. <==
  current version: 4.6.14
  latest version: 4.7.10

Please update conda by running

    $ conda update -n base conda


ERROR conda.core.link:_execute(568): An error occurred while installing package 'defaults::libgfortran-ng-7.3.0-hdf63c60_0'.
AssertionError()
Attempting to roll back.

Rolling back transaction: ...working... done

AssertionError()

The command '/bin/sh -c export PATH="/opt/conda/bin:${PATH}" &&     : 'Make sure we get the (working) conda we want before installing the rest.' &&     sed -nE         -e 's/\s*#.*$//'         -e 's/^(conda([><!=~ ].+)?)$/\1/p'         /tmp/repo/bioconda_utils/bioconda_utils-requirements.txt         | xargs -r conda install -y &&     conda install -y --file /tmp/repo/bioconda_utils/bioconda_utils-requirements.txt &&     conda clean -y -it' returned a non-zero code: 1
Exited with code 1

This is an intermitted failure that I saw once before last week. Meh, if it happens too often, I might be forced to inverstigate :/ ....

@mbargull
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Ready to review/merge.
TODO: tests. I won't add those right now, but opened gh-594 to track this TODO.

@mbargull mbargull requested a review from dpryan79 July 24, 2019 10:14
@dpryan79
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👍 LGTM

@bgruening bgruening merged commit ce02dec into master Jul 26, 2019
@bgruening bgruening deleted the fixes branch July 26, 2019 19:24
@bgruening
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Thanks!

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4 participants