Installation Errors

[felipehcoutinho]

Hi, first I would like to congratulate you and your team on putting together this amazing tool.

I ran on some issues when installing it from git with the specified commands. I ran:

git clone https://github.com/WeiliWw/VirHostMatcher-Net.git rohit@flamingo:~/felipe$ cd VirHostMatcher-Net/ CC=g++ python setup.py install --install-platlib=./src/

And received the following errors:

running install running build running build_ext building 'tools' extension g++ -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/rohit/.local/lib/python2.7/site-packages/numpy/core/include -I./src/tools/ -I/usr/include/python2.7 -c ./src/tools/tools.cpp -o build/temp.linux-x86_64-2.7/./src/tools/tools.o -w -std=c++11 ./src/tools/tools.cpp:55:27: error: variable ‘PyModuleDef toolsmodule’ has initializer but incomplete type static struct PyModuleDef toolsmodule = { ^ ./src/tools/tools.cpp:56:5: error: ‘PyModuleDef_HEAD_INIT’ was not declared in this scope PyModuleDef_HEAD_INIT, ^ ./src/tools/tools.cpp: In function ‘void PyInit_tools()’: ./src/tools/tools.cpp:67:40: error: ‘PyModule_Create’ was not declared in this scope return PyModule_Create(&toolsmodule); ^ ./src/tools/tools.cpp:67:40: error: return-statement with a value, in function returning 'void' [-fpermissive] error: command 'g++' failed with exit status 1

Below are my system specs: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 144 On-line CPU(s) list: 0-143 Thread(s) per core: 2 Core(s) per socket: 18 Socket(s): 4 NUMA node(s): 4 Vendor ID: GenuineIntel CPU family: 6 Model: 85 Model name: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz Stepping: 4 CPU MHz: 2600.730 CPU max MHz: 2301,0000 CPU min MHz: 1000,0000 BogoMIPS: 4602.37 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 25344K NUMA node0 CPU(s): 0-17,72-89 NUMA node1 CPU(s): 18-35,90-107 NUMA node2 CPU(s): 36-53,108-125 NUMA node3 CPU(s): 54-71,126-143

And the output of pip freeze:

adium-theme-ubuntu==0.3.4 asn1crypto==0.24.0 awscli==1.15.4 backports.lzma==0.0.3 bcbio-gff==0.6.4 beautifulsoup4==4.4.1 biolib==0.0.46 biom-format==2.1.7 biopython==1.66 botocore==1.10.4 certifi==2017.11.5 cffi==1.11.2 chardet==3.0.4 checkm-genome==1.0.11 Click==7.0 colorama==0.3.7 comparem==0.0.23 crcmod==1.7 cryptography==2.1.4 cssselect==0.9.1 cvxopt==1.1.4 cycler==0.10.0 decorator==4.0.6 DendroPy==4.3.0 docutils==0.14 enum34==1.1.6 ete2==2.3.10 flye==2.7b0 future==0.16.0 futures==3.2.0 gmpy==1.17 gtdbtk==0.1.3 h5py==2.8.0 helperlibs==0.1.9 html5lib==0.999 HTSeq==0.12.4 humann2==2.8.1 idna==2.6 ipaddress==1.0.19 ipython==2.4.1 jdcal==1.0 Jinja2==2.8 jmespath==0.9.3 joblib==0.9.4 kraken-biom==1.0.1 lxml==3.5.0 MarkupSafe==0.23 matplotlib==1.5.3 mercurial==4.7.2 mpld3==0.3 mpmath==0.19 ncbi-genome-download==0.2.5 networkx==1.11 nose==1.3.7 numexpr==2.4.3 numpy==1.16.6 openpyxl==2.3.0 pandas==0.23.4 patsy==0.4.1 pexpect==4.0.1 Pillow==3.1.2 Pmw==1.3.2 ptyprocess==0.5 py==1.4.31 pyasn1==0.4.2 pycparser==2.18 pycrypto==2.6.1 pycurl==7.43.0 pyExcelerator==0.6.4.1 pyglet==1.1.4 pymol==1.7.2.1 PyMySQL==0.7.2 pyOpenSSL==17.5.0 pyparsing==2.0.3 pyqi==0.3.2 pyquery==1.2.9 pysam==0.16.0.1 Pyste==0.9.10 pysvg==0.2.2 pytest==2.8.7 python-dateutil==2.6.1 pytz==2014.10 PyYAML==3.12 pyzmq==15.2.0 reportlab==3.3.0 requests==2.18.4 rsa==3.4.2 s3transfer==0.1.13 scikit-learn==0.17 scipy==0.17.0 simplegeneric==0.8.1 simplejson==3.8.1 six==1.11.0 statsmodels==0.6.1 sympy==0.7.6.1 tables==3.2.2 tornado==4.2.1 tqdm==4.43.0 unity-lens-photos==1.0 urllib3==1.22 vboxapi==1.0 virtualenv==15.0.1 WebOb==1.5.1 xlrd==0.9.4 xlwt==0.7.5

Regards,

Felipe

[WeiliWw]

Hi Felipe,

Thanks for sharing the error info! Seems you are using Python2. However, we need Python3.4+ to work with our software. Please check the Dependencies in README for details.

Best, Weili

[WXYWD]

Hi, I have some trouble when I run the pymol.Could you please help me sovle it? Thanks. $ pymol

:1: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses QFactoryLoader::QFactoryLoader() checking directory path "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms" ... QFactoryLoader::QFactoryLoader() looking at "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqeglfs.so" Found metadata in lib /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqeglfs.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "eglfs" ] }, "archreq": 0, "className": "QEglFSIntegrationPlugin", "debug": false, "version": 330752 } Got keys from plugin meta data ("eglfs") QFactoryLoader::QFactoryLoader() looking at "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqlinuxfb.so" Found metadata in lib /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqlinuxfb.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "linuxfb" ] }, "archreq": 0, "className": "QLinuxFbIntegrationPlugin", "debug": false, "version": 330752 } Got keys from plugin meta data ("linuxfb") QFactoryLoader::QFactoryLoader() looking at "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqminimal.so" Found metadata in lib /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqminimal.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "minimal" ] }, "archreq": 0, "className": "QMinimalIntegrationPlugin", "debug": false, "version": 330752 } Got keys from plugin meta data ("minimal") QFactoryLoader::QFactoryLoader() looking at "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqminimalegl.so" Found metadata in lib /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqminimalegl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "minimalegl" ] }, "archreq": 0, "className": "QMinimalEglIntegrationPlugin", "debug": false, "version": 330752 } Got keys from plugin meta data ("minimalegl") QFactoryLoader::QFactoryLoader() looking at "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqoffscreen.so" Found metadata in lib /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqoffscreen.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "offscreen" ] }, "archreq": 0, "className": "QOffscreenIntegrationPlugin", "debug": false, "version": 330752 } Got keys from plugin meta data ("offscreen") QFactoryLoader::QFactoryLoader() looking at "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqvnc.so" Found metadata in lib /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqvnc.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "vnc" ] }, "archreq": 0, "className": "QVncIntegrationPlugin", "debug": false, "version": 330752 } Got keys from plugin meta data ("vnc") QFactoryLoader::QFactoryLoader() looking at "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqxcb.so" Found metadata in lib /usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqxcb.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "xcb" ] }, "archreq": 0, "className": "QXcbIntegrationPlugin", "debug": false, "version": 330752 } Got keys from plugin meta data ("xcb") QFactoryLoader::QFactoryLoader() checking directory path "/usr/bin/platforms" ... loaded library "/usr/lib/x86_64-linux-gnu/qt5/plugins/platforms/libqxcb.so" qt.qpa.xcb: could not connect to display qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb. Aborted

[WeiliWw]

Seems this pymol command is not related to our software.