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gem-pasteur / macsyfinder

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
GNU General Public License v3.0
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sudo python setup.py install: "build/scripts-2.7/macsyview: No such file or directory" #27

Closed vbrover closed 5 years ago

vbrover commented 5 years ago

Thank you! Could build using python 2.7.15.

New issue:

$ cd macsyfinder-macsyfinder-1.0.5
$ sudo python setup.py install
running install
moving build/lib/macsypy/config.py.tmp -> build/lib/macsypy/config.py
moving build/lib/macsypy/registries.py.tmp -> build/lib/macsypy/registries.py
moving build/lib/macsypy/__init__.py.tmp -> build/lib/macsypy/__init__.py
running build
running build_py
running build_scripts
macsyview not found

Unit tests are available. It is _highly_ recommended to run tests now.
to run test, run 'python setup.py test -vv'
running install_lib
creating /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/database.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/gene.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/macsypy_error.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/report.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/search_genes.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/search_systems.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/system.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/system_parser.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/utils.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/__init__.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/config.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/gene.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/report.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/database.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/macsypy_error.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/system.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/registries.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/utils.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/system_parser.pyc -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/config.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/registries.py -> /usr/lib/python2.7/site-packages/macsypy
copying build/lib/macsypy/__init__.py -> /usr/lib/python2.7/site-packages/macsypy
byte-compiling /usr/lib/python2.7/site-packages/macsypy/search_genes.py to search_genes.pyc
byte-compiling /usr/lib/python2.7/site-packages/macsypy/search_systems.py to search_systems.pyc
byte-compiling /usr/lib/python2.7/site-packages/macsypy/config.py to config.pyc
byte-compiling /usr/lib/python2.7/site-packages/macsypy/registries.py to registries.pyc
byte-compiling /usr/lib/python2.7/site-packages/macsypy/__init__.py to __init__.pyc
running install_scripts
copying build/scripts-2.7/macsyfinder -> /usr/bin
changing mode of /usr/bin/macsyfinder to 755
running install_data
creating /usr/local/share/macsyfinder
creating /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIA.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIB.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIC.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeID.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIE.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIF.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIIA.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIIB.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIIIA.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIIIB.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIIIU.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIIU.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeIU.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS-TypeU.xml -> /usr/local/share/macsyfinder/DEF
copying data/DEF/CAS.xml -> /usr/local/share/macsyfinder/DEF
creating /usr/local/share/macsyfinder/profiles
copying data/profiles/cas10_TypeIIIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas10_TypeIIIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas10d_TypeID.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeI-II-III.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeIC.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeID.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeIE.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeIF.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeII.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas1_TypeU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas2_TypeI-II-III.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas2_TypeIE.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas3-cas2_TypeIF.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas3_TypeI.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas3_TypeID.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas3_TypeIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas3a_TypeI.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas4_TypeI-II.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas4_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas4_TypeU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas5_TypeI.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas5_TypeIE.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas5a2_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas5a_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas5b2_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas5b_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas5c2_TypeIC.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas5c_TypeIC.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas6_TypeI-III.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas6_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas6_TypeIE.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas6_TypeIF.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas7_TypeI.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas7_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas7_TypeIE.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas7b2_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas7b3_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas7b_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas7c2_TypeIC.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas7c_TypeIC.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8a1a2_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8a1a3_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8a1b2_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8a1b3_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8a1b_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8a2a2_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8a2a_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8b_TypeIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8c2_TypeIC.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas8c_TypeIC.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas9_TypeII.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cas9_TypeIIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/casRa_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cmr1_TypeIIIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cmr3_TypeIIIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cmr4_TypeIIIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cmr5_TypeIIIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cmr6_TypeIIIB.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cpf1_TypeU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csa5_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csaX_TypeIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csb1_TypeIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csb2_TypeIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csb3_TypeIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csc1_TypeID.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csc2_TypeID.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cse1_TypeIE.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/cse2_TypeIE.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csf1_TypeU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csf2_TypeU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csf3_TypeU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csf4_TypeU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csm2_TypeIIIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csm3_TypeIIIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csm4_TypeIIIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csm5_TypeIIIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csm6_TypeIIIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csn2_TypeIIA.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csx10_TypeIIIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csx16_TypeIIIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csx17_TypeIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csx1u2_TypeIIIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csx1u_TypeIIIU.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csy1_TypeIF.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csy2_TypeIF.hmm -> /usr/local/share/macsyfinder/profiles
copying data/profiles/csy3_TypeIF.hmm -> /usr/local/share/macsyfinder/profiles
creating /usr/local/share/macsyfinder/sequence_data
copying data/sequence_data/datatest_gembase.fasta -> /usr/local/share/macsyfinder/sequence_data
copying data/sequence_data/datatest_gembase.topology -> /usr/local/share/macsyfinder/sequence_data
copying data/sequence_data/results.macsyfinder.json -> /usr/local/share/macsyfinder/sequence_data
creating /usr/local/share/macsyfinder/macsyview
creating /usr/local/share/macsyfinder/macsyview/app
WARNING the document macsyview/app/ cannot be found, installation skipped
running install_egg_info
Writing /usr/lib/python2.7/site-packages/macsyfinder-1.0.5-py2.7.egg-info
running install_doc
creating /usr/local/share/doc
creating /usr/local/share/doc/macsyfinder
creating /usr/local/share/doc/macsyfinder/html
WARNING the document doc/_build/html/ cannot be found, installation skipped
creating /usr/local/share/doc/macsyfinder/pdf
WARNING the document doc/_build/latex/Macsyfinder.pdf cannot be found, installation skipped
running install_conf
creating /etc/macsyfinder
copying etc/macsyfinder.conf -> /etc/macsyfinder/macsyfinder.conf.new
moving /etc/macsyfinder/macsyfinder.conf.new.tmp -> /etc/macsyfinder/macsyfinder.conf.new
running install_viewer
error: build/scripts-2.7/macsyview: No such file or directory

Error code = 1.

bneron commented 5 years ago

if you want to build macsyfinder from the github repository you must add --no-viewer option during the installation phase as the viewer is in an other repository. to check all available instalation options python setup.py install --help

vbrover commented 4 years ago

I was following the instructions on the https://github.com/gem-pasteur/macsyfinder page. This worked:

sudo python setup.py install --no-viewer

Thank you!