snayfach / MicrobeCensus

MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
http://genomebiology.com/2015/16/1/51
GNU General Public License v3.0
41 stars 16 forks source link

Something wrong when put 'python setup.py install' #30

Closed Rooobben closed 1 year ago

Rooobben commented 1 year ago

/envs/ham/lib/python3.7/site-packages/setuptools/command/install.py: 37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other s tandards-based tools. setuptools.SetuptoolsDeprecationWarning, /envs/ham/lib/python3.7/site-packages/setuptools/command/easy_instal l.py:147: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. EasyInstallDeprecationWarning, /envs/ham/lib/python3.7/site-packages/pkg_resources/init.py:125: PkgResourcesDeprecationWarning: 4.0.0-unsupported is an invalid version and will not be suppor ted in a future release PkgResourcesDeprecationWarning, running bdist_egg running egg_info creating MicrobeCensus.egg-info writing MicrobeCensus.egg-info/PKG-INFO writing dependency_links to MicrobeCensus.egg-info/dependency_links.txt writing requirements to MicrobeCensus.egg-info/requires.txt writing top-level names to MicrobeCensus.egg-info/top_level.txt writing manifest file 'MicrobeCensus.egg-info/SOURCES.txt' reading manifest file 'MicrobeCensus.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'training/README.txt' adding license file 'LICENSE.txt' writing manifest file 'MicrobeCensus.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/microbe_census copying microbe_census/microbe_census.py -> build/lib/microbe_census copying microbe_census/init.py -> build/lib/microbe_census creating build/lib/tests copying tests/test_microbe_census.py -> build/lib/tests copying tests/init.py -> build/lib/tests creating build/lib/microbe_census/data copying microbe_census/data/pars.map -> build/lib/microbe_census/data copying microbe_census/data/rapdb_2.15 -> build/lib/microbe_census/data copying microbe_census/data/read_len.map -> build/lib/microbe_census/data copying microbe_census/data/gene_fam.map -> build/lib/microbe_census/data copying microbe_census/data/coefficients.map -> build/lib/microbe_census/data copying microbe_census/data/rapdb_2.15.info -> build/lib/microbe_census/data copying microbe_census/data/gene_len.map -> build/lib/microbe_census/data copying microbe_census/data/weights.map -> build/lib/microbe_census/data creating build/lib/microbe_census/bin copying microbe_census/bin/rapsearch_Darwin_2.15 -> build/lib/microbe_census/bin copying microbe_census/bin/rapsearch_Linux_2.15 -> build/lib/microbe_census/bin copying microbe_census/bin/prerapsearch_Darwin_2.15 -> build/lib/microbe_census/bin copying microbe_census/bin/prerapsearch_Linux_2.15 -> build/lib/microbe_census/bin creating build/lib/microbe_census/example copying microbe_census/example/example.fa.gz -> build/lib/microbe_census/example copying microbe_census/example/example.fq.gz -> build/lib/microbe_census/example creating build/lib/tests/data copying tests/data/metagenome.fa.gz -> build/lib/tests/data copying tests/data/community.txt -> build/lib/tests/data creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/microbe_census creating build/bdist.linux-x86_64/egg/microbe_census/data copying build/lib/microbe_census/data/pars.map -> build/bdist.linux-x86_64/egg/microbe_census/d ata copying build/lib/microbe_census/data/rapdb_2.15 -> build/bdist.linux-x86_64/egg/microbe_census /data copying build/lib/microbe_census/data/read_len.map -> build/bdist.linux-x86_64/egg/microbe_cens us/data copying build/lib/microbe_census/data/gene_fam.map -> build/bdist.linux-x86_64/egg/microbe_cens us/data copying build/lib/microbe_census/data/coefficients.map -> build/bdist.linux-x8664/egg/microbe census/data copying build/lib/microbe_census/data/rapdb_2.15.info -> build/bdist.linux-x86_64/egg/microbe_c ensus/data copying build/lib/microbe_census/data/gene_len.map -> build/bdist.linux-x86_64/egg/microbe_cens us/data copying build/lib/microbe_census/data/weights.map -> build/bdist.linux-x86_64/egg/microbe_censu s/data creating build/bdist.linux-x86_64/egg/microbe_census/example copying build/lib/microbe_census/example/example.fa.gz -> build/bdist.linux-x8664/egg/microbe census/example copying build/lib/microbe_census/example/example.fq.gz -> build/bdist.linux-x8664/egg/microbe census/example copying build/lib/microbe_census/microbe_census.py -> build/bdist.linux-x86_64/egg/microbe_cens us creating build/bdist.linux-x86_64/egg/microbe_census/bin copying build/lib/microbe_census/bin/rapsearch_Darwin_2.15 -> build/bdist.linux-x86_64/egg/micr obe_census/bin copying build/lib/microbe_census/bin/rapsearch_Linux_2.15 -> build/bdist.linux-x86_64/egg/micro be_census/bin copying build/lib/microbe_census/bin/prerapsearch_Darwin_2.15 -> build/bdist.linux-x86_64/egg/m icrobe_census/bin copying build/lib/microbe_census/bin/prerapsearch_Linux_2.15 -> build/bdist.linux-x86_64/egg/mi crobe_census/bin copying build/lib/microbe_census/init.py -> build/bdist.linux-x86_64/egg/microbe_census creating build/bdist.linux-x86_64/egg/tests creating build/bdist.linux-x86_64/egg/tests/data copying build/lib/tests/data/metagenome.fa.gz -> build/bdist.linux-x86_64/egg/tests/data copying build/lib/tests/data/community.txt -> build/bdist.linux-x86_64/egg/tests/data copying build/lib/tests/test_microbe_census.py -> build/bdist.linux-x86_64/egg/tests copying build/lib/tests/init.py -> build/bdist.linux-x86_64/egg/tests byte-compiling build/bdist.linux-x86_64/egg/microbe_census/microbe_census.py to microbe_census. cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/microbe_census/init.py to init.cpython-37.p yc byte-compiling build/bdist.linux-x86_64/egg/tests/test_microbe_census.py to test_microbe_census .cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/tests/init.py to init.cpython-37.pyc changing mode of build/bdist.linux-x86_64/egg/microbe_census/bin/rapsearch_Darwin_2.15 to 1141 changing mode of build/bdist.linux-x86_64/egg/microbe_census/bin/rapsearch_Linux_2.15 to 1141 changing mode of build/bdist.linux-x86_64/egg/microbe_census/bin/prerapsearch_Darwin_2.15 to 10 41 changing mode of build/bdist.linux-x86_64/egg/microbe_census/bin/prerapsearch_Linux_2.15 to 114 1 creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/scripts-3.7 copying and adjusting scripts/run_microbe_census.py -> build/scripts-3.7 changing mode of build/scripts-3.7/run_microbe_census.py from 664 to 775 creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-3.7/run_microbe_census.py -> build/bdist.linux-x86_64/egg/EGG-INFO/script s changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/run_microbe_census.py to 775 copying MicrobeCensus.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying MicrobeCensus.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MicrobeCensus.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MicrobeCensus.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MicrobeCensus.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... microbe_census.pycache.microbe_census.cpython-37: module references file tests.pycache.test_microbe_census.cpython-37: module references file creating dist creating 'dist/MicrobeCensus-1.1.0-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it error: [Errno 13] Permission denied: 'build/bdist.linux-x86_64/egg/microbe_census/bin/prerapsea rch_Darwin_2.15'

Then I used "MicrobeCensus/build/scripts-3.7/run_microbe_census.py", it prompted me "ModuleNotFoundError: No module named 'microbe_cencus'"

P.S. I can't sudo

wanxn518 commented 1 year ago

I also encountered the same problem, please have any good solution, thank you very much