Erros when downloading genewalk even with versions higher than 3.5 #63

Felipe-Leite · 2021-07-12T14:48:55Z

Felipe-Leite
Jul 12, 2021

Hi! I tried many time to download Genewalk whitout success. I tried Python 3.9.6 and 3.7. Do I need a virtual environment when using updated versions?

THis is what I get:
Python 3.9.6 (v3.9.6:db3ff76da1, Jun 28 2021, 11:49:53)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

exit()
(tutorial-env) Felipes-MacBook-Pro:~ felipedesouzaleite$ pip3 install genewalk
Collecting genewalk
Using cached genewalk-1.5.3-py2.py3-none-any.whl (43 kB)
Requirement already satisfied: networkx>=2.1 in ./tutorial-env/lib/python3.9/site-packages (from genewalk) (2.6.1)
Requirement already satisfied: seaborn in ./tutorial-env/lib/python3.9/site-packages (from genewalk) (0.11.1)
Requirement already satisfied: scipy>=1.3.0 in ./tutorial-env/lib/python3.9/site-packages (from genewalk) (1.7.0)
Requirement already satisfied: matplotlib in ./tutorial-env/lib/python3.9/site-packages (from genewalk) (3.4.2)
Requirement already satisfied: goatools in ./tutorial-env/lib/python3.9/site-packages (from genewalk) (1.1.6)
Requirement already satisfied: plotly>=4.0.0 in ./tutorial-env/lib/python3.9/site-packages (from genewalk) (5.1.0)
Collecting gensim<4
Using cached gensim-3.8.3.tar.gz (23.4 MB)
Requirement already satisfied: pandas in ./tutorial-env/lib/python3.9/site-packages (from genewalk) (1.3.0)
Requirement already satisfied: numpy in ./tutorial-env/lib/python3.9/site-packages (from genewalk) (1.21.0)
Requirement already satisfied: six>=1.5.0 in ./tutorial-env/lib/python3.9/site-packages (from gensim<4->genewalk) (1.16.0)
Requirement already satisfied: smart_open>=1.8.1 in ./tutorial-env/lib/python3.9/site-packages (from gensim<4->genewalk) (5.1.0)
Requirement already satisfied: python-dateutil>=2.7 in ./tutorial-env/lib/python3.9/site-packages (from matplotlib->genewalk) (2.8.1)
Requirement already satisfied: pillow>=6.2.0 in ./tutorial-env/lib/python3.9/site-packages (from matplotlib->genewalk) (8.3.1)
Requirement already satisfied: cycler>=0.10 in ./tutorial-env/lib/python3.9/site-packages (from matplotlib->genewalk) (0.10.0)
Requirement already satisfied: pyparsing>=2.2.1 in ./tutorial-env/lib/python3.9/site-packages (from matplotlib->genewalk) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in ./tutorial-env/lib/python3.9/site-packages (from matplotlib->genewalk) (1.3.1)
Requirement already satisfied: pytz>=2017.3 in ./tutorial-env/lib/python3.9/site-packages (from pandas->genewalk) (2021.1)
Requirement already satisfied: tenacity>=6.2.0 in ./tutorial-env/lib/python3.9/site-packages (from plotly>=4.0.0->genewalk) (8.0.0)
Requirement already satisfied: xlsxwriter in ./tutorial-env/lib/python3.9/site-packages (from goatools->genewalk) (1.4.4)
Requirement already satisfied: statsmodels in ./tutorial-env/lib/python3.9/site-packages (from goatools->genewalk) (0.12.2)
Requirement already satisfied: xlrd==1.2.0 in ./tutorial-env/lib/python3.9/site-packages (from goatools->genewalk) (1.2.0)
Requirement already satisfied: docopt in ./tutorial-env/lib/python3.9/site-packages (from goatools->genewalk) (0.6.2)
Requirement already satisfied: pydot in ./tutorial-env/lib/python3.9/site-packages (from goatools->genewalk) (1.4.2)
Requirement already satisfied: requests in ./tutorial-env/lib/python3.9/site-packages (from goatools->genewalk) (2.25.1)
Requirement already satisfied: wget in ./tutorial-env/lib/python3.9/site-packages (from goatools->genewalk) (3.2)
Requirement already satisfied: certifi>=2017.4.17 in ./tutorial-env/lib/python3.9/site-packages (from requests->goatools->genewalk) (2021.5.30)
Requirement already satisfied: idna<3,>=2.5 in ./tutorial-env/lib/python3.9/site-packages (from requests->goatools->genewalk) (2.10)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./tutorial-env/lib/python3.9/site-packages (from requests->goatools->genewalk) (1.26.6)
Requirement already satisfied: chardet<5,>=3.0.2 in ./tutorial-env/lib/python3.9/site-packages (from requests->goatools->genewalk) (4.0.0)
Requirement already satisfied: patsy>=0.5 in ./tutorial-env/lib/python3.9/site-packages (from statsmodels->goatools->genewalk) (0.5.1)
Using legacy 'setup.py install' for gensim, since package 'wheel' is not installed.
Installing collected packages: gensim, genewalk
Running setup.py install for gensim ... error
ERROR: Command errored out with exit status 1:
command: /Users/felipedesouzaleite/tutorial-env/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/t1/5tpwp76556g0tdw2dr2w157c0000gn/T/pip-install-twht3der/gensim_1295893271d04cfcacc5557c5be9e321/setup.py'"'"'; file='"'"'/private/var/folders/t1/5tpwp76556g0tdw2dr2w157c0000gn/T/pip-install-twht3der/gensim_1295893271d04cfcacc5557c5be9e321/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 /private/var/folders/t1/5tpwp76556g0tdw2dr2w157c0000gn/T/pip-record-ykqeapqp/install-record.txt --single-version-externally-managed --compile --install-headers /Users/felipedesouzaleite/tutorial-env/include/site/python3.9/gensim
cwd: /private/var/folders/t1/5tpwp76556g0tdw2dr2w157c0000gn/T/pip-install-twht3der/gensim_1295893271d04cfcacc5557c5be9e321/
Complete output (459 lines):
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.9
creating build/lib.macosx-10.9-x86_64-3.9/gensim
copying gensim/interfaces.py -> build/lib.macosx-10.9-x86_64-3.9/gensim
copying gensim/downloader.py -> build/lib.macosx-10.9-x86_64-3.9/gensim
copying gensim/matutils.py -> build/lib.macosx-10.9-x86_64-3.9/gensim
copying gensim/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim
copying gensim/utils.py -> build/lib.macosx-10.9-x86_64-3.9/gensim
copying gensim/nosy.py -> build/lib.macosx-10.9-x86_64-3.9/gensim
creating build/lib.macosx-10.9-x86_64-3.9/gensim/similarities
copying gensim/similarities/index.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/similarities
copying gensim/similarities/docsim.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/similarities
copying gensim/similarities/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/similarities
copying gensim/similarities/nmslib.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/similarities
copying gensim/similarities/levenshtein.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/similarities
copying gensim/similarities/termsim.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/similarities
creating build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_text_analysis.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_glove2word2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_parsing.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_tmdiff.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_utils.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_matutils.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_keywords.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_word2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_segmentation.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_lsimodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_coherencemodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_miislita.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_wordrank_wrapper.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_phrases.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_BM25.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_sklearn_api.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_dtm.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_tfidfmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_poincare.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_rpmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_corpora_hashdictionary.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/simspeed2.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_aggregation.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_varembed_wrapper.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_lee.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_big.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_translation_matrix.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/basetmtests.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_ldaseqmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_datatype.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_summarization.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_ldavowpalwabbit_wrapper.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_similarity_metrics.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_ldamodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_nmf.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_lda_callback.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/utils.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_keyedvectors.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_ldamallet_wrapper.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_fasttext_wrapper.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_corpora_dictionary.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_d2vmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/svd_error.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_logentropy_model.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_doc2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_similarities.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_keras_integration.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_direct_confirmation.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_api.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_atmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_corpora.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_indirect_confirmation.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_probability_estimation.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_fasttext.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_utils_any2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_scripts.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_normmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_hdpmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/test_sharded_corpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
copying gensim/test/simspeed.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/test
creating build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/bm25.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/textcleaner.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/graph.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/keywords.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/commons.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/summarizer.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/pagerank_weighted.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/mz_entropy.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
copying gensim/summarization/syntactic_unit.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/summarization
creating build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/poincare.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/basemodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/phrases.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/_fasttext_bin.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/word2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/normmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/translation_matrix.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/lsimodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/rpmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/logentropy_model.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/keyedvectors.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/lda_worker.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/fasttext.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/tfidfmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/doc2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/callbacks.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/hdpmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/ldamulticore.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/ldaseqmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/lsi_dispatcher.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/lda_dispatcher.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/utils_any2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/base_any2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/ldamodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/nmf.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/atmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/lsi_worker.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/coherencemodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
creating build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/hdp.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/phrases.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/lsimodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/rpmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/ftmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/ldaseqmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/text2bow.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/ldamodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/w2vmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/tfidf.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/atmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
copying gensim/sklearn_api/d2vmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/sklearn_api
creating build/lib.macosx-10.9-x86_64-3.9/gensim/viz
copying gensim/viz/poincare.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/viz
copying gensim/viz/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/viz
creating build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/make_wikicorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/word2vec2tensor.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/package_info.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/make_wiki_online_lemma.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/segment_wiki.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/make_wiki_online.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/make_wiki.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/make_wiki_lemma.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/make_wiki_online_nodebug.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/glove2word2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
copying gensim/scripts/word2vec_standalone.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/scripts
creating build/lib.macosx-10.9-x86_64-3.9/gensim/parsing
copying gensim/parsing/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/parsing
copying gensim/parsing/preprocessing.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/parsing
copying gensim/parsing/porter.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/parsing
creating build/lib.macosx-10.9-x86_64-3.9/gensim/topic_coherence
copying gensim/topic_coherence/direct_confirmation_measure.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/topic_coherence
copying gensim/topic_coherence/aggregation.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/topic_coherence
copying gensim/topic_coherence/text_analysis.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/topic_coherence
copying gensim/topic_coherence/probability_estimation.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/topic_coherence
copying gensim/topic_coherence/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/topic_coherence
copying gensim/topic_coherence/indirect_confirmation_measure.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/topic_coherence
copying gensim/topic_coherence/segmentation.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/topic_coherence
creating build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/sharded_corpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/textcorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/wikicorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/csvcorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/malletcorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/mmcorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/ucicorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/indexedcorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/lowcorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/bleicorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/dictionary.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/svmlightcorpus.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/hashdictionary.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
creating build/lib.macosx-10.9-x86_64-3.9/gensim/models/wrappers
copying gensim/models/wrappers/dtmmodel.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/wrappers
copying gensim/models/wrappers/ldavowpalwabbit.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/wrappers
copying gensim/models/wrappers/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/wrappers
copying gensim/models/wrappers/varembed.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/wrappers
copying gensim/models/wrappers/fasttext.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/wrappers
copying gensim/models/wrappers/ldamallet.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/wrappers
copying gensim/models/wrappers/wordrank.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/wrappers
creating build/lib.macosx-10.9-x86_64-3.9/gensim/models/deprecated
copying gensim/models/deprecated/old_saveload.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/deprecated
copying gensim/models/deprecated/word2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/deprecated
copying gensim/models/deprecated/init.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/deprecated
copying gensim/models/deprecated/fasttext_wrapper.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/deprecated
copying gensim/models/deprecated/keyedvectors.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/deprecated
copying gensim/models/deprecated/fasttext.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/deprecated
copying gensim/models/deprecated/doc2vec.py -> build/lib.macosx-10.9-x86_64-3.9/gensim/models/deprecated
running egg_info
writing gensim.egg-info/PKG-INFO
writing dependency_links to gensim.egg-info/dependency_links.txt
writing requirements to gensim.egg-info/requires.txt
writing top-level names to gensim.egg-info/top_level.txt
adding license file 'COPYING' (matched pattern 'COPYING*')
reading manifest file 'gensim.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'COPYING.LESSER'
warning: no files found matching 'ez_setup.py'
warning: no files found matching 'gensim/models/doc2vec_inner.c'
writing manifest file 'gensim.egg-info/SOURCES.txt'
copying gensim/_matutils.c -> build/lib.macosx-10.9-x86_64-3.9/gensim
copying gensim/_matutils.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim
creating build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/EN.1-10.cbow1_wind5_hs0_neg10_size300_smpl1e-05.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/IT.1-10.cbow1_wind5_hs0_neg10_size300_smpl1e-05.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/OPUS_en_it_europarl_train_one2ten.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/alldata-id-10.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/atmodel_3_0_1_model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/atmodel_3_0_1_model.expElogbeta.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/atmodel_3_0_1_model.id2word -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/atmodel_3_0_1_model.state -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/bgwiki-latest-pages-articles-shortened.xml.bz2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/compatible-hash-false.model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/compatible-hash-true.model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/cp852_fasttext.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/crime-and-punishment.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/crime-and-punishment.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/crime-and-punishment.vec -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/d2v-lee-v0.13.0 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/doc2vec_old -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/doc2vec_old_sep -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/doc2vec_old_sep.syn0_lockf.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/doc2vec_old_sep.syn1neg.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/dtm_test.dict -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/dtm_test.mm -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/enwiki-latest-pages-articles1.xml-p000000010p000030302-shortened.bz2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/enwiki-table-markup.xml.bz2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/euclidean_vectors.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/fasttext_old -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/fasttext_old_sep -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/fasttext_old_sep.syn0_lockf.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/fasttext_old_sep.syn1neg.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/fb-ngrams.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ft_kv_3.6.0.model.gz -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ft_model_2.3.0 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/head500.noblanks.cor -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/head500.noblanks.cor.bz2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/head500.noblanks.cor_tfidf.model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/head500.noblanks.cor_wordids.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/high_precision.kv.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/high_precision.kv.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/large_tag_doc_10_iter50 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lda_3_0_1_model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lda_3_0_1_model.expElogbeta.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lda_3_0_1_model.id2word -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lda_3_0_1_model.state -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldamodel_python_2_7 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldamodel_python_2_7.expElogbeta.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldamodel_python_2_7.id2word -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldamodel_python_2_7.state -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldamodel_python_3_5 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldamodel_python_3_5.expElogbeta.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldamodel_python_3_5.id2word -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldamodel_python_3_5.state -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldavowpalwabbit.dict.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/ldavowpalwabbit.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lee.cor -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lee_background.cor -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lee_fasttext -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lee_fasttext.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lee_fasttext.vec -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/lee_fasttext_new.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/miIslita.cor -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/mihalcea_tarau.kw.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/mihalcea_tarau.kwpos.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/mihalcea_tarau.summ.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/mihalcea_tarau.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/mini_newsgroup -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/nmf_model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/non_ascii_fasttext.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/old_keyedvectors_320.dat -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/pang_lee_polarity.cor -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/pang_lee_polarity_fasttext.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/pang_lee_polarity_fasttext.vec -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/para2para_text1.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/para2para_text2.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phraser-3.6.0.model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phraser-no-common-terms.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phraser-no-scoring.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phraser-scoring-str.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phrases-3.6.0.model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phrases-no-common-terms.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phrases-no-scoring.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phrases-scoring-str.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phrases-transformer-new-v3-5-0.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/phrases-transformer-v3-5-0.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/poincare_cp852.tsv -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/poincare_hypernyms.tsv -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/poincare_hypernyms_large.tsv -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/poincare_test_3.4.0 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/poincare_utf8.tsv -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/poincare_vectors.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/pre_0_13_2_model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/pre_0_13_2_model.state -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/pretrained.vec -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/questions-words.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/reproduce.dat -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/reproduce.dat.gz -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/similarities0-1.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/simlex999.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/small_tag_doc_5_iter50 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_corpus_ok.mm -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_corpus_small.mm -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_glove.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_mmcorpus_corrupt.mm -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_mmcorpus_no_index.mm -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_mmcorpus_no_index.mm.bz2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_mmcorpus_no_index.mm.gz -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_mmcorpus_overflow.mm -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_mmcorpus_with_index.mm -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/test_mmcorpus_with_index.mm.index -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.blei -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.blei.index -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.blei.vocab -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.low -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.low.index -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.mallet -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.mallet.index -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.mm -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.mm.index -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.svmlight -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.svmlight.index -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.uci -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.uci.index -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.uci.vocab -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus.xml.bz2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testcorpus_serialization.mm.index -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testlowdistinctwords.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testrepeatedkeywords.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/testsummarization_unrelated.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/tfidf_model.tst -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/tfidf_model.tst.bz2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/tfidf_model_3_2.tst -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/toy-data.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/toy-model-pretrained.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/toy-model.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/toy-model.vec -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/varembed_lee_subcorpus.cor -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/varembed_morfessor.bin -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/varembed_vectors.pkl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/w2v-lee-v0.12.0 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/w2v_keyedvectors_load_test.modeldata -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/w2v_keyedvectors_load_test.vocab -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_3.3 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_old -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_old_sep -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_old_sep.syn0_lockf.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_old_sep.syn1neg.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_c -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_py2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_py3 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_py3_4 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py2.neg_labels.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py2.syn0.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py2.syn0_lockf.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py2.syn1neg.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3.neg_labels.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3.syn0.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3.syn0_lockf.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3.syn1neg.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3_4 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3_4.neg_labels.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3_4.syn0.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3_4.syn0_lockf.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/word2vec_pre_kv_sep_py3_4.syn1neg.npy -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
copying gensim/test/test_data/wordsim353.tsv -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data
creating build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/DTM
copying gensim/test/test_data/DTM/ldaseq_3_0_1_model -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/DTM
copying gensim/test/test_data/DTM/sstats_test.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/DTM
creating build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/PathLineSentences
copying gensim/test/test_data/PathLineSentences/1.txt -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/PathLineSentences
copying gensim/test/test_data/PathLineSentences/2.txt.bz2 -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/PathLineSentences
creating build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.12.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.12.1.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.12.2.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.12.3.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.12.4.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.13.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.13.1.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.13.2.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.13.3.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_0.13.4.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_1.0.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_1.0.1.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_2.0.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_2.1.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_2.2.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_2.3.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_3.0.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_3.1.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_3.2.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_3.3.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
copying gensim/test/test_data/old_d2v_models/d2v_3.4.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_d2v_models
creating build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.12.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.12.1.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.12.2.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.12.3.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.12.4.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.13.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.13.1.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.13.2.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.13.3.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_0.13.4.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_1.0.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_1.0.1.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_2.0.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_2.1.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_2.2.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_2.3.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_3.0.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_3.1.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_3.2.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_3.3.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/test/test_data/old_w2v_models/w2v_3.4.0.mdl -> build/lib.macosx-10.9-x86_64-3.9/gensim/test/test_data/old_w2v_models
copying gensim/models/_utils_any2vec.c -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/_utils_any2vec.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/doc2vec_corpusfile.cpp -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/doc2vec_corpusfile.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/doc2vec_inner.cpp -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/doc2vec_inner.pxd -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/doc2vec_inner.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/fast_line_sentence.h -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/fasttext_corpusfile.cpp -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/fasttext_corpusfile.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/fasttext_inner.c -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/fasttext_inner.pxd -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/fasttext_inner.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/nmf_pgd.c -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/nmf_pgd.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/stdint_wrapper.h -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/voidptr.h -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/word2vec_corpusfile.cpp -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/word2vec_corpusfile.pxd -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/word2vec_corpusfile.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/word2vec_inner.c -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/word2vec_inner.pxd -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/models/word2vec_inner.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/models
copying gensim/corpora/_mmreader.c -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
copying gensim/corpora/_mmreader.pyx -> build/lib.macosx-10.9-x86_64-3.9/gensim/corpora
running build_ext
building 'gensim.models.word2vec_inner' extension
creating build/temp.macosx-10.9-x86_64-3.9
creating build/temp.macosx-10.9-x86_64-3.9/gensim
creating build/temp.macosx-10.9-x86_64-3.9/gensim/models
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/Users/felipedesouzaleite/tutorial-env/include -I/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9 -I/Users/felipedesouzaleite/tutorial-env/lib/python3.9/site-packages/numpy/core/include -c gensim/models/word2vec_inner.c -o build/temp.macosx-10.9-x86_64-3.9/gensim/models/word2vec_inner.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command '/usr/bin/gcc' failed with exit code 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/felipedesouzaleite/tutorial-env/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/t1/5tpwp76556g0tdw2dr2w157c0000gn/T/pip-install-twht3der/gensim_1295893271d04cfcacc5557c5be9e321/setup.py'"'"'; file='"'"'/private/var/folders/t1/5tpwp76556g0tdw2dr2w157c0000gn/T/pip-install-twht3der/gensim_1295893271d04cfcacc5557c5be9e321/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 /private/var/folders/t1/5tpwp76556g0tdw2dr2w157c0000gn/T/pip-record-ykqeapqp/install-record.txt --single-version-externally-managed --compile --install-headers /Users/felipedesouzaleite/tutorial-env/include/site/python3.9/gensim Check the logs for full command output.

bgyori · 2021-07-12T15:20:49Z

bgyori
Jul 12, 2021
Maintainer

Hi @Felipe-Leite, the issue seems to be with the installation of the Gensim package (https://github.com/RaRe-Technologies/gensim). Based on this page: https://ma.ttias.be/mac-os-xcrun-error-invalid-active-developer-path-missing-xcrun/, you could try running

xcode-select --install

to see if that helps with the xcode error.

2 replies

Felipe-Leite Jul 12, 2021
Author

Thanks, that worked!

I tried to run the QKI_forGW file to test but ran into another issue (could it be the python version?):

Felipes-MacBook-Pro:~ felipedesouzaleite$ genewalk --project qki --genes /Users/felipedesouzaleite/Desktop/GeneWalk/QKI_forGW.csv --id_type mgi_id
INFO: [2021-07-12 18:54:10] matplotlib.font_manager - Generating new fontManager, this may take some time...
INFO: [2021-07-12 18:54:10] matplotlib.font_manager - Failed to extract font properties from /System/Library/Fonts/Supplemental/NISC18030.ttf: In FT2Font: Could not set the fontsize (error code 0x17)
INFO: [2021-07-12 18:54:11] matplotlib.font_manager - Failed to extract font properties from /System/Library/Fonts/Apple Color Emoji.ttc: In FT2Font: Could not set the fontsize (error code 0x17)
INFO: [2021-07-12 18:54:11] matplotlib.font_manager - Failed to extract font properties from /System/Library/Fonts/LastResort.otf: tuple indices must be integers or slices, not str
INFO: [2021-07-12 18:54:13] genewalk.cli - Creating qki folder at /Users/felipedesouzaleite/genewalk/qki
INFO: [2021-07-12 18:54:13] genewalk.resources - Using /Users/felipedesouzaleite/genewalk/resources as resource folder.
INFO: [2021-07-12 18:54:13] genewalk.resources - Downloading https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_status&col=md_eg_id&col=md_prot_id&col=md_mgd_id&col=md_rgd_id&col=gd_pub_ensembl_id&status=Approved&status=Entry%20Withdrawn&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit into /Users/felipedesouzaleite/genewalk/resources/hgnc_entries.tsv
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1318, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1400, in connect
server_hostname=server_hostname)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ssl.py", line 407, in wrap_socket
_context=self, _session=session)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ssl.py", line 817, in init
self.do_handshake()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ssl.py", line 1077, in do_handshake
self._sslobj.do_handshake()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ssl.py", line 689, in do_handshake
self._sslobj.do_handshake()
ssl.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:847)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.6/bin/genewalk", line 11, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/genewalk/cli.py", line 157, in main
run_main(args)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/genewalk/cli.py", line 195, in run_main
genes = read_gene_list(args.genes, args.id_type, rm)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/genewalk/gene_lists.py", line 31, in read_gene_list
gene_mapper = GeneMapper(resource_manager)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/genewalk/gene_lists.py", line 232, in init
self.hgnc_file = self.resource_manager.get_hgnc()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/genewalk/resources.py", line 78, in get_hgnc
download_url(url, fname)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/genewalk/resources.py", line 125, in download_url
urllib.request.urlretrieve(url, fname)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 248, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 223, in urlopen
return opener.open(url, data, timeout)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 526, in open
response = self._open(req, data)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 544, in _open
'_open', req)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain
result = func(*args)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1361, in https_open
context=self._context, check_hostname=self._check_hostname)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1320, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:847)>

ri23 Jul 12, 2021
Maintainer

Hi @Felipe-Leite

This is an issue with your SSL certificate, which is a problem unrelated to GeneWalk.
Please see the workaround answered before, in case you cannot adjust your SSL certificate.
#44 (comment)

Felipe-Leite · 2021-07-13T12:35:17Z

Felipe-Leite
Jul 13, 2021
Author

Great, it worked. Of notice, I used QKI_for GW list and I got several warning message like this: WARNING: [2021-07-12 21:50:17] genewalk.gene_lists - Could not get HGNC ID for MGI ID 2686053 Otherwise, it worked very well. Also, is there a way to make GW consider the fold change in the analyses? Is it a problem to have long non-coding RNA, pseudogenes, etc within the input list? Att, Felipe de Souza Leite, PhD Genetics and Genomics - Kunkel's lab Boston Children's Hospital

…

________________________________ Pathology - Pourquié's Lab Brigham & Women's Hospital

______________________________ Centro de Pesquisa sobre o Genoma Humano e Células-Tronco Universidade de São Paulo (USP) São Paulo, Brasil.

On Jul 12, 2021, at 7:09 PM, Robert Ietswaart ***@***.***> wrote: Hi @Felipe-Leite <https://github.com/Felipe-Leite> This is an issue with your SSL certificate, which is a problem unrelated to GeneWalk. Please see the workaround answered before, in case you cannot adjust your SSL certificate. #44 (comment) <#44 (comment)> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#63 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEQGLJ4KFVBX3PQTXKGMIVLTXNYZTANCNFSM5AHAEQTA>.

0 replies

Felipe-Leite · 2021-07-13T12:55:38Z

Felipe-Leite
Jul 13, 2021
Author

I’m sorry, I just notice that the warning messages are normal. On Tue, Jul 13, 2021 at 8:35 AM Felipe de Souza Leite < ***@***.***> wrote:

…

Great, it worked. Of notice, I used QKI_for GW list and I got several warning message like this: WARNING: [2021-07-12 21:50:17] genewalk.gene_lists - Could not get HGNC ID for MGI ID 2686053 Otherwise, it worked very well. Also, is there a way to make GW consider the fold change in the analyses? Is it a problem to have long non-coding RNA, pseudogenes, etc within the input list? Att, Felipe de Souza Leite, PhD Genetics and Genomics - Kunkel's lab Boston Children's Hospital ________________________________ Pathology - Pourquié's Lab Brigham & Women's Hospital ______________________________ Centro de Pesquisa sobre o Genoma Humano e Células-Tronco Universidade de São Paulo (USP) São Paulo, Brasil. On Jul 12, 2021, at 7:09 PM, Robert Ietswaart ***@***.***> wrote: Hi @Felipe-Leite <https://github.com/Felipe-Leite> This is an issue with your SSL certificate, which is a problem unrelated to GeneWalk. Please see the workaround answered before, in case you cannot adjust your SSL certificate. #44 (comment) <#44 (comment)> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#63 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEQGLJ4KFVBX3PQTXKGMIVLTXNYZTANCNFSM5AHAEQTA> .

1 reply

ri23 Jul 13, 2021
Maintainer

Hi @Felipe-Leite
Great that it works,
regarding the fold changes: GW does not take them into account, in case they are important for your analysis you can determine the input list for GW based on a fold change cut off for instance. For bulk RNAseq with enough replicates to ensure statistical power, we have used a cut off based on the DEseq p-adj values. In the end, how you decide your input list is totally up to you.

non-coding RNA and pseudogenes etc: this is fine to include, but bear in mind that these genes often do not have any GO annotations associated. In that case, GW can not make any relevance prediction. Also sometimes these genes do not have a UniProt ID associated, in that case the gene will be automatically filtered out by GW with a similar warning message as you got for MGI ID 2686053. If you are lacking statistical power with DE (not getting many DE genes), I would recommend prefiltering for protein coding genes and then run DE and base the GW input list on that. But again, this is up totally up to you.

Good luck,
Robert

Felipe-Leite · 2021-07-13T15:15:18Z

Felipe-Leite
Jul 13, 2021
Author

Thanks, that’s great. Congratulations on the work. Att, Felipe de Souza Leite, PhD Genetics and Genomics - Kunkel's lab Boston Children's Hospital

…

________________________________ Pathology - Pourquié's Lab Brigham & Women's Hospital

______________________________ Centro de Pesquisa sobre o Genoma Humano e Células-Tronco Universidade de São Paulo (USP) São Paulo, Brasil.

On Jul 13, 2021, at 11:08 AM, Robert Ietswaart ***@***.***> wrote: Hi @Felipe-Leite <https://github.com/Felipe-Leite> Great that it works, regarding the fold changes: GW does not take them into account, in case they are important for your analysis you can determine the input list for GW based on a fold change cut off for instance. For bulk RNAseq with enough replicates to ensure statistical power, we have used a cut off based on the DEseq p-adj values. In the end, how you decide your input list is totally up to you. non-coding RNA and pseudogenes etc: this is fine to include, but bear in mind that these genes often do not have any GO annotations associated. In that case, GW can not make any relevance prediction. Also sometimes these genes do not have a UniProt ID associated, in that case the gene will be automatically filtered out by GW with a similar warning message as you got for MGI ID 2686053. If you are lacking statistical power with DE (not getting many DE genes), I would recommend prefiltering for protein coding genes and then run DE and base the GW input list on that. But again, this is up totally up to you. Good luck, Robert — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#63 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEQGLJ3L5IFQUF3AYDGC5U3TXRJH7ANCNFSM5AHAEQTA>.

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Erros when downloading genewalk even with versions higher than 3.5 #63

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Erros when downloading genewalk even with versions higher than 3.5 #63

Felipe-Leite Jul 12, 2021

Replies: 4 comments · 3 replies

bgyori Jul 12, 2021 Maintainer

Felipe-Leite Jul 12, 2021 Author

ri23 Jul 12, 2021 Maintainer

Felipe-Leite Jul 13, 2021 Author

Felipe-Leite Jul 13, 2021 Author

ri23 Jul 13, 2021 Maintainer

Felipe-Leite Jul 13, 2021 Author

Felipe-Leite
Jul 12, 2021

Replies: 4 comments 3 replies

bgyori
Jul 12, 2021
Maintainer

Felipe-Leite Jul 12, 2021
Author

ri23 Jul 12, 2021
Maintainer

Felipe-Leite
Jul 13, 2021
Author

Felipe-Leite
Jul 13, 2021
Author

ri23 Jul 13, 2021
Maintainer

Felipe-Leite
Jul 13, 2021
Author