{"action":"created","issue":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/9534","repository_url":"https://api.github.com/repos/bioconda/bioconda-recipes","labels_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/9534/labels{/name}","comments_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/9534/comments","events_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/9534/events","html_url":"https://github.com/bioconda/bioconda-recipes/issues/9534","id":334719204,"node_id":"MDU6SXNzdWUzMzQ3MTkyMDQ=","number":9534,"title":"First Bioconda package: Problems trying to run tests","user":{"login":"ignaciot","id":2243614,"node_id":"MDQ6VXNlcjIyNDM2MTQ=","avatar_url":"https://avatars3.githubusercontent.com/u/2243614?v=4","gravatar_id":"","url":"https://api.github.com/users/ignaciot","html_url":"https://github.com/ignaciot","followers_url":"https://api.github.com/users/ignaciot/followers","following_url":"https://api.github.com/users/ignaciot/following{/other_user}","gists_url":"https://api.github.com/users/ignaciot/gists{/gist_id}","starred_url":"https://api.github.com/users/ignaciot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ignaciot/subscriptions","organizations_url":"https://api.github.com/users/ignaciot/orgs","repos_url":"https://api.github.com/users/ignaciot/repos","events_url":"https://api.github.com/users/ignaciot/events{/privacy}","received_events_url":"https://api.github.com/users/ignaciot/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-06-22T02:05:22Z","updated_at":"2018-06-22T14:59:04Z","closed_at":null,"author_association":"NONE","body":"Hi guys, this is my first attempt at submitting a package to Bioconda, so I apologize in advance if I'm missing something really obvious. I have a proper PyPI package that I'd like to include in Bioconda as well, I followed the instructions up to forking this repository and when trying to run the local tests, I'm running into errors with both the \"Circle CI\" and \"bootstrap\" methods.\r\n\r\nWith the first one, I get an exception regarding conda.version (I can import conda but don't seem to have a conda.version package, is this part of something else?):\r\n\r\n```\r\n$ circleci build\r\n\r\n====>> Spin up Environment\r\nBuild-agent version 0.0.5895-01cdb92 (2018-05-29T20:07:10+0000)\r\nStarting container bioconda/bioconda-utils-build-env\r\n  using image bioconda/bioconda-utils-build-env@sha256:969aad03c0b5661ed55d2eadb938295706a4cf45191dc47e2dfe4c57f4d2d436\r\n\r\nUsing build environment variables:\r\n  BASH_ENV=/tmp/.bash_env-localbuild-1529630969\r\n  CI=true\r\n  CIRCLECI=true\r\n  CIRCLE_BRANCH=dastk\r\n  CIRCLE_BUILD_NUM=\r\n  CIRCLE_JOB=build\r\n  CIRCLE_NODE_INDEX=0\r\n  CIRCLE_NODE_TOTAL=1\r\n  CIRCLE_REPOSITORY_URL=https://github.com/ignaciot/bioconda-recipes.git\r\n  CIRCLE_SHA1=671f6dbc52adca025f10fa000b2566ff2908d9d1\r\n  CIRCLE_SHELL_ENV=/tmp/.bash_env-localbuild-1529630969\r\n  CIRCLE_WORKING_DIRECTORY=~/project\r\n\r\n====>> Checkout code\r\n  #!/bin/sh\r\nmkdir -p /root/project && cp -r /tmp/_circleci_local_build_repo/. /root/project\r\n====>> Setup ssh\r\n  #!/bin/bash -eo pipefail\r\nmkdir -p ~/.ssh\r\nssh-keyscan -H github.com >> ~/.ssh/known_hosts\r\n\r\n# github.com SSH-2.0-libssh_0.7.0\r\n====>> Setup base system\r\n  #!/bin/bash -eo pipefail\r\ncat >> $BASH_ENV <<EOF\r\nif [[ \\$- == *u* ]] ; then\r\n    set +u ; . /tmp/repo/docker-entrypoint-source ; set -u\r\nelse\r\n    . /tmp/repo/docker-entrypoint-source\r\nfi\r\nEOF\r\n\r\n====>> Download common definitions\r\n  #!/bin/bash -eo pipefail\r\ncurl -s https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh > .circleci/common.sh\r\n# TODO remove this temporal override before merging the PR into master\r\necho -e 'MINICONDA_VER=4.4.10\\nBIOCONDA_UTILS_TAG=cb3-migration' > .circleci/common.sh\r\n\r\n====>> Setup bioconda-utils\r\n  #!/bin/bash -eo pipefail\r\n.circleci/setup.sh\r\nFetching package metadata ...............\r\nSolving package specifications: .\r\n\r\nPackage plan for installation in environment /opt/conda:\r\n\r\nThe following NEW packages will be INSTALLED:\r\n\r\n    intel-openmp:   2018.0.3-0                    defaults\r\n    libgcc-ng:      7.2.0-hdf63c60_3              defaults\r\n    libgfortran-ng: 7.2.0-hdf63c60_3              defaults\r\n    mkl:            2018.0.3-1                    defaults\r\n    mkl_fft:        1.0.2-py36_0                  conda-forge\r\n    mkl_random:     1.0.1-py36_0                  conda-forge\r\n    numpy-base:     1.14.5-py36hdbf6ddf_0         defaults\r\n\r\nThe following packages will be UPDATED:\r\n\r\n    conda:          4.3.33-py36_0                 conda-forge --> 4.5.4-py36_0          conda-forge\r\n    conda-build:    2.1.18-py36_0                 conda-forge --> 3.10.6-py36_0         conda-forge\r\n    git:            2.14.2-3                      conda-forge --> 2.17.1-0              conda-forge\r\n    numpy:          1.14.3-py36_blas_openblas_200 conda-forge [blas_openblas] --> 1.14.5-py36hcd700cb_0 defaults\r\n    tini:           0.18.0-0                      conda-forge --> 0.18.0-h470a237_1     conda-forge\r\n\r\nThe following packages will be DOWNGRADED:\r\n\r\n    blas:           1.1-openblas                  conda-forge --> 1.0-mkl               defaults\r\n\r\nProceed ([y]/n)?\r\nblas-1.0-mkl.t 100% || Time: 0:00:00   3.99 MB/ss\r\nintel-openmp-2 100% || Time: 0:00:00   5.12 MB/ss\r\nlibgcc-ng-7.2. 100% || Time: 0:00:00  12.43 MB/ss\r\nlibgfortran-ng 100% || Time: 0:00:00  20.93 MB/ss\r\nmkl-2018.0.3-1 100% || Time: 0:00:12  16.75 MB/ss\r\ntini-0.18.0-h4 100% || Time: 0:00:00  11.17 MB/ss\r\ngit-2.17.1-0.t 100% || Time: 0:00:09   1.97 MB/ss\r\nnumpy-base-1.1 100% || Time: 0:00:00  23.04 MB/ss\r\nconda-4.5.4-py 100% || Time: 0:00:00   2.84 MB/ss\r\nconda-build-3. 100% || Time: 0:00:00   1.25 MB/ss\r\nmkl_fft-1.0.2- 100% || Time: 0:00:00   2.55 MB/ss\r\nmkl_random-1.0 100% || Time: 0:00:00   4.58 MB/ss\r\nnumpy-1.14.5-p 100% || Time: 0:00:00  25.17 MB/ss\r\nremote: Counting objects: 709, done.\r\nremote: Compressing objects: 100% (38/38), done.\r\nremote: Total 709 (delta 405), reused 441 (delta 404), pack-reused 265\r\nReceiving objects: 100% (709/709), 143.32 KiB | 13.03 MiB/s, done.\r\nResolving deltas: 100% (405/405), completed with 296 local objects.\r\nFrom https://github.com/bioconda/bioconda-recipes\r\n * [new branch]          master     -> __upstream__obeubaimpb/master\r\n====>> Linting\r\n  #!/bin/bash -eo pipefail\r\nbioconda-utils lint --loglevel debug --full-report recipes config.yml --git-range master HEAD\r\nTraceback (most recent call last):\r\n  File \"/opt/conda/bin/bioconda-utils\", line 11, in <module>\r\n    load_entry_point('bioconda-utils==0+untagged.1.gf35d935', 'console_scripts', 'bioconda-utils')()\r\n  File \"/opt/conda/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 476, in load_entry_point\r\n    return get_distribution(dist).load_entry_point(group, name)\r\n  File \"/opt/conda/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2700, in load_entry_point\r\n    return ep.load()\r\n  File \"/opt/conda/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2318, in load\r\n    return self.resolve()\r\n  File \"/opt/conda/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2324, in resolve\r\n    module = __import__(self.module_name, fromlist=['__name__'], level=0)\r\n  File \"/opt/conda/lib/python3.6/site-packages/bioconda_utils/cli.py\", line 15, in <module>\r\n    from . import utils\r\n  File \"/opt/conda/lib/python3.6/site-packages/bioconda_utils/utils.py\", line 25, in <module>\r\n    from conda.version import VersionOrder\r\nModuleNotFoundError: No module named 'conda.version'\r\nError: Exited with code 1\r\nStep failed\r\nTask failed\r\n```\r\n\r\nWith the bootstrap method, I get an error from the setup.sh script, because it's attempting to execute `common.sh` which isn't present:\r\n\r\n```\r\n$ ./bootstrap.py /tmp/miniconda\r\n.circleci/setup.sh: line 13: conda: command not found\r\nTraceback (most recent call last):\r\n  File \"./bootstrap.py\", line 104, in <module>\r\n    sp.check_call(['.circleci/setup.sh'], env=env)\r\n  File \"/Users/ignaciot/miniconda3/lib/python3.6/subprocess.py\", line 291, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nsubprocess.CalledProcessError: Command '['.circleci/setup.sh']' returned non-zero exit status 127.\r\n```\r\n\r\nAny clues would be greatly appreciated! I'm trying to run this on python 3:\r\n\r\n```\r\n$ python --version\r\nPython 3.6.5 :: Anaconda, Inc.\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/comments/399471812","html_url":"https://github.com/bioconda/bioconda-recipes/issues/9534#issuecomment-399471812","issue_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/9534","id":399471812,"node_id":"MDEyOklzc3VlQ29tbWVudDM5OTQ3MTgxMg==","user":{"login":"daler","id":115406,"node_id":"MDQ6VXNlcjExNTQwNg==","avatar_url":"https://avatars1.githubusercontent.com/u/115406?v=4","gravatar_id":"","url":"https://api.github.com/users/daler","html_url":"https://github.com/daler","followers_url":"https://api.github.com/users/daler/followers","following_url":"https://api.github.com/users/daler/following{/other_user}","gists_url":"https://api.github.com/users/daler/gists{/gist_id}","starred_url":"https://api.github.com/users/daler/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daler/subscriptions","organizations_url":"https://api.github.com/users/daler/orgs","repos_url":"https://api.github.com/users/daler/repos","events_url":"https://api.github.com/users/daler/events{/privacy}","received_events_url":"https://api.github.com/users/daler/received_events","type":"User","site_admin":false},"created_at":"2018-06-22T14:59:04Z","updated_at":"2018-06-22T14:59:04Z","author_association":"MEMBER","body":"@ignaciot please try #9541, but note that the `adjustText` and `DateTime` dependencies specified by DAStk are not currently available as conda packages. As these are general-purpose packages, they should be added conda-forge first."}}
{"actor":{"display_login":"daler"}}