Failed installation: ignore_missing_bp.o: file not recognized #1

lldelisle · 2019-10-08T08:56:46Z

Hi,
I would be interested to use your package, unfortunately, I did not managed to install it.
I tried to create a conda environment with it:

conda create -n pybedgraph cython pybigwig pip
conda activate pybedgraph
pip install pyBedGraph
Collecting pyBedGraph
  Using cached https://files.pythonhosted.org/packages/00/ef/9005f4916c3ffeb21be99d4e173c1e84aa1aaaa9248f2ed6552057848e2c/pyBedGraph-0.5.32.tar.gz
Requirement already satisfied: numpy>=1.16.4 in ./.conda/envs/pybedgraph/lib/python3.7/site-packages (from pyBedGraph) (1.17.2)
Requirement already satisfied: pyBigWig>=0.3.16 in ./.conda/envs/pybedgraph/lib/python3.7/site-packages (from pyBedGraph) (0.3.17)
Requirement already satisfied: cython>=0.29.12 in ./.conda/envs/pybedgraph/lib/python3.7/site-packages (from pyBedGraph) (0.29.13)
Building wheels for collected packages: pyBedGraph
  Building wheel for pyBedGraph (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/ldelisle/.conda/envs/pybedgraph/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-p109m_zy/pyBedGraph/setup.py'"'"'; __file__='"'"'/tmp/pip-install-p109m_zy/pyBedGraph/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-ynxa743a --python-tag cp37                                                                             
       cwd: /tmp/pip-install-p109m_zy/pyBedGraph/                                                                                    
  Complete output (24 lines):                                                                                                        
  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/pyBedGraph                                                                                     
  copying pyBedGraph/__init__.py -> build/lib.linux-x86_64-3.7/pyBedGraph                                                            
  copying pyBedGraph/Chrom_Data_Complete.py -> build/lib.linux-x86_64-3.7/pyBedGraph                                                 
  copying pyBedGraph/Chrom_Data.py -> build/lib.linux-x86_64-3.7/pyBedGraph                                                          
  copying pyBedGraph/Benchmark.py -> build/lib.linux-x86_64-3.7/pyBedGraph                                                           
  copying pyBedGraph/BedGraph.py -> build/lib.linux-x86_64-3.7/pyBedGraph                                                            
  running build_ext                                                                                                                  
  building 'pyBedGraph.ignore_missing_bp' extension                                                                                  
  creating build/temp.linux-x86_64-3.7                                                                                               
  creating build/temp.linux-x86_64-3.7/pyBedGraph                                                                                    
  gcc -pthread -B /home/ldelisle/.conda/envs/pybedgraph/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -c pyBedGraph/ignore_missing_bp.c -o build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o
  gcc -pthread -shared -B /home/ldelisle/.conda/envs/pybedgraph/compiler_compat -L/home/ldelisle/.conda/envs/pybedgraph/lib -Wl,-rpath=/home/ldelisle/.conda/envs/pybedgraph/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o -o build/lib.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.cpython-37m-x86_64-linux-gnu.so
  /home/ldelisle/.conda/envs/pybedgraph/compiler_compat/ld: build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: unable to initialize decompress status for section .debug_info
  /home/ldelisle/.conda/envs/pybedgraph/compiler_compat/ld: build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: unable to initialize decompress status for section .debug_info
  /home/ldelisle/.conda/envs/pybedgraph/compiler_compat/ld: build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: unable to initialize decompress status for section .debug_info
  /home/ldelisle/.conda/envs/pybedgraph/compiler_compat/ld: build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: unable to initialize decompress status for section .debug_info
  build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: file not recognized: file format not recognized
  collect2: error: ld returned 1 exit status
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pyBedGraph
  Running setup.py clean for pyBedGraph
Failed to build pyBedGraph
Installing collected packages: pyBedGraph
  Running setup.py install for pyBedGraph ... error
    ERROR: Command errored out with exit status 1:
     command: /home/ldelisle/.conda/envs/pybedgraph/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-p109m_zy/pyBedGraph/setup.py'"'"'; __file__='"'"'/tmp/pip-install-p109m_zy/pyBedGraph/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-rf0hjb_5/install-record.txt --single-version-externally-managed --compile
         cwd: /tmp/pip-install-p109m_zy/pyBedGraph/
    Complete output (24 lines):
    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/pyBedGraph
    copying pyBedGraph/__init__.py -> build/lib.linux-x86_64-3.7/pyBedGraph
    copying pyBedGraph/Chrom_Data_Complete.py -> build/lib.linux-x86_64-3.7/pyBedGraph
    copying pyBedGraph/Chrom_Data.py -> build/lib.linux-x86_64-3.7/pyBedGraph
    copying pyBedGraph/Benchmark.py -> build/lib.linux-x86_64-3.7/pyBedGraph
    copying pyBedGraph/BedGraph.py -> build/lib.linux-x86_64-3.7/pyBedGraph
    running build_ext
    building 'pyBedGraph.ignore_missing_bp' extension
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/pyBedGraph
    gcc -pthread -B /home/ldelisle/.conda/envs/pybedgraph/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -c pyBedGraph/ignore_missing_bp.c -o build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o
    gcc -pthread -shared -B /home/ldelisle/.conda/envs/pybedgraph/compiler_compat -L/home/ldelisle/.conda/envs/pybedgraph/lib -Wl,-rpath=/home/ldelisle/.conda/envs/pybedgraph/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o -o build/lib.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.cpython-37m-x86_64-linux-gnu.so
    /home/ldelisle/.conda/envs/pybedgraph/compiler_compat/ld: build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: unable to initialize decompress status for section .debug_info
    /home/ldelisle/.conda/envs/pybedgraph/compiler_compat/ld: build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: unable to initialize decompress status for section .debug_info
    /home/ldelisle/.conda/envs/pybedgraph/compiler_compat/ld: build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: unable to initialize decompress status for section .debug_info
    /home/ldelisle/.conda/envs/pybedgraph/compiler_compat/ld: build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: unable to initialize decompress status for section .debug_info
    build/temp.linux-x86_64-3.7/pyBedGraph/ignore_missing_bp.o: file not recognized: file format not recognized
    collect2: error: ld returned 1 exit status
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/ldelisle/.conda/envs/pybedgraph/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-p109m_zy/pyBedGraph/setup.py'"'"'; __file__='"'"'/tmp/pip-install-p109m_zy/pyBedGraph/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-rf0hjb_5/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

python
Python 3.7.3 | packaged by conda-forge | (default, Jul  1 2019, 21:52:21) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyBigWig
>>> pyBigWig.__version__
'0.3.17'
>>> import Cython
>>> Cython.__version__
'0.29.13'
>>> import numpy
>>> numpy.__version__
'1.17.2'

Many thanks,

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

henrybzhang · 2019-10-08T18:52:39Z

Could you also give run conda -V? I am able to run your commands successfully.

hirow@hirow-Aspire-VX5-591G:~$ conda create -n pybedgraph cython pybigwig pip
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - pybigwig

Current channels:

  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

hirow@hirow-Aspire-VX5-591G:~$ conda create -n pybedgraph cython pip
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.10
  latest version: 4.7.12

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/hirow/anaconda3/envs/pybedgraph

  added / updated specs:
    - cython
    - pip


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.8.28-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  cython             pkgs/main/linux-64::cython-0.29.13-py37he6710b0_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_2
  pip                pkgs/main/linux-64::pip-19.2.3-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate pybedgraph
#
# To deactivate an active environment, use
#
#     $ conda deactivate

hirow@hirow-Aspire-VX5-591G:~$ conda activate pybedgraph
(pybedgraph) hirow@hirow-Aspire-VX5-591G:~$ pip -V
pip 19.2.3 from /home/hirow/anaconda3/envs/pybedgraph/lib/python3.7/site-packages/pip (python 3.7)
(pybedgraph) hirow@hirow-Aspire-VX5-591G:~$ which pip
/home/hirow/anaconda3/envs/pybedgraph/bin/pip
(pybedgraph) hirow@hirow-Aspire-VX5-591G:~$ pip install pybedgraph
Collecting pybedgraph
  Downloading https://files.pythonhosted.org/packages/00/ef/9005f4916c3ffeb21be99d4e173c1e84aa1aaaa9248f2ed6552057848e2c/pyBedGraph-0.5.32.tar.gz (358kB)
     |████████████████████████████████| 368kB 5.5MB/s 
Collecting numpy>=1.16.4 (from pybedgraph)
  Downloading https://files.pythonhosted.org/packages/ba/e0/46e2f0540370f2661b044647fa447fef2ecbcc8f7cdb4329ca2feb03fb23/numpy-1.17.2-cp37-cp37m-manylinux1_x86_64.whl (20.3MB)
     |████████████████████████████████| 20.3MB 24.9MB/s 
Collecting pyBigWig>=0.3.16 (from pybedgraph)
  Downloading https://files.pythonhosted.org/packages/b0/e2/cf945d541a10bb9c675f986d5bf0b0268544721054d17cc6260cfcfb3685/pyBigWig-0.3.17.tar.gz (64kB)
     |████████████████████████████████| 71kB 6.0MB/s 
Requirement already satisfied: cython>=0.29.12 in ./anaconda3/envs/pybedgraph/lib/python3.7/site-packages (from pybedgraph) (0.29.13)
Building wheels for collected packages: pybedgraph, pyBigWig
  Building wheel for pybedgraph (setup.py) ... done
  Created wheel for pybedgraph: filename=pyBedGraph-0.5.32-cp37-cp37m-linux_x86_64.whl size=1239217 sha256=16791111c8bd18cf6a09cbcd17572dbc41f9884c109a239f7f674ad3a05fde99
  Stored in directory: /home/hirow/.cache/pip/wheels/ee/ea/23/7fce95bd55bef6fa44d3412e36645c447b2508d2de7973c779
  Building wheel for pyBigWig (setup.py) ... done
  Created wheel for pyBigWig: filename=pyBigWig-0.3.17-cp37-cp37m-linux_x86_64.whl size=162339 sha256=6282353e6e6bf60add1502abfd65faa10d85cc0b77769e39503f53dad740b40c
  Stored in directory: /home/hirow/.cache/pip/wheels/fb/27/2d/ac3e2e2d17894877fd3c4595ebd6fbd25ad805bfeab333f19b
Successfully built pybedgraph pyBigWig
Installing collected packages: numpy, pyBigWig, pybedgraph
Successfully installed numpy-1.17.2 pyBigWig-0.3.17 pybedgraph-0.5.32
(pybedgraph) hirow@hirow-Aspire-VX5-591G:~$ conda -V
conda 4.7.10
(pybedgraph) hirow@hirow-Aspire-VX5-591G:~$ python
Python 3.7.4 (default, Aug 13 2019, 20:35:49) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyBigWig
>>> pyBigWig.__version__
'0.3.17'
>>> import cython
>>> cython.__version__
'0.29.13'
>>> import numpy
>>> numpy.__version__
'1.17.2'

Another user also had a similar error, so I would greatly appreciate any extra information you can provide.

lldelisle · 2019-10-09T05:54:10Z

Hi,
pybigwig is part of bioconda channel that's why you could not load it.
I did as you did:

conda create -n pybedgraph cython pip

I got exactly the same packages:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h516909a_1
  ca-certificates    conda-forge/linux-64::ca-certificates-2019.9.11-hecc5488_0
  certifi            conda-forge/linux-64::certifi-2019.9.11-py37_0
  cython             conda-forge/linux-64::cython-0.29.13-py37he1b5a44_0
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1006
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
  openssl            conda-forge/linux-64::openssl-1.1.1c-h516909a_0
  pip                conda-forge/linux-64::pip-19.2.3-py37_0
  python             conda-forge/linux-64::python-3.7.3-h33d41f4_1
  readline           conda-forge/linux-64::readline-8.0-hf8c457e_0
  setuptools         conda-forge/linux-64::setuptools-41.4.0-py37_0
  sqlite             conda-forge/linux-64::sqlite-3.30.0-hcee41ef_0
  tk                 conda-forge/linux-64::tk-8.6.9-hed695b0_1003
  wheel              conda-forge/linux-64::wheel-0.33.6-py37_0
  xz                 conda-forge/linux-64::xz-5.2.4-h14c3975_1001
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1006

I also have the same conda version:

==> WARNING: A newer version of conda exists. <==
  current version: 4.7.10
  latest version: 4.7.12

But still the same error when building pybedgraph.
I am on linux and I guess you are on mac...
I use miniconda and you use anaconda but this should not change anything as it is just the number of packages which are included by default...

henrybzhang · 2019-10-09T07:46:13Z

I am also using Linux, specifically Ubuntu 19.04.

I looked around and saw anaconda/anaconda-project#183 (comment).
A potential workaround from that is conda install gxx_linux-64. Could you try that and see if it helps?

lldelisle · 2019-10-09T14:11:27Z

I have a new error and I cannot compile pybigwig... I hope it helps:

pip install pybedgraph
Collecting pybedgraph
Requirement already satisfied: numpy>=1.16.4 in ./.conda/envs/pybedgraph/lib/python3.7/site-packages (from pybedgraph) (1.17.2)
Requirement already satisfied: cython>=0.29.12 in ./.conda/envs/pybedgraph/lib/python3.7/site-packages (from pybedgraph) (0.29.13)
Collecting pyBigWig>=0.3.16 (from pybedgraph)
  Using cached https://files.pythonhosted.org/packages/b0/e2/cf945d541a10bb9c675f986d5bf0b0268544721054d17cc6260cfcfb3685/pyBigWig-0.3.17.tar.gz
Building wheels for collected packages: pyBigWig
  Building wheel for pyBigWig (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/ldelisle/.conda/envs/pybedgraph/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cj_ulcb1/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cj_ulcb1/pyBigWig/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-ib20jim3 --python-tag cp37
       cwd: /tmp/pip-install-cj_ulcb1/pyBigWig/
  Complete output (71 lines):
  /home/ldelisle/.conda/envs/pybedgraph/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'
    warnings.warn(msg)
  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/pyBigWigTest
  copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.7/pyBigWigTest
  copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-3.7/pyBigWigTest
  running egg_info
  writing pyBigWig.egg-info/PKG-INFO
  writing dependency_links to pyBigWig.egg-info/dependency_links.txt
  writing requirements to pyBigWig.egg-info/requires.txt
  writing top-level names to pyBigWig.egg-info/top_level.txt
  reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
  copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.7/pyBigWigTest
  copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.7/pyBigWigTest
  running build_ext
  building 'pyBigWig' extension
  Warning: Can't read registry to find the necessary compiler setting
  Make sure that Python modules winreg, win32api or win32con are installed.
  C compiler: /home/ldelisle/.conda/envs/pybedgraph/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC
  
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/libBigWig
  compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -I/home/ldelisle/.conda/envs/pybedgraph/lib/python3.7/site-packages/numpy/core/include -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -c'
  x86_64-conda_cos6-linux-gnu-cc: libBigWig/io.c
  x86_64-conda_cos6-linux-gnu-cc: libBigWig/bwWrite.c
  x86_64-conda_cos6-linux-gnu-cc: libBigWig/bwValues.cx86_64-conda_cos6-linux-gnu-cc: libBigWig/bwStats.c
  
  libBigWig/io.c:2:10: fatal error: curl/curl.h: No such file or directory
   #include <curl/curl.h>
            ^~~~~~~~~~~~~
  compilation terminated.
  x86_64-conda_cos6-linux-gnu-cc: libBigWig/bwRead.c
  In file included from libBigWig/bigWig.h:1:0,
                   from libBigWig/bwValues.c:1:
  libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
   #include <curl/curl.h>
            ^~~~~~~~~~~~~
  compilation terminated.
  In file included from libBigWig/bigWig.h:1:0,
                   from libBigWig/bwStats.c:1:
  libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
   #include <curl/curl.h>
            ^~~~~~~~~~~~~
  compilation terminated.
  x86_64-conda_cos6-linux-gnu-cc: pyBigWig.c
  In file included from libBigWig/bigWig.h:1:0,
                   from libBigWig/bwRead.c:1:
  libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
   #include <curl/curl.h>
            ^~~~~~~~~~~~~
  compilation terminated.
  In file included from libBigWig/bigWig.h:1:0,
                   from libBigWig/bwWrite.c:6:
  libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
   #include <curl/curl.h>
            ^~~~~~~~~~~~~
  compilation terminated.
  In file included from libBigWig/bigWig.h:1:0,
                   from pyBigWig.h:3,
                   from pyBigWig.c:3:
  libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory                                                                                                   
   #include <curl/curl.h>                                                                                                                                                          
            ^~~~~~~~~~~~~
  compilation terminated.
  error: Command "/home/ldelisle/.conda/envs/pybedgraph/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -I/home/ldelisle/.conda/envs/pybedgraph/lib/python3.7/site-packages/numpy/core/include -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -c libBigWig/io.c -o build/temp.linux-x86_64-3.7/libBigWig/io.o" failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pyBigWig
  Running setup.py clean for pyBigWig
Failed to build pyBigWig
Installing collected packages: pyBigWig, pybedgraph
  Running setup.py install for pyBigWig ... error
    ERROR: Command errored out with exit status 1:
     command: /home/ldelisle/.conda/envs/pybedgraph/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cj_ulcb1/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cj_ulcb1/pyBigWig/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-8nvptvam/install-record.txt --single-version-externally-managed --compile
         cwd: /tmp/pip-install-cj_ulcb1/pyBigWig/
    Complete output (71 lines):
    /home/ldelisle/.conda/envs/pybedgraph/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier'
      warnings.warn(msg)
    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/pyBigWigTest
    copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.7/pyBigWigTest
    copying pyBigWigTest/__init__.py -> build/lib.linux-x86_64-3.7/pyBigWigTest
    running egg_info
    writing pyBigWig.egg-info/PKG-INFO
    writing dependency_links to pyBigWig.egg-info/dependency_links.txt
    writing requirements to pyBigWig.egg-info/requires.txt
    writing top-level names to pyBigWig.egg-info/top_level.txt
    reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
    copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.7/pyBigWigTest
    copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.7/pyBigWigTest
    running build_ext
    building 'pyBigWig' extension
    Warning: Can't read registry to find the necessary compiler setting
    Make sure that Python modules winreg, win32api or win32con are installed.
    C compiler: /home/ldelisle/.conda/envs/pybedgraph/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC
    
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/libBigWig
    compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -I/home/ldelisle/.conda/envs/pybedgraph/lib/python3.7/site-packages/numpy/core/include -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -c'
    x86_64-conda_cos6-linux-gnu-cc: libBigWig/io.cx86_64-conda_cos6-linux-gnu-cc: libBigWig/bwWrite.c
    x86_64-conda_cos6-linux-gnu-cc: libBigWig/bwValues.c
    x86_64-conda_cos6-linux-gnu-cc: libBigWig/bwStats.c
    
    In file included from libBigWig/bigWig.h:1:0,
                     from libBigWig/bwStats.c:1:
    libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
     #include <curl/curl.h>
              ^~~~~~~~~~~~~
    compilation terminated.
    In file included from libBigWig/bigWig.h:1:0,
                     from libBigWig/bwValues.c:1:
    libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
     #include <curl/curl.h>
              ^~~~~~~~~~~~~
    libBigWig/io.c:2:10: fatal error: curl/curl.h: No such file or directory
     #include <curl/curl.h>
              ^~~~~~~~~~~~~
    compilation terminated.
    compilation terminated.
    x86_64-conda_cos6-linux-gnu-cc: libBigWig/bwRead.c
    x86_64-conda_cos6-linux-gnu-cc: pyBigWig.c
    In file included from libBigWig/bigWig.h:1:0,
                     from libBigWig/bwRead.c:1:
    libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
     #include <curl/curl.h>
              ^~~~~~~~~~~~~
    compilation terminated.
    In file included from libBigWig/bigWig.h:1:0,
                     from libBigWig/bwWrite.c:6:
    libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
     #include <curl/curl.h>
              ^~~~~~~~~~~~~
    compilation terminated.
    In file included from libBigWig/bigWig.h:1:0,
                     from pyBigWig.h:3,
                     from pyBigWig.c:3:
    libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
     #include <curl/curl.h>
              ^~~~~~~~~~~~~
    compilation terminated.
    error: Command "/home/ldelisle/.conda/envs/pybedgraph/bin/x86_64-conda_cos6-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -I/home/ldelisle/.conda/envs/pybedgraph/lib/python3.7/site-packages/numpy/core/include -I/home/ldelisle/.conda/envs/pybedgraph/include/python3.7m -c libBigWig/bwValues.c -o build/temp.linux-x86_64-3.7/libBigWig/bwValues.o" failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/ldelisle/.conda/envs/pybedgraph/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cj_ulcb1/pyBigWig/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cj_ulcb1/pyBigWig/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-8nvptvam/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

henrybzhang · 2019-10-10T00:39:35Z

I am not quite sure how to fix that error. Perhaps conda install curl? However, pyBedGraph does not need pyBigWig to function so I will remove the dependency in setup.py.

I also plan on adding pyBedGraph to the Bioconda channel so this hopefully won't continue to create new problems.

henrybzhang · 2019-12-18T22:04:57Z

@lldelisle I added the package on Bioconda. Hopefully it works on your end!

Merge

henrybzhang closed this as completed Oct 20, 2019

henrybzhang reopened this Dec 16, 2019

henrybzhang closed this as completed Dec 18, 2019

henrybzhang pushed a commit that referenced this issue Apr 3, 2020

Merge pull request #1 from TheJacksonLaboratory/master

57a8653

Merge

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Failed installation: ignore_missing_bp.o: file not recognized #1

Failed installation: ignore_missing_bp.o: file not recognized #1

lldelisle commented Oct 8, 2019

henrybzhang commented Oct 8, 2019

lldelisle commented Oct 9, 2019

henrybzhang commented Oct 9, 2019

lldelisle commented Oct 9, 2019

henrybzhang commented Oct 10, 2019

henrybzhang commented Dec 18, 2019

Failed installation: ignore_missing_bp.o: file not recognized #1

Failed installation: ignore_missing_bp.o: file not recognized #1

Comments

lldelisle commented Oct 8, 2019

henrybzhang commented Oct 8, 2019

lldelisle commented Oct 9, 2019

henrybzhang commented Oct 9, 2019

lldelisle commented Oct 9, 2019

henrybzhang commented Oct 10, 2019

henrybzhang commented Dec 18, 2019