Installation errors

[slevu]

Hi, I cannot install hivclustering on OSX 10.10.5 with Python3 installed. After cloning HyPhy, the first step of installing dependencies (cd [hyphy]/src/lib and python3 setup.py install) is throwing me the following errors. Thanks for your help. Stephane

... 14 warnings generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DSQLITE_PTR_SIZE=sizeof(long) -DUNIX -DMP -DMP2 -D_SLKP_LFENGINEREWRITE -DAFYP_REWRITE_BGM -DHEADLESS -D_HYPHYLIBDIRECTORY="/usr/local/lib/hyphy" -D__HYPHY_64__ -I/Users/stephanelevu/Documents/hyphy/src/core/include -I/Users/stephanelevu/Documents/hyphy/src/new/include -I/Users/stephanelevu/Documents/hyphy/src/gui/include -I/Users/stephanelevu/Documents/hyphy/src/lib/Link -I/Users/stephanelevu/Documents/hyphy/contrib -I/Users/stephanelevu/Documents/hyphy/contrib/SQLite-3.8.2 -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c /Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp -o build/temp.macosx-10.6-intel-3.5/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.o -Wno-int-to-pointer-cast -Wno-char-subscripts -Wno-sign-compare -Wno-parentheses -Wno-uninitialized -Wno-unused-variable -Wno-shorten-64-to-32 -fsigned-char -O3 -fpermissive -fPIC /Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:2376:23: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] res = SWIG_AddCast(res);

/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:2379:23: warning: 
      explicitly assigning value of variable of type 'int' to itself
      [-Wself-assign]
                  res = SWIG_AddCast(res);  
                  ~~~ ^              ~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5636:5: error: 
      cannot initialize a member subobject of type 'unaryfunc' (aka 'PyObject
      _(_)(PyObject _)') with an rvalue of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)'): different number of parameters (1 vs 2)
    (binaryfunc) 0,                           /_ nb_add _/
    ^~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5637:5: error: 
      cannot initialize a member subobject of type 'unaryfunc' (aka 'PyObject
      *(_)(PyObject _)') with an rvalue of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)'): different number of parameters (1 vs 2)
    (binaryfunc) 0,                           /_ nb_subtract _/
    ^~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5638:5: error: 
      cannot initialize a member subobject of type 'unaryfunc' (aka 'PyObject
      *(_)(PyObject _)') with an rvalue of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)'): different number of parameters (1 vs 2)
    (binaryfunc) 0,                           /_ nb_multiply _/
    ^~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5691:5: error: 
      cannot initialize a member subobject of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)') with an rvalue of type 'lenfunc' (aka
      'Py_ssize_t (_)(PyObject _)'): different number of parameters (2 vs 1)
    (lenfunc) 0,                              /_ mp_length _/
    ^~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5693:5: error: 
      cannot initialize a member subobject of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)') with an rvalue of type 'objobjargproc' (aka
      'int (_)(PyObject _, PyObject *, PyObject *)'): different number of
      parameters (2 vs 3)
    (objobjargproc) 0,                        /_ mp_ass_subscript _/
    ^~~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5698:5: error: 
      cannot initialize a member subobject of type 'objobjargproc' (aka 'int
      (_)(PyObject _, PyObject *, PyObject *)') with an rvalue of type
      'ssizeargfunc' (aka 'PyObject *(_)(PyObject _, Py_ssize_t)'): different
      number of parameters (3 vs 2)
    (ssizeargfunc) 0,                         /_ sq_repeat _/
    ^~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5723:5: error: 
      cannot initialize a member subobject of type 'lenfunc' (aka 'Py_ssize_t
      (_)(PyObject _)') with an rvalue of type 'getbufferproc' (aka 'int
      (_)(PyObject _, Py_buffer *, int)'): different number of parameters
      (1 vs 3)
    (getbufferproc) 0,                        /_ bf_getbuffer _/
    ^~~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5724:5: error: 
      cannot initialize a member subobject of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)') with an rvalue of type 'releasebufferproc'
      (aka 'void (_)(PyObject _, Py_buffer *)'): type mismatch at 2nd parameter
      ('PyObject *' (aka '_object *') vs 'Py_buffer *' (aka 'bufferinfo *'))
    (releasebufferproc) 0,                    /_ bf_releasebuffer _/
    ^~~~~~~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5727:5: error: 
      cannot initialize a member subobject of type 'getbufferproc' (aka 'int
      (_)(PyObject _, Py_buffer *, int)') with an rvalue of type 'PyObject *'
      (aka '_object *')
    (PyObject_) 0,                            /\* ht_name _/
    ^~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5728:5: error: 
      cannot initialize a member subobject of type 'releasebufferproc' (aka
      'void (_)(PyObject _, Py_buffer *)') with an rvalue of type 'PyObject *'
      (aka '_object *')
    (PyObject_) 0,                            /\* ht_slots _/
    ^~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5727:5: warning: 
      suggest braces around initialization of subobject [-Wmissing-braces](PyObject*) 0,                            /_ ht_name _/
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5834:5: error: 
      cannot initialize a member subobject of type 'unaryfunc' (aka 'PyObject
      *(_)(PyObject _)') with an rvalue of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)'): different number of parameters (1 vs 2)
    (binaryfunc) 0,                           /_ nb_add _/
    ^~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5835:5: error: 
      cannot initialize a member subobject of type 'unaryfunc' (aka 'PyObject
      *(_)(PyObject _)') with an rvalue of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)'): different number of parameters (1 vs 2)
    (binaryfunc) 0,                           /_ nb_subtract _/
    ^~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5836:5: error: 
      cannot initialize a member subobject of type 'unaryfunc' (aka 'PyObject
      *(_)(PyObject _)') with an rvalue of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)'): different number of parameters (1 vs 2)
    (binaryfunc) 0,                           /_ nb_multiply _/
    ^~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5889:5: error: 
      cannot initialize a member subobject of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)') with an rvalue of type 'lenfunc' (aka
      'Py_ssize_t (_)(PyObject _)'): different number of parameters (2 vs 1)
    (lenfunc) 0,                              /_ mp_length _/
    ^~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5891:5: error: 
      cannot initialize a member subobject of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)') with an rvalue of type 'objobjargproc' (aka
      'int (_)(PyObject _, PyObject *, PyObject *)'): different number of
      parameters (2 vs 3)
    (objobjargproc) 0,                        /_ mp_ass_subscript _/
    ^~~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5896:5: error: 
      cannot initialize a member subobject of type 'objobjargproc' (aka 'int
      (_)(PyObject _, PyObject *, PyObject *)') with an rvalue of type
      'ssizeargfunc' (aka 'PyObject *(_)(PyObject _, Py_ssize_t)'): different
      number of parameters (3 vs 2)
    (ssizeargfunc) 0,                         /_ sq_repeat _/
    ^~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5921:5: error: 
      cannot initialize a member subobject of type 'lenfunc' (aka 'Py_ssize_t
      (_)(PyObject _)') with an rvalue of type 'getbufferproc' (aka 'int
      (_)(PyObject _, Py_buffer *, int)'): different number of parameters
      (1 vs 3)
    (getbufferproc) 0,                        /_ bf_getbuffer _/
    ^~~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5922:5: error: 
      cannot initialize a member subobject of type 'binaryfunc' (aka 'PyObject
      *(_)(PyObject _, PyObject *)') with an rvalue of type 'releasebufferproc'
      (aka 'void (_)(PyObject _, Py_buffer *)'): type mismatch at 2nd parameter
      ('PyObject *' (aka '_object *') vs 'Py_buffer *' (aka 'bufferinfo *'))
    (releasebufferproc) 0,                    /_ bf_releasebuffer _/
    ^~~~~~~~~~~~~~~~~~~~~
/Users/stephanelevu/Documents/hyphy/src/lib/SWIGWrappers/THyPhy_py3.cpp:5925:5: error: 
      cannot initialize a member subobject of type 'getbufferproc' (aka 'int
      (_)(PyObject _, Py_buffer *, int)') with an rvalue of type 'PyObject *'
      (aka '_object *')
    (PyObject_) 0,                            /\* ht_name */
    ^~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
3 warnings and 20 errors generated.
error: command '/usr/bin/clang' failed with exit status 1

[spond]

Hi @slevu ,

This could be a version incompatibility somewhere. @stevenweaver should be able to help you out

Sergei

[stevenweaver]

Hi Stephane,

Yes, this is an issue that appears when attempting to install with Python 3.5. I will see if I can apply a patch, and will report back shortly.

Regards, Steven

[stevenweaver]

Hello Stephane,

I've applied a patch for python 3.5 compatibility. Please ensure that you are using gcc for compilation as well. This can be achieved by using the following commands:

brew install gcc
export CC=/usr/local/bin/gcc-5;export CXX=/usr/local/bin/g++-5;
python3 setup.py install

Please let me know if you run into additional issues.

Regards, Steven

[slevu]

Hi Steven, Many thanks for taking care of it. Having updated to gcc-5 and launched your proposed commands, I still have some issues (see below). Best regards Stephane

---

running install running build running build_py running build_ext building '_HyPhy' extension /usr/local/bin/gcc-5 -fno-strict-aliasing -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DSQLITE_PTR_SIZE=sizeof(long) -DUNIX -DMP -DMP2 -D_SLKP_LFENGINEREWRITE -DAFYP_REWRITE_BGM -DHEADLESS -D_HYPHYLIBDIRECTORY="/usr/local/lib/hyphy" -D__HYPHY_64__ -I/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/include -I/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/new/include -I/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/gui/include -I/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/lib/Link -I/Volumes/hiv_mol_epi/stephane/softwares/hyphy/contrib -I/Volumes/hiv_mol_epi/stephane/softwares/hyphy/contrib/SQLite-3.8.2 -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c /Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/alignment.cpp -o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/alignment.o -Wno-int-to-pointer-cast -Wno-char-subscripts -Wno-sign-compare -Wno-parentheses -Wno-uninitialized -Wno-unused-variable -Wno-shorten-64-to-32 -fsigned-char -O3 -fpermissive -fPIC cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ cc1plus: warning: unrecognized command line option '-Wno-shorten-64-to-32'

---

and a series of errors like this one:

---

/var/folders/rl/hw3ws1bn0p5__9gbg1wgtql80000gp/T//ccPVcxIp.s:49:8: error: register %r15 is only available in 64-bit mode pushq %r15

[stevenweaver]

Hello Stephane,

The warnings are acceptable for now. I will create an issue to suppress warning statements when the package is being installed for production use.

There are two items in standard error that seem peculiar to me:

1. temp.macosx-10.6-intel-3.5 is implying that the version of OSX you are using may be 10.6 as opposed to 10.10.
2. intel means that you are attempting to compile a universal version of HyPhy. (both 32-bit and 64-bit versions).

Can you please make sure you are using OSX 10.10?

Additionally, you might be able to use the following command, but I'm unable to check if it will work since I don't have access to OSX 10.6.

arch -x86_64 python3 setup.py install

Please let me know if this is helpful.

Regards, Steven

[slevu]

Hi Steven, I am certain to use OSX 10.10.5 and I don't know why the build is (still) evoking 10.6. The arch -x86_64 instruction seemed to help for the installation of HyPhy. After the warnings, I end up with these messages:

---

/usr/bin/clang++ -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/alignment.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/avllist.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/avllistx.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/avllistxl.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/baseobj.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/batchlan.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/batchlan2.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/batchlanhelpers.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/batchlanruntime.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/calcnode.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/calcnode2.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/category.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/constant.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/error.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/fisher_exact.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/formula.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/fstring.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/likefunc.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/likefunc2.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/likefuncocl.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/list.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/mathobj.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/matrix.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/nexus.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/operation.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/parser.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/parser2.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/polynoml.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/regex.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/sequence.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/simplelist.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/site.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/stack.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/strings.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/trie.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/variable.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/variablecontainer.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/core/_hyExecutionContext.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/new/bayesgraph.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/new/bayesgraph2.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/new/bgm.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/new/bgm2.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/new/scfg.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/contrib/SQLite-3.8.2/shell.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/contrib/SQLite-3.8.2/sqlite3.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/gui/preferences.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/lib/Link/THyPhy.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/lib/SWIGWrappers/THyPhy_py3.o build/temp.macosx-10.6-intel-3.5/Volumes/hiv_mol_epi/stephane/softwares/hyphy/src/utils/hyphyunixutils.o -lpthread -lssl -lcrypto -lcurl -o build/lib.macosx-10.6-intel-3.5/_HyPhy.cpython-35m-darwin.so running install_lib creating /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/HyPhy copying build/lib.macosx-10.6-intel-3.5/HyPhy/init.py -> /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/HyPhy copying build/lib.macosx-10.6-intel-3.5/_HyPhy.cpython-35m-darwin.so -> /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages byte-compiling /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/HyPhy/init.py to init.cpython-35.pyc running install_egg_info Writing /Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/HyPhy-0.1.1-py3.5.egg-info

---

But for step 2, I cannot find the install.sh mentioned and the installation of hivclustering still fails. Many thanks for your help. Best regards, Stephane