Error in pip install fitsne #109

Zifeng-L · 2020-10-29T06:46:51Z

Hi, here.
I tried to install Fit-SNE by the command line "pip install fitsne". However, there seemed to be somthing wrong with gcc.
pip install fitsne

Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Collecting fitsne
  Downloading https://pypi.tuna.tsinghua.edu.cn/packages/92/d4/e19298eb37d1b56d5b0675daf0443a42a17000258ab55797035b8ece2aeb/fitsne-1.1.1.tar.gz (151 kB)
     |████████████████████████████████| 151 kB 1.6 MB/s 
Requirement already satisfied: numpy in ./anaconda2/envs/pegasus/lib/python3.7/site-packages (from fitsne) (1.18.5)
Requirement already satisfied: cython in ./anaconda2/envs/pegasus/lib/python3.7/site-packages (from fitsne) (0.29.21)
Building wheels for collected packages: fitsne
  Building wheel for fitsne (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /cluster/home/zfli/anaconda2/envs/pegasus/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-yunl5jsw/fitsne/setup.py'"'"'; __file__='"'"'/tmp/pip-install-yunl5jsw/fitsne/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-9yw0krtm
       cwd: /tmp/pip-install-yunl5jsw/fitsne/
  Complete output (33 lines):
  Warning: passing language='c++' to cythonize() is deprecated. Instead, put "# distutils: language=c++" in your .pyx or .pxd file(s)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.7
  creating build/lib.linux-x86_64-3.7/fitsne
  copying fitsne/__init__.py -> build/lib.linux-x86_64-3.7/fitsne
  copying fitsne/_version.py -> build/lib.linux-x86_64-3.7/fitsne
  copying fitsne/cywrap.py -> build/lib.linux-x86_64-3.7/fitsne
  running build_ext
  building 'fitsne.cppwrap' extension
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/fitsne
  creating build/temp.linux-x86_64-3.7/fitsne/src
  gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/cppwrap.cpp -o build/temp.linux-x86_64-3.7/fitsne/cppwrap.o -std=c++11 -O3 -pthread -lfftw3 -lm
  cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
  gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/src/nbodyfft.cpp -o build/temp.linux-x86_64-3.7/fitsne/src/nbodyfft.o -std=c++11 -O3 -pthread -lfftw3 -lm
  cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
  In file included from fitsne/src/nbodyfft.cpp:4:
  fitsne/src/nbodyfft.h:7:10: fatal error: fftw3.h: No such file or directory
      7 | #include <fftw3.h>
        |          ^~~~~~~~~
  compilation terminated.
  Warning: passing language='c++' to cythonize() is deprecated. Instead, put "# distutils: language=c++" in your .pyx or .pxd file(s)
  running bdist_wheel
  running build
  running build_py
  running build_ext
  building 'fitsne.cppwrap' extension
  gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/cppwrap.cpp -o build/temp.linux-x86_64-3.7/fitsne/cppwrap.o -std=c++11 -O3 -pthread -lfftw3 -lm -stdlib=libc++
  gcc: error: unrecognized command-line option ‘-stdlib=libc++’
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for fitsne
  Running setup.py clean for fitsne
Failed to build fitsne
Installing collected packages: fitsne
    Running setup.py install for fitsne ... error
    ERROR: Command errored out with exit status 1:
     command: /cluster/home/zfli/anaconda2/envs/pegasus/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-yunl5jsw/fitsne/setup.py'"'"'; __file__='"'"'/tmp/pip-install-yunl5jsw/fitsne/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-obe2addf/install-record.txt --single-version-externally-managed --compile --install-headers /cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m/fitsne
         cwd: /tmp/pip-install-yunl5jsw/fitsne/
    Complete output (33 lines):
    Warning: passing language='c++' to cythonize() is deprecated. Instead, put "# distutils: language=c++" in your .pyx or .pxd file(s)
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.7
    creating build/lib.linux-x86_64-3.7/fitsne
    copying fitsne/__init__.py -> build/lib.linux-x86_64-3.7/fitsne
    copying fitsne/_version.py -> build/lib.linux-x86_64-3.7/fitsne
    copying fitsne/cywrap.py -> build/lib.linux-x86_64-3.7/fitsne
    running build_ext
    building 'fitsne.cppwrap' extension
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/fitsne
    creating build/temp.linux-x86_64-3.7/fitsne/src
    gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/cppwrap.cpp -o build/temp.linux-x86_64-3.7/fitsne/cppwrap.o -std=c++11 -O3 -pthread -lfftw3 -lm
    cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/src/nbodyfft.cpp -o build/temp.linux-x86_64-3.7/fitsne/src/nbodyfft.o -std=c++11 -O3 -pthread -lfftw3 -lm
    cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    In file included from fitsne/src/nbodyfft.cpp:4:
    fitsne/src/nbodyfft.h:7:10: fatal error: fftw3.h: No such file or directory
        7 | #include <fftw3.h>
          |          ^~~~~~~~~
    compilation terminated.
    Warning: passing language='c++' to cythonize() is deprecated. Instead, put "# distutils: language=c++" in your .pyx or .pxd file(s)
    running install
    running build
    running build_py
    running build_ext
    building 'fitsne.cppwrap' extension
    gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/cppwrap.cpp -o build/temp.linux-x86_64-3.7/fitsne/cppwrap.o -std=c++11 -O3 -pthread -lfftw3 -lm -stdlib=libc++
    gcc: error: unrecognized command-line option ‘-stdlib=libc++’
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /cluster/home/zfli/anaconda2/envs/pegasus/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-yunl5jsw/fitsne/setup.py'"'"'; __file__='"'"'/tmp/pip-install-yunl5jsw/fitsne/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-obe2addf/install-record.txt --single-version-externally-managed --compile --install-headers /cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m/fitsne Check the logs for full command output.

version information:
gcc version 10.2.0 (GCC)

The text was updated successfully, but these errors were encountered:

pavlin-policar · 2020-10-29T08:03:30Z

Try to remove the problematic flag -stdlib=libc++ from the compiler arguments. I add that flag for Mac compilers, but I think it isn't necessary with GCC.

Zifeng-L · 2020-10-29T08:41:15Z

remove the problematic flag

Sorry to disturb you again. How to remove the problematic flag -stdlib=libc++ from the compiler arguments when installing fitsne? Should I download the sources and install locally?

pavlin-policar · 2020-10-29T13:05:23Z

You should probably clone the repository https://github.com/KlugerLab/pyFIt-SNE and change thesetup.py file accordingly. However, I'm not sure how up-to-date that repository is. Whenever I use this C++ implementation of FIt-SNE, I follow the instructions here and don't bother with the PyPI package. It's kind of a pain to set up.

Zifeng-L · 2020-10-30T02:48:20Z

thanks a lot!!!

Zifeng-L · 2020-10-30T05:52:24Z

Sorry to reopen this issue again. I tried to remove the problematic flag -stdlib=libc++ from the compiler arguments, there was still something wrong with C++. Is my setup.py codes wrong?
My all steps were as follows.
git clone https://github.com/KlugerLab/pyFIt-SNE.git
Then I changed the setup.py codes.

from setuptools import setup, find_packages  # from distutils.core import setup
from setuptools.extension import Extension
from Cython.Build import cythonize
from os import path
from os import environ
from sys import platform

__version__ = "0.0.0"
exec(open('fitsne/_version.py').read())
here = path.abspath(path.dirname(__file__))
with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
    long_description = f.read()

author="George Linderman, Gioele La Manno"
author_email="[email protected], [email protected]"
url="https://github.com/KlugerLab/FIt-SNE"
download_url="https://github.com/KlugerLab/pyFIt-SNE/archive/%s.tar.gz"%__version__
keywords=["tSNE", "embedding"]
description="Fast Fourier Transform-accelerated Interpolation-based t-SNE (FIt-SNE)"
license="BSD3"

#Try...except because for some OS X setups, the compilation fails without -stdlib=libc++
try: 
    if platform == "darwin":
        extensions = [Extension("fitsne.cppwrap",
                                ["fitsne/cppwrap.pyx", "fitsne/src/nbodyfft.cpp", "fitsne/src/sptree.cpp", "fitsne/src/tsne.cpp"],
                                language="c++",
                                extra_compile_args=["-std=c++11", "-O3", '-pthread', "-lfftw3", "-lm"],
                                extra_link_args=['-lfftw3', '-lm',"-mmacosx-version-min=10.9"])]
    else:
        extensions = [Extension("fitsne.cppwrap",
                                ["fitsne/cppwrap.pyx", "fitsne/src/nbodyfft.cpp", "fitsne/src/sptree.cpp", "fitsne/src/tsne.cpp"],
                                language="c++",
                                extra_compile_args=["-std=c++11", "-O3", '-pthread', "-lfftw3", "-lm"],
                                extra_link_args=['-lfftw3', '-lm'])]
    extensions = cythonize(extensions, language="c++",  include_path=[])

    # package_data = {}
    __version__ = "0.0.0"
    exec(open('fitsne/_version.py').read())

    setup(name="fitsne",
          version=__version__,
          packages=find_packages(),
          install_requires=['numpy', 'cython'],
          ext_modules=extensions,
          # package_data=package_data,
          # metadata
          author=author, 
          author_email=author_email, 
          url=url,
          download_url=download_url,
          keywords=keywords,
          description=description, 
          long_description=long_description,
          license=license) 

except:
    extensions = [Extension("fitsne.cppwrap",
                            ["fitsne/cppwrap.pyx", "fitsne/src/nbodyfft.cpp", "fitsne/src/sptree.cpp", "fitsne/src/tsne.cpp"],
                            language="c++",
                            extra_compile_args=["-std=c++11", "-O3", '-pthread', "-lfftw3", "-lm"],
                            extra_link_args=['-lfftw3', '-lm'])]
    extensions = cythonize(extensions, language="c++",  include_path=[])

    setup(name="fitsne",
          version=__version__,
          packages=find_packages(),
          install_requires=['numpy', 'cython'],
          ext_modules=extensions,
          author=author, 
          author_email=author_email, 
          url=url,
          download_url=download_url,
          keywords=keywords,
          description=description, 
          long_description=long_description,
          license=license)

Then I run setup.py in python.

Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Obtaining file:///cluster/home/zfli/apps/pyFIt-SNE
Requirement already satisfied: numpy in /cluster/home/zfli/anaconda2/envs/pegasus/lib/python3.7/site-packages (from fitsne==1.1.0) (1.18.5)
Requirement already satisfied: cython in /cluster/home/zfli/anaconda2/envs/pegasus/lib/python3.7/site-packages (from fitsne==1.1.0) (0.29.21)
Installing collected packages: fitsne
  Running setup.py develop for fitsne
    ERROR: Command errored out with exit status 1:
     command: /cluster/home/zfli/anaconda2/envs/pegasus/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/cluster/home/zfli/apps/pyFIt-SNE/setup.py'"'"'; __file__='"'"'/cluster/home/zfli/apps/pyFIt-SNE/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
         cwd: /cluster/home/zfli/apps/pyFIt-SNE/
    Complete output (51 lines):
    Warning: passing language='c++' to cythonize() is deprecated. Instead, put "# distutils: language=c++" in your .pyx or .pxd file(s)
    running develop
    running egg_info
    creating fitsne.egg-info
    writing fitsne.egg-info/PKG-INFO
    writing dependency_links to fitsne.egg-info/dependency_links.txt
    writing requirements to fitsne.egg-info/requires.txt
    writing top-level names to fitsne.egg-info/top_level.txt
    writing manifest file 'fitsne.egg-info/SOURCES.txt'
    reading manifest file 'fitsne.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching 'LICENSE'
    writing manifest file 'fitsne.egg-info/SOURCES.txt'
    running build_ext
    building 'fitsne.cppwrap' extension
    creating build
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/fitsne
    creating build/temp.linux-x86_64-3.7/fitsne/src
    gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/cppwrap.cpp -o build/temp.linux-x86_64-3.7/fitsne/cppwrap.o -std=c++11 -O3 -pthread -lfftw3 -lm
    cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/src/nbodyfft.cpp -o build/temp.linux-x86_64-3.7/fitsne/src/nbodyfft.o -std=c++11 -O3 -pthread -lfftw3 -lm
    cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    In file included from fitsne/src/nbodyfft.cpp:4:
    fitsne/src/nbodyfft.h:7:10: fatal error: fftw3.h: No such file or directory
        7 | #include <fftw3.h>
          |          ^~~~~~~~~
    compilation terminated.
    Warning: passing language='c++' to cythonize() is deprecated. Instead, put "# distutils: language=c++" in your .pyx or .pxd file(s)
    running develop
    running egg_info
    writing fitsne.egg-info/PKG-INFO
    writing dependency_links to fitsne.egg-info/dependency_links.txt
    writing requirements to fitsne.egg-info/requires.txt
    writing top-level names to fitsne.egg-info/top_level.txt
    reading manifest file 'fitsne.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching 'LICENSE'
    writing manifest file 'fitsne.egg-info/SOURCES.txt'
    running build_ext
    building 'fitsne.cppwrap' extension
    gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/cppwrap.cpp -o build/temp.linux-x86_64-3.7/fitsne/cppwrap.o -std=c++11 -O3 -pthread -lfftw3 -lm
    cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    gcc -pthread -B /cluster/home/zfli/anaconda2/envs/pegasus/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ifitsne -I/cluster/home/zfli/anaconda2/envs/pegasus/include/python3.7m -c fitsne/src/nbodyfft.cpp -o build/temp.linux-x86_64-3.7/fitsne/src/nbodyfft.o -std=c++11 -O3 -pthread -lfftw3 -lm
    cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    In file included from fitsne/src/nbodyfft.cpp:4:
    fitsne/src/nbodyfft.h:7:10: fatal error: fftw3.h: No such file or directory
        7 | #include <fftw3.h>
          |          ^~~~~~~~~
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /cluster/home/zfli/anaconda2/envs/pegasus/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/cluster/home/zfli/apps/pyFIt-SNE/setup.py'"'"'; __file__='"'"'/cluster/home/zfli/apps/pyFIt-SNE/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.

pavlin-policar · 2020-10-30T08:24:33Z

Well, now it seems like it doesn't find FFTW. I don't really know how to solve that without diving into it. Installation and distribution problems like this are exactly why I developed openTSNE. If you're okay with a marginal decrease in speed, you can use that, and it's completely painless to install.

ghuls · 2021-01-27T15:31:48Z

fitsne/cppwrap.py need this at the beginning to satisfy cython:

# distutils: language=c++

Modify PyPi package and install it

# Get fitsne pip package.
wget https://files.pythonhosted.org/packages/92/d4/e19298eb37d1b56d5b0675daf0443a42a17000258ab55797035b8ece2aeb/fitsne-1.1.1.tar.gz

# Extract tar ball.
tar xzf fitsne-1.1.1.tar.gz

cd fitsne-1.1.1

Create file ../fitsne-pypi.patch with content:

--- fitsne-1.1.1/setup.py       2018-11-17 12:42:11.000000000 +0100
+++ fitsne-1.1.1-patched/setup.py       2021-01-27 16:14:57.148976000 +0100
@@ -24,16 +24,14 @@
     if platform == "darwin":
         extensions = [Extension("fitsne.cppwrap",
                                 ["fitsne/cppwrap.pyx", "fitsne/src/nbodyfft.cpp", "fitsne/src/sptree.cpp", "fitsne/src/tsne.cpp"],
-                                language="c++",
                                 extra_compile_args=["-std=c++11", "-O3", '-pthread', "-lfftw3", "-lm"],
-                                extra_link_args=['-lfftw3', '-lm',"-mmacosx-version-min=10.9"])]
+                                extra_link_args=['-lfftw3', '-lm', "-mmacosx-version-min=10.9"])]
     else:
         extensions = [Extension("fitsne.cppwrap",
                                 ["fitsne/cppwrap.pyx", "fitsne/src/nbodyfft.cpp", "fitsne/src/sptree.cpp", "fitsne/src/tsne.cpp"],
-                                language="c++",
                                 extra_compile_args=["-std=c++11", "-O3", '-pthread', "-lfftw3", "-lm"],
                                 extra_link_args=['-lfftw3', '-lm'])]
-    extensions = cythonize(extensions, language="c++",  include_path=[])
+    extensions = cythonize(extensions, language_level="3",  include_path=[])

     # package_data = {}
     __version__ = "0.0.0"
@@ -58,10 +56,9 @@
 except:
     extensions = [Extension("fitsne.cppwrap",
                             ["fitsne/cppwrap.pyx", "fitsne/src/nbodyfft.cpp", "fitsne/src/sptree.cpp", "fitsne/src/tsne.cpp"],
-                            language="c++",
                             extra_compile_args=["-std=c++11","-stdlib=libc++", "-O3", '-pthread', "-lfftw3", "-lm"],
                             extra_link_args=['-lfftw3', '-lm'])]
-    extensions = cythonize(extensions, language="c++",  include_path=[])
+    extensions = cythonize(extensions, language_level="3",  include_path=[])

     setup(name="fitsne",
           version=__version__,

--- fitsne-1.1.1/fitsne/cppwrap.pyx     2020-01-07 22:11:12.000000000 +0100
+++ fitsne-1.1.1-patched/fitsne/cppwrap.pyx     2021-01-27 16:11:46.431525000 +0100
@@ -1,3 +1,5 @@
+# distutils: language=c++
+
 import cython
 from libcpp cimport bool

# Patch extracted PyPi package.
patch -p1 < ../fitsne-pypi.patch

# Install package.
python setup.py install

cflerin · 2021-02-05T18:50:36Z

I had the same problem as the original post. For me, this error:

    In file included from fitsne/src/nbodyfft.cpp:4:
    fitsne/src/nbodyfft.h:7:10: fatal error: fftw3.h: No such file or directory
     #include <fftw3.h>
              ^~~~~~~~~
    compilation terminated.

turned out to be the main source of the problem. This was solved by installing the libfftw3-dev package (using apt in Debian). After this, I could do

pip install fitsne

without any errors.

Package/system info:

Debian GNU/Linux 10 (buster)
Cython 0.29.21
gcc version 8.3.0 (Debian 8.3.0-6)

JANHMS · 2022-04-12T00:12:24Z

Solution of cflerin above worked for me within a Docker container

Zifeng-L closed this as completed Oct 30, 2020

Zifeng-L reopened this Oct 30, 2020

Zifeng-L closed this as completed Oct 30, 2020

Zifeng-L reopened this Oct 30, 2020

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Error in pip install fitsne #109

Error in pip install fitsne #109

Zifeng-L commented Oct 29, 2020

pavlin-policar commented Oct 29, 2020

Zifeng-L commented Oct 29, 2020

pavlin-policar commented Oct 29, 2020

Zifeng-L commented Oct 30, 2020

Zifeng-L commented Oct 30, 2020

pavlin-policar commented Oct 30, 2020

ghuls commented Jan 27, 2021 •

edited

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cflerin commented Feb 5, 2021

JANHMS commented Apr 12, 2022 •

edited

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Error in pip install fitsne #109

Error in pip install fitsne #109

Comments

Zifeng-L commented Oct 29, 2020

pavlin-policar commented Oct 29, 2020

Zifeng-L commented Oct 29, 2020

pavlin-policar commented Oct 29, 2020

Zifeng-L commented Oct 30, 2020

Zifeng-L commented Oct 30, 2020

pavlin-policar commented Oct 30, 2020

ghuls commented Jan 27, 2021 • edited Loading

Modify PyPi package and install it

cflerin commented Feb 5, 2021

JANHMS commented Apr 12, 2022 • edited Loading

ghuls commented Jan 27, 2021 •

edited

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JANHMS commented Apr 12, 2022 •

edited

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