I have just done a fresh install of bioconda-utils in a new conda installation. When I use bioconda-utils build --docker
on a Linux machine I get the errors below. If I remove the --docker
option, it works.
bioconda-utils build recipes config.yml --docker --loglevel=info --packages cgat-scripts --loglevel=debug
14:58:17 BIOCONDA INFO DOCKER: Pulling docker image condaforge/linux-anvil
14:58:19 BIOCONDA DEBUG DOCKER: stdout+stderr:
Using default tag: latest
latest: Pulling from condaforge/linux-anvil
Digest: sha256:dd53ef1792f777fa8b2abf30221bf9beb6cb6a81d158d498f0219c4d475696cd
Status: Image is up to date for condaforge/linux-anvil:latest
14:58:19 BIOCONDA INFO DOCKER: Done pulling image
14:58:19 BIOCONDA INFO DOCKER: Building image "tmp-bioconda-builder" from /tmp/tmpwfwm7ysb
14:58:19 BIOCONDA DEBUG Dockerfile:
FROM condaforge/linux-anvil
COPY requirements.txt /tmp/requirements.txt
RUN /opt/conda/bin/conda config --add channels defaults
RUN /opt/conda/bin/conda config --add channels conda-forge
RUN /opt/conda/bin/conda config --add channels bioconda
RUN /opt/conda/bin/conda install --file /tmp/requirements.txt
....
15:02:19 BIOCONDA INFO DOCKER: Built docker image tag=tmp-bioconda-builder
15:02:19 BIOCONDA INFO blacklist: blast/2.2.21, cap-mirseq, denovogear, detonate, mgkit, mothur/1.36.1, perl-font-afm, r-histonehmm
15:02:19 BIOCONDA DEBUG get_recipes(recipes, package='['cgat-scripts']'): cgat-scripts
15:02:19 BIOCONDA DEBUG recipes/cgat-scripts
15:02:19 BIOCONDA DEBUG recipes: ['recipes/cgat-scripts']
15:02:19 BIOCONDA INFO Filtering recipes
15:02:21 BIOCONDA DEBUG recipes: ['recipes/cgat-scripts']
15:02:22 BIOCONDA DEBUG FILTER: building cgat-scripts-0.2.7-np112py27r3.3.2_0.tar.bz2 because it is not in channels and does not define skip
15:02:22 BIOCONDA DEBUG FILTER: building cgat-scripts-0.2.7-np112py35r3.3.2_0.tar.bz2 because it is not in channels and does not define skip
15:02:22 BIOCONDA DEBUG FILTER: building cgat-scripts-0.2.7-np112py36r3.3.2_0.tar.bz2 because it is not in channels and does not define skip
Filtering 1 of 1 (100.0%) recipes/cgat-scripts
recipes/cgat-scripts
15:02:22 BIOCONDA INFO Building and testing 1 recipes in total
15:02:22 BIOCONDA INFO Recipes to build:
cgat-scripts
15:02:22 BIOCONDA INFO Building and testing subdag 1 of 1 (1 recipes)
15:02:22 BIOCONDA INFO BUILD START recipes/cgat-scripts, env: CONDA_ALLOW_SOFTLINKS=false;CONDA_BOOST=1.61;CONDA_DEFAULT_ENV=root;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin;CONDA_PERL=5.22.0;CONDA_PREFIX=/conda/sebastian/py3;CONDA_PS1_BACKUP=\n\[\]\[\][\d \t] \u@\h:\w\n\$ \[\];CONDA_PY=27;CONDA_R=3.3.2;CONDA_ROOT=/conda/sebastian/py3;LANG=C;MACOSX_DEPLOYMENT_TARGET=10.9;PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin
15:02:22 BIOCONDA DEBUG build_args: ['--no-anaconda-upload']
15:02:22 BIOCONDA DEBUG channel_args: ['--channel', 'bioconda', '--channel', 'conda-forge', '--channel', 'defaults']
15:02:23 BIOCONDA DEBUG DOCKER: Container build script:
#!/bin/bash
set -e
conda install conda-build=2.1.16 conda=4.3.21 > /dev/null 2>&1
# Add the host's mounted conda-bld dir so that we can use its contents as
# dependencies for building this recipe.
#
# Note that if the directory didn't exist on the host, then the staging area
# will exist in the container but will be empty. Channels expect at least
# a linux-64 and noarch directory within that directory, so we make sure it
# exists before adding the channel.
mkdir -p /opt/host-conda-bld/linux-64
mkdir -p /opt/host-conda-bld/noarch
conda config --add channels file:///opt/host-conda-bld > /dev/null 2>&1
# The actual building...
# we explicitly point to the meta.yaml, in order to keep
# conda-build from building all subdirectories
conda build --channel bioconda --channel conda-forge --channel defaults --no-anaconda-upload /opt/recipe/meta.yaml 2>&1
# Identify the output package
OUTPUT_DIR=$(dirname $(conda build /opt/recipe/meta.yaml --output 2> /dev/null))
OUTPUT=$OUTPUT_DIR/cgat-scripts-0.2.7-np112py27r3.3.2_0.tar.bz2
# Some args to conda-build make it run and exit 0 without creating a package
# (e.g., -h or --skip-existing), so check to see if there's anything to copy
# over first.
if [[ -e $OUTPUT ]]; then
# Copy over the recipe from where the container built it to the mounted
# conda-bld dir from the host. The arch will be either linux-64 or noarch.
cp $OUTPUT /opt/host-conda-bld/linux-64
# Ensure permissions are correct on the host.
HOST_USER=1362
chown $HOST_USER:$HOST_USER /opt/host-conda-bld/linux-64/$(basename $OUTPUT)
conda index /opt/host-conda-bld/linux-64 > /dev/null 2>&1
fi
15:02:23 BIOCONDA DEBUG DOCKER: cmd: ['docker', 'run', '--net', 'host', '--rm', '-v', '/tmp/tmpxn2pcntf/build_script.bash:/opt/build_script.bash', '-v', '/conda/sebastian/py3/conda-bld:/opt/host-conda-bld', '-v', '/conda/sebastian/bioconda-recipes/recipes/cgat-scripts:/opt/recipe', '-e', 'CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin', '-e', 'CONDA_PREFIX=/conda/sebastian/py3', '-e', 'CONDA_GSL=1.16', '-e', 'CONDA_DEFAULT_ENV=root', '-e', 'CONDA_GMP=5.1', '-e', 'PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin', '-e', 'CONDA_ROOT=/conda/sebastian/py3', '-e', 'MACOSX_DEPLOYMENT_TARGET=10.9', '-e', 'CONDA_PY=27', '-e', 'CONDA_ALLOW_SOFTLINKS=false', '-e', 'CONDA_BOOST=1.61', '-e', 'LANG=C', '-e', 'CONDA_HDF5=1.8.17', '-e', 'CONDA_NPY=112', '-e', 'CONDA_HTSLIB=1.5', '-e', 'CONDA_PERL=5.22.0', '-e', 'CONDA_NCURSES=5.9', '-e', 'CONDA_R=3.3.2', '-e', 'CONDA_PS1_BACKUP=\\n\\[\x1b[1m\\]\\[\x1b[32m\\][\\d \\t] \\u@\\h:\\w\\n\\$ \\[\x1b(B\x1b[m\\]', 'tmp-bioconda-builder', '/bin/bash', '/opt/build_script.bash']
.15:02:39 BIOCONDA ERROR COMMAND FAILED: docker run --net host --rm -v /tmp/tmpxn2pcntf/build_script.bash:/opt/build_script.bash -v /conda/sebastian/py3/conda-bld:/opt/host-conda-bld -v /conda/sebastian/bioconda-recipes/recipes/cgat-scripts:/opt/recipe -e CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin -e CONDA_PREFIX=/conda/sebastian/py3 -e CONDA_GSL=1.16 -e CONDA_DEFAULT_ENV=root -e CONDA_GMP=5.1 -e PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin -e CONDA_ROOT=/conda/sebastian/py3 -e MACOSX_DEPLOYMENT_TARGET=10.9 -e CONDA_PY=27 -e CONDA_ALLOW_SOFTLINKS=false -e CONDA_BOOST=1.61 -e LANG=C -e CONDA_HDF5=1.8.17 -e CONDA_NPY=112 -e CONDA_HTSLIB=1.5 -e CONDA_PERL=5.22.0 -e CONDA_NCURSES=5.9 -e CONDA_R=3.3.2 -e CONDA_PS1_BACKUP=\n\[\]\[\][\d \t] \u@\h:\w\n\$ \[\] tmp-bioconda-builder /bin/bash /opt/build_script.bash
15:02:39 BIOCONDA ERROR STDOUT+STDERR:
bash: cannot set terminal process group (-1): Inappropriate ioctl for device
bash: no job control in this shell
Can't read /etc/scl/prefixes/devtoolset-2, devtoolset-2 is probably not installed.
bash: uname: command not found
bash: uname: command not found
CondaValueError: Could not find environment: /conda/sebastian/py3
bash: sed: command not found
bash: grep: command not found
bash: grep: command not found
/opt/build_script.bash: line 14: mkdir: command not found
15:03:23 BIOCONDA ERROR BUILD FAILED recipes/cgat-scripts, CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PERL=5.22.0;CONDA_PY=27;CONDA_R=3.3.2;MACOSX_DEPLOYMENT_TARGET=10.9
15:03:24 BIOCONDA INFO BUILD START recipes/cgat-scripts, env: CONDA_ALLOW_SOFTLINKS=false;CONDA_BOOST=1.61;CONDA_DEFAULT_ENV=root;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin;CONDA_PERL=5.22.0;CONDA_PREFIX=/conda/sebastian/py3;CONDA_PS1_BACKUP=\n\[\]\[\][\d \t] \u@\h:\w\n\$ \[\];CONDA_PY=35;CONDA_R=3.3.2;CONDA_ROOT=/conda/sebastian/py3;LANG=C;MACOSX_DEPLOYMENT_TARGET=10.9;PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin
15:03:24 BIOCONDA DEBUG build_args: ['--no-anaconda-upload']
15:03:24 BIOCONDA DEBUG channel_args: ['--channel', 'bioconda', '--channel', 'conda-forge', '--channel', 'defaults']
15:03:24 BIOCONDA DEBUG DOCKER: Container build script:
#!/bin/bash
set -e
conda install conda-build=2.1.16 conda=4.3.21 > /dev/null 2>&1
# Add the host's mounted conda-bld dir so that we can use its contents as
# dependencies for building this recipe.
#
# Note that if the directory didn't exist on the host, then the staging area
# will exist in the container but will be empty. Channels expect at least
# a linux-64 and noarch directory within that directory, so we make sure it
# exists before adding the channel.
mkdir -p /opt/host-conda-bld/linux-64
mkdir -p /opt/host-conda-bld/noarch
conda config --add channels file:///opt/host-conda-bld > /dev/null 2>&1
# The actual building...
# we explicitly point to the meta.yaml, in order to keep
# conda-build from building all subdirectories
conda build --channel bioconda --channel conda-forge --channel defaults --no-anaconda-upload /opt/recipe/meta.yaml 2>&1
# Identify the output package
OUTPUT_DIR=$(dirname $(conda build /opt/recipe/meta.yaml --output 2> /dev/null))
OUTPUT=$OUTPUT_DIR/cgat-scripts-0.2.7-np112py35r3.3.2_0.tar.bz2
# Some args to conda-build make it run and exit 0 without creating a package
# (e.g., -h or --skip-existing), so check to see if there's anything to copy
# over first.
if [[ -e $OUTPUT ]]; then
# Copy over the recipe from where the container built it to the mounted
# conda-bld dir from the host. The arch will be either linux-64 or noarch.
cp $OUTPUT /opt/host-conda-bld/linux-64
# Ensure permissions are correct on the host.
HOST_USER=1362
chown $HOST_USER:$HOST_USER /opt/host-conda-bld/linux-64/$(basename $OUTPUT)
conda index /opt/host-conda-bld/linux-64 > /dev/null 2>&1
fi
15:03:24 BIOCONDA DEBUG DOCKER: cmd: ['docker', 'run', '--net', 'host', '--rm', '-v', '/tmp/tmpfzn1vnjs/build_script.bash:/opt/build_script.bash', '-v', '/conda/sebastian/py3/conda-bld:/opt/host-conda-bld', '-v', '/conda/sebastian/bioconda-recipes/recipes/cgat-scripts:/opt/recipe', '-e', 'CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin', '-e', 'CONDA_PREFIX=/conda/sebastian/py3', '-e', 'CONDA_GSL=1.16', '-e', 'CONDA_DEFAULT_ENV=root', '-e', 'CONDA_GMP=5.1', '-e', 'PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin', '-e', 'CONDA_ROOT=/conda/sebastian/py3', '-e', 'MACOSX_DEPLOYMENT_TARGET=10.9', '-e', 'CONDA_PY=35', '-e', 'CONDA_ALLOW_SOFTLINKS=false', '-e', 'CONDA_BOOST=1.61', '-e', 'LANG=C', '-e', 'CONDA_HDF5=1.8.17', '-e', 'CONDA_NPY=112', '-e', 'CONDA_HTSLIB=1.5', '-e', 'CONDA_PERL=5.22.0', '-e', 'CONDA_NCURSES=5.9', '-e', 'CONDA_R=3.3.2', '-e', 'CONDA_PS1_BACKUP=\\n\\[\x1b[1m\\]\\[\x1b[32m\\][\\d \\t] \\u@\\h:\\w\\n\\$ \\[\x1b(B\x1b[m\\]', 'tmp-bioconda-builder', '/bin/bash', '/opt/build_script.bash']
.15:03:40 BIOCONDA ERROR COMMAND FAILED: docker run --net host --rm -v /tmp/tmpfzn1vnjs/build_script.bash:/opt/build_script.bash -v /conda/sebastian/py3/conda-bld:/opt/host-conda-bld -v /conda/sebastian/bioconda-recipes/recipes/cgat-scripts:/opt/recipe -e CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin -e CONDA_PREFIX=/conda/sebastian/py3 -e CONDA_GSL=1.16 -e CONDA_DEFAULT_ENV=root -e CONDA_GMP=5.1 -e PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin -e CONDA_ROOT=/conda/sebastian/py3 -e MACOSX_DEPLOYMENT_TARGET=10.9 -e CONDA_PY=35 -e CONDA_ALLOW_SOFTLINKS=false -e CONDA_BOOST=1.61 -e LANG=C -e CONDA_HDF5=1.8.17 -e CONDA_NPY=112 -e CONDA_HTSLIB=1.5 -e CONDA_PERL=5.22.0 -e CONDA_NCURSES=5.9 -e CONDA_R=3.3.2 -e CONDA_PS1_BACKUP=\n\[\]\[\][\d \t] \u@\h:\w\n\$ \[\] tmp-bioconda-builder /bin/bash /opt/build_script.bash
15:03:40 BIOCONDA ERROR STDOUT+STDERR:
bash: cannot set terminal process group (-1): Inappropriate ioctl for device
bash: no job control in this shell
Can't read /etc/scl/prefixes/devtoolset-2, devtoolset-2 is probably not installed.
bash: uname: command not found
bash: uname: command not found
CondaValueError: Could not find environment: /conda/sebastian/py3
bash: sed: command not found
bash: grep: command not found
bash: grep: command not found
/opt/build_script.bash: line 14: mkdir: command not found
15:04:25 BIOCONDA ERROR BUILD FAILED recipes/cgat-scripts, CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PERL=5.22.0;CONDA_PY=35;CONDA_R=3.3.2;MACOSX_DEPLOYMENT_TARGET=10.9
15:04:26 BIOCONDA INFO BUILD START recipes/cgat-scripts, env: CONDA_ALLOW_SOFTLINKS=false;CONDA_BOOST=1.61;CONDA_DEFAULT_ENV=root;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin;CONDA_PERL=5.22.0;CONDA_PREFIX=/conda/sebastian/py3;CONDA_PS1_BACKUP=\n\[\]\[\][\d \t] \u@\h:\w\n\$ \[\];CONDA_PY=36;CONDA_R=3.3.2;CONDA_ROOT=/conda/sebastian/py3;LANG=C;MACOSX_DEPLOYMENT_TARGET=10.9;PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin
15:04:26 BIOCONDA DEBUG build_args: ['--no-anaconda-upload']
15:04:26 BIOCONDA DEBUG channel_args: ['--channel', 'bioconda', '--channel', 'conda-forge', '--channel', 'defaults']
15:04:26 BIOCONDA DEBUG DOCKER: Container build script:
#!/bin/bash
set -e
conda install conda-build=2.1.16 conda=4.3.21 > /dev/null 2>&1
# Add the host's mounted conda-bld dir so that we can use its contents as
# dependencies for building this recipe.
#
# Note that if the directory didn't exist on the host, then the staging area
# will exist in the container but will be empty. Channels expect at least
# a linux-64 and noarch directory within that directory, so we make sure it
# exists before adding the channel.
mkdir -p /opt/host-conda-bld/linux-64
mkdir -p /opt/host-conda-bld/noarch
conda config --add channels file:///opt/host-conda-bld > /dev/null 2>&1
# The actual building...
# we explicitly point to the meta.yaml, in order to keep
# conda-build from building all subdirectories
conda build --channel bioconda --channel conda-forge --channel defaults --no-anaconda-upload /opt/recipe/meta.yaml 2>&1
# Identify the output package
OUTPUT_DIR=$(dirname $(conda build /opt/recipe/meta.yaml --output 2> /dev/null))
OUTPUT=$OUTPUT_DIR/cgat-scripts-0.2.7-np112py36r3.3.2_0.tar.bz2
# Some args to conda-build make it run and exit 0 without creating a package
# (e.g., -h or --skip-existing), so check to see if there's anything to copy
# over first.
if [[ -e $OUTPUT ]]; then
# Copy over the recipe from where the container built it to the mounted
# conda-bld dir from the host. The arch will be either linux-64 or noarch.
cp $OUTPUT /opt/host-conda-bld/linux-64
# Ensure permissions are correct on the host.
HOST_USER=1362
chown $HOST_USER:$HOST_USER /opt/host-conda-bld/linux-64/$(basename $OUTPUT)
conda index /opt/host-conda-bld/linux-64 > /dev/null 2>&1
fi
15:04:26 BIOCONDA DEBUG DOCKER: cmd: ['docker', 'run', '--net', 'host', '--rm', '-v', '/tmp/tmpko472l2m/build_script.bash:/opt/build_script.bash', '-v', '/conda/sebastian/py3/conda-bld:/opt/host-conda-bld', '-v', '/conda/sebastian/bioconda-recipes/recipes/cgat-scripts:/opt/recipe', '-e', 'CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin', '-e', 'CONDA_PREFIX=/conda/sebastian/py3', '-e', 'CONDA_GSL=1.16', '-e', 'CONDA_DEFAULT_ENV=root', '-e', 'CONDA_GMP=5.1', '-e', 'PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin', '-e', 'CONDA_ROOT=/conda/sebastian/py3', '-e', 'MACOSX_DEPLOYMENT_TARGET=10.9', '-e', 'CONDA_PY=36', '-e', 'CONDA_ALLOW_SOFTLINKS=false', '-e', 'CONDA_BOOST=1.61', '-e', 'LANG=C', '-e', 'CONDA_HDF5=1.8.17', '-e', 'CONDA_NPY=112', '-e', 'CONDA_HTSLIB=1.5', '-e', 'CONDA_PERL=5.22.0', '-e', 'CONDA_NCURSES=5.9', '-e', 'CONDA_R=3.3.2', '-e', 'CONDA_PS1_BACKUP=\\n\\[\x1b[1m\\]\\[\x1b[32m\\][\\d \\t] \\u@\\h:\\w\\n\\$ \\[\x1b(B\x1b[m\\]', 'tmp-bioconda-builder', '/bin/bash', '/opt/build_script.bash']
.15:04:43 BIOCONDA ERROR COMMAND FAILED: docker run --net host --rm -v /tmp/tmpko472l2m/build_script.bash:/opt/build_script.bash -v /conda/sebastian/py3/conda-bld:/opt/host-conda-bld -v /conda/sebastian/bioconda-recipes/recipes/cgat-scripts:/opt/recipe -e CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin -e CONDA_PREFIX=/conda/sebastian/py3 -e CONDA_GSL=1.16 -e CONDA_DEFAULT_ENV=root -e CONDA_GMP=5.1 -e PATH=/conda/sebastian/py3/bin:/usr/lib64/qt-3.3/bin:/ifs/apps/system/git-2.13.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/ifs/home/sebastian/bin -e CONDA_ROOT=/conda/sebastian/py3 -e MACOSX_DEPLOYMENT_TARGET=10.9 -e CONDA_PY=36 -e CONDA_ALLOW_SOFTLINKS=false -e CONDA_BOOST=1.61 -e LANG=C -e CONDA_HDF5=1.8.17 -e CONDA_NPY=112 -e CONDA_HTSLIB=1.5 -e CONDA_PERL=5.22.0 -e CONDA_NCURSES=5.9 -e CONDA_R=3.3.2 -e CONDA_PS1_BACKUP=\n\[\]\[\][\d \t] \u@\h:\w\n\$ \[\] tmp-bioconda-builder /bin/bash /opt/build_script.bash
15:04:43 BIOCONDA ERROR STDOUT+STDERR:
bash: cannot set terminal process group (-1): Inappropriate ioctl for device
bash: no job control in this shell
Can't read /etc/scl/prefixes/devtoolset-2, devtoolset-2 is probably not installed.
bash: uname: command not found
bash: uname: command not found
CondaValueError: Could not find environment: /conda/sebastian/py3
bash: sed: command not found
bash: grep: command not found
bash: grep: command not found
/opt/build_script.bash: line 14: mkdir: command not found
15:05:26 BIOCONDA ERROR BUILD FAILED recipes/cgat-scripts, CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PERL=5.22.0;CONDA_PY=36;CONDA_R=3.3.2;MACOSX_DEPLOYMENT_TARGET=10.9
15:05:28 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
15:05:28 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe cgat-scripts-0.2.7-np112py27r3.3.2_0.tar.bz2, environment CONDA_GSL=1.16;CONDA_GMP=5.1;MACOSX_DEPLOYMENT_TARGET=10.9;CONDA_PY=27;CONDA_BOOST=1.61;CONDA_HDF5=1.8.17;CONDA_NPY=112;CONDA_HTSLIB=1.5;CONDA_PERL=5.22.0;CONDA_R=3.3.2;CONDA_NCURSES=5.9
15:05:28 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe cgat-scripts-0.2.7-np112py35r3.3.2_0.tar.bz2, environment CONDA_GSL=1.16;CONDA_GMP=5.1;MACOSX_DEPLOYMENT_TARGET=10.9;CONDA_PY=35;CONDA_BOOST=1.61;CONDA_HDF5=1.8.17;CONDA_NPY=112;CONDA_HTSLIB=1.5;CONDA_PERL=5.22.0;CONDA_R=3.3.2;CONDA_NCURSES=5.9
15:05:28 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe cgat-scripts-0.2.7-np112py36r3.3.2_0.tar.bz2, environment CONDA_GSL=1.16;CONDA_GMP=5.1;MACOSX_DEPLOYMENT_TARGET=10.9;CONDA_PY=36;CONDA_BOOST=1.61;CONDA_HDF5=1.8.17;CONDA_NPY=112;CONDA_HTSLIB=1.5;CONDA_PERL=5.22.0;CONDA_R=3.3.2;CONDA_NCURSES=5.9