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kr-colab / diploSHIC

feature-based deep learning for the identification of selective sweeps
MIT License
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installing warning #1

Closed conniecl closed 5 years ago

conniecl commented 6 years ago

Hi, While installing diploS/HIC according to the suggestion, some warnings appeared. I'm wondering if these warnings will affect the performance of diploS/HIC. Here is the installing message:

[maize@login1 diploSHIC]$ ../anaconda3/bin/python setup.py install
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "shicstats" sources
creating build
creating build/src.linux-x86_64-3.6
f2py options: []
f2py: ./shicstats.pyf
Reading fortran codes...
    Reading file './shicstats.pyf' (format:free)
Line #6 in ./shicstats.pyf:"    intent(c)"
    All arguments will have attribute intent(c)
Line #14 in ./shicstats.pyf:"    intent(c)"
    All arguments will have attribute intent(c)
Line #21 in ./shicstats.pyf:"    intent(c)"
    All arguments will have attribute intent(c)
Line #28 in ./shicstats.pyf:"    intent(c)"
    All arguments will have attribute intent(c)
Line #36 in ./shicstats.pyf:"    intent(c)"
    All arguments will have attribute intent(c)
Line #44 in ./shicstats.pyf:"    intent(c)"
    All arguments will have attribute intent(c)
crackline: groupcounter=1 groupname={0: '', 1: 'python module', 2: 'interface', 3: 'subroutine'}
crackline: Mismatch of blocks encountered. Trying to fix it by assuming "end" statement.
Post-processing...
    Block: shicstats
            Block: computeR2Matrix
            Block: omega
            Block: ZnS
            Block: pairwiseDiffs
            Block: pairwiseDiffsDiplo
            Block: getHaplotypeFreqSpec
Post-processing (stage 2)...
Building modules...
    Building module "shicstats"...
        Constructing wrapper function "computeR2Matrix"...
          r2Matrix = computeR2Matrix(haps)
        Constructing wrapper function "omega"...
          omegaMax = omega(r2Matrix)
        Constructing wrapper function "ZnS"...
          zns = ZnS(r2Matrix)
        Constructing wrapper function "pairwiseDiffs"...
          diffLs = pairwiseDiffs(haps)
        Constructing wrapper function "pairwiseDiffsDiplo"...
          diffLs = pairwiseDiffsDiplo(haps)
        Constructing wrapper function "getHaplotypeFreqSpec"...
          hapCounts = getHaplotypeFreqSpec(haps)
    Wrote C/API module "shicstats" to file "build/src.linux-x86_64-3.6/shicstatsmodule.c"
  adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs.
creating build/src.linux-x86_64-3.6/build
creating build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6
copying /home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6
copying /home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6
build_src: building npy-pkg config files
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'shicstats' extension
compiling C sources
C compiler: gcc -pthread -B /home/maize/software/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/home/maize/software/anaconda3/include/python3.6m -c'
gcc: build/src.linux-x86_64-3.6/shicstatsmodule.c
In file included from /home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.h:13,
                 from build/src.linux-x86_64-3.6/shicstatsmodule.c:19:
/home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
build/src.linux-x86_64-3.6/shicstatsmodule.c:105:12: warning: ‘f2py_size’ defined but not used [-Wunused-function]
 static int f2py_size(PyArrayObject* var, ...)
            ^
gcc: ./utils.c
gcc: build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c
In file included from /home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.h:13,
                 from build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c:2:
/home/maize/software/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c: In function ‘format_def’:
build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c:138:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (size < sizeof(notalloc)) {
                  ^
creating build/lib.linux-x86_64-3.6
gcc -pthread -shared -B /home/maize/software/anaconda3/compiler_compat -L/home/maize/software/anaconda3/lib -Wl,-rpath=/home/maize/software/anaconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/shicstatsmodule.o build/temp.linux-x86_64-3.6/utils.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o -L/home/maize/software/anaconda3/lib -lpython3.6m -o build/lib.linux-x86_64-3.6/shicstats.cpython-36m-x86_64-linux-gnu.so
running install_lib
copying build/lib.linux-x86_64-3.6/shicstats.cpython-36m-x86_64-linux-gnu.so -> /home/maize/software/anaconda3/lib/python3.6/site-packages
running install_egg_info
Writing /home/maize/software/anaconda3/lib/python3.6/site-packages/UNKNOWN-0.0.0-py3.6.egg-info
running install_clib
customize UnixCCompiler

By the way, I can get the help file by using../anaconda3/bin/python diploSHIC.py -h. And while running the train test command: ../anaconda3/bin/python diploSHIC.py train training/ testing/ fooModel --epochs 10, everything seems OK. But while running the predict test command:../anaconda3/bin/python diploSHIC.py predict fooModel.json fooModel.weights.hdf5 testEmpirical.fvec testEmpirical.preds, a CPU problem raised.I guess it about the problem of TensorFlow I installed?

Using TensorFlow backend.
2018-05-15 10:03:10.435351: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
Loaded model from disk
9 predictions complete

Hope can get some advice, and thanks in advance.

andrewkern commented 6 years ago

hi there. it looks like these warnings are coming from numpy. what version of numpy do you currently have installed? I doubt this will cause issues for diploSHIC.

conniecl commented 6 years ago

Hi, sorry about the late reply, the version of numpy I used is 1.13.3. And it's the version which contained in Anaconda3-5.0.1.

andrewkern commented 6 years ago

strange. it looks like the numpy warnings on install show numpy v 1.7. the tensorflow warnings are indeed the because of installing tf with a binary rather than compiling on your machine. that would slow things a bit but it shouldn't be a big deal.

conniecl commented 6 years ago

OK. Thanks, I'll have a try

andrewkern commented 5 years ago

no this is for python 3.x