CarlinLiao
commented
1 year ago Not directly related, but have you been getting errors when running force-rebuild-data-loaded-images? Could be a stale version of the test databases running properly with my local tests but not accurately reflecting the newest changes to the db.
11.14 Fetched 101 MB in 10s (10.4 MB/s)
11.14 E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/main/m/mysql-8.0/libmysqlclient21_8.0.34-0ubuntu0.22.04.1_amd64.deb 404 Not Found [IP: 185.125.190.39 80]
11.14 E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/main/m/mysql-8.0/libmysqlclient-dev_8.0.34-0ubuntu0.22.04.1_amd64.deb 404 Not Found [IP: 185.125.190.39 80]
11.14 E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
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development_prereqs.Dockerfile:28
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26 | COPY pyproject.toml.unversioned .
27 | RUN python -m pip install toml
28 | >>> RUN apt install libgdal-dev -y
29 | RUN python -c 'import toml; c = toml.load("pyproject.toml.unversioned"); print("\n".join(c["project"]["dependencies"]))' | python -m pip install -r /dev/stdin
30 | RUN python -c 'import toml; c = toml.load("pyproject.toml.unversioned"); print("\n".join(c["project"]["optional-dependencies"]["all"]))' | python -m pip install -r /dev/stdin
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ERROR: failed to solve: process "/bin/sh -c apt install libgdal-dev -y" did not complete successfully: exit code: 1000.917 After this operation, 13.2 MB of additional disk space will be used.
0.917 Get:1 http://deb.debian.org/debian-security bookworm-security/main amd64 libssl-dev amd64 3.0.11-1~deb12u2 [2,430 kB]
1.189 Err:2 http://apt.postgresql.org/pub/repos/apt bookworm-pgdg/main amd64 libpq-dev amd64 16.0-1.pgdg120+1
1.189 404 Not Found [IP: 217.196.149.55 80]
1.192 E: Failed to fetch http://apt.postgresql.org/pub/repos/apt/pool/main/p/postgresql-16/libpq-dev_16.0-1.pgdg120%2b1_amd64.deb 404 Not Found [IP: 217.196.149.55 80]
1.192 E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
1.192 Fetched 2,430 kB in 0s (7,762 kB/s)
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Dockerfile:9
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7 | RUN apt install python3-venv -y
8 | RUN apt install python3-pip -y
9 | >>> RUN apt install -y libpq-dev
10 | RUN apt install -y libgdal-dev
11 | RUN python3 -m pip install --break-system-packages psycopg2==2.9.6
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ERROR: failed to solve: process "/bin/sh -c apt install -y libpq-dev" did not complete successfully: exit code: 100
jimmymathews
Thank you for resolving the Nextflow script to Bash issue. Resolving this has re-revealed a problem I noticed earlier.
It's interesting because this error doesn't occur when the cggnn workflow test, so my first thought would be a difference between the test database and
scstudies. Does this have to do with the removal of indexing you mentioned earlier this week @jimmymathews?Originally posted by @CarlinLiao in https://github.com/nadeemlab/SPT/issues/241#issuecomment-1802251462