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dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.
MIT License
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Error in "run-all-rpbp-instances" #100

Closed yuan777 closed 2 years ago

yuan777 commented 4 years ago

when i run the command "run-all-rpbp-instances", it always get the wrong like this

_rpbp/lib/python3.6/site-packages/rpbp/orf_profile_construction/create_orf_profiles.py:76: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. config = yaml.load(open(args.config)) WARNING misc.shell_utils 2019-07-31 23:42:26,711 : All output files ['./without-rrna-mapping/c-elegans-rep-1.test-unique.bam'] already exist. Skipping call: create-base-genome-profile ./c-elegans.test-chrI.rep-1.fastq.gz c-elegans-test.yaml c-elegans-rep-1 --num-cpus 1 --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --star-executable STAR --star-read-files-command zcat --mem 2G WARNING misc.shell_utils 2019-07-31 23:42:26,712 : All output files ['./metagene-profiles/c-elegans-rep-1.test-unique.metagene-profile.csv.gz'] already exist. Skipping call: extract-metagene-profiles ./without-rrna-mapping/c-elegans-rep-1.test-unique.bam ./WBcel235.79.chrI/WBcel235.79.chrI.annotated.bed.gz ./metagene-profiles/c-elegans-rep-1.test-unique.metagene-profile.csv.gz --num-cpus 1 --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --start-upstream 50 --start-downstream 20 --end-upstream 50 --end-downstream 20 Traceback (most recent call last): File "rpbp/bin/estimate-metagene-profile-bayes-factors", line 10, in sys.exit(main()) File "rpbp/lib/python3.6/site-packages/riboutils/estimate_metagene_profile_bayes_factors.py", line 222, in main progress_bar=True File "rpbp/lib/python3.6/site-packages/misc/parallel.py", line 101, in apply_parallel_groups for name,group in tqdm.tqdm(groups, total=len(groups), leave=True, file=sys.stdout)) File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 921, in call if self.dispatch_one_batch(iterator): File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch self._dispatch(tasks) File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 716, in _dispatch job = self._backend.apply_async(batch, callback=cb) File "rpbp/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 182, in apply_async result = ImmediateResult(func) File "rpbp/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 549, in init self.results = batch() File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 225, in call for func, args, kwargs in self.items] File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 225, in for func, args, kwargs in self.items] File "rpbp/lib/python3.6/site-packages/riboutils/estimate_metagene_profile_bayes_factors.py", line 114, in estimate_profile_bayes_factors iterations=args.iterations,chains=args.chains,seed=args.seed) File "rpbp/lib/python3.6/site-packages/riboutils/estimate_metagene_profile_bayes_factors.py", line 63, in estimate_marginal_likelihoods for pm in periodic_models] File "rpbp/lib/python3.6/site-packages/riboutils/estimate_metagene_profile_bayes_factors.py", line 63, in for pm in periodic_models] File "rpbp/lib/python3.6/site-packages/pystan/model.py", line 671, in sampling fit = self.fit_class(data) AttributeError: 'StanModel' object has no attribute 'fit_class'

Traceback (most recent call last): File "rpbp/bin/create-orf-profiles", line 11, in load_entry_point('rpbp==1.1.12', 'console_scripts', 'create-orf-profiles')() File "rpbp/lib/python3.6/site-packages/rpbp/orf_profile_construction/create_orf_profiles.py", line 228, in main file_checkers=file_checkers, overwrite=args.overwrite, call=call) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 345, in call_if_not_exists ret_code = check_call(cmd, call=call, raise_on_error=raise_on_error) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 193, in check_call return check_call_step(cmd, call=call, raise_on_error=raise_on_error) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 176, in check_call_step raise subprocess.CalledProcessError(ret_code, cmd) subprocess.CalledProcessError: Command 'estimate-metagene-profile-bayes-factors ./metagene-profiles/c-elegans-rep-1.test-unique.metagene-profile.csv.gz ./metagene-profiles/c-elegans-rep-1.test-unique.metagene-periodicity-bayes-factors.csv.gz --num-cpus 1 --periodic-models /home/YDH/.local/share/rpbp/rpbp_models/periodic/start-high-low-low.pkl --nonperiodic-models /home/YDH/.local/share/rpbp/rpbp_models/nonperiodic/no-periodicity.pkl /home/YDH/.local/share/rpbp/rpbp_models/nonperiodic/start-high-high-low.pkl /home/YDH/.local/share/rpbp/rpbp_models/nonperiodic/start-high-low-high.pkl --periodic-offset-start -20 --periodic-offset-end 0 --metagene-profile-length 21 --seed 8675309 --chains 2 --iterations 500 --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET' returned non-zero exit status 1. rpbp/lib/python3.6/site-packages/rpbp/run_rpbp_pipeline.py:61: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. config = yaml.load(open(args.config)) Traceback (most recent call last): File "rpbp/bin/run-rpbp-pipeline", line 11, in load_entry_point('rpbp==1.1.12', 'console_scripts', 'run-rpbp-pipeline')() File "rpbp/lib/python3.6/site-packages/rpbp/run_rpbp_pipeline.py", line 143, in main shell_utils.check_call(cmd) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 193, in check_call return check_call_step(cmd, call=call, raise_on_error=raise_on_error) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 176, in check_call_step raise subprocess.CalledProcessError(ret_code, cmd) subprocess.CalledProcessError: Command 'create-orf-profiles ./c-elegans.test-chrI.rep-1.fastq.gz c-elegans-test.yaml c-elegans-rep-1 --num-cpus 1 --mem 2G --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --star-executable STAR --star-read-files-command zcat ' returned non-zero exit status 1. rpbp/lib/python3.6/site-packages/rpbp/run_all_rpbp_instances.py:70: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. config = yaml.load(open(args.config)) Traceback (most recent call last): File "rpbp/bin/run-all-rpbp-instances", line 11, in load_entry_point('rpbp==1.1.12', 'console_scripts', 'run-all-rpbp-instances')() File "rpbp/lib/python3.6/site-packages/rpbp/run_all_rpbp_instances.py", line 183, in main job_id = slurm.check_sbatch(cmd, args=args) File "rpbp/lib/python3.6/site-packages/misc/slurm.py", line 188, in check_sbatch shell_utils.check_call(cmd, call=call) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 193, in check_call return check_call_step(cmd, call=call, raise_on_error=raise_on_error) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 176, in check_call_step raise subprocess.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'run-rpbp-pipeline ./c-elegans.test-chrI.rep-1.fastq.gz c-elegans-test.yaml c-elegans-rep-1 --num-cpus 1 --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --star-executable STAR --star-read-files-command zcat --mem 2G' returned non-zero exit status 1.

anyone can tell me how to resolve this problem?

eboileau commented 4 years ago

Hi @yuan777, please use the dev branch, and recompile the Stan models, see Installation. Please make sure that you have the right version of all packages/dependencies. We will soon add these to the main branch.

yuan777 commented 4 years ago

@eboileau thanks for your response, i do install all the packages with the proper version according to the installation required, and i reinstall the pystan from version 2.16 to 2.17 , because the rpbp required 2.16, so i return it. i return the command as you suggested, when i run the "create-orf-profiles", it has the same error. the error is following: rpbp/lib/python3.6/site-packages/rpbp/orf_profile_construction/create_orf_profiles.py:76: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. config = yaml.load(open(args.config)) WARNING misc.shell_utils 2019-08-01 04:46:50,845 : All output files ['./c-elegans-chrI-example/without-rrna-mapping/rep-1.test-unique.bam'] already exist. Skipping call: create-base-genome-profile c-elegans.test-chrI.rep-1.fastq.gz c-elegans-test.yaml rep-1 --num-cpus 1 --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --star-executable STAR --star-read-files-command zcat --mem 2G WARNING misc.shell_utils 2019-08-01 04:46:50,846 : All output files ['./c-elegans-chrI-example/metagene-profiles/rep-1.test-unique.metagene-profile.csv.gz'] already exist. Skipping call: extract-metagene-profiles ./c-elegans-chrI-example/without-rrna-mapping/rep-1.test-unique.bam ./c-elegans-chrI-example/WBcel235.79.chrI/WBcel235.79.chrI.annotated.bed.gz ./c-elegans-chrI-example/metagene-profiles/rep-1.test-unique.metagene-profile.csv.gz --num-cpus 1 --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --start-upstream 50 --start-downstream 20 --end-upstream 50 --end-downstream 20 Traceback (most recent call last): File "rpbp/bin/estimate-metagene-profile-bayes-factors", line 10, in sys.exit(main()) File "rpbp/lib/python3.6/site-packages/riboutils/estimate_metagene_profile_bayes_factors.py", line 222, in main progress_bar=True File "rpbp/lib/python3.6/site-packages/misc/parallel.py", line 101, in apply_parallel_groups for name,group in tqdm.tqdm(groups, total=len(groups), leave=True, file=sys.stdout)) File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 921, in call if self.dispatch_one_batch(iterator): File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch self._dispatch(tasks) File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 716, in _dispatch job = self._backend.apply_async(batch, callback=cb) File "rpbp/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 182, in apply_async result = ImmediateResult(func) File "rpbp/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 549, in init self.results = batch() File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 225, in call for func, args, kwargs in self.items] File "rpbp/lib/python3.6/site-packages/joblib/parallel.py", line 225, in for func, args, kwargs in self.items] File "rpbp/lib/python3.6/site-packages/riboutils/estimate_metagene_profile_bayes_factors.py", line 114, in estimate_profile_bayes_factors iterations=args.iterations,chains=args.chains,seed=args.seed) File "rpbp/lib/python3.6/site-packages/riboutils/estimate_metagene_profile_bayes_factors.py", line 63, in estimate_marginal_likelihoods for pm in periodic_models] File "rpbp/lib/python3.6/site-packages/riboutils/estimate_metagene_profile_bayes_factors.py", line 63, in for pm in periodic_models] File "rpbp/lib/python3.6/site-packages/pystan/model.py", line 671, in sampling fit = self.fit_class(data) AttributeError: 'StanModel' object has no attribute 'fit_class' Traceback (most recent call last): File "rpbp/bin/create-orf-profiles", line 11, in load_entry_point('rpbp==1.1.12', 'console_scripts', 'create-orf-profiles')() File "rpbp/lib/python3.6/site-packages/rpbp/orf_profile_construction/create_orf_profiles.py", line 228, in main file_checkers=file_checkers, overwrite=args.overwrite, call=call) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 345, in call_if_not_exists ret_code = check_call(cmd, call=call, raise_on_error=raise_on_error) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 193, in check_call return check_call_step(cmd, call=call, raise_on_error=raise_on_error) File "rpbp/lib/python3.6/site-packages/misc/shell_utils.py", line 176, in check_call_step raise subprocess.CalledProcessError(ret_code, cmd) subprocess.CalledProcessError: Command 'estimate-metagene-profile-bayes-factors ./c-elegans-chrI-example/metagene-profiles/rep-1.test-unique.metagene-profile.csv.gz ./c-elegans-chrI-example/metagene-profiles/rep-1.test-unique.metagene-periodicity-bayes-factors.csv.gz --num-cpus 1 --periodic-models /home/YDH/.local/share/rpbp/rpbp_models/periodic/start-high-low-low.pkl --nonperiodic-models /home/YDH/.local/share/rpbp/rpbp_models/nonperiodic/no-periodicity.pkl /home/YDH/.local/share/rpbp/rpbp_models/nonperiodic/start-high-high-low.pkl /home/YDH/.local/share/rpbp/rpbp_models/nonperiodic/start-high-low-high.pkl --periodic-offset-start -20 --periodic-offset-end 0 --metagene-profile-length 21 --seed 8675309 --chains 2 --iterations 500 --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET' returned non-zero exit status 1.

eboileau commented 4 years ago

You did not install the dev branch, this is still the main branch. There has been minor changes in API, so meanwhile you need to use dev.

After cloning the repo, you need to git checkout dev before installing. Please follow the latest instructions. I advise you do this in a new virtual environment.

eboileau commented 4 years ago

...and use the --force-recompile flag, see Installation.

yuan777 commented 4 years ago

i follow your suggestion and installation, my step is : first used conda create visual environment and activated the new environment, then use conda install flexbar; bowtie2; samtools.and next clone the git repository, get into the rp-bp dirctory, and run git checkout dev, all is ok, final run _pip --verbose install -r requirements.txt --install-option="--force-recompile" 2>&1 | tee install.log_ , it makes error:

Created temporary directory: /tmp/pip-ephem-wheel-cache-re452es9 Created temporary directory: /tmp/pip-req-tracker-mgfeiiq7 Created requirements tracker '/tmp/pip-req-tracker-mgfeiiq7' Created temporary directory: /tmp/pip-install-dlp3fajt Collecting pbio from git+https://github.com/dieterich-lab/pybio-utils.git@dev#egg=pbio (from -r requirements.txt (line 6)) Cloning https://github.com/dieterich-lab/pybio-utils.git (to revision dev) to /tmp/pip-install-dlp3fajt/pbio ~/miniconda3/envs/rpbp/lib/python3.6/site-packages/pip/_internal/commands/install.py:243: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options. cmdoptions.check_install_build_global(options) Running command git clone -q https://github.com/dieterich-lab/pybio-utils.git /tmp/pip-install-dlp3fajt/pbio Running command git show-ref dev b84a9f3e55357a2102b2851a82baf0724791acf4 refs/remotes/origin/dev Running command git symbolic-ref -q HEAD refs/heads/master Running command git checkout -b dev --track origin/dev Switched to a new branch 'dev' Branch 'dev' set up to track remote branch 'dev' from 'origin'. Added pbio from git+https://github.com/dieterich-lab/pybio-utils.git@dev#egg=pbio (from -r requirements.txt (line 6)) to build tracker '/tmp/pip-req-tracker-mgfeiiq7' Running setup.py (path:/tmp/pip-install-dlp3fajt/pbio/setup.py) egg_info for package pbio Running command python setup.py egg_info running egg_info creating pip-egg-info/pbio.egg-info writing pip-egg-info/pbio.egg-info/PKG-INFO writing dependency_links to pip-egg-info/pbio.egg-info/dependency_links.txt writing entry points to pip-egg-info/pbio.egg-info/entry_points.txt writing requirements to pip-egg-info/pbio.egg-info/requires.txt writing top-level names to pip-egg-info/pbio.egg-info/top_level.txt writing manifest file 'pip-egg-info/pbio.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/pbio.egg-info/SOURCES.txt' writing manifest file 'pip-egg-info/pbio.egg-info/SOURCES.txt' Source in /tmp/pip-install-dlp3fajt/pbio has version 1.0.0, which satisfies requirement pbio from git+https://github.com/dieterich-lab/pybio-utils.git@dev#egg=pbio (from -r requirements.txt (line 6)) Removed pbio from git+https://github.com/dieterich-lab/pybio-utils.git@dev#egg=pbio (from -r requirements.txt (line 6)) from build tracker '/tmp/pip-req-tracker-mgfeiiq7' Requirement already satisfied: sklearn in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (0.0) Requirement already satisfied: appdirs in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (1.4.3) Requirement already satisfied: tqdm in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (4.32.2) Requirement already satisfied: mygene in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (3.1.0) Requirement already satisfied: openpyxl in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (2.6.2) Requirement already satisfied: fastparquet in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (0.3.2) Requirement already satisfied: more_itertools in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (7.2.0) Requirement already satisfied: matplotlib in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (3.1.1) Requirement already satisfied: matplotlib_venn in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (0.11.5) Requirement already satisfied: seaborn in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pbio->-r requirements.txt (line 6)) (0.9.0) Requirement already satisfied: scikit-learn in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from sklearn->pbio->-r requirements.txt (line 6)) (0.21.3) Requirement already satisfied: biothings_client>=0.2.0 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from mygene->pbio->-r requirements.txt (line 6)) (0.2.0) Requirement already satisfied: et-xmlfile in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from openpyxl->pbio->-r requirements.txt (line 6)) (1.0.1) Requirement already satisfied: jdcal in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from openpyxl->pbio->-r requirements.txt (line 6)) (1.4.1) Requirement already satisfied: pandas>=0.19 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from fastparquet->pbio->-r requirements.txt (line 6)) (0.25.0) Requirement already satisfied: numba>=0.28 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from fastparquet->pbio->-r requirements.txt (line 6)) (0.45.1) Requirement already satisfied: numpy>=1.11 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from fastparquet->pbio->-r requirements.txt (line 6)) (1.17.0) Requirement already satisfied: thrift>=0.11.0 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from fastparquet->pbio->-r requirements.txt (line 6)) (0.11.0) Requirement already satisfied: six in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from fastparquet->pbio->-r requirements.txt (line 6)) (1.12.0) Requirement already satisfied: python-dateutil>=2.1 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from matplotlib->pbio->-r requirements.txt (line 6)) (2.8.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from matplotlib->pbio->-r requirements.txt (line 6)) (2.4.2) Requirement already satisfied: cycler>=0.10 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from matplotlib->pbio->-r requirements.txt (line 6)) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from matplotlib->pbio->-r requirements.txt (line 6)) (1.1.0) Requirement already satisfied: scipy in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from matplotlib_venn->pbio->-r requirements.txt (line 6)) (1.3.0) Requirement already satisfied: joblib>=0.11 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from scikit-learn->sklearn->pbio->-r requirements.txt (line 6)) (0.13.2) Requirement already satisfied: requests>=2.3.0 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from biothings_client>=0.2.0->mygene->pbio->-r requirements.txt (line 6)) (2.22.0) Requirement already satisfied: nose in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from biothings_client>=0.2.0->mygene->pbio->-r requirements.txt (line 6)) (1.3.7) Requirement already satisfied: pytz>=2017.2 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from pandas>=0.19->fastparquet->pbio->-r requirements.txt (line 6)) (2019.2) Requirement already satisfied: llvmlite>=0.29.0dev0 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from numba>=0.28->fastparquet->pbio->-r requirements.txt (line 6)) (0.29.0) Requirement already satisfied: setuptools in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->pbio->-r requirements.txt (line 6)) (41.0.1) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from requests>=2.3.0->biothings_client>=0.2.0->mygene->pbio->-r requirements.txt (line 6)) (3.0.4) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from requests>=2.3.0->biothings_client>=0.2.0->mygene->pbio->-r requirements.txt (line 6)) (1.25.3) Requirement already satisfied: idna<2.9,>=2.5 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from requests>=2.3.0->biothings_client>=0.2.0->mygene->pbio->-r requirements.txt (line 6)) (2.8) Requirement already satisfied: certifi>=2017.4.17 in ~/miniconda3/envs/rpbp/lib/python3.6/site-packages (from requests>=2.3.0->biothings_client>=0.2.0->mygene->pbio->-r requirements.txt (line 6)) (2019.6.16) Skipping bdist_wheel for pbio, due to binaries being disabled for it. Installing collected packages: pbio Created temporary directory: /tmp/pip-record-i2w1k4zj Running setup.py install for pbio: started Running command ~/miniconda3/envs/rpbp/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dlp3fajt/pbio/setup.py'"'"'; file='"'"'/tmp/pip-install-dlp3fajt/pbio/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-i2w1k4zj/install-record.txt --single-version-externally-managed --compile --force-recompile usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help

error: option --force-recompile not recognized

Running setup.py install for pbio: finished with status 'error' Cleaning up... Removing source in /tmp/pip-install-dlp3fajt/pbio Removed build tracker '/tmp/pip-req-tracker-mgfeiiq7' ERROR: Command errored out with exit status 1: ~/miniconda3/envs/rpbp/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dlp3fajt/pbio/setup.py'"'"'; file='"'"'/tmp/pip-install-dlp3fajt/pbio/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-i2w1k4zj/install-record.txt --single-version-externally-managed --compile --force-recompile Check the logs for full command output. Exception information: Traceback (most recent call last): File "~/miniconda3/envs/rpbp/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 188, in main status = self.run(options, args) File "~/miniconda3/envs/rpbp/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 407, in run use_user_site=options.use_user_site, File "~/miniconda3/envs/rpbp/lib/python3.6/site-packages/pip/_internal/req/init.py", line 58, in install_given_reqs **kwargs File "~/miniconda3/envs/rpbp/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 959, in install spinner=spinner, File "~/miniconda3/envs/rpbp/lib/python3.6/site-packages/pip/_internal/utils/misc.py", line 934, in call_subprocess raise InstallationError(exc_msg) pip._internal.exceptions.InstallationError: Command errored out with exit status 1: ~/miniconda3/envs/rpbp/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dlp3fajt/pbio/setup.py'"'"'; file='"'"'/tmp/pip-install-dlp3fajt/pbio/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-i2w1k4zj/install-record.txt --single-version-externally-managed --compile --force-recompile Check the logs for full command output.

eboileau commented 4 years ago

Hi @yuan777, there are 2 things. First, when issuing the pip install command, the period/dot is required, it is the local project path (rp-bp), after requirements.txt:

pip --verbose install -r requirements.txt . --install-option="--force-recompile" 2>&1 | tee install.log

Second, and this a problem, the install-option seems to leak across lines (this issue is not specific to rp-bp, it has been reported and discussed in various places). Clearly, I tested the current install and it worked, so I'm not sure why this is occurring again now. I will need to investigate. Meanwhile, there are 2 workarounds, which I think should do temporarily:

  1. Delete the compiled models, if necessary (under $HOME/.local/share/rpbp/rpbp_models), or leave as is, but do NOT use the --install-option="--force-recompile", or
  2. Install pbio and all other dependencies separately, then install rpbp.

In all cases, I strongly suggest to pip install numpy (in your virtual environment) before installing rpbp.

yuan777 commented 4 years ago

@eboileau thanks for your response, i will try it according to your suggestions.