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Failing CircleCI Build
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| $ circleci build | |
| ====>> Spin up Environment | |
| Build-agent version 0.0.4710-44beb0a (2018-02-27T20:05:34+0000) | |
| Starting container bioconda/bioconda-utils-build-env | |
| using image bioconda/bioconda-utils-build-env@sha256:1754002c070d602a3f80d4cb029129081d88487c97026a279b873b003d48bdb8 | |
| Using build environment variables: | |
| BASH_ENV=/tmp/.bash_env-localbuild-1520100701 | |
| CI=true | |
| CIRCLECI=true | |
| CIRCLE_BRANCH=ENH_RepeatmaskerOSX | |
| CIRCLE_BUILD_NUM= | |
| CIRCLE_JOB=build | |
| CIRCLE_NODE_INDEX=0 | |
| CIRCLE_NODE_TOTAL=1 | |
| CIRCLE_REPOSITORY_URL= | |
| CIRCLE_SHA1=5623b956715bd33d96401abe40b3d9073d681f1d | |
| CIRCLE_SHELL_ENV=/tmp/.bash_env-localbuild-1520100701 | |
| CIRCLE_WORKING_DIRECTORY=~/project | |
| ====>> Checkout code | |
| #!/bin/sh | |
| mkdir -p /root/project && cp -r /tmp/_circleci_local_build_repo/. /root/project | |
| ====>> Setup ssh | |
| #!/bin/bash -eo pipefail | |
| mkdir -p ~/.ssh | |
| ssh-keyscan -H github.com >> ~/.ssh/known_hosts | |
| # github.com SSH-2.0-libssh_0.7.0 | |
| ====>> Setup base system | |
| #!/bin/bash -eo pipefail | |
| cat >> $BASH_ENV <<EOF | |
| if [[ \$- == *u* ]] ; then | |
| set +u ; . /tmp/repo/docker-entrypoint-source ; set -u | |
| else | |
| . /tmp/repo/docker-entrypoint-source | |
| fi | |
| EOF | |
| ====>> Download common definitions | |
| #!/bin/bash -eo pipefail | |
| curl -s https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh > .circleci/common.sh | |
| ====>> Setup bioconda-utils | |
| #!/bin/bash -eo pipefail | |
| .circleci/setup.sh | |
| remote: Counting objects: 9, done. | |
| remote: Compressing objects: 100% (7/7), done. | |
| remote: Total 9 (delta 3), reused 0 (delta 0), pack-reused 2 | |
| Unpacking objects: 100% (9/9), done. | |
| From https://github.com/bioconda/bioconda-recipes | |
| * [new branch] master -> __upstream__lifcdwmajd/master | |
| .circleci/setup.sh: line 28: docker: command not found | |
| Error: Exited with code 127 | |
| Step failed | |
| Task failed |
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| $ circleci build | |
| ====>> Spin up Environment | |
| Build-agent version 0.0.4710-44beb0a (2018-02-27T20:05:34+0000) | |
| Starting container bioconda/bioconda-utils-build-env | |
| using image bioconda/bioconda-utils-build-env@sha256:1754002c070d602a3f80d4cb029129081d88487c97026a279b873b003d48bdb8 | |
| Using build environment variables: | |
| BASH_ENV=/tmp/.bash_env-localbuild-1520361875 | |
| CI=true | |
| CIRCLECI=true | |
| CIRCLE_BRANCH=ENH_RepeatmaskerOSX | |
| CIRCLE_BUILD_NUM= | |
| CIRCLE_JOB=build | |
| CIRCLE_NODE_INDEX=0 | |
| CIRCLE_NODE_TOTAL=1 | |
| CIRCLE_REPOSITORY_URL= | |
| CIRCLE_SHA1=b618c3a0ab901bca8907065e12da13b60d352445 | |
| CIRCLE_SHELL_ENV=/tmp/.bash_env-localbuild-1520361875 | |
| CIRCLE_WORKING_DIRECTORY=~/project | |
| ====>> Checkout code | |
| #!/bin/sh | |
| mkdir -p /root/project && cp -r /tmp/_circleci_local_build_repo/. /root/project | |
| ====>> Setup ssh | |
| #!/bin/bash -eo pipefail | |
| mkdir -p ~/.ssh | |
| ssh-keyscan -H github.com >> ~/.ssh/known_hosts | |
| # github.com SSH-2.0-libssh_0.7.0 | |
| ====>> Setup base system | |
| #!/bin/bash -eo pipefail | |
| cat >> $BASH_ENV <<EOF | |
| if [[ \$- == *u* ]] ; then | |
| set +u ; . /tmp/repo/docker-entrypoint-source ; set -u | |
| else | |
| . /tmp/repo/docker-entrypoint-source | |
| fi | |
| EOF | |
| ====>> Download common definitions | |
| #!/bin/bash -eo pipefail | |
| curl -s https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh > .circleci/common.sh | |
| Traceback (most recent call last): | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 170, in main | |
| import conda.cli.activate as activate | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/activate.py", line 12, in <module> | |
| from ..utils import shells | |
| File "/opt/conda/lib/python3.6/site-packages/conda/utils.py", line 15, in <module> | |
| from .gateways.disk.read import compute_md5sum | |
| File "/opt/conda/lib/python3.6/site-packages/conda/gateways/disk/read.py", line 22, in <module> | |
| from ...models.channel import Channel | |
| File "/opt/conda/lib/python3.6/site-packages/conda/models/channel.py", line 8, in <module> | |
| from ..base.context import context | |
| File "/opt/conda/lib/python3.6/site-packages/conda/base/context.py", line 20, in <module> | |
| from ..common.configuration import (Configuration, LoadError, MapParameter, PrimitiveParameter, | |
| File "/opt/conda/lib/python3.6/site-packages/conda/common/configuration.py", line 50, in <module> | |
| from ruamel_yaml.comments import CommentedSeq, CommentedMap | |
| ValueError: source code string cannot contain null bytes | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "/opt/conda/bin/conda", line 6, in <module> | |
| sys.exit(conda.cli.main()) | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 178, in main | |
| init_loggers() | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 84, in init_loggers | |
| from ..console import setup_verbose_handlers | |
| File "/opt/conda/lib/python3.6/site-packages/conda/console.py", line 9, in <module> | |
| from .base.context import context | |
| File "/opt/conda/lib/python3.6/site-packages/conda/base/context.py", line 20, in <module> | |
| from ..common.configuration import (Configuration, LoadError, MapParameter, PrimitiveParameter, | |
| File "/opt/conda/lib/python3.6/site-packages/conda/common/configuration.py", line 50, in <module> | |
| from ruamel_yaml.comments import CommentedSeq, CommentedMap | |
| ValueError: source code string cannot contain null bytes | |
| ====>> Setup bioconda-utils | |
| #!/bin/bash -eo pipefail | |
| .circleci/setup.sh | |
| Traceback (most recent call last): | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 170, in main | |
| import conda.cli.activate as activate | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/activate.py", line 12, in <module> | |
| from ..utils import shells | |
| File "/opt/conda/lib/python3.6/site-packages/conda/utils.py", line 15, in <module> | |
| from .gateways.disk.read import compute_md5sum | |
| File "/opt/conda/lib/python3.6/site-packages/conda/gateways/disk/read.py", line 22, in <module> | |
| from ...models.channel import Channel | |
| File "/opt/conda/lib/python3.6/site-packages/conda/models/channel.py", line 8, in <module> | |
| from ..base.context import context | |
| File "/opt/conda/lib/python3.6/site-packages/conda/base/context.py", line 20, in <module> | |
| from ..common.configuration import (Configuration, LoadError, MapParameter, PrimitiveParameter, | |
| File "/opt/conda/lib/python3.6/site-packages/conda/common/configuration.py", line 50, in <module> | |
| from ruamel_yaml.comments import CommentedSeq, CommentedMap | |
| ValueError: source code string cannot contain null bytes | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "/opt/conda/bin/conda", line 6, in <module> | |
| sys.exit(conda.cli.main()) | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 178, in main | |
| init_loggers() | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 84, in init_loggers | |
| from ..console import setup_verbose_handlers | |
| File "/opt/conda/lib/python3.6/site-packages/conda/console.py", line 9, in <module> | |
| from .base.context import context | |
| File "/opt/conda/lib/python3.6/site-packages/conda/base/context.py", line 20, in <module> | |
| from ..common.configuration import (Configuration, LoadError, MapParameter, PrimitiveParameter, | |
| File "/opt/conda/lib/python3.6/site-packages/conda/common/configuration.py", line 50, in <module> | |
| from ruamel_yaml.comments import CommentedSeq, CommentedMap | |
| ValueError: source code string cannot contain null bytes | |
| Traceback (most recent call last): | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 170, in main | |
| import conda.cli.activate as activate | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/activate.py", line 12, in <module> | |
| from ..utils import shells | |
| File "/opt/conda/lib/python3.6/site-packages/conda/utils.py", line 15, in <module> | |
| from .gateways.disk.read import compute_md5sum | |
| File "/opt/conda/lib/python3.6/site-packages/conda/gateways/disk/read.py", line 22, in <module> | |
| from ...models.channel import Channel | |
| File "/opt/conda/lib/python3.6/site-packages/conda/models/channel.py", line 8, in <module> | |
| from ..base.context import context | |
| File "/opt/conda/lib/python3.6/site-packages/conda/base/context.py", line 20, in <module> | |
| from ..common.configuration import (Configuration, LoadError, MapParameter, PrimitiveParameter, | |
| File "/opt/conda/lib/python3.6/site-packages/conda/common/configuration.py", line 50, in <module> | |
| from ruamel_yaml.comments import CommentedSeq, CommentedMap | |
| ValueError: source code string cannot contain null bytes | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "/opt/conda/bin/conda", line 6, in <module> | |
| sys.exit(conda.cli.main()) | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 178, in main | |
| init_loggers() | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 84, in init_loggers | |
| from ..console import setup_verbose_handlers | |
| File "/opt/conda/lib/python3.6/site-packages/conda/console.py", line 9, in <module> | |
| from .base.context import context | |
| File "/opt/conda/lib/python3.6/site-packages/conda/base/context.py", line 20, in <module> | |
| from ..common.configuration import (Configuration, LoadError, MapParameter, PrimitiveParameter, | |
| File "/opt/conda/lib/python3.6/site-packages/conda/common/configuration.py", line 50, in <module> | |
| from ruamel_yaml.comments import CommentedSeq, CommentedMap | |
| ValueError: source code string cannot contain null bytes | |
| Traceback (most recent call last): | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 170, in main | |
| import conda.cli.activate as activate | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/activate.py", line 12, in <module> | |
| from ..utils import shells | |
| File "/opt/conda/lib/python3.6/site-packages/conda/utils.py", line 15, in <module> | |
| from .gateways.disk.read import compute_md5sum | |
| File "/opt/conda/lib/python3.6/site-packages/conda/gateways/disk/read.py", line 22, in <module> | |
| from ...models.channel import Channel | |
| File "/opt/conda/lib/python3.6/site-packages/conda/models/channel.py", line 8, in <module> | |
| from ..base.context import context | |
| File "/opt/conda/lib/python3.6/site-packages/conda/base/context.py", line 20, in <module> | |
| from ..common.configuration import (Configuration, LoadError, MapParameter, PrimitiveParameter, | |
| File "/opt/conda/lib/python3.6/site-packages/conda/common/configuration.py", line 50, in <module> | |
| from ruamel_yaml.comments import CommentedSeq, CommentedMap | |
| ValueError: source code string cannot contain null bytes | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "/opt/conda/bin/conda", line 6, in <module> | |
| sys.exit(conda.cli.main()) | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 178, in main | |
| init_loggers() | |
| File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 84, in init_loggers | |
| from ..console import setup_verbose_handlers | |
| File "/opt/conda/lib/python3.6/site-packages/conda/console.py", line 9, in <module> | |
| from .base.context import context | |
| File "/opt/conda/lib/python3.6/site-packages/conda/base/context.py", line 20, in <module> | |
| from ..common.configuration import (Configuration, LoadError, MapParameter, PrimitiveParameter, | |
| File "/opt/conda/lib/python3.6/site-packages/conda/common/configuration.py", line 50, in <module> | |
| from ruamel_yaml.comments import CommentedSeq, CommentedMap | |
| ValueError: source code string cannot contain null bytes | |
| Error: Exited with code 1 | |
| Step failed | |
| Task failed |
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