erinijapranckeviciene
commented
6 years ago Hi, I have exactly the same ERROR as guillaumecharbonnier when running bootstrap.py as in "Test locally" on two different machines with docker and --no-docker.
Closed guillaumecharbonnier closed 5 years ago
erinijapranckeviciene
commented
6 years ago Hi, I have exactly the same ERROR as guillaumecharbonnier when running bootstrap.py as in "Test locally" on two different machines with docker and --no-docker.
pjbriggs
commented
6 years ago Just encountered the same HTTP 404 NOT FOUND error running ./bootstrap.py /tmp/miniconda as reported above, when following the local test instructions from https://bioconda.github.io/contribute-a-recipe.html#bootstrap-method.
EDIT
The problem (for the specific issue of the HTTP 404 error at least) looks to be here in bootstrap.py:
# TODO: this mimics the override in the "common" job in .circleci/config.yaml
with open('.circleci/common.sh', 'w') as fout:
fout.write("MINICONDA_VER=4.5.4\nBIOCONDA_UTILS_TAG=cb3-migration\n")The cb3-migration "tag" seems to be pointing to something that no longer exists in the https://github.com/bioconda/bioconda-utils repo.
erinijapranckeviciene
commented
6 years ago Hi @guillaumecharbonnier @pjbriggs
I am not sure if my thinking was correct, but it seemed that the "cb3-migration" in bootstrap.py line 55 represents a branch in bioconda/bioconda-utils:
line 54 with open('.circleci/common.sh', 'w') as fout: line 55 fout.write("MINICONDA_VER=4.5.4\nBIOCONDA_UTILS_TAG=cb3-migration\n")
In bootstrap.py I have replaced it in line 55 with : fout.write("MINICONDA_VER=4.5.4\nBIOCONDA_UTILS_TAG=bioconda-recipes-local-build\n")
and the bootstrap.py finished executing. I can source ~/.config/bioconda/activate
I don't know whether I will encounter more problems down the road, bit for now this is how I solved it. The bioconda team could chime in about the proper fix.
pjbriggs
commented
6 years ago Thanks @erinijapranckeviciene! Your patch also seems to be working for me, at least I'm able to get to the next stage for now. Hopefully it will get fixed at source soon.
dcroote
commented
6 years ago fout.write("MINICONDA_VER=4.5.4\nBIOCONDA_UTILS_TAG=master\n")
also worked for me
pjbriggs
commented
6 years ago Some more observations:
Using BIOCONDA_UTILS_TAG=bioconda-recipes-local-build worked okay for me using the linting command, but I encountered another problem when trying the mulled tests (i.e. bioconda-utils build recipes config.yml --docker --mulled-test --git-range master):
09:18:04 BIOCONDA ERROR STDOUT+STDERR: usage: mulled-build [-h] [--involucro-path INVOLUCRO_PATH] [--dry-run] [--verbose] [--singularity] [--singularity-image-dir SINGULARITY_IMAGE_DIR] [-n NAMESPACE] [-r REPOSITORY_TEMPLATE] [-c CHANNELS] [--conda-version CONDA_VERSION] [--oauth-token OAUTH_TOKEN] [--check-published] [--hash {v1,v2}] [--name-override NAME_OVERRIDE] [--image-build IMAGE_BUILD] [--repository-name REPOSITORY_NAME] [--test TEST] [--test-files TEST_FILES] COMMAND TARGETS mulled-build: error: unrecognized arguments: --extra-channels file:///tmp/miniconda/miniconda/conda-bld,conda-forge,defaults
Dropping the --mulled-test option seems to work okay.
BIOCONDA_UTILS_TAG=master (as suggested by @dcroote above) doesn't give this error when using --mulled-test (I get different errors but it's possible that these could problems with the recipe I'm testing).erinijapranckeviciene
commented
6 years ago thank you for more info and improved solution @pjbriggs @dcroote . I haven't invoked the mulled tests yet, what exactly mulled tests are for?
pjbriggs
commented
6 years ago Hello @erinijapranckeviciene I'm not sure precisely what the mulled tests are, only that in the documentation for local testing they are referred to as being "more stringent" than e.g. testing using the CircleCI client: https://bioconda.github.io/contribute-a-recipe.html#bootstrap-method Hope that helps!
erinijapranckeviciene
commented
6 years ago Thank you @pjbriggs . Yes, me too- "master" produced no errors with --mulled-test. I was just wandering whether there is a possibility to run tests for macos within linux bioconda? Something like special option to bioconda-utils? Otherwise I believe one should install VM, install macos , clone the bioconda-recipies, install miniconda via bootstrap and only then run the tests with docker? Indeed my question might be beyond the scope of this issue, then please ignore.
pjbriggs
commented
6 years ago @erinijapranckeviciene testing on macos is outside my experience so I can't offer any help there - sorry!
guillaumecharbonnier
commented
5 years ago
I have tried with no success to set up the local building test. With circleci build, I do not seem to have gcc in the build environment. Here is an example with fastree recipe incremented by 1.
When trying the boostrap method, I get a broken url error: