docker-compose up ERROR

Hi, Gabe, I met an issue when I run the docker-compose up command
executor failed running [/bin/bash -o pipefail -c python -m pip install -r requirements.txt]: exit code: 1
ERROR: Service 'jupyter-notebook' failed to build : Build failed

I uninstalled all jupyter related packages using pip, but it doesn't solve the issue.

Hi there! Can you provide the full trace? What OS are you running?

My bad. I am using Mac OS Catalina.
(base) Ruijis-iMac-Pro:mortar ruijisun$ docker-compose up
Building jupyter-notebook
[+] Building 10.7s (7/15)
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 37B                                                                                0.0s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 34B                                                                                0.0s
 => [internal] load metadata for docker.io/jupyter/scipy-notebook:latest                                                                    1.0s
 => [ 1/11] FROM docker.io/jupyter/scipy-notebook@sha256:0d3c4df52908c00c47e0da99148648772c3c13e58c3125ec9c7db941abb76d85                   0.0s
 => [internal] load build context                                                                                0.0s
 => => transferring context: 1.03kB                                                                                0.0s
 => CACHED [ 2/11] COPY notebooks/requirements.txt .                                                                                0.0s
 => ERROR [ 3/11] RUN python -m pip install -r requirements.txt                                                                             9.5s
------
 > [ 3/11] RUN python -m pip install -r requirements.txt:
#7 0.532 WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
#7 0.725 Collecting pymortar>=2.0.3
#7 1.045   Downloading pymortar-2.0.4-py3-none-any.whl (10.0 kB)
#7 1.166 Collecting plotly
#7 1.173   Downloading plotly-5.1.0-py2.py3-none-any.whl (20.6 MB)
#7 2.053 Collecting python-snappy<0.7.0,>=0.6.0
#7 2.062   Downloading python_snappy-0.6.0-cp39-cp39-manylinux2010_x86_64.whl (54 kB)
#7 2.067 Requirement already satisfied: pandas<2.0,>=1.1 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.3->-r requirements.txt (line 1)) (1.3.0)
#7 2.183 Collecting pyarrow<4.0.0,>=3.0.0
#7 2.191   Downloading pyarrow-3.0.0-cp39-cp39-manylinux2014_x86_64.whl (20.7 MB)
#7 2.794 Collecting zstd<2.0.0,>=1.5.0
#7 2.803   Downloading zstd-<IP_ADDRESS>.tar.gz (528 kB)
#7 3.168 Requirement already satisfied: requests<3.0.0,>=2.25.0 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.3->-r requirements.txt (line 1)) (2.25.1)
#7 3.198 Collecting rdflib<6.0.0,>=5.0.0
#7 3.212   Downloading rdflib-5.0.0-py3-none-any.whl (231 kB)
#7 3.386 Collecting brickschema<0.5,>=0.4
#7 3.396   Downloading brickschema-0.4.1-py3-none-any.whl (372 kB)
#7 3.437 Collecting googleapis-common-protos<2.0.0,>=1.52.0
#7 3.448   Downloading googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
#7 3.507 Collecting Flask<2.0.0,>=1.1.2
#7 3.518   Downloading Flask-1.1.4-py2.py3-none-any.whl (94 kB)
#7 3.557 Collecting typer[all]<0.4.0,>=0.3.2
#7 3.567   Downloading typer-0.3.2-py3-none-any.whl (21 kB)
#7 3.600 Collecting xlrd<2.0.0,>=1.2.0
#7 3.611   Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
#7 3.618 Requirement already satisfied: PyYAML<6.0.0,>=5.3.1 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (5.4.1)
#7 3.726 Collecting pyshacl<0.15.0,>=0.14.2
#7 3.736   Downloading pyshacl-0.14.5-py3-none-any.whl (194 kB)
#7 3.818 Collecting owlrl<6.0,>=5.2
#7 3.827   Downloading owlrl-5.2.1-py3-none-any.whl (56 kB)
#7 3.852 Collecting tabulate<0.9.0,>=0.8.7
#7 3.860   Downloading tabulate-0.8.9-py3-none-any.whl (25 kB)
#7 3.975 Collecting pytest<7.0,>=6.2
#7 3.985   Downloading pytest-6.2.4-py3-none-any.whl (280 kB)
#7 4.077 Collecting click-spinner<0.2.0,>=0.1.10
#7 4.085   Downloading click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB)
#7 4.138 Collecting importlib-resources<4.0.0,>=3.3.0
#7 4.146   Downloading importlib_resources-3.3.1-py2.py3-none-any.whl (26 kB)
#7 4.150 Requirement already satisfied: sqlalchemy<2.0,>=1.3 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.4.20)
#7 4.192 Collecting Jinja2<3.0.0,>=2.11.2
#7 4.201   Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
#7 4.252 Collecting itsdangerous<2.0,>=0.24
#7 4.260   Downloading itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
#7 4.300 Collecting click<8.0,>=5.1
#7 4.307   Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
#7 4.387 Collecting Werkzeug<2.0,>=0.15
#7 4.397   Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
#7 4.416 Requirement already satisfied: protobuf>=3.12.0 in /opt/conda/lib/python3.9/site-packages (from googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (3.17.2)
#7 4.433 Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/lib/python3.9/site-packages (from Jinja2<3.0.0,>=2.11.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.0.1)
#7 4.515 Collecting rdflib-jsonld>=0.4.0
#7 4.522   Downloading rdflib-jsonld-0.5.0.tar.gz (55 kB)
#7 4.826 Requirement already satisfied: numpy>=1.17.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.21.0)
#7 4.827 Requirement already satisfied: python-dateutil>=2.7.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.8.1)
#7 4.828 Requirement already satisfied: pytz>=2017.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (2021.1)
#7 4.833 Requirement already satisfied: six>=1.9 in /opt/conda/lib/python3.9/site-packages (from protobuf>=3.12.0->googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.16.0)
#7 4.900 Collecting pluggy<1.0.0a1,>=0.12
#7 4.909   Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
#7 4.914 Requirement already satisfied: packaging in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (21.0)
#7 4.935 Collecting toml
#7 4.942   Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
#7 4.959 Collecting iniconfig
#7 4.966   Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
#7 4.969 Requirement already satisfied: attrs>=19.2.0 in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (21.2.0)
#7 5.008 Collecting py>=1.8.2
#7 5.015   Downloading py-1.10.0-py2.py3-none-any.whl (97 kB)
#7 5.086 Requirement already satisfied: pyparsing in /opt/conda/lib/python3.9/site-packages (from rdflib<6.0.0,>=5.0.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.4.7)
#7 5.108 Collecting isodate
#7 5.116   Downloading isodate-0.6.0-py2.py3-none-any.whl (45 kB)
#7 5.146 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.26.6)
#7 5.148 Requirement already satisfied: chardet<5,>=3.0.2 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (4.0.0)
#7 5.149 Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2021.5.30)
#7 5.150 Requirement already satisfied: idna<3,>=2.5 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.10)
#7 5.249 Requirement already satisfied: greenlet!=0.4.17 in /opt/conda/lib/python3.9/site-packages (from sqlalchemy<2.0,>=1.3->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.1.0)
#7 5.333 Collecting shellingham<2.0.0,>=1.3.0
#7 5.340   Downloading shellingham-1.4.0-py2.py3-none-any.whl (9.4 kB)
#7 5.379 Collecting colorama<0.5.0,>=0.4.3
#7 5.387   Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
#7 5.534 Collecting tenacity>=6.2.0
#7 5.548   Downloading tenacity-8.0.1-py3-none-any.whl (24 kB)
#7 5.606 Building wheels for collected packages: rdflib-jsonld, zstd
#7 5.607   Building wheel for rdflib-jsonld (setup.py): started
#7 6.599   Building wheel for rdflib-jsonld (setup.py): finished with status 'done'
#7 6.600   Created wheel for rdflib-jsonld: filename=rdflib_jsonld-0.5.0-py2.py3-none-any.whl size=15348 sha256=0062f4f154ec276dad48b8f8f726814780ee1476da5afbaec3eb1b1c57e9a1be
#7 6.600   Stored in directory: /tmp/pip-ephem-wheel-cache-puw8nme3/wheels/70/d3/7a/5421158e60102a4f13bcb5770cbeb95d45c97f3c4b92e7197f
#7 6.602   Building wheel for zstd (setup.py): started
#7 6.871   Building wheel for zstd (setup.py): finished with status 'error'
#7 6.872   ERROR: Command errored out with exit status 1:
#7 6.872    command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5otktiao/zstd_24cdddd84d0640f38920cc8d9ed331a4/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5otktiao/zstd_24cdddd84d0640f38920cc8d9ed331a4/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-mak4d381
#7 6.872        cwd: /tmp/pip-install-5otktiao/zstd_24cdddd84d0640f38920cc8d9ed331a4/
#7 6.872   Complete output (14 lines):
#7 6.872   running bdist_wheel
#7 6.872   running build
#7 6.872   running build_ext
#7 6.872   building 'zstd' extension
#7 6.872   creating build
#7 6.872   creating build/temp.linux-x86_64-3.9
#7 6.872   creating build/temp.linux-x86_64-3.9/src
#7 6.872   creating build/temp.linux-x86_64-3.9/zstd
#7 6.872   creating build/temp.linux-x86_64-3.9/zstd/lib
#7 6.872   creating build/temp.linux-x86_64-3.9/zstd/lib/common
#7 6.872   creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#7 6.872   creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#7 6.872   gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#7 6.872   error: command 'gcc' failed: No such file or directory
#7 6.872   ----------------------------------------
#7 6.872   ERROR: Failed building wheel for zstd
#7 6.872   Running setup.py clean for zstd
#7 7.126 Successfully built rdflib-jsonld
#7 7.126 Failed to build zstd
#7 7.932 Installing collected packages: isodate, rdflib, rdflib-jsonld, click, Werkzeug, typer, toml, shellingham, py, pluggy, owlrl, Jinja2, itsdangerous, iniconfig, colorama, xlrd, tabulate, pytest, pyshacl, importlib-resources, Flask, click-spinner, zstd, tenacity, python-snappy, pyarrow, googleapis-common-protos, brickschema, pymortar, plotly
#7 8.195   Attempting uninstall: click
#7 8.196     Found existing installation: click 8.0.1
#7 8.202     Uninstalling click-8.0.1:
#7 8.208       Successfully uninstalled click-8.0.1
#7 8.517   Attempting uninstall: Jinja2
#7 8.518     Found existing installation: Jinja2 3.0.1
#7 8.526     Uninstalling Jinja2-3.0.1:
#7 8.534       Successfully uninstalled Jinja2-3.0.1
#7 8.637   Attempting uninstall: xlrd
#7 8.638     Found existing installation: xlrd 2.0.1
#7 8.642     Uninstalling xlrd-2.0.1:
#7 8.650       Successfully uninstalled xlrd-2.0.1
#7 9.005     Running setup.py install for zstd: started
#7 9.273     Running setup.py install for zstd: finished with status 'error'
#7 9.273     ERROR: Command errored out with exit status 1:
#7 9.273      command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5otktiao/zstd_24cdddd84d0640f38920cc8d9ed331a4/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5otktiao/zstd_24cdddd84d0640f38920cc8d9ed331a4/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-31ob0hpc/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd
#7 9.273          cwd: /tmp/pip-install-5otktiao/zstd_24cdddd84d0640f38920cc8d9ed331a4/
#7 9.273     Complete output (14 lines):
#7 9.273     running install
#7 9.273     running build
#7 9.273     running build_ext
#7 9.273     building 'zstd' extension
#7 9.273     creating build
#7 9.273     creating build/temp.linux-x86_64-3.9
#7 9.273     creating build/temp.linux-x86_64-3.9/src
#7 9.273     creating build/temp.linux-x86_64-3.9/zstd
#7 9.273     creating build/temp.linux-x86_64-3.9/zstd/lib
#7 9.273     creating build/temp.linux-x86_64-3.9/zstd/lib/common
#7 9.273     creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#7 9.273     creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#7 9.273     gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#7 9.273     error: command 'gcc' failed: No such file or directory
#7 9.273     ----------------------------------------
#7 9.274 ERROR: Command errored out with exit status 1: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-5otktiao/zstd_24cdddd84d0640f38920cc8d9ed331a4/setup.py'"'"'; __file__='"'"'/tmp/pip-install-5otktiao/zstd_24cdddd84d0640f38920cc8d9ed331a4/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-31ob0hpc/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd Check the logs for full command output.
------
executor failed running [/bin/bash -o pipefail -c python -m pip install -r requirements.txt]: exit code: 1
ERROR: Service 'jupyter-notebook' failed to build : Build failed

I think the issue might be the mistaken inclusion of the zstd dependency; can you pull the latest code from this repo and try rebuilding? There's a new beta release of pymortar that should avoid the dependency

I fetched the latest code and ran docker-compose up. I got the same error. I also ran docker-compose up --build to rebuild the image, then similar error shown up. Below are the details of these two steps:
(base) ruijisun:~/Documents/GitHub/mortar 😂😂😂 $ docker-compose up
Building jupyter-notebook
[+] Building 11.6s (8/16)
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 438B                                                                                0.0s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 34B                                                                                0.0s
 => [internal] load metadata for docker.io/jupyter/scipy-notebook:latest                                                                     1.0s
 => [auth] jupyter/scipy-notebook:pull token for registry-1.docker.io                                                                        0.0s
 => [ 1/11] FROM docker.io/jupyter/scipy-notebook@sha256:0d3c4df52908c00c47e0da99148648772c3c13e58c3125ec9c7db941abb76d85                    0.0s
 => [internal] load build context                                                                                0.0s
 => => transferring context: 818B                                                                                0.0s
 => CACHED [ 2/11] COPY notebooks/requirements.txt .                                                                                0.0s
 => ERROR [ 3/11] RUN python -m pip install -r requirements.txt                                                                             10.5s
------
 > [ 3/11] RUN python -m pip install -r requirements.txt:
#8 0.622 WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
#8 0.791 Collecting pymortar>=2.0.3
#8 0.851   Downloading pymortar-2.0.4-py3-none-any.whl (10.0 kB)
#8 0.993 Collecting plotly
#8 1.002   Downloading plotly-5.1.0-py2.py3-none-any.whl (20.6 MB)
#8 1.771 Collecting googleapis-common-protos<2.0.0,>=1.52.0
#8 1.781   Downloading googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
#8 1.789 Requirement already satisfied: requests<3.0.0,>=2.25.0 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.3->-r requirements.txt (line 1)) (2.25.1)
#8 1.931 Collecting pyarrow<4.0.0,>=3.0.0
#8 1.939   Downloading pyarrow-3.0.0-cp39-cp39-manylinux2014_x86_64.whl (20.7 MB)
#8 2.555 Collecting zstd<2.0.0,>=1.5.0
#8 2.567   Downloading zstd-<IP_ADDRESS>.tar.gz (528 kB)
#8 2.987 Collecting rdflib<6.0.0,>=5.0.0
#8 2.998   Downloading rdflib-5.0.0-py3-none-any.whl (231 kB)
#8 3.047 Collecting python-snappy<0.7.0,>=0.6.0
#8 3.057   Downloading python_snappy-0.6.0-cp39-cp39-manylinux2010_x86_64.whl (54 kB)
#8 3.191 Collecting brickschema<0.5,>=0.4
#8 3.205   Downloading brickschema-0.4.1-py3-none-any.whl (372 kB)
#8 3.216 Requirement already satisfied: pandas<2.0,>=1.1 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.3->-r requirements.txt (line 1)) (1.3.0)
#8 3.277 Collecting Jinja2<3.0.0,>=2.11.2
#8 3.287   Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
#8 3.340 Collecting pyshacl<0.15.0,>=0.14.2
#8 3.355   Downloading pyshacl-0.14.5-py3-none-any.whl (194 kB)
#8 3.423 Collecting importlib-resources<4.0.0,>=3.3.0
#8 3.440   Downloading importlib_resources-3.3.1-py2.py3-none-any.whl (26 kB)
#8 3.479 Collecting xlrd<2.0.0,>=1.2.0
#8 3.490   Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
#8 3.513 Collecting owlrl<6.0,>=5.2
#8 3.524   Downloading owlrl-5.2.1-py3-none-any.whl (56 kB)
#8 3.559 Collecting typer[all]<0.4.0,>=0.3.2
#8 3.567   Downloading typer-0.3.2-py3-none-any.whl (21 kB)
#8 3.571 Requirement already satisfied: sqlalchemy<2.0,>=1.3 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.4.20)
#8 3.598 Collecting tabulate<0.9.0,>=0.8.7
#8 3.607   Downloading tabulate-0.8.9-py3-none-any.whl (25 kB)
#8 3.628 Collecting click-spinner<0.2.0,>=0.1.10
#8 3.637   Downloading click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB)
#8 3.640 Requirement already satisfied: PyYAML<6.0.0,>=5.3.1 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (5.4.1)
#8 3.679 Collecting Flask<2.0.0,>=1.1.2
#8 3.689   Downloading Flask-1.1.4-py2.py3-none-any.whl (94 kB)
#8 3.833 Collecting pytest<7.0,>=6.2
#8 3.843   Downloading pytest-6.2.4-py3-none-any.whl (280 kB)
#8 3.918 Collecting click<8.0,>=5.1
#8 3.927   Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
#8 4.012 Collecting Werkzeug<2.0,>=0.15
#8 4.023   Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
#8 4.067 Collecting itsdangerous<2.0,>=0.24
#8 4.076   Downloading itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
#8 4.086 Requirement already satisfied: protobuf>=3.12.0 in /opt/conda/lib/python3.9/site-packages (from googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (3.17.2)
#8 4.107 Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/lib/python3.9/site-packages (from Jinja2<3.0.0,>=2.11.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.0.1)
#8 4.138 Collecting rdflib-jsonld>=0.4.0
#8 4.147   Downloading rdflib-jsonld-0.5.0.tar.gz (55 kB)
#8 4.525 Requirement already satisfied: numpy>=1.17.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.21.0)
#8 4.526 Requirement already satisfied: python-dateutil>=2.7.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.8.1)
#8 4.528 Requirement already satisfied: pytz>=2017.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (2021.1)
#8 4.535 Requirement already satisfied: six>=1.9 in /opt/conda/lib/python3.9/site-packages (from protobuf>=3.12.0->googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.16.0)
#8 4.632 Collecting py>=1.8.2
#8 4.641   Downloading py-1.10.0-py2.py3-none-any.whl (97 kB)
#8 4.648 Requirement already satisfied: attrs>=19.2.0 in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (21.2.0)
#8 4.682 Collecting pluggy<1.0.0a1,>=0.12
#8 4.689   Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
#8 4.708 Collecting iniconfig
#8 4.718   Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
#8 4.742 Collecting toml
#8 4.750   Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
#8 4.752 Requirement already satisfied: packaging in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (21.0)
#8 4.835 Requirement already satisfied: pyparsing in /opt/conda/lib/python3.9/site-packages (from rdflib<6.0.0,>=5.0.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.4.7)
#8 4.858 Collecting isodate
#8 4.866   Downloading isodate-0.6.0-py2.py3-none-any.whl (45 kB)
#8 4.889 Requirement already satisfied: chardet<5,>=3.0.2 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (4.0.0)
#8 4.890 Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2021.5.30)
#8 4.892 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.26.6)
#8 4.893 Requirement already satisfied: idna<3,>=2.5 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.10)
#8 4.981 Requirement already satisfied: greenlet!=0.4.17 in /opt/conda/lib/python3.9/site-packages (from sqlalchemy<2.0,>=1.3->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.1.0)
#8 5.070 Collecting colorama<0.5.0,>=0.4.3
#8 5.078   Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
#8 5.119 Collecting shellingham<2.0.0,>=1.3.0
#8 5.130   Downloading shellingham-1.4.0-py2.py3-none-any.whl (9.4 kB)
#8 5.263 Collecting tenacity>=6.2.0
#8 5.271   Downloading tenacity-8.0.1-py3-none-any.whl (24 kB)
#8 5.336 Building wheels for collected packages: rdflib-jsonld, zstd
#8 5.337   Building wheel for rdflib-jsonld (setup.py): started
#8 6.529   Building wheel for rdflib-jsonld (setup.py): finished with status 'done'
#8 6.530   Created wheel for rdflib-jsonld: filename=rdflib_jsonld-0.5.0-py2.py3-none-any.whl size=15348 sha256=45a8e88ecefb2574ce727d41dfcd929d7b347c36deb642dada5540b1e44df5a8
#8 6.530   Stored in directory: /tmp/pip-ephem-wheel-cache-gj7y49ub/wheels/70/d3/7a/5421158e60102a4f13bcb5770cbeb95d45c97f3c4b92e7197f
#8 6.533   Building wheel for zstd (setup.py): started
#8 6.865   Building wheel for zstd (setup.py): finished with status 'error'
#8 6.865   ERROR: Command errored out with exit status 1:
#8 6.865    command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ny5ki8o6/zstd_9f8863164cdc4704835fc5071a042f98/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ny5ki8o6/zstd_9f8863164cdc4704835fc5071a042f98/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-qnx0oqd1
#8 6.865        cwd: /tmp/pip-install-ny5ki8o6/zstd_9f8863164cdc4704835fc5071a042f98/
#8 6.865   Complete output (14 lines):
#8 6.865   running bdist_wheel
#8 6.865   running build
#8 6.865   running build_ext
#8 6.865   building 'zstd' extension
#8 6.865   creating build
#8 6.865   creating build/temp.linux-x86_64-3.9
#8 6.865   creating build/temp.linux-x86_64-3.9/src
#8 6.865   creating build/temp.linux-x86_64-3.9/zstd
#8 6.865   creating build/temp.linux-x86_64-3.9/zstd/lib
#8 6.865   creating build/temp.linux-x86_64-3.9/zstd/lib/common
#8 6.865   creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#8 6.865   creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#8 6.865   gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#8 6.865   error: command 'gcc' failed: No such file or directory
#8 6.865   ----------------------------------------
#8 6.865   ERROR: Failed building wheel for zstd
#8 6.865   Running setup.py clean for zstd
#8 7.191 Successfully built rdflib-jsonld
#8 7.191 Failed to build zstd
#8 8.172 Installing collected packages: isodate, rdflib, rdflib-jsonld, click, Werkzeug, typer, toml, shellingham, py, pluggy, owlrl, Jinja2, itsdangerous, iniconfig, colorama, xlrd, tabulate, pytest, pyshacl, importlib-resources, Flask, click-spinner, zstd, tenacity, python-snappy, pyarrow, googleapis-common-protos, brickschema, pymortar, plotly
#8 8.403   Attempting uninstall: click
#8 8.404     Found existing installation: click 8.0.1
#8 8.411     Uninstalling click-8.0.1:
#8 8.420       Successfully uninstalled click-8.0.1
#8 8.784   Attempting uninstall: Jinja2
#8 8.785     Found existing installation: Jinja2 3.0.1
#8 8.796     Uninstalling Jinja2-3.0.1:
#8 8.808       Successfully uninstalled Jinja2-3.0.1
#8 8.935   Attempting uninstall: xlrd
#8 8.935     Found existing installation: xlrd 2.0.1
#8 8.940     Uninstalling xlrd-2.0.1:
#8 8.950       Successfully uninstalled xlrd-2.0.1
#8 9.431     Running setup.py install for zstd: started
#8 9.768     Running setup.py install for zstd: finished with status 'error'
#8 9.769     ERROR: Command errored out with exit status 1:
#8 9.769      command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ny5ki8o6/zstd_9f8863164cdc4704835fc5071a042f98/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ny5ki8o6/zstd_9f8863164cdc4704835fc5071a042f98/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-kf46v45s/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd
#8 9.769          cwd: /tmp/pip-install-ny5ki8o6/zstd_9f8863164cdc4704835fc5071a042f98/
#8 9.769     Complete output (14 lines):
#8 9.769     running install
#8 9.769     running build
#8 9.769     running build_ext
#8 9.769     building 'zstd' extension
#8 9.769     creating build
#8 9.769     creating build/temp.linux-x86_64-3.9
#8 9.769     creating build/temp.linux-x86_64-3.9/src
#8 9.769     creating build/temp.linux-x86_64-3.9/zstd
#8 9.769     creating build/temp.linux-x86_64-3.9/zstd/lib
#8 9.769     creating build/temp.linux-x86_64-3.9/zstd/lib/common
#8 9.769     creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#8 9.769     creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#8 9.769     gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#8 9.769     error: command 'gcc' failed: No such file or directory
#8 9.769     ----------------------------------------
#8 9.770 ERROR: Command errored out with exit status 1: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ny5ki8o6/zstd_9f8863164cdc4704835fc5071a042f98/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ny5ki8o6/zstd_9f8863164cdc4704835fc5071a042f98/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-kf46v45s/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd Check the logs for full command output.
------
executor failed running [/bin/bash -o pipefail -c python -m pip install -r requirements.txt]: exit code: 1
ERROR: Service 'jupyter-notebook' failed to build : Build failed

(base) ruijisun:~/Documents/GitHub/mortar 😂😂😂 $ docker-compose up --build
Building pg
[+] Building 1.6s (19/19) FINISHED
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 1.55kB                                                                                0.0s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 2B                                                                                0.0s
 => [internal] load metadata for docker.io/library/postgres:12                                                                               1.0s
 => [auth] library/postgres:pull token for registry-1.docker.io                                                                              0.0s
 => [internal] load build context                                                                                0.0s
 => => transferring context: 18.50kB                                                                                0.0s
 => [ 1/13] FROM docker.io/library/postgres:12@sha256:65e488c552d36b6482a7d5e044925962024fe816a7d797f7c0a153ac842b9aab                       0.0s
 => CACHED [ 2/13] RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selections                                        0.0s
 => CACHED [ 3/13] RUN apt-get update && apt-get install -y       postgresql-plpython3-12       python3-dev       python3-pip       softwar  0.0s
 => CACHED [ 4/13] RUN mkdir /data/                                                                                0.0s
 => CACHED [ 5/13] RUN cat /usr/share/postgresql/postgresql.conf.sample > /data/postgresql.conf                                              0.0s
 => CACHED [ 6/13] RUN sh -c "echo 'deb https://packagecloud.io/timescale/timescaledb/debian/ `lsb_release -c -s` main' > /etc/apt/sources.  0.0s
 => CACHED [ 7/13] RUN wget --quiet -O - https://packagecloud.io/timescale/timescaledb/gpgkey | apt-key add -                                0.0s
 => CACHED [ 8/13] RUN apt-get update && apt-get install -y timescaledb-2-postgresql-12                                                      0.0s
 => CACHED [ 9/13] RUN timescaledb-tune --quiet --yes --conf-path=/data/postgresql.conf                                                      0.0s
 => [10/13] ADD install_timescale.sh /docker-entrypoint-initdb.d/001_install.sh                                                              0.0s
 => [11/13] ADD setup.sql /docker-entrypoint-initdb.d/002_setup.sql                                                                          0.0s
 => [12/13] ADD backfill.sql /docker-entrypoint-initdb.d/003_backfill.sql                                                                    0.0s
 => [13/13] RUN pg_lsclusters                                                                                0.4s
 => exporting to image                                                                                0.1s
 => => exporting layers                                                                                0.0s
 => => writing image sha256:4435dac37a1cb8ac5fe3022fe1c306a14da9dd0d44ba3724f7591d895c964069                                                 0.0s
 => => naming to docker.io/mortar/pg                                                                                0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building mortar-server
[+] Building 11.8s (17/17) FINISHED
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 295B                                                                                0.0s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 34B                                                                                0.0s
 => [internal] load metadata for docker.io/library/ubuntu:19.10                                                                              1.0s
 => [internal] load metadata for docker.io/library/golang:latest                                                                             1.0s
 => [auth] library/ubuntu:pull token for registry-1.docker.io                                                                                0.0s
 => [auth] library/golang:pull token for registry-1.docker.io                                                                                0.0s
 => [builder 1/7] FROM docker.io/library/golang@sha256:773f15a2f2368be3ef88bfc29cc602bac5bd918f1f6cd14b24502d8760e04173                      0.0s
 => CACHED [stage-1 1/2] FROM docker.io/library/ubuntu:19.10@sha256:f332c4057e21ec71cc8b20b05328d476104a069bfa6882877e0920e8140edcf0         0.0s
 => [internal] load build context                                                                                0.0s
 => => transferring context: 79.78kB                                                                                0.0s
 => CACHED [builder 2/7] WORKDIR /app                                                                                0.0s
 => [builder 3/7] COPY main.go .                                                                                0.0s
 => [builder 4/7] COPY go.mod .                                                                                0.0s
 => [builder 5/7] COPY go.sum .                                                                                0.0s
 => [builder 6/7] COPY internal internal                                                                                0.0s
 => [builder 7/7] RUN go build -o mortar-server                                                                                10.4s
 => [stage-1 2/2] COPY --from=builder /app/mortar-server .                                                                                0.0s
 => exporting to image                                                                                0.1s
 => => exporting layers                                                                                0.1s
 => => writing image sha256:68563662aa2601cc975cf697f37aaefbd49782a012c225f4a2848e0677e744dd                                                 0.0s
 => => naming to docker.io/mortar/server2                                                                                0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building reasoner
[+] Building 193.7s (14/14) FINISHED
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 251B                                                                                0.0s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 34B                                                                                0.0s
 => [internal] load metadata for docker.io/library/debian:buster-slim                                                                        1.0s
 => [internal] load metadata for docker.io/library/rust:latest                                                                               1.0s
 => [auth] library/debian:pull token for registry-1.docker.io                                                                                0.0s
 => [auth] library/rust:pull token for registry-1.docker.io                                                                                0.0s
 => [stage-1 1/2] FROM docker.io/library/debian:buster-slim@sha256:a6bbc75c36b0d9d82ae4b64219b48c3027b7a101e9334b2ffb3bc71dbe94f552          0.0s
 => [internal] load build context                                                                                0.0s
 => => transferring context: 12.43kB                                                                                0.0s
 => [builder 1/4] FROM docker.io/library/rust@sha256:6ab4e79e374047846637c0266a9147bcac4a575b68bcbcaaad2f2e41175288a8                        0.0s
 => CACHED [builder 2/4] WORKDIR /app                                                                                0.0s
 => [builder 3/4] COPY reasoner .                                                                                0.0s
 => [builder 4/4] RUN cargo build --release                                                                                192.4s
 => CACHED [stage-1 2/2] COPY --from=builder /app/target/release/reasoner .                                                                  0.0s
 => exporting to image                                                                                0.0s
 => => exporting layers                                                                                0.0s
 => => writing image sha256:c9dd936edd0e95c952ee6edeb437f29049fdf35a711e21b230d392583bdedde0                                                 0.0s
 => => naming to docker.io/mortar/reasoner                                                                                0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building jupyter-notebook
[+] Building 12.1s (8/16)
 => [internal] load build definition from Dockerfile                                                                                0.0s
 => => transferring dockerfile: 438B                                                                                0.0s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 34B                                                                                0.0s
 => [internal] load metadata for docker.io/jupyter/scipy-notebook:latest                                                                     0.9s
 => [auth] jupyter/scipy-notebook:pull token for registry-1.docker.io                                                                        0.0s
 => [internal] load build context                                                                                0.1s
 => => transferring context: 2.62MB                                                                                0.1s
 => [ 1/11] FROM docker.io/jupyter/scipy-notebook@sha256:0d3c4df52908c00c47e0da99148648772c3c13e58c3125ec9c7db941abb76d85                    0.0s
 => CACHED [ 2/11] COPY notebooks/requirements.txt .                                                                                0.0s
 => ERROR [ 3/11] RUN python -m pip install -r requirements.txt                                                                             11.0s
------
 > [ 3/11] RUN python -m pip install -r requirements.txt:
#8 1.169 WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
#8 1.364 Collecting pymortar>=2.0.3
#8 1.413   Downloading pymortar-2.0.4-py3-none-any.whl (10.0 kB)
#8 1.562 Collecting plotly
#8 1.571   Downloading plotly-5.1.0-py2.py3-none-any.whl (20.6 MB)
#8 2.489 Collecting pyarrow<4.0.0,>=3.0.0
#8 2.497   Downloading pyarrow-3.0.0-cp39-cp39-manylinux2014_x86_64.whl (20.7 MB)
#8 3.163 Collecting brickschema<0.5,>=0.4
#8 3.174   Downloading brickschema-0.4.1-py3-none-any.whl (372 kB)
#8 3.208 Collecting zstd<2.0.0,>=1.5.0
#8 3.218   Downloading zstd-<IP_ADDRESS>.tar.gz (528 kB)
#8 3.736 Collecting python-snappy<0.7.0,>=0.6.0
#8 3.747   Downloading python_snappy-0.6.0-cp39-cp39-manylinux2010_x86_64.whl (54 kB)
#8 3.751 Requirement already satisfied: pandas<2.0,>=1.1 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.3->-r requirements.txt (line 1)) (1.3.0)
#8 3.753 Requirement already satisfied: requests<3.0.0,>=2.25.0 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.3->-r requirements.txt (line 1)) (2.25.1)
#8 3.784 Collecting googleapis-common-protos<2.0.0,>=1.52.0
#8 3.795   Downloading googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
#8 3.824 Collecting rdflib<6.0.0,>=5.0.0
#8 3.834   Downloading rdflib-5.0.0-py3-none-any.whl (231 kB)
#8 3.861 Requirement already satisfied: sqlalchemy<2.0,>=1.3 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.4.20)
#8 3.923 Collecting importlib-resources<4.0.0,>=3.3.0
#8 3.934   Downloading importlib_resources-3.3.1-py2.py3-none-any.whl (26 kB)
#8 3.963 Collecting tabulate<0.9.0,>=0.8.7
#8 3.970   Downloading tabulate-0.8.9-py3-none-any.whl (25 kB)
#8 4.021 Collecting pyshacl<0.15.0,>=0.14.2
#8 4.031   Downloading pyshacl-0.14.5-py3-none-any.whl (194 kB)
#8 4.081 Collecting Flask<2.0.0,>=1.1.2
#8 4.090   Downloading Flask-1.1.4-py2.py3-none-any.whl (94 kB)
#8 4.134 Collecting Jinja2<3.0.0,>=2.11.2
#8 4.144   Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
#8 4.168 Collecting owlrl<6.0,>=5.2
#8 4.177   Downloading owlrl-5.2.1-py3-none-any.whl (56 kB)
#8 4.213 Collecting typer[all]<0.4.0,>=0.3.2
#8 4.221   Downloading typer-0.3.2-py3-none-any.whl (21 kB)
#8 4.364 Collecting pytest<7.0,>=6.2
#8 4.375   Downloading pytest-6.2.4-py3-none-any.whl (280 kB)
#8 4.414 Collecting xlrd<2.0.0,>=1.2.0
#8 4.422   Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
#8 4.450 Collecting click-spinner<0.2.0,>=0.1.10
#8 4.459   Downloading click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB)
#8 4.461 Requirement already satisfied: PyYAML<6.0.0,>=5.3.1 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (5.4.1)
#8 4.534 Collecting click<8.0,>=5.1
#8 4.543   Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
#8 4.607 Collecting Werkzeug<2.0,>=0.15
#8 4.617   Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
#8 4.688 Collecting itsdangerous<2.0,>=0.24
#8 4.696   Downloading itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
#8 4.712 Requirement already satisfied: protobuf>=3.12.0 in /opt/conda/lib/python3.9/site-packages (from googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (3.17.2)
#8 4.734 Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/lib/python3.9/site-packages (from Jinja2<3.0.0,>=2.11.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.0.1)
#8 4.765 Collecting rdflib-jsonld>=0.4.0
#8 4.776   Downloading rdflib-jsonld-0.5.0.tar.gz (55 kB)
#8 5.170 Requirement already satisfied: numpy>=1.17.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.21.0)
#8 5.172 Requirement already satisfied: python-dateutil>=2.7.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.8.1)
#8 5.173 Requirement already satisfied: pytz>=2017.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.3->-r requirements.txt (line 1)) (2021.1)
#8 5.182 Requirement already satisfied: six>=1.9 in /opt/conda/lib/python3.9/site-packages (from protobuf>=3.12.0->googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.16.0)
#8 5.228 Requirement already satisfied: packaging in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (21.0)
#8 5.279 Collecting py>=1.8.2
#8 5.288   Downloading py-1.10.0-py2.py3-none-any.whl (97 kB)
#8 5.318 Collecting toml
#8 5.326   Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
#8 5.329 Requirement already satisfied: attrs>=19.2.0 in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (21.2.0)
#8 5.365 Collecting pluggy<1.0.0a1,>=0.12
#8 5.372   Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
#8 5.393 Collecting iniconfig
#8 5.401   Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
#8 5.515 Collecting isodate
#8 5.524   Downloading isodate-0.6.0-py2.py3-none-any.whl (45 kB)
#8 5.528 Requirement already satisfied: pyparsing in /opt/conda/lib/python3.9/site-packages (from rdflib<6.0.0,>=5.0.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.4.7)
#8 5.551 Requirement already satisfied: chardet<5,>=3.0.2 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (4.0.0)
#8 5.553 Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2021.5.30)
#8 5.555 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.26.6)
#8 5.557 Requirement already satisfied: idna<3,>=2.5 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.3->-r requirements.txt (line 1)) (2.10)
#8 5.645 Requirement already satisfied: greenlet!=0.4.17 in /opt/conda/lib/python3.9/site-packages (from sqlalchemy<2.0,>=1.3->brickschema<0.5,>=0.4->pymortar>=2.0.3->-r requirements.txt (line 1)) (1.1.0)
#8 5.735 Collecting shellingham<2.0.0,>=1.3.0
#8 5.744   Downloading shellingham-1.4.0-py2.py3-none-any.whl (9.4 kB)
#8 5.789 Collecting colorama<0.5.0,>=0.4.3
#8 5.799   Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
#8 5.925 Collecting tenacity>=6.2.0
#8 5.934   Downloading tenacity-8.0.1-py3-none-any.whl (24 kB)
#8 6.003 Building wheels for collected packages: rdflib-jsonld, zstd
#8 6.004   Building wheel for rdflib-jsonld (setup.py): started
#8 7.262   Building wheel for rdflib-jsonld (setup.py): finished with status 'done'
#8 7.263   Created wheel for rdflib-jsonld: filename=rdflib_jsonld-0.5.0-py2.py3-none-any.whl size=15348 sha256=e63e959c3b70ecedaf8b71d0bebbf9cea64b31f91ff438ad4ca7366d23ef0c11
#8 7.263   Stored in directory: /tmp/pip-ephem-wheel-cache-nhep7_89/wheels/70/d3/7a/5421158e60102a4f13bcb5770cbeb95d45c97f3c4b92e7197f
#8 7.266   Building wheel for zstd (setup.py): started
#8 7.607   Building wheel for zstd (setup.py): finished with status 'error'
#8 7.608   ERROR: Command errored out with exit status 1:
#8 7.608    command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-q6egm6w1/zstd_449220f2a0574f09aaa6a80f5d5c104f/setup.py'"'"'; __file__='"'"'/tmp/pip-install-q6egm6w1/zstd_449220f2a0574f09aaa6a80f5d5c104f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-rdv7kexv
#8 7.608        cwd: /tmp/pip-install-q6egm6w1/zstd_449220f2a0574f09aaa6a80f5d5c104f/
#8 7.608   Complete output (14 lines):
#8 7.608   running bdist_wheel
#8 7.608   running build
#8 7.608   running build_ext
#8 7.608   building 'zstd' extension
#8 7.608   creating build
#8 7.608   creating build/temp.linux-x86_64-3.9
#8 7.608   creating build/temp.linux-x86_64-3.9/src
#8 7.608   creating build/temp.linux-x86_64-3.9/zstd
#8 7.608   creating build/temp.linux-x86_64-3.9/zstd/lib
#8 7.608   creating build/temp.linux-x86_64-3.9/zstd/lib/common
#8 7.608   creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#8 7.608   creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#8 7.608   gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#8 7.608   error: command 'gcc' failed: No such file or directory
#8 7.608   ----------------------------------------
#8 7.608   ERROR: Failed building wheel for zstd
#8 7.609   Running setup.py clean for zstd
#8 7.929 Successfully built rdflib-jsonld
#8 7.929 Failed to build zstd
#8 8.987 Installing collected packages: isodate, rdflib, rdflib-jsonld, click, Werkzeug, typer, toml, shellingham, py, pluggy, owlrl, Jinja2, itsdangerous, iniconfig, colorama, xlrd, tabulate, pytest, pyshacl, importlib-resources, Flask, click-spinner, zstd, tenacity, python-snappy, pyarrow, googleapis-common-protos, brickschema, pymortar, plotly
#8 9.226   Attempting uninstall: click
#8 9.227     Found existing installation: click 8.0.1
#8 9.236     Uninstalling click-8.0.1:
#8 9.258       Successfully uninstalled click-8.0.1
#8 9.634   Attempting uninstall: Jinja2
#8 9.635     Found existing installation: Jinja2 3.0.1
#8 9.647     Uninstalling Jinja2-3.0.1:
#8 9.678       Successfully uninstalled Jinja2-3.0.1
#8 9.809   Attempting uninstall: xlrd
#8 9.809     Found existing installation: xlrd 2.0.1
#8 9.816     Uninstalling xlrd-2.0.1:
#8 9.840       Successfully uninstalled xlrd-2.0.1
#8 10.33     Running setup.py install for zstd: started
#8 10.67     Running setup.py install for zstd: finished with status 'error'
#8 10.67     ERROR: Command errored out with exit status 1:
#8 10.67      command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-q6egm6w1/zstd_449220f2a0574f09aaa6a80f5d5c104f/setup.py'"'"'; __file__='"'"'/tmp/pip-install-q6egm6w1/zstd_449220f2a0574f09aaa6a80f5d5c104f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-8o8b1c85/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd
#8 10.67          cwd: /tmp/pip-install-q6egm6w1/zstd_449220f2a0574f09aaa6a80f5d5c104f/
#8 10.67     Complete output (14 lines):
#8 10.67     running install
#8 10.67     running build
#8 10.67     running build_ext
#8 10.67     building 'zstd' extension
#8 10.67     creating build
#8 10.67     creating build/temp.linux-x86_64-3.9
#8 10.67     creating build/temp.linux-x86_64-3.9/src
#8 10.67     creating build/temp.linux-x86_64-3.9/zstd
#8 10.67     creating build/temp.linux-x86_64-3.9/zstd/lib
#8 10.67     creating build/temp.linux-x86_64-3.9/zstd/lib/common
#8 10.67     creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#8 10.67     creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#8 10.67     gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#8 10.67     error: command 'gcc' failed: No such file or directory
#8 10.67     ----------------------------------------
#8 10.67 ERROR: Command errored out with exit status 1: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-q6egm6w1/zstd_449220f2a0574f09aaa6a80f5d5c104f/setup.py'"'"'; __file__='"'"'/tmp/pip-install-q6egm6w1/zstd_449220f2a0574f09aaa6a80f5d5c104f/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-8o8b1c85/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd Check the logs for full command output.
------
executor failed running [/bin/bash -o pipefail -c python -m pip install -r requirements.txt]: exit code: 1
ERROR: Service 'jupyter-notebook' failed to build : Build failed

What are the contents of notebooks/requirements.txt?

You may need to explicitly kill the docker image cache

I notice that the cache has been disabled, and the directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. Maybe something wrong here?

The contents of notebooks/requirements.txt :
pymortar>=2.0.4
plotly

The details of docker-compose up and docker-compose up --build:

[(base) ruijisun:~/Documents/GitHub/mortar 😂😂😂 $ docker-compose up
Building jupyter-notebook
[+] Building 51.5s (8/16)
 => [internal] load build definition from Dockerfile                                                 0.0s
 => => transferring dockerfile: 37B                                                                  0.0s
 => [internal] load .dockerignore                                                                    0.0s
 => => transferring context: 34B                                                                     0.0s
 => [internal] load metadata for docker.io/jupyter/scipy-notebook:latest                             1.6s
 => [auth] jupyter/scipy-notebook:pull token for registry-1.docker.io                                0.0s
 => [ 1/11] FROM docker.io/jupyter/scipy-notebook@sha256:0d3c4df52908c00c47e0da99148648772c3c13e58c  0.0s
 => [internal] load build context                                                                    0.0s
 => => transferring context: 818B                                                                    0.0s
 => CACHED [ 2/11] COPY notebooks/requirements.txt .                                                 0.0s
 => ERROR [ 3/11] RUN python -m pip install -r requirements.txt                                     49.7s
------
 > [ 3/11] RUN python -m pip install -r requirements.txt:
#8 0.687 WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
#8 1.248 Collecting pymortar>=2.0.4
#8 1.500   Downloading pymortar-2.0.4-py3-none-any.whl (10.0 kB)
#8 1.770 Collecting plotly
#8 1.849   Downloading plotly-5.1.0-py2.py3-none-any.whl (20.6 MB)
#8 15.11 Requirement already satisfied: pandas<2.0,>=1.1 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.4->-r requirements.txt (line 1)) (1.3.0)
#8 15.35 Collecting zstd<2.0.0,>=1.5.0
#8 15.43   Downloading zstd-<IP_ADDRESS>.tar.gz (528 kB)
#8 16.46 Collecting googleapis-common-protos<2.0.0,>=1.52.0
#8 16.53   Downloading googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
#8 16.97 Collecting python-snappy<0.7.0,>=0.6.0
#8 17.05   Downloading python_snappy-0.6.0-cp39-cp39-manylinux2010_x86_64.whl (54 kB)
#8 17.14 Requirement already satisfied: requests<3.0.0,>=2.25.0 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.4->-r requirements.txt (line 1)) (2.25.1)
#8 17.43 Collecting brickschema<0.5,>=0.4
#8 17.50   Downloading brickschema-0.4.1-py3-none-any.whl (372 kB)
#8 18.04 Collecting rdflib<6.0.0,>=5.0.0
#8 18.11   Downloading rdflib-5.0.0-py3-none-any.whl (231 kB)
#8 18.66 Collecting pyarrow<4.0.0,>=3.0.0
#8 18.73   Downloading pyarrow-3.0.0-cp39-cp39-manylinux2014_x86_64.whl (20.7 MB)
#8 35.22 Collecting Jinja2<3.0.0,>=2.11.2
#8 35.29   Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
#8 35.57 Collecting typer[all]<0.4.0,>=0.3.2
#8 35.65   Downloading typer-0.3.2-py3-none-any.whl (21 kB)
#8 35.94 Collecting pytest<7.0,>=6.2
#8 36.02   Downloading pytest-6.2.4-py3-none-any.whl (280 kB)
#8 36.64 Collecting owlrl<6.0,>=5.2
#8 36.73   Downloading owlrl-5.2.1-py3-none-any.whl (56 kB)
#8 36.96 Collecting click-spinner<0.2.0,>=0.1.10
#8 37.03   Downloading click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB)
#8 37.11 Collecting tabulate<0.9.0,>=0.8.7
#8 37.18   Downloading tabulate-0.8.9-py3-none-any.whl (25 kB)
#8 37.20 Requirement already satisfied: sqlalchemy<2.0,>=1.3 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.4.20)
#8 37.32 Collecting Flask<2.0.0,>=1.1.2
#8 37.39   Downloading Flask-1.1.4-py2.py3-none-any.whl (94 kB)
#8 37.62 Collecting xlrd<2.0.0,>=1.2.0
#8 37.70   Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
#8 38.11 Collecting pyshacl<0.15.0,>=0.14.2
#8 38.16   Downloading pyshacl-0.14.5-py3-none-any.whl (194 kB)
#8 38.52 Requirement already satisfied: PyYAML<6.0.0,>=5.3.1 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (5.4.1)
#8 38.77 Collecting importlib-resources<4.0.0,>=3.3.0
#8 38.83   Downloading importlib_resources-3.3.1-py2.py3-none-any.whl (26 kB)
#8 39.19 Collecting Werkzeug<2.0,>=0.15
#8 39.29   Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
#8 40.06 Collecting click<8.0,>=5.1
#8 40.16   Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
#8 40.33 Collecting itsdangerous<2.0,>=0.24
#8 40.41   Downloading itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
#8 40.43 Requirement already satisfied: protobuf>=3.12.0 in /opt/conda/lib/python3.9/site-packages (from googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (3.17.2)
#8 40.45 Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/lib/python3.9/site-packages (from Jinja2<3.0.0,>=2.11.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.0.1)
#8 40.59 Collecting rdflib-jsonld>=0.4.0
#8 40.67   Downloading rdflib-jsonld-0.5.0.tar.gz (55 kB)
#8 41.17 Requirement already satisfied: numpy>=1.17.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.21.0)
#8 41.17 Requirement already satisfied: python-dateutil>=2.7.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.8.1)
#8 41.18 Requirement already satisfied: pytz>=2017.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (2021.1)
#8 41.18 Requirement already satisfied: six>=1.9 in /opt/conda/lib/python3.9/site-packages (from protobuf>=3.12.0->googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.16.0)
#8 41.43 Collecting py>=1.8.2
#8 41.49   Downloading py-1.10.0-py2.py3-none-any.whl (97 kB)
#8 41.87 Collecting iniconfig
#8 41.97   Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
#8 42.34 Collecting pluggy<1.0.0a1,>=0.12
#8 42.41   Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
#8 42.59 Collecting toml
#8 42.68   Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
#8 42.69 Requirement already satisfied: attrs>=19.2.0 in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (21.2.0)
#8 42.70 Requirement already satisfied: packaging in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (21.0)
#8 42.78 Requirement already satisfied: pyparsing in /opt/conda/lib/python3.9/site-packages (from rdflib<6.0.0,>=5.0.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.4.7)
#8 42.89 Collecting isodate
#8 42.98   Downloading isodate-0.6.0-py2.py3-none-any.whl (45 kB)
#8 43.21 Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2021.5.30)
#8 43.21 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.26.6)
#8 43.21 Requirement already satisfied: idna<3,>=2.5 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.10)
#8 43.21 Requirement already satisfied: chardet<5,>=3.0.2 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (4.0.0)
#8 43.30 Requirement already satisfied: greenlet!=0.4.17 in /opt/conda/lib/python3.9/site-packages (from sqlalchemy<2.0,>=1.3->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.1.0)
#8 43.53 Collecting shellingham<2.0.0,>=1.3.0
#8 43.66   Downloading shellingham-1.4.0-py2.py3-none-any.whl (9.4 kB)
#8 43.83 Collecting colorama<0.5.0,>=0.4.3
#8 43.91   Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
#8 44.20 Collecting tenacity>=6.2.0
#8 44.28   Downloading tenacity-8.0.1-py3-none-any.whl (24 kB)
#8 44.43 Building wheels for collected packages: rdflib-jsonld, zstd
#8 44.43   Building wheel for rdflib-jsonld (setup.py): started
#8 45.66   Building wheel for rdflib-jsonld (setup.py): finished with status 'done'
#8 45.66   Created wheel for rdflib-jsonld: filename=rdflib_jsonld-0.5.0-py2.py3-none-any.whl size=15348 sha256=3cb0a80e3a0f810c6f8a9a8b0877a478c0efbb881afe18fc63434c691bc151c3
#8 45.66   Stored in directory: /tmp/pip-ephem-wheel-cache-r01mqojb/wheels/70/d3/7a/5421158e60102a4f13bcb5770cbeb95d45c97f3c4b92e7197f
#8 45.66   Building wheel for zstd (setup.py): started
#8 46.01   Building wheel for zstd (setup.py): finished with status 'error'
#8 46.01   ERROR: Command errored out with exit status 1:
#8 46.01    command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"'; __file__='"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-t80za9tt
#8 46.01        cwd: /tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/
#8 46.01   Complete output (14 lines):
#8 46.01   running bdist_wheel
#8 46.01   running build
#8 46.01   running build_ext
#8 46.01   building 'zstd' extension
#8 46.01   creating build
#8 46.01   creating build/temp.linux-x86_64-3.9
#8 46.01   creating build/temp.linux-x86_64-3.9/src
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd/lib
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd/lib/common
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#8 46.01   gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#8 46.01   error: command 'gcc' failed: No such file or directory
#8 46.01   ----------------------------------------
#8 46.01   ERROR: Failed building wheel for zstd
#8 46.01   Running setup.py clean for zstd
#8 46.31 Successfully built rdflib-jsonld
#8 46.31 Failed to build zstd
#8 47.33 Installing collected packages: isodate, rdflib, rdflib-jsonld, click, Werkzeug, typer, toml, shellingham, py, pluggy, owlrl, Jinja2, itsdangerous, iniconfig, colorama, xlrd, tabulate, pytest, pyshacl, importlib-resources, Flask, click-spinner, zstd, tenacity, python-snappy, pyarrow, googleapis-common-protos, brickschema, pymortar, plotly
#8 47.58   Attempting uninstall: click
#8 47.58     Found existing installation: click 8.0.1
#8 47.59     Uninstalling click-8.0.1:
#8 47.60       Successfully uninstalled click-8.0.1
#8 48.00   Attempting uninstall: Jinja2
#8 48.00     Found existing installation: Jinja2 3.0.1
#8 48.01     Uninstalling Jinja2-3.0.1:
#8 48.03       Successfully uninstalled Jinja2-3.0.1
#8 48.17   Attempting uninstall: xlrd
#8 48.17     Found existing installation: xlrd 2.0.1
#8 48.17     Uninstalling xlrd-2.0.1:
#8 48.18       Successfully uninstalled xlrd-2.0.1
#8 48.70     Running setup.py install for zstd: started
#8 49.06     Running setup.py install for zstd: finished with status 'error'
#8 49.06     ERROR: Command errored out with exit status 1:
#8 49.06      command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"'; __file__='"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vk1dr5ed/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd
#8 49.06          cwd: /tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/
#8 49.06     Complete output (14 lines):
#8 49.06     running install
#8 49.06     running build
#8 49.06     running build_ext
#8 49.06     building 'zstd' extension
#8 49.06     creating build
#8 49.06     creating build/temp.linux-x86_64-3.9
#8 49.06     creating build/temp.linux-x86_64-3.9/src
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd/lib
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd/lib/common
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#8 49.06     gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#8 49.06     error: command 'gcc' failed: No such file or directory
#8 49.06     ----------------------------------------
#8 49.06 ERROR: Command errored out with exit status 1: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"'; __file__='"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-vk1dr5ed/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd Check the logs for full command output.
------
executor failed running [/bin/bash -o pipefail -c python -m pip install -r requirements.txt]: exit code: 1
ERROR: Service 'jupyter-notebook' failed to build : Build failed
(base) ruijisun:~/Documents/GitHub/mortar 😂😂😂 $ docker-compose up --build
Building pg
[+] Building 1.7s (19/19) FINISHED
 => [internal] load build definition from Dockerfile                                                 0.0s
 => => transferring dockerfile: 37B                                                                  0.0s
 => [internal] load .dockerignore                                                                    0.0s
 => => transferring context: 2B                                                                      0.0s
 => [internal] load metadata for docker.io/library/postgres:12                                       1.5s
 => [auth] library/postgres:pull token for registry-1.docker.io                                      0.0s
 => [internal] load build context                                                                    0.0s
 => => transferring context: 103B                                                                    0.0s
 => [ 1/13] FROM docker.io/library/postgres:12@sha256:65e488c552d36b6482a7d5e044925962024fe816a7d79  0.0s
 => CACHED [ 2/13] RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selectio  0.0s
 => CACHED [ 3/13] RUN apt-get update && apt-get install -y       postgresql-plpython3-12       pyt  0.0s
 => CACHED [ 4/13] RUN mkdir /data/                                                                  0.0s
 => CACHED [ 5/13] RUN cat /usr/share/postgresql/postgresql.conf.sample > /data/postgresql.conf      0.0s
 => CACHED [ 6/13] RUN sh -c "echo 'deb https://packagecloud.io/timescale/timescaledb/debian/ `lsb_  0.0s
 => CACHED [ 7/13] RUN wget --quiet -O - https://packagecloud.io/timescale/timescaledb/gpgkey | apt  0.0s
 => CACHED [ 8/13] RUN apt-get update && apt-get install -y timescaledb-2-postgresql-12              0.0s
 => CACHED [ 9/13] RUN timescaledb-tune --quiet --yes --conf-path=/data/postgresql.conf              0.0s
 => CACHED [10/13] ADD install_timescale.sh /docker-entrypoint-initdb.d/001_install.sh               0.0s
 => CACHED [11/13] ADD setup.sql /docker-entrypoint-initdb.d/002_setup.sql                           0.0s
 => CACHED [12/13] ADD backfill.sql /docker-entrypoint-initdb.d/003_backfill.sql                     0.0s
 => CACHED [13/13] RUN pg_lsclusters                                                                 0.0s
 => exporting to image                                                                               0.0s
 => => exporting layers                                                                              0.0s
 => => writing image sha256:4435dac37a1cb8ac5fe3022fe1c306a14da9dd0d44ba3724f7591d895c964069         0.0s
 => => naming to docker.io/mortar/pg                                                                 0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building mortar-server
[+] Building 1.8s (17/17) FINISHED
 => [internal] load build definition from Dockerfile                                                 0.0s
 => => transferring dockerfile: 295B                                                                 0.0s
 => [internal] load .dockerignore                                                                    0.0s
 => => transferring context: 34B                                                                     0.0s
 => [internal] load metadata for docker.io/library/ubuntu:19.10                                      1.6s
 => [internal] load metadata for docker.io/library/golang:latest                                     1.6s
 => [auth] library/ubuntu:pull token for registry-1.docker.io                                        0.0s
 => [auth] library/golang:pull token for registry-1.docker.io                                        0.0s
 => [builder 1/7] FROM docker.io/library/golang@sha256:773f15a2f2368be3ef88bfc29cc602bac5bd918f1f6c  0.0s
 => [stage-1 1/2] FROM docker.io/library/ubuntu:19.10@sha256:f332c4057e21ec71cc8b20b05328d476104a06  0.0s
 => [internal] load build context                                                                    0.0s
 => => transferring context: 79.78kB                                                                 0.0s
 => CACHED [builder 2/7] WORKDIR /app                                                                0.0s
 => CACHED [builder 3/7] COPY main.go .                                                              0.0s
 => CACHED [builder 4/7] COPY go.mod .                                                               0.0s
 => CACHED [builder 5/7] COPY go.sum .                                                               0.0s
 => CACHED [builder 6/7] COPY internal internal                                                      0.0s
 => CACHED [builder 7/7] RUN go build -o mortar-server                                               0.0s
 => CACHED [stage-1 2/2] COPY --from=builder /app/mortar-server .                                    0.0s
 => exporting to image                                                                               0.0s
 => => exporting layers                                                                              0.0s
 => => writing image sha256:68563662aa2601cc975cf697f37aaefbd49782a012c225f4a2848e0677e744dd         0.0s
 => => naming to docker.io/mortar/server2                                                            0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building reasoner
[+] Building 1.9s (14/14) FINISHED
 => [internal] load build definition from Dockerfile                                                 0.0s
 => => transferring dockerfile: 251B                                                                 0.0s
 => [internal] load .dockerignore                                                                    0.0s
 => => transferring context: 34B                                                                     0.0s
 => [internal] load metadata for docker.io/library/debian:buster-slim                                1.7s
 => [internal] load metadata for docker.io/library/rust:latest                                       1.7s
 => [auth] library/debian:pull token for registry-1.docker.io                                        0.0s
 => [auth] library/rust:pull token for registry-1.docker.io                                          0.0s
 => [builder 1/4] FROM docker.io/library/rust@sha256:6ab4e79e374047846637c0266a9147bcac4a575b68bcbc  0.0s
 => [internal] load build context                                                                    0.0s
 => => transferring context: 12.43kB                                                                 0.0s
 => [stage-1 1/2] FROM docker.io/library/debian:buster-slim@sha256:a6bbc75c36b0d9d82ae4b64219b48c30  0.0s
 => CACHED [builder 2/4] WORKDIR /app                                                                0.0s
 => CACHED [builder 3/4] COPY reasoner .                                                             0.0s
 => CACHED [builder 4/4] RUN cargo build --release                                                   0.0s
 => CACHED [stage-1 2/2] COPY --from=builder /app/target/release/reasoner .                          0.0s
 => exporting to image                                                                               0.0s
 => => exporting layers                                                                              0.0s
 => => writing image sha256:c9dd936edd0e95c952ee6edeb437f29049fdf35a711e21b230d392583bdedde0         0.0s
 => => naming to docker.io/mortar/reasoner                                                           0.0s

Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building jupyter-notebook
[+] Building 113.8s (7/15)
 => [internal] load build definition from Dockerfile                                                 0.0s
 => => transferring dockerfile: 438B                                                                 0.0s
 => [internal] load .dockerignore                                                                    0.0s
 => => transferring context: 34B                                                                     0.0s
 => [internal] load metadata for docker.io/jupyter/scipy-notebook:latest                             0.9s
 => [internal] load build context                                                                    0.1s
 => => transferring context: 2.62MB                                                                  0.1s
 => [ 1/11] FROM docker.io/jupyter/scipy-notebook@sha256:0d3c4df52908c00c47e0da99148648772c3c13e58c  0.0s
 => CACHED [ 2/11] COPY notebooks/requirements.txt .                                                 0.0s
 => ERROR [ 3/11] RUN python -m pip install -r requirements.txt                                    112.7s
------
 > [ 3/11] RUN python -m pip install -r requirements.txt:
#7 0.680 WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
#7 1.236 Collecting pymortar>=2.0.4
#7 1.545   Downloading pymortar-2.0.4-py3-none-any.whl (10.0 kB)
#7 2.084 Collecting plotly
#7 2.165   Downloading plotly-5.1.0-py2.py3-none-any.whl (20.6 MB)
#7 41.40 Collecting python-snappy<0.7.0,>=0.6.0
#7 41.47   Downloading python_snappy-0.6.0-cp39-cp39-manylinux2010_x86_64.whl (54 kB)
#7 41.76 Collecting googleapis-common-protos<2.0.0,>=1.52.0
#7 41.82   Downloading googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
#7 43.29 Collecting pyarrow<4.0.0,>=3.0.0
#7 43.37   Downloading pyarrow-3.0.0-cp39-cp39-manylinux2014_x86_64.whl (20.7 MB)
#7 94.09 Collecting brickschema<0.5,>=0.4
#7 94.18   Downloading brickschema-0.4.1-py3-none-any.whl (372 kB)
#7 95.16 Collecting rdflib<6.0.0,>=5.0.0
#7 95.25   Downloading rdflib-5.0.0-py3-none-any.whl (231 kB)
#7 95.66 Requirement already satisfied: pandas<2.0,>=1.1 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.4->-r requirements.txt (line 1)) (1.3.0)
#7 95.74 Collecting zstd<2.0.0,>=1.5.0
#7 95.82   Downloading zstd-<IP_ADDRESS>.tar.gz (528 kB)
#7 97.02 Requirement already satisfied: requests<3.0.0,>=2.25.0 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.4->-r requirements.txt (line 1)) (2.25.1)
#7 97.33 Collecting importlib-resources<4.0.0,>=3.3.0
#7 97.42   Downloading importlib_resources-3.3.1-py2.py3-none-any.whl (26 kB)
#7 97.76 Collecting pytest<7.0,>=6.2
#7 97.83   Downloading pytest-6.2.4-py3-none-any.whl (280 kB)
#7 98.53 Collecting Flask<2.0.0,>=1.1.2
#7 98.65   Downloading Flask-1.1.4-py2.py3-none-any.whl (94 kB)
#7 98.99 Collecting Jinja2<3.0.0,>=2.11.2
#7 99.06   Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
#7 99.39 Collecting tabulate<0.9.0,>=0.8.7
#7 99.47   Downloading tabulate-0.8.9-py3-none-any.whl (25 kB)
#7 99.53 Requirement already satisfied: PyYAML<6.0.0,>=5.3.1 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (5.4.1)
#7 99.60 Collecting owlrl<6.0,>=5.2
#7 99.68   Downloading owlrl-5.2.1-py3-none-any.whl (56 kB)
#7 99.91 Collecting xlrd<2.0.0,>=1.2.0
#7 99.99   Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
#7 100.5 Collecting pyshacl<0.15.0,>=0.14.2
#7 100.6   Downloading pyshacl-0.14.5-py3-none-any.whl (194 kB)
#7 101.3 Collecting click-spinner<0.2.0,>=0.1.10
#7 101.4   Downloading click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB)
#7 101.5 Collecting typer[all]<0.4.0,>=0.3.2
#7 101.6   Downloading typer-0.3.2-py3-none-any.whl (21 kB)
#7 101.6 Requirement already satisfied: sqlalchemy<2.0,>=1.3 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.4.20)
#7 101.8 Collecting Werkzeug<2.0,>=0.15
#7 101.9   Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
#7 102.6 Collecting itsdangerous<2.0,>=0.24
#7 102.7   Downloading itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
#7 103.0 Collecting click<8.0,>=5.1
#7 103.1   Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
#7 103.4 Requirement already satisfied: protobuf>=3.12.0 in /opt/conda/lib/python3.9/site-packages (from googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (3.17.2)
#7 103.5 Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/lib/python3.9/site-packages (from Jinja2<3.0.0,>=2.11.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.0.1)
#7 103.5 Collecting rdflib-jsonld>=0.4.0
#7 103.6   Downloading rdflib-jsonld-0.5.0.tar.gz (55 kB)
#7 104.2 Requirement already satisfied: numpy>=1.17.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.21.0)
#7 104.2 Requirement already satisfied: python-dateutil>=2.7.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.8.1)
#7 104.2 Requirement already satisfied: pytz>=2017.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (2021.1)
#7 104.2 Requirement already satisfied: six>=1.9 in /opt/conda/lib/python3.9/site-packages (from protobuf>=3.12.0->googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.16.0)
#7 104.4 Collecting toml
#7 104.5   Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
#7 104.6 Collecting iniconfig
#7 104.7   Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
#7 104.8 Collecting pluggy<1.0.0a1,>=0.12
#7 104.9   Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
#7 104.9 Requirement already satisfied: packaging in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (21.0)
#7 105.1 Collecting py>=1.8.2
#7 105.2   Downloading py-1.10.0-py2.py3-none-any.whl (97 kB)
#7 105.6 Requirement already satisfied: attrs>=19.2.0 in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (21.2.0)
#7 105.8 Collecting isodate
#7 105.9   Downloading isodate-0.6.0-py2.py3-none-any.whl (45 kB)
#7 106.0 Requirement already satisfied: pyparsing in /opt/conda/lib/python3.9/site-packages (from rdflib<6.0.0,>=5.0.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.4.7)
#7 106.0 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.26.6)
#7 106.0 Requirement already satisfied: chardet<5,>=3.0.2 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (4.0.0)
#7 106.0 Requirement already satisfied: idna<3,>=2.5 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.10)
#7 106.0 Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2021.5.30)
#7 106.1 Requirement already satisfied: greenlet!=0.4.17 in /opt/conda/lib/python3.9/site-packages (from sqlalchemy<2.0,>=1.3->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.1.0)
#7 106.3 Collecting colorama<0.5.0,>=0.4.3
#7 106.4   Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
#7 106.6 Collecting shellingham<2.0.0,>=1.3.0
#7 106.7   Downloading shellingham-1.4.0-py2.py3-none-any.whl (9.4 kB)
#7 107.0 Collecting tenacity>=6.2.0
#7 107.1   Downloading tenacity-8.0.1-py3-none-any.whl (24 kB)
#7 107.3 Building wheels for collected packages: rdflib-jsonld, zstd
#7 107.3   Building wheel for rdflib-jsonld (setup.py): started
#7 108.6   Building wheel for rdflib-jsonld (setup.py): finished with status 'done'
#7 108.6   Created wheel for rdflib-jsonld: filename=rdflib_jsonld-0.5.0-py2.py3-none-any.whl size=15348 sha256=51660f53fb320b9a65a0f12a69512a5c89c7918c5f0e68d065d7a54e0889f1c6
#7 108.6   Stored in directory: /tmp/pip-ephem-wheel-cache-91vnxz74/wheels/70/d3/7a/5421158e60102a4f13bcb5770cbeb95d45c97f3c4b92e7197f
#7 108.6   Building wheel for zstd (setup.py): started
#7 108.9   Building wheel for zstd (setup.py): finished with status 'error'
#7 108.9   ERROR: Command errored out with exit status 1:
#7 108.9    command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-xtk2zg0l/zstd_5c6751cb2a024d6583b7da7913bf3bce/setup.py'"'"'; __file__='"'"'/tmp/pip-install-xtk2zg0l/zstd_5c6751cb2a024d6583b7da7913bf3bce/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-v1c_lb66
#7 108.9        cwd: /tmp/pip-install-xtk2zg0l/zstd_5c6751cb2a024d6583b7da7913bf3bce/
#7 108.9   Complete output (14 lines):
#7 108.9   running bdist_wheel
#7 108.9   running build
#7 108.9   running build_ext
#7 108.9   building 'zstd' extension
#7 108.9   creating build
#7 108.9   creating build/temp.linux-x86_64-3.9
#7 108.9   creating build/temp.linux-x86_64-3.9/src
#7 108.9   creating build/temp.linux-x86_64-3.9/zstd
#7 108.9   creating build/temp.linux-x86_64-3.9/zstd/lib
#7 108.9   creating build/temp.linux-x86_64-3.9/zstd/lib/common
#7 108.9   creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#7 108.9   creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#7 108.9   gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#7 108.9   error: command 'gcc' failed: No such file or directory
#7 108.9   ----------------------------------------
#7 108.9   ERROR: Failed building wheel for zstd
#7 108.9   Running setup.py clean for zstd
#7 109.2 Successfully built rdflib-jsonld
#7 109.2 Failed to build zstd
#7 110.3 Installing collected packages: isodate, rdflib, rdflib-jsonld, click, Werkzeug, typer, toml, shellingham, py, pluggy, owlrl, Jinja2, itsdangerous, iniconfig, colorama, xlrd, tabulate, pytest, pyshacl, importlib-resources, Flask, click-spinner, zstd, tenacity, python-snappy, pyarrow, googleapis-common-protos, brickschema, pymortar, plotly
#7 110.6   Attempting uninstall: click
#7 110.6     Found existing installation: click 8.0.1
#7 110.6     Uninstalling click-8.0.1:
#7 110.6       Successfully uninstalled click-8.0.1
#7 111.0   Attempting uninstall: Jinja2
#7 111.0     Found existing installation: Jinja2 3.0.1
#7 111.0     Uninstalling Jinja2-3.0.1:
#7 111.0       Successfully uninstalled Jinja2-3.0.1
#7 111.2   Attempting uninstall: xlrd
#7 111.2     Found existing installation: xlrd 2.0.1
#7 111.2     Uninstalling xlrd-2.0.1:
#7 111.2       Successfully uninstalled xlrd-2.0.1
#7 111.7     Running setup.py install for zstd: started
#7 112.1     Running setup.py install for zstd: finished with status 'error'
#7 112.1     ERROR: Command errored out with exit status 1:
#7 112.1      command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-xtk2zg0l/zstd_5c6751cb2a024d6583b7da7913bf3bce/setup.py'"'"'; __file__='"'"'/tmp/pip-install-xtk2zg0l/zstd_5c6751cb2a024d6583b7da7913bf3bce/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-gzhrrnpr/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd
#7 112.1          cwd: /tmp/pip-install-xtk2zg0l/zstd_5c6751cb2a024d6583b7da7913bf3bce/
#7 112.1     Complete output (14 lines):
#7 112.1     running install
#7 112.1     running build
#7 112.1     running build_ext
#7 112.1     building 'zstd' extension
#7 112.1     creating build
#7 112.1     creating build/temp.linux-x86_64-3.9
#7 112.1     creating build/temp.linux-x86_64-3.9/src
#7 112.1     creating build/temp.linux-x86_64-3.9/zstd
#7 112.1     creating build/temp.linux-x86_64-3.9/zstd/lib
#7 112.1     creating build/temp.linux-x86_64-3.9/zstd/lib/common
#7 112.1     creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#7 112.1     creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#7 112.1     gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#7 112.1     error: command 'gcc' failed: No such file or directory
#7 112.1     ----------------------------------------
#7 112.1 ERROR: Command errored out with exit status 1: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-xtk2zg0l/zstd_5c6751cb2a024d6583b7da7913bf3bce/setup.py'"'"'; __file__='"'"'/tmp/pip-install-xtk2zg0l/zstd_5c6751cb2a024d6583b7da7913bf3bce/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-gzhrrnpr/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd Check the logs for full command output.
------
executor failed running [/bin/bash -o pipefail -c python -m pip install -r requirements.txt]: exit code: 1
ERROR: Service 'jupyter-notebook' failed to build : Build failed

That file is not up to date. When did you last pull from the master branch?
On Wed, Jul 14, 2021, 2:07 PM Ruiji Sun (Ricky) @.***>
wrote:

I notice that the cache has been disabled, and the directory
'/home/jovyan/.cache/pip' or its parent directory is not owned or is not
writable by the current user. Maybe something wrong here?

The contents of notebooks/requirements.txt :
pymortar>=2.0.4
plotly
The details of docker-compose up and docker-compose up --build:
[(base) ruijisun:~/Documents/GitHub/mortar 😂😂😂 $ docker-compose up
Building jupyter-notebook
[+] Building 51.5s (8/16)
=> [internal] load build definition from Dockerfile                                                 0.0s
=> => transferring dockerfile: 37B                                                                  0.0s
=> [internal] load .dockerignore                                                                    0.0s
=> => transferring context: 34B                                                                     0.0s
=> [internal] load metadata for docker.io/jupyter/scipy-notebook:latest                             1.6s
=> [auth] jupyter/scipy-notebook:pull token for registry-1.docker.io                                0.0s
=> [ 1/11] FROM @.***:0d3c4df52908c00c47e0da99148648772c3c13e58c  0.0s
=> [internal] load build context                                                                    0.0s
=> => transferring context: 818B                                                                    0.0s
=> CACHED [ 2/11] COPY notebooks/requirements.txt .                                                 0.0s
=> ERROR [ 3/11] RUN python -m pip install -r requirements.txt                                     49.7s

[ 3/11] RUN python -m pip install -r requirements.txt:

#8 0.687 WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
#8 1.248 Collecting pymortar>=2.0.4
#8 1.500   Downloading pymortar-2.0.4-py3-none-any.whl (10.0 kB)
#8 1.770 Collecting plotly
#8 1.849   Downloading plotly-5.1.0-py2.py3-none-any.whl (20.6 MB)
#8 15.11 Requirement already satisfied: pandas<2.0,>=1.1 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.4->-r requirements.txt (line 1)) (1.3.0)
#8 15.35 Collecting zstd<2.0.0,>=1.5.0
#8 15.43   Downloading zstd-<IP_ADDRESS>.tar.gz (528 kB)
#8 16.46 Collecting googleapis-common-protos<2.0.0,>=1.52.0
#8 16.53   Downloading googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
#8 16.97 Collecting python-snappy<0.7.0,>=0.6.0
#8 17.05   Downloading python_snappy-0.6.0-cp39-cp39-manylinux2010_x86_64.whl (54 kB)
#8 17.14 Requirement already satisfied: requests<3.0.0,>=2.25.0 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.4->-r requirements.txt (line 1)) (2.25.1)
#8 17.43 Collecting brickschema<0.5,>=0.4
#8 17.50   Downloading brickschema-0.4.1-py3-none-any.whl (372 kB)
#8 18.04 Collecting rdflib<6.0.0,>=5.0.0
#8 18.11   Downloading rdflib-5.0.0-py3-none-any.whl (231 kB)
#8 18.66 Collecting pyarrow<4.0.0,>=3.0.0
#8 18.73   Downloading pyarrow-3.0.0-cp39-cp39-manylinux2014_x86_64.whl (20.7 MB)
#8 35.22 Collecting Jinja2<3.0.0,>=2.11.2
#8 35.29   Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
#8 35.57 Collecting typer[all]<0.4.0,>=0.3.2
#8 35.65   Downloading typer-0.3.2-py3-none-any.whl (21 kB)
#8 35.94 Collecting pytest<7.0,>=6.2
#8 36.02   Downloading pytest-6.2.4-py3-none-any.whl (280 kB)
#8 36.64 Collecting owlrl<6.0,>=5.2
#8 36.73   Downloading owlrl-5.2.1-py3-none-any.whl (56 kB)
#8 36.96 Collecting click-spinner<0.2.0,>=0.1.10
#8 37.03   Downloading click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB)
#8 37.11 Collecting tabulate<0.9.0,>=0.8.7
#8 37.18   Downloading tabulate-0.8.9-py3-none-any.whl (25 kB)
#8 37.20 Requirement already satisfied: sqlalchemy<2.0,>=1.3 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.4.20)
#8 37.32 Collecting Flask<2.0.0,>=1.1.2
#8 37.39   Downloading Flask-1.1.4-py2.py3-none-any.whl (94 kB)
#8 37.62 Collecting xlrd<2.0.0,>=1.2.0
#8 37.70   Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
#8 38.11 Collecting pyshacl<0.15.0,>=0.14.2
#8 38.16   Downloading pyshacl-0.14.5-py3-none-any.whl (194 kB)
#8 38.52 Requirement already satisfied: PyYAML<6.0.0,>=5.3.1 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (5.4.1)
#8 38.77 Collecting importlib-resources<4.0.0,>=3.3.0
#8 38.83   Downloading importlib_resources-3.3.1-py2.py3-none-any.whl (26 kB)
#8 39.19 Collecting Werkzeug<2.0,>=0.15
#8 39.29   Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
#8 40.06 Collecting click<8.0,>=5.1
#8 40.16   Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
#8 40.33 Collecting itsdangerous<2.0,>=0.24
#8 40.41   Downloading itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
#8 40.43 Requirement already satisfied: protobuf>=3.12.0 in /opt/conda/lib/python3.9/site-packages (from googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (3.17.2)
#8 40.45 Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/lib/python3.9/site-packages (from Jinja2<3.0.0,>=2.11.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.0.1)
#8 40.59 Collecting rdflib-jsonld>=0.4.0
#8 40.67   Downloading rdflib-jsonld-0.5.0.tar.gz (55 kB)
#8 41.17 Requirement already satisfied: numpy>=1.17.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.21.0)
#8 41.17 Requirement already satisfied: python-dateutil>=2.7.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.8.1)
#8 41.18 Requirement already satisfied: pytz>=2017.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (2021.1)
#8 41.18 Requirement already satisfied: six>=1.9 in /opt/conda/lib/python3.9/site-packages (from protobuf>=3.12.0->googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.16.0)
#8 41.43 Collecting py>=1.8.2
#8 41.49   Downloading py-1.10.0-py2.py3-none-any.whl (97 kB)
#8 41.87 Collecting iniconfig
#8 41.97   Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
#8 42.34 Collecting pluggy<1.0.0a1,>=0.12
#8 42.41   Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
#8 42.59 Collecting toml
#8 42.68   Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
#8 42.69 Requirement already satisfied: attrs>=19.2.0 in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (21.2.0)
#8 42.70 Requirement already satisfied: packaging in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (21.0)
#8 42.78 Requirement already satisfied: pyparsing in /opt/conda/lib/python3.9/site-packages (from rdflib<6.0.0,>=5.0.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.4.7)
#8 42.89 Collecting isodate
#8 42.98   Downloading isodate-0.6.0-py2.py3-none-any.whl (45 kB)
#8 43.21 Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2021.5.30)
#8 43.21 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.26.6)
#8 43.21 Requirement already satisfied: idna<3,>=2.5 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.10)
#8 43.21 Requirement already satisfied: chardet<5,>=3.0.2 in /opt/conda/lib/python3.9/site-packages (from requests<3.0.0,>=2.25.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (4.0.0)
#8 43.30 Requirement already satisfied: greenlet!=0.4.17 in /opt/conda/lib/python3.9/site-packages (from sqlalchemy<2.0,>=1.3->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.1.0)
#8 43.53 Collecting shellingham<2.0.0,>=1.3.0
#8 43.66   Downloading shellingham-1.4.0-py2.py3-none-any.whl (9.4 kB)
#8 43.83 Collecting colorama<0.5.0,>=0.4.3
#8 43.91   Downloading colorama-0.4.4-py2.py3-none-any.whl (16 kB)
#8 44.20 Collecting tenacity>=6.2.0
#8 44.28   Downloading tenacity-8.0.1-py3-none-any.whl (24 kB)
#8 44.43 Building wheels for collected packages: rdflib-jsonld, zstd
#8 44.43   Building wheel for rdflib-jsonld (setup.py): started
#8 45.66   Building wheel for rdflib-jsonld (setup.py): finished with status 'done'
#8 45.66   Created wheel for rdflib-jsonld: filename=rdflib_jsonld-0.5.0-py2.py3-none-any.whl size=15348 sha256=3cb0a80e3a0f810c6f8a9a8b0877a478c0efbb881afe18fc63434c691bc151c3
#8 45.66   Stored in directory: /tmp/pip-ephem-wheel-cache-r01mqojb/wheels/70/d3/7a/5421158e60102a4f13bcb5770cbeb95d45c97f3c4b92e7197f
#8 45.66   Building wheel for zstd (setup.py): started
#8 46.01   Building wheel for zstd (setup.py): finished with status 'error'
#8 46.01   ERROR: Command errored out with exit status 1:
#8 46.01    command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"'; file='"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-t80za9tt
#8 46.01        cwd: /tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/
#8 46.01   Complete output (14 lines):
#8 46.01   running bdist_wheel
#8 46.01   running build
#8 46.01   running build_ext
#8 46.01   building 'zstd' extension
#8 46.01   creating build
#8 46.01   creating build/temp.linux-x86_64-3.9
#8 46.01   creating build/temp.linux-x86_64-3.9/src
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd/lib
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd/lib/common
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#8 46.01   creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#8 46.01   gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#8 46.01   error: command 'gcc' failed: No such file or directory
#8 46.01   ----------------------------------------
#8 46.01   ERROR: Failed building wheel for zstd
#8 46.01   Running setup.py clean for zstd
#8 46.31 Successfully built rdflib-jsonld
#8 46.31 Failed to build zstd
#8 47.33 Installing collected packages: isodate, rdflib, rdflib-jsonld, click, Werkzeug, typer, toml, shellingham, py, pluggy, owlrl, Jinja2, itsdangerous, iniconfig, colorama, xlrd, tabulate, pytest, pyshacl, importlib-resources, Flask, click-spinner, zstd, tenacity, python-snappy, pyarrow, googleapis-common-protos, brickschema, pymortar, plotly
#8 47.58   Attempting uninstall: click
#8 47.58     Found existing installation: click 8.0.1
#8 47.59     Uninstalling click-8.0.1:
#8 47.60       Successfully uninstalled click-8.0.1
#8 48.00   Attempting uninstall: Jinja2
#8 48.00     Found existing installation: Jinja2 3.0.1
#8 48.01     Uninstalling Jinja2-3.0.1:
#8 48.03       Successfully uninstalled Jinja2-3.0.1
#8 48.17   Attempting uninstall: xlrd
#8 48.17     Found existing installation: xlrd 2.0.1
#8 48.17     Uninstalling xlrd-2.0.1:
#8 48.18       Successfully uninstalled xlrd-2.0.1
#8 48.70     Running setup.py install for zstd: started
#8 49.06     Running setup.py install for zstd: finished with status 'error'
#8 49.06     ERROR: Command errored out with exit status 1:
#8 49.06      command: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"'; file='"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-vk1dr5ed/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd
#8 49.06          cwd: /tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/
#8 49.06     Complete output (14 lines):
#8 49.06     running install
#8 49.06     running build
#8 49.06     running build_ext
#8 49.06     building 'zstd' extension
#8 49.06     creating build
#8 49.06     creating build/temp.linux-x86_64-3.9
#8 49.06     creating build/temp.linux-x86_64-3.9/src
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd/lib
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd/lib/common
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd/lib/compress
#8 49.06     creating build/temp.linux-x86_64-3.9/zstd/lib/decompress
#8 49.06     gcc -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/include -fPIC -O2 -isystem /opt/conda/include -fPIC -I/opt/conda/include/python3.9 -c src/python-zstd.c -o build/temp.linux-x86_64-3.9/src/python-zstd.o -O2 -DVERSION="<IP_ADDRESS>" -DZSTD_MULTITHREAD=1 -Izstd/lib -Izstd/lib/common -Izstd/lib/compress -Izstd/lib/decompress -DZSTD_TRACE=0
#8 49.06     error: command 'gcc' failed: No such file or directory
#8 49.06     ----------------------------------------
#8 49.06 ERROR: Command errored out with exit status 1: /opt/conda/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"'; file='"'"'/tmp/pip-install-97w5nqub/zstd_a3ad46b88e8d4d89bbdf6010ed892e8b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-vk1dr5ed/install-record.txt --single-version-externally-managed --compile --install-headers /opt/conda/include/python3.9/zstd Check the logs for full command output.

executor failed running [/bin/bash -o pipefail -c python -m pip install -r requirements.txt]: exit code: 1
ERROR: Service 'jupyter-notebook' failed to build : Build failed
(base) ruijisun:~/Documents/GitHub/mortar 😂😂😂 $ docker-compose up --build
Building pg
[+] Building 1.7s (19/19) FINISHED
=> [internal] load build definition from Dockerfile                                                 0.0s
=> => transferring dockerfile: 37B                                                                  0.0s
=> [internal] load .dockerignore                                                                    0.0s
=> => transferring context: 2B                                                                      0.0s
=> [internal] load metadata for docker.io/library/postgres:12                                       1.5s
=> [auth] library/postgres:pull token for registry-1.docker.io                                      0.0s
=> [internal] load build context                                                                    0.0s
=> => transferring context: 103B                                                                    0.0s
=> [ 1/13] FROM @.***:65e488c552d36b6482a7d5e044925962024fe816a7d79  0.0s
=> CACHED [ 2/13] RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selectio  0.0s
=> CACHED [ 3/13] RUN apt-get update && apt-get install -y       postgresql-plpython3-12       pyt  0.0s
=> CACHED [ 4/13] RUN mkdir /data/                                                                  0.0s
=> CACHED [ 5/13] RUN cat /usr/share/postgresql/postgresql.conf.sample > /data/postgresql.conf      0.0s
=> CACHED [ 6/13] RUN sh -c "echo 'deb https://packagecloud.io/timescale/timescaledb/debian/ `lsb_  0.0s
=> CACHED [ 7/13] RUN wget --quiet -O - https://packagecloud.io/timescale/timescaledb/gpgkey | apt  0.0s
=> CACHED [ 8/13] RUN apt-get update && apt-get install -y timescaledb-2-postgresql-12              0.0s
=> CACHED [ 9/13] RUN timescaledb-tune --quiet --yes --conf-path=/data/postgresql.conf              0.0s
=> CACHED [10/13] ADD install_timescale.sh /docker-entrypoint-initdb.d/001_install.sh               0.0s
=> CACHED [11/13] ADD setup.sql /docker-entrypoint-initdb.d/002_setup.sql                           0.0s
=> CACHED [12/13] ADD backfill.sql /docker-entrypoint-initdb.d/003_backfill.sql                     0.0s
=> CACHED [13/13] RUN pg_lsclusters                                                                 0.0s
=> exporting to image                                                                               0.0s
=> => exporting layers                                                                              0.0s
=> => writing image sha256:4435dac37a1cb8ac5fe3022fe1c306a14da9dd0d44ba3724f7591d895c964069         0.0s
=> => naming to docker.io/mortar/pg                                                                 0.0s
Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building mortar-server
[+] Building 1.8s (17/17) FINISHED
=> [internal] load build definition from Dockerfile                                                 0.0s
=> => transferring dockerfile: 295B                                                                 0.0s
=> [internal] load .dockerignore                                                                    0.0s
=> => transferring context: 34B                                                                     0.0s
=> [internal] load metadata for docker.io/library/ubuntu:19.10                                      1.6s
=> [internal] load metadata for docker.io/library/golang:latest                                     1.6s
=> [auth] library/ubuntu:pull token for registry-1.docker.io                                        0.0s
=> [auth] library/golang:pull token for registry-1.docker.io                                        0.0s
=> [builder 1/7] FROM @.***:773f15a2f2368be3ef88bfc29cc602bac5bd918f1f6c  0.0s
=> [stage-1 1/2] FROM @.***:f332c4057e21ec71cc8b20b05328d476104a06  0.0s
=> [internal] load build context                                                                    0.0s
=> => transferring context: 79.78kB                                                                 0.0s
=> CACHED [builder 2/7] WORKDIR /app                                                                0.0s
=> CACHED [builder 3/7] COPY main.go .                                                              0.0s
=> CACHED [builder 4/7] COPY go.mod .                                                               0.0s
=> CACHED [builder 5/7] COPY go.sum .                                                               0.0s
=> CACHED [builder 6/7] COPY internal internal                                                      0.0s
=> CACHED [builder 7/7] RUN go build -o mortar-server                                               0.0s
=> CACHED [stage-1 2/2] COPY --from=builder /app/mortar-server .                                    0.0s
=> exporting to image                                                                               0.0s
=> => exporting layers                                                                              0.0s
=> => writing image sha256:68563662aa2601cc975cf697f37aaefbd49782a012c225f4a2848e0677e744dd         0.0s
=> => naming to docker.io/mortar/server2                                                            0.0s
Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building reasoner
[+] Building 1.9s (14/14) FINISHED
=> [internal] load build definition from Dockerfile                                                 0.0s
=> => transferring dockerfile: 251B                                                                 0.0s
=> [internal] load .dockerignore                                                                    0.0s
=> => transferring context: 34B                                                                     0.0s
=> [internal] load metadata for docker.io/library/debian:buster-slim                                1.7s
=> [internal] load metadata for docker.io/library/rust:latest                                       1.7s
=> [auth] library/debian:pull token for registry-1.docker.io                                        0.0s
=> [auth] library/rust:pull token for registry-1.docker.io                                          0.0s
=> [builder 1/4] FROM @.***:6ab4e79e374047846637c0266a9147bcac4a575b68bcbc  0.0s
=> [internal] load build context                                                                    0.0s
=> => transferring context: 12.43kB                                                                 0.0s
=> [stage-1 1/2] FROM @.***:a6bbc75c36b0d9d82ae4b64219b48c30  0.0s
=> CACHED [builder 2/4] WORKDIR /app                                                                0.0s
=> CACHED [builder 3/4] COPY reasoner .                                                             0.0s
=> CACHED [builder 4/4] RUN cargo build --release                                                   0.0s
=> CACHED [stage-1 2/2] COPY --from=builder /app/target/release/reasoner .                          0.0s
=> exporting to image                                                                               0.0s
=> => exporting layers                                                                              0.0s
=> => writing image sha256:c9dd936edd0e95c952ee6edeb437f29049fdf35a711e21b230d392583bdedde0         0.0s
=> => naming to docker.io/mortar/reasoner                                                           0.0s
Use 'docker scan' to run Snyk tests against images to find vulnerabilities and learn how to fix them
Building jupyter-notebook
[+] Building 113.8s (7/15)
=> [internal] load build definition from Dockerfile                                                 0.0s
=> => transferring dockerfile: 438B                                                                 0.0s
=> [internal] load .dockerignore                                                                    0.0s
=> => transferring context: 34B                                                                     0.0s
=> [internal] load metadata for docker.io/jupyter/scipy-notebook:latest                             0.9s
=> [internal] load build context                                                                    0.1s
=> => transferring context: 2.62MB                                                                  0.1s
=> [ 1/11] FROM @.***:0d3c4df52908c00c47e0da99148648772c3c13e58c  0.0s
=> CACHED [ 2/11] COPY notebooks/requirements.txt .                                                 0.0s
=> ERROR [ 3/11] RUN python -m pip install -r requirements.txt                                    112.7s

[ 3/11] RUN python -m pip install -r requirements.txt:

#7 0.680 WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
#7 1.236 Collecting pymortar>=2.0.4
#7 1.545   Downloading pymortar-2.0.4-py3-none-any.whl (10.0 kB)
#7 2.084 Collecting plotly
#7 2.165   Downloading plotly-5.1.0-py2.py3-none-any.whl (20.6 MB)
#7 41.40 Collecting python-snappy<0.7.0,>=0.6.0
#7 41.47   Downloading python_snappy-0.6.0-cp39-cp39-manylinux2010_x86_64.whl (54 kB)
#7 41.76 Collecting googleapis-common-protos<2.0.0,>=1.52.0
#7 41.82   Downloading googleapis_common_protos-1.53.0-py2.py3-none-any.whl (198 kB)
#7 43.29 Collecting pyarrow<4.0.0,>=3.0.0
#7 43.37   Downloading pyarrow-3.0.0-cp39-cp39-manylinux2014_x86_64.whl (20.7 MB)
#7 94.09 Collecting brickschema<0.5,>=0.4
#7 94.18   Downloading brickschema-0.4.1-py3-none-any.whl (372 kB)
#7 95.16 Collecting rdflib<6.0.0,>=5.0.0
#7 95.25   Downloading rdflib-5.0.0-py3-none-any.whl (231 kB)
#7 95.66 Requirement already satisfied: pandas<2.0,>=1.1 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.4->-r requirements.txt (line 1)) (1.3.0)
#7 95.74 Collecting zstd<2.0.0,>=1.5.0
#7 95.82   Downloading zstd-<IP_ADDRESS>.tar.gz (528 kB)
#7 97.02 Requirement already satisfied: requests<3.0.0,>=2.25.0 in /opt/conda/lib/python3.9/site-packages (from pymortar>=2.0.4->-r requirements.txt (line 1)) (2.25.1)
#7 97.33 Collecting importlib-resources<4.0.0,>=3.3.0
#7 97.42   Downloading importlib_resources-3.3.1-py2.py3-none-any.whl (26 kB)
#7 97.76 Collecting pytest<7.0,>=6.2
#7 97.83   Downloading pytest-6.2.4-py3-none-any.whl (280 kB)
#7 98.53 Collecting Flask<2.0.0,>=1.1.2
#7 98.65   Downloading Flask-1.1.4-py2.py3-none-any.whl (94 kB)
#7 98.99 Collecting Jinja2<3.0.0,>=2.11.2
#7 99.06   Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
#7 99.39 Collecting tabulate<0.9.0,>=0.8.7
#7 99.47   Downloading tabulate-0.8.9-py3-none-any.whl (25 kB)
#7 99.53 Requirement already satisfied: PyYAML<6.0.0,>=5.3.1 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (5.4.1)
#7 99.60 Collecting owlrl<6.0,>=5.2
#7 99.68   Downloading owlrl-5.2.1-py3-none-any.whl (56 kB)
#7 99.91 Collecting xlrd<2.0.0,>=1.2.0
#7 99.99   Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
#7 100.5 Collecting pyshacl<0.15.0,>=0.14.2
#7 100.6   Downloading pyshacl-0.14.5-py3-none-any.whl (194 kB)
#7 101.3 Collecting click-spinner<0.2.0,>=0.1.10
#7 101.4   Downloading click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB)
#7 101.5 Collecting typer[all]<0.4.0,>=0.3.2
#7 101.6   Downloading typer-0.3.2-py3-none-any.whl (21 kB)
#7 101.6 Requirement already satisfied: sqlalchemy<2.0,>=1.3 in /opt/conda/lib/python3.9/site-packages (from brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.4.20)
#7 101.8 Collecting Werkzeug<2.0,>=0.15
#7 101.9   Downloading Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB)
#7 102.6 Collecting itsdangerous<2.0,>=0.24
#7 102.7   Downloading itsdangerous-1.1.0-py2.py3-none-any.whl (16 kB)
#7 103.0 Collecting click<8.0,>=5.1
#7 103.1   Downloading click-7.1.2-py2.py3-none-any.whl (82 kB)
#7 103.4 Requirement already satisfied: protobuf>=3.12.0 in /opt/conda/lib/python3.9/site-packages (from googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (3.17.2)
#7 103.5 Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/lib/python3.9/site-packages (from Jinja2<3.0.0,>=2.11.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.0.1)
#7 103.5 Collecting rdflib-jsonld>=0.4.0
#7 103.6   Downloading rdflib-jsonld-0.5.0.tar.gz (55 kB)
#7 104.2 Requirement already satisfied: numpy>=1.17.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.21.0)
#7 104.2 Requirement already satisfied: python-dateutil>=2.7.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (2.8.1)
#7 104.2 Requirement already satisfied: pytz>=2017.3 in /opt/conda/lib/python3.9/site-packages (from pandas<2.0,>=1.1->pymortar>=2.0.4->-r requirements.txt (line 1)) (2021.1)
#7 104.2 Requirement already satisfied: six>=1.9 in /opt/conda/lib/python3.9/site-packages (from protobuf>=3.12.0->googleapis-common-protos<2.0.0,>=1.52.0->pymortar>=2.0.4->-r requirements.txt (line 1)) (1.16.0)
#7 104.4 Collecting toml
#7 104.5   Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
#7 104.6 Collecting iniconfig
#7 104.7   Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
#7 104.8 Collecting pluggy<1.0.0a1,>=0.12
#7 104.9   Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
#7 104.9 Requirement already satisfied: packaging in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (21.0)
#7 105.1 Collecting py>=1.8.2
#7 105.2   Downloading py-1.10.0-py2.py3-none-any.whl (97 kB)
#7 105.6 Requirement already satisfied: attrs>=19.2.0 in /opt/conda/lib/python3.9/site-packages (from pytest<7.0,>=6.2->brickschema<0.5,>=0.4->pymortar>=2.0.4->-r requirements.txt (line 1)) (21.2.0)
#7 105.8 Collecting isodate
#7 105.9   Downloading isodate-0.6.0-py2.py3-none-any.whl (45 kB)