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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Linux installation Error #193

Open GeneVector5 opened 11 months ago

GeneVector5 commented 11 months ago

I ran pip install -e . based on the tutorial and at the very end of the installation, I got this red text error message that I am having a hard time understanding. Does anyone know why this error is happening and how to resolve it?

  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 /tmp/tmpuu4a31nk get_requires_for_build_wheel /tmp/tmp_qyf3mvn
       cwd: /tmp/pip-install-0f7xkt3r/pysam
  Complete output (162 lines):
  # pysam: cython is available - using cythonize if necessary
  # pysam: htslib mode is shared
  # pysam: HTSLIB_CONFIGURE_OPTIONS=None
  # pysam: (sysconfig) CC=x86_64-linux-gnu-gcc -pthread
  # pysam: (sysconfig) CFLAGS=-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
  # pysam: (sysconfig) LDFLAGS=-Wl,-Bsymbolic-functions  -Wl,-z,relro -g -fwrapv -O2
  checking for gcc... x86_64-linux-gnu-gcc -pthread
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether x86_64-linux-gnu-gcc -pthread accepts -g... yes
  checking for x86_64-linux-gnu-gcc -pthread option to accept ISO C89... none needed
  checking for ranlib... ranlib
  checking for grep that handles long lines and -e... /usr/bin/grep
  checking for C compiler warning flags... unknown
  configure: Default CFLAGS_ARM/X86: -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
  checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes
  checking whether C compiler accepts -mavx2... yes
  checking whether C compiler accepts -mavx512f... yes
  checking whether C compiler supports ARM Neon... no
  checking for pkg-config... no
  checking for special C compiler options needed for large files... no
  checking for _FILE_OFFSET_BITS value needed for large files... no
  checking shared library type for unknown-Linux... plain .so
  checking whether the linker supports versioned symbols... no
  checking whether the compiler accepts -fvisibility=hidden... yes
  checking how to run the C preprocessor... x86_64-linux-gnu-gcc -pthread -E
  checking for egrep... /usr/bin/grep -E
  checking for ANSI C header files... yes
  checking for sys/types.h... yes
  checking for sys/stat.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for memory.h... yes
  checking for strings.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for unistd.h... yes
  checking for stdlib.h... (cached) yes
  checking for unistd.h... (cached) yes
  checking for sys/param.h... yes
  checking for getpagesize... yes
  checking for working mmap... yes
  checking for gmtime_r... yes
  checking for fsync... yes
  checking for drand48... yes
  checking for srand48_deterministic... no
  checking whether fdatasync is declared... yes
  checking for fdatasync... yes
  checking for library containing log... -lm
  checking for zlib.h... yes
  checking for inflate in -lz... yes
  checking for library containing recv... none required
  checking for bzlib.h... yes
  checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
  checking for lzma.h... no
  checking for lzma_easy_buffer_encode in -llzma... no
  configure: error: liblzma development files not found

  The CRAM format may use LZMA2 compression, which is implemented in HTSlib
  by using compression routines from liblzma <http://tukaani.org/xz/>.

  Building HTSlib requires liblzma development files to be installed on the
  build machine; you may need to ensure a package such as liblzma-dev (on Debian
  or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
  xz (via Homebrew on macOS) is installed; or build XZ Utils from source.

  Either configure with --disable-lzma (which will make some CRAM files
  produced elsewhere unreadable) or resolve this error to build HTSlib.
  checking for gcc... x86_64-linux-gnu-gcc -pthread
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether x86_64-linux-gnu-gcc -pthread accepts -g... yes
  checking for x86_64-linux-gnu-gcc -pthread option to accept ISO C89... none needed
  checking for ranlib... ranlib
  checking for grep that handles long lines and -e... /usr/bin/grep
  checking for C compiler warning flags... unknown
  configure: Default CFLAGS_ARM/X86: -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g   -fstack-protector-strong -Wformat -Werror=format-security  -g -fwrapv -O2    -fPIC
  checking whether C compiler accepts -mssse3 -mpopcnt -msse4.1... yes
  checking whether C compiler accepts -mavx2... yes
  checking whether C compiler accepts -mavx512f... yes
  checking whether C compiler supports ARM Neon... no
  checking for pkg-config... no
  checking for special C compiler options needed for large files... no
  checking for _FILE_OFFSET_BITS value needed for large files... no
  checking shared library type for unknown-Linux... plain .so
  checking whether the linker supports versioned symbols... no
  checking whether the compiler accepts -fvisibility=hidden... yes
  checking how to run the C preprocessor... x86_64-linux-gnu-gcc -pthread -E
  checking for egrep... /usr/bin/grep -E
  checking for ANSI C header files... yes
  checking for sys/types.h... yes
  checking for sys/stat.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for memory.h... yes
  checking for strings.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for unistd.h... yes
  checking for stdlib.h... (cached) yes
  checking for unistd.h... (cached) yes
  checking for sys/param.h... yes
  checking for getpagesize... yes
  checking for working mmap... yes
  checking for gmtime_r... yes
  checking for fsync... yes
  checking for drand48... yes
  checking for srand48_deterministic... no
  checking whether fdatasync is declared... yes
  checking for fdatasync... yes
  checking for library containing log... -lm
  checking for zlib.h... yes
  checking for inflate in -lz... yes
  checking for library containing recv... none required
  checking for bzlib.h... yes
  checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
  checking for lzma.h... no
  checking for lzma_easy_buffer_encode in -llzma... no
  configure: error: liblzma development files not found

  The CRAM format may use LZMA2 compression, which is implemented in HTSlib
  by using compression routines from liblzma <http://tukaani.org/xz/>.

  Building HTSlib requires liblzma development files to be installed on the
  build machine; you may need to ensure a package such as liblzma-dev (on Debian
  or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or
  xz (via Homebrew on macOS) is installed; or build XZ Utils from source.

  Either configure with --disable-lzma (which will make some CRAM files
  produced elsewhere unreadable) or resolve this error to build HTSlib.
  config.mk:2: *** Resolve configure error first.  Stop.
  # pysam: htslib configure options: None
  Traceback (most recent call last):
    File "/tmp/tmpuu4a31nk", line 280, in <module>
      main()
    File "/tmp/tmpuu4a31nk", line 263, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/tmp/tmpuu4a31nk", line 114, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/tmp/pip-build-env-f_dhcvaf/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
      return self._get_build_requires(config_settings, requirements=['wheel'])
    File "/tmp/pip-build-env-f_dhcvaf/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
      self.run_setup()
    File "/tmp/pip-build-env-f_dhcvaf/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 487, in run_setup
      super(_BuildMetaLegacyBackend,
    File "/tmp/pip-build-env-f_dhcvaf/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 338, in run_setup
      exec(code, locals())
    File "<string>", line 383, in <module>
    File "<string>", line 79, in run_make_print_config
    File "/usr/lib/python3.8/subprocess.py", line 415, in check_output
      return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
    File "/usr/lib/python3.8/subprocess.py", line 516, in run
      raise CalledProcessError(retcode, process.args,
  subprocess.CalledProcessError: Command '['make', '-s', 'print-config']' returned non-zero exit status 2.
  ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 /tmp/tmpuu4a31nk get_requires_for_build_wheel /tmp/tmp_qyf3mvn Check the logs for full command output.
SeppeDeWinter commented 11 months ago

@GeneVector5

Could you show the entire output of the command please?

Best,

Seppe

crossworlds423 commented 10 months ago

Hi Seppe, I attached a textfile showing the entire command outputwhen trying to install it again entire_ouput.txt

(base) sark@instance-4:~/scenicplus/scenicplus$ ls
Dockerfile       LICENSE.txt                        README.md         docs       requirements.txt  setup.py
Dockerfile_meme  Miniconda3-latest-Linux-x86_64.sh  cytoscape_styles  notebooks  resources         src
(base) sark@instance-4:~/scenicplus/scenicplus$ pip install -e .
Obtaining file:///home/sark/scenicplus/scenicplus
  Preparing metadata (setup.py) ... done
Collecting pycisTopic@ git+https://github.com/aertslab/pycisTopic@master (from scenicplus==1.0.1.dev3+g3741a4b)
  Cloning https://github.com/aertslab/pycisTopic (to revision master) to /tmp/pip-install-siptfp5b/pycistopic_db79979192484785bc77519333c715b4
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-siptfp5b/pycistopic_db79979192484785bc77519333c715b4
  Resolved https://github.com/aertslab/pycisTopic to commit e563fb6647380e1d510bed38779adc2034ec6292
  Preparing metadata (setup.py) ... done
Collecting pycistarget@ git+https://github.com/aertslab/pycistarget@master (from scenicplus==1.0.1.dev3+g3741a4b)
  Cloning https://github.com/aertslab/pycistarget (to revision master) to /tmp/pip-install-siptfp5b/pycistarget_0d2e7ca989b4443aae089e72e17326bf
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycistarget /tmp/pip-install-siptfp5b/pycistarget_0d2e7ca989b4443aae089e72e17326bf
  Resolved https://github.com/aertslab/pycistarget to commit 3fde1ce5e16241f00078bee920d8a805ccbf2360
  Preparing metadata (setup.py) ... done
Collecting pyscenic@ git+https://github.com/aertslab/pySCENIC@master (from scenicplus==1.0.1.dev3+g3741a4b)
  Cloning https://github.com/aertslab/pySCENIC (to revision master) to /tmp/pip-install-siptfp5b/pyscenic_7e9b6e8801d14aab917bb2430461ab74
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pySCENIC /tmp/pip-install-siptfp5b/pyscenic_7e9b6e8801d14aab917bb2430461ab74
  Resolved https://github.com/aertslab/pySCENIC to commit 31d51a1625f12fb3c6e92bc48ecc9d401524c22a
  Preparing metadata (setup.py) ... done
Collecting loomxpy@ git+https://github.com/aertslab/LoomXpy@main (from scenicplus==1.0.1.dev3+g3741a4b)
  Cloning https://github.com/aertslab/LoomXpy (to revision main) to /tmp/pip-install-siptfp5b/loomxpy_c97b0c3b8c814e239c1c1639d2a4282e
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/LoomXpy /tmp/pip-install-siptfp5b/loomxpy_c97b0c3b8c814e239c1c1639d2a4282e
  Resolved https://github.com/aertslab/LoomXpy to commit 61995ff10940968eac2cee8fe48300ab477a15d0
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pandas==1.5 (from scenicplus==1.0.1.dev3+g3741a4b)
  Downloading pandas-1.5.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 128.9 MB/s eta 0:00:00
Requirement already satisfied: numpy in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (1.24.4)
Requirement already satisfied: tqdm in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (4.65.0)
Collecting ray (from scenicplus==1.0.1.dev3+g3741a4b)
  Downloading ray-2.6.3-cp311-cp311-manylinux2014_x86_64.whl (57.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.1/57.1 MB 33.6 MB/s eta 0:00:00
Collecting attr (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached attr-0.3.2-py2.py3-none-any.whl (3.3 kB)
Collecting typing (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached typing-3.7.4.3.tar.gz (78 kB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: matplotlib in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (3.7.2)
Requirement already satisfied: scikit-learn in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (1.3.0)
Collecting statistics (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached statistics-1.0.3.5.tar.gz (8.3 kB)
  Preparing metadata (setup.py) ... done
Collecting pyranges (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached pyranges-0.0.129-py3-none-any.whl (1.5 MB)
Requirement already satisfied: scipy in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (1.11.2)
Collecting pybiomart (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached pybiomart-0.2.0-py3-none-any.whl (10 kB)
Requirement already satisfied: requests in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (2.29.0)
Collecting arboreto (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached arboreto-0.1.6-py2.py3-none-any.whl (15 kB)
Collecting gseapy==0.10.8 (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached gseapy-0.10.8-py3-none-any.whl (526 kB)
Requirement already satisfied: networkx in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (3.1)
Collecting ctxcore (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached ctxcore-0.2.0-py3-none-any.whl (5.8 MB)
Requirement already satisfied: seaborn in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (0.12.2)
Collecting pyBigWig (from scenicplus==1.0.1.dev3+g3741a4b)
  Downloading pyBigWig-0.3.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 213.3/213.3 kB 40.2 MB/s eta 0:00:00
Collecting plotly (from scenicplus==1.0.1.dev3+g3741a4b)
  Downloading plotly-5.16.1-py2.py3-none-any.whl (15.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.6/15.6 MB 101.5 MB/s eta 0:00:00
Collecting adjustText (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached adjustText-0.8-py3-none-any.whl (9.1 kB)
Collecting MACS2 (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached MACS2-2.2.9.1.tar.gz (2.0 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting lxml (from scenicplus==1.0.1.dev3+g3741a4b)
  Downloading lxml-4.9.3-cp311-cp311-manylinux_2_28_x86_64.whl (7.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 148.1 MB/s eta 0:00:00
Collecting tspex (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached tspex-0.6.3.tar.gz (24 kB)
  Preparing metadata (setup.py) ... done
Collecting kaleido (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached kaleido-0.2.1-py2.py3-none-manylinux1_x86_64.whl (79.9 MB)
Collecting pyvis (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached pyvis-0.3.2-py3-none-any.whl (756 kB)
Collecting pygam (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached pygam-0.9.0-py3-none-any.whl (522 kB)
Requirement already satisfied: scanpy~=1.9 in /home/sark/miniconda3/lib/python3.11/site-packages (from scenicplus==1.0.1.dev3+g3741a4b) (1.9.3)
Collecting cython (from scenicplus==1.0.1.dev3+g3741a4b)
  Downloading Cython-3.0.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/3.6 MB 154.7 MB/s eta 0:00:00
Collecting plotnine (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached plotnine-0.12.2-py3-none-any.whl (1.3 MB)
Collecting mudata (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached mudata-0.2.3-py3-none-any.whl (24 kB)
Collecting sphinx_rtd_theme (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl (2.8 MB)
Collecting nbsphinx (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached nbsphinx-0.9.2-py3-none-any.whl (30 kB)
Collecting nbsphinx_link (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached nbsphinx_link-1.3.0-py2.py3-none-any.whl (5.2 kB)
Collecting numpydoc (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached numpydoc-1.5.0-py3-none-any.whl (52 kB)
Collecting sphinx_book_theme (from scenicplus==1.0.1.dev3+g3741a4b)
  Using cached sphinx_book_theme-1.0.1-py3-none-any.whl (396 kB)
Collecting bioservices (from gseapy==0.10.8->scenicplus==1.0.1.dev3+g3741a4b)
  Using cached bioservices-1.11.2.tar.gz (191 kB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: joblib in /home/sark/miniconda3/lib/python3.11/site-packages (from gseapy==0.10.8->scenicplus==1.0.1.dev3+g3741a4b) (1.3.2)
Requirement already satisfied: python-dateutil>=2.8.1 in /home/sark/miniconda3/lib/python3.11/site-packages (from pandas==1.5->scenicplus==1.0.1.dev3+g3741a4b) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /home/sark/miniconda3/lib/python3.11/site-packages (from pandas==1.5->scenicplus==1.0.1.dev3+g3741a4b) (2023.3)
Requirement already satisfied: anndata>=0.7.4 in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (0.9.2)
Requirement already satisfied: h5py>=3 in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (3.9.0)
Requirement already satisfied: statsmodels>=0.10.0rc2 in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (0.14.0)
Requirement already satisfied: patsy in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (0.5.3)
Requirement already satisfied: natsort in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (8.4.0)
Requirement already satisfied: numba>=0.41.0 in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (0.57.1)
Requirement already satisfied: umap-learn>=0.3.10 in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (0.5.3)
Requirement already satisfied: packaging in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (23.0)
Requirement already satisfied: session-info in /home/sark/miniconda3/lib/python3.11/site-packages (from scanpy~=1.9->scenicplus==1.0.1.dev3+g3741a4b) (1.0.0)
Requirement already satisfied: contourpy>=1.0.1 in /home/sark/miniconda3/lib/python3.11/site-packages (from matplotlib->scenicplus==1.0.1.dev3+g3741a4b) (1.1.0)
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Collecting pure-eval (from stack-data->IPython->pycistarget@ git+https://github.com/aertslab/pycistarget@master->scenicplus==1.0.1.dev3+g3741a4b)
  Using cached pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting xyzservices>=2021.09.1 (from bokeh>=2.4.2->dask[complete]->arboreto->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading xyzservices-2023.7.0-py3-none-any.whl (56 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.7/56.7 kB 13.2 MB/s eta 0:00:00
Requirement already satisfied: pycparser in /home/sark/miniconda3/lib/python3.11/site-packages (from cffi>=1.12->cryptography<40,>=38.0.0->pyopenssl->pycisTopic@ git+https://github.com/aertslab/pycisTopic@master->scenicplus==1.0.1.dev3+g3741a4b) (2.21)
Collecting googleapis-common-protos<2.0.dev0,>=1.56.2 (from google-api-core<3.0.0,>=1.0.0->opencensus->ray->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading googleapis_common_protos-1.60.0-py2.py3-none-any.whl (227 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 227.6/227.6 kB 44.3 MB/s eta 0:00:00
Collecting google-auth<3.0.dev0,>=2.14.1 (from google-api-core<3.0.0,>=1.0.0->opencensus->ray->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading google_auth-2.22.0-py2.py3-none-any.whl (181 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 181.8/181.8 kB 36.2 MB/s eta 0:00:00
Collecting zope.event (from gevent->grequests->bioservices->gseapy==0.10.8->scenicplus==1.0.1.dev3+g3741a4b)
  Using cached zope.event-5.0-py3-none-any.whl (6.8 kB)
Collecting zope.interface (from gevent->grequests->bioservices->gseapy==0.10.8->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading zope.interface-6.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (249 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 249.0/249.0 kB 41.5 MB/s eta 0:00:00
Collecting greenlet>=2.0.0 (from gevent->grequests->bioservices->gseapy==0.10.8->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading greenlet-2.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (618 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 618.8/618.8 kB 71.0 MB/s eta 0:00:00
Collecting cachetools<6.0,>=2.0.0 (from google-auth<3.0.dev0,>=2.14.1->google-api-core<3.0.0,>=1.0.0->opencensus->ray->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading cachetools-5.3.1-py3-none-any.whl (9.3 kB)
Collecting pyasn1-modules>=0.2.1 (from google-auth<3.0.dev0,>=2.14.1->google-api-core<3.0.0,>=1.0.0->opencensus->ray->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading pyasn1_modules-0.3.0-py2.py3-none-any.whl (181 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 181.3/181.3 kB 37.2 MB/s eta 0:00:00
Collecting rsa<5,>=3.1.4 (from google-auth<3.0.dev0,>=2.14.1->google-api-core<3.0.0,>=1.0.0->opencensus->ray->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading rsa-4.9-py3-none-any.whl (34 kB)
Collecting pyasn1<0.6.0,>=0.4.6 (from pyasn1-modules>=0.2.1->google-auth<3.0.dev0,>=2.14.1->google-api-core<3.0.0,>=1.0.0->opencensus->ray->scenicplus==1.0.1.dev3+g3741a4b)
  Downloading pyasn1-0.5.0-py2.py3-none-any.whl (83 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.9/83.9 kB 21.6 MB/s eta 0:00:00
Building wheels for collected packages: loomxpy, pyscenic, MACS2, pycistarget, pycisTopic, statistics, tspex, typing, loompy, annoy, bioservices, bs4, future, interlap, lda, multiprocessing_on_dill, pandoc, pybedtools, pyfasta, easydev, fbpca, globre, gpustat, intervaltree, numpy-groupies
  Building wheel for loomxpy (pyproject.toml) ... done
  Created wheel for loomxpy: filename=loomxpy-0.4.2-py3-none-any.whl size=28168 sha256=e0f93017fc4915fa36170ea7cb0ab9a20e04b7e0f9cc3385f0143c229863a965
  Stored in directory: /tmp/pip-ephem-wheel-cache-ndtitar1/wheels/7a/3a/8a/21d26a485464c1c66d81da84ae8c8536ebf9629f2d4ec480da
  Building wheel for pyscenic (setup.py) ... done
  Created wheel for pyscenic: filename=pyscenic-0.12.1+6.g31d51a1-py3-none-any.whl size=7100120 sha256=adce726f342126b29759231b51bbd4fb567f0eef8e88d012f10186e9447fdab5
  Stored in directory: /tmp/pip-ephem-wheel-cache-ndtitar1/wheels/34/b0/cc/4961f5e29900a4e897551d3390658f02f1f34d13813d49b852
  Building wheel for MACS2 (pyproject.toml) ... done
  Created wheel for MACS2: filename=MACS2-2.2.9.1-cp311-cp311-linux_x86_64.whl size=1827964 sha256=cbe16401bfd63f7c6e4b5a681502118e8f26671ae8d6d3ed913bf82b55d688c0
  Stored in directory: /home/sark/.cache/pip/wheels/fa/c0/cd/e20c4ce750b1247dc1432a11eaca830948bab4e5326997636d
  Building wheel for pycistarget (setup.py) ... done
  Created wheel for pycistarget: filename=pycistarget-1.0.3.dev1+g3fde1ce-py3-none-any.whl size=36176 sha256=868ae08840852d49cef23e287914a2cb405db37ac721a677005815ddeed06889
  Stored in directory: /tmp/pip-ephem-wheel-cache-ndtitar1/wheels/98/d5/e5/b9ac1a59c8e10c78f6f3a4ac9c4bed2b2b1f0261f80e38e707
  Building wheel for pycisTopic (setup.py) ... done
  Created wheel for pycisTopic: filename=pycisTopic-1.0.3.dev18+ge563fb6-py3-none-any.whl size=95772 sha256=9237508f70a7893739c938cc19ca199aa8df1bad1f6bcdf5831467706a989a82
  Stored in directory: /tmp/pip-ephem-wheel-cache-ndtitar1/wheels/c1/1e/de/f36b8117c897a2188e60f92702c5187735bdf63170152daee1
  Building wheel for statistics (setup.py) ... done
  Created wheel for statistics: filename=statistics-1.0.3.5-py3-none-any.whl size=7438 sha256=ac336439656dda1d3f03a4347c00eb8b7383874284dec2846d27281a094ebdb0
  Stored in directory: /home/sark/.cache/pip/wheels/a7/30/34/fceae1c718a4e749dd51f479c5720c0671519887e824915e90
  Building wheel for tspex (setup.py) ... done
  Created wheel for tspex: filename=tspex-0.6.3-py3-none-any.whl size=27193 sha256=3be511c8b2b780a53a5e6eac083a729f371accc16888e1e1aece03db4721abc6
  Stored in directory: /home/sark/.cache/pip/wheels/a1/b4/f9/b710c768e5eee193e1d1ce1a7ce96e451753bc40284558869b
  Building wheel for typing (setup.py) ... done
  Created wheel for typing: filename=typing-3.7.4.3-py3-none-any.whl size=26304 sha256=813b2cc72ff4e85229eb1608521cccde58c1f5af36dfd5e5dfdc532108f1e625
  Stored in directory: /home/sark/.cache/pip/wheels/9d/67/2f/53e3ef32ec48d11d7d60245255e2d71e908201d20c880c08ee
  Building wheel for loompy (setup.py) ... done
  Created wheel for loompy: filename=loompy-3.0.7-py3-none-any.whl size=52018 sha256=1f379c5503e200b7537d84eec1af22eca985f819a57fca73b5c346d6cf26f820
  Stored in directory: /home/sark/.cache/pip/wheels/ff/b3/90/a44cf2ed988f70e1f1d9868910ea5cb0e144c0c3493cf67352
  Building wheel for annoy (setup.py) ... done
  Created wheel for annoy: filename=annoy-1.17.3-cp311-cp311-linux_x86_64.whl size=77476 sha256=9f666fe0ebea6617fb0916e62f96519a271ce2008bc3982b8417414bc289bc85
  Stored in directory: /home/sark/.cache/pip/wheels/33/e5/58/0a3e34b92bedf09b4c57e37a63ff395ade6f6c1099ba59877c
  Building wheel for bioservices (setup.py) ... done
  Created wheel for bioservices: filename=bioservices-1.11.2-py3-none-any.whl size=223237 sha256=fbd52368e926150ff3d285aaecb11a9d5253086c008c0e74e7c8c60af2f976b5
  Stored in directory: /home/sark/.cache/pip/wheels/7f/99/8b/4bad72b741806a29f19ee46b1483ceb7498f8d07df2286a986
  Building wheel for bs4 (setup.py) ... done
  Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1256 sha256=c9fcc8b24793bc8a470adfea83b31f53395871042244696d80baf2ffc49649cd
  Stored in directory: /home/sark/.cache/pip/wheels/d4/c8/5b/b5be9c20e5e4503d04a6eac8a3cd5c2393505c29f02bea0960
  Building wheel for future (setup.py) ... done
  Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492025 sha256=030b6102762fc1a19c14b4b00533b9be137f24a313280ecd5d25ae1970935654
  Stored in directory: /home/sark/.cache/pip/wheels/da/19/ca/9d8c44cd311a955509d7e13da3f0bea42400c469ef825b580b
  Building wheel for interlap (setup.py) ... done
  Created wheel for interlap: filename=interlap-0.2.7-py3-none-any.whl size=6281 sha256=74b7875be0d85202bc4cd60306c178350669f25c78f365a19c97e29473caaa3b
  Stored in directory: /home/sark/.cache/pip/wheels/dd/c0/23/cb81b8babdc3a0b751c69ebf227f83b0e1640bef7ffedf0386
  Building wheel for lda (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [168 lines of output]
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!

              ********************************************************************************
              Usage of dash-separated 'description-file' will not be supported in future
              versions. Please use the underscore name 'description_file' instead.

              By 2023-Sep-26, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

      !!
        opt = self.warn_dash_deprecation(opt, section)
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!

              ********************************************************************************
              Usage of dash-separated 'author-email' will not be supported in future
              versions. Please use the underscore name 'author_email' instead.

              By 2023-Sep-26, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

      !!
        opt = self.warn_dash_deprecation(opt, section)
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!

              ********************************************************************************
              Usage of dash-separated 'pre-hook.sdist_pre_hook' will not be supported in future
              versions. Please use the underscore name 'pre_hook.sdist_pre_hook' instead.

              By 2023-Sep-26, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

      !!
        opt = self.warn_dash_deprecation(opt, section)
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
      !!

              ********************************************************************************
              Requirements should be satisfied by a PEP 517 installer.
              If you are using pip, you can try `pip install --use-pep517`.
              ********************************************************************************

      !!
        dist.fetch_build_eggs(dist.setup_requires)
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/command/develop.py:40: EasyInstallDeprecationWarning: easy_install command is deprecated.
      !!

              ********************************************************************************
              Please avoid running ``setup.py`` and ``easy_install``.
              Instead, use pypa/build, pypa/installer, pypa/build or
              other standards-based tools.

              See https://github.com/pypa/setuptools/issues/917 for details.
              ********************************************************************************

      !!
        easy_install.initialize_options(self)
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
      !!

              ********************************************************************************
              Please avoid running ``setup.py`` directly.
              Instead, use pypa/build, pypa/installer, pypa/build or
              other standards-based tools.

              See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
              ********************************************************************************

      !!
        self.initialize_options()
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!

              ********************************************************************************
              Usage of dash-separated 'description-file' will not be supported in future
              versions. Please use the underscore name 'description_file' instead.

              By 2023-Sep-26, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

      !!
        opt = self.warn_dash_deprecation(opt, section)
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!

              ********************************************************************************
              Usage of dash-separated 'author-email' will not be supported in future
              versions. Please use the underscore name 'author_email' instead.

              By 2023-Sep-26, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

      !!
        opt = self.warn_dash_deprecation(opt, section)
      /home/sark/miniconda3/lib/python3.11/site-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
      !!

              ********************************************************************************
              Usage of dash-separated 'pre-hook.sdist_pre_hook' will not be supported in future
              versions. Please use the underscore name 'pre_hook.sdist_pre_hook' instead.

              By 2023-Sep-26, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

      !!
        opt = self.warn_dash_deprecation(opt, section)
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-311
      creating build/lib.linux-x86_64-cpython-311/lda
      copying lda/__init__.py -> build/lib.linux-x86_64-cpython-311/lda
      copying lda/lda.py -> build/lib.linux-x86_64-cpython-311/lda
      copying lda/datasets.py -> build/lib.linux-x86_64-cpython-311/lda
      copying lda/utils.py -> build/lib.linux-x86_64-cpython-311/lda
      copying lda/_setup_hooks.py -> build/lib.linux-x86_64-cpython-311/lda
      creating build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/__init__.py -> build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/test_lda_sparse.py -> build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/test_lda_reuters.py -> build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/test_lda.py -> build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/test_lda_transform.py -> build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/test_datasets.py -> build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/test_utils.py -> build/lib.linux-x86_64-cpython-311/lda/tests
      running egg_info
      writing lda.egg-info/PKG-INFO
      writing dependency_links to lda.egg-info/dependency_links.txt
      writing requirements to lda.egg-info/requires.txt
      writing top-level names to lda.egg-info/top_level.txt
      [pbr] Reusing existing SOURCES.txt
      copying lda/_lda.c -> build/lib.linux-x86_64-cpython-311/lda
      copying lda/_lda.pyx -> build/lib.linux-x86_64-cpython-311/lda
      copying lda/gamma.c -> build/lib.linux-x86_64-cpython-311/lda
      copying lda/gamma.h -> build/lib.linux-x86_64-cpython-311/lda
      copying lda/tests/reuters.ldac -> build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/reuters.titles -> build/lib.linux-x86_64-cpython-311/lda/tests
      copying lda/tests/reuters.tokens -> build/lib.linux-x86_64-cpython-311/lda/tests
      running build_ext
      building 'lda._lda' extension
      creating build/temp.linux-x86_64-cpython-311
      creating build/temp.linux-x86_64-cpython-311/lda
      gcc -pthread -B /home/sark/miniconda3/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/sark/miniconda3/include -fPIC -O2 -isystem /home/sark/miniconda3/include -fPIC -I/home/sark/miniconda3/include/python3.11 -c lda/_lda.c -o build/temp.linux-x86_64-cpython-311/lda/_lda.o
      lda/_lda.c:196:12: fatal error: longintrepr.h: No such file or directory
        196 |   #include "longintrepr.h"
            |            ^~~~~~~~~~~~~~~
      compilation terminated.
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for lda
  Running setup.py clean for lda
  Building wheel for multiprocessing_on_dill (setup.py) ... done
  Created wheel for multiprocessing_on_dill: filename=multiprocessing_on_dill-3.5.0a4-py3-none-any.whl size=64023 sha256=5f3500efab9e1e59643ed8c179e16cb65d82b1c4943e2fa4fc813ed234c48df0
  Stored in directory: /home/sark/.cache/pip/wheels/55/31/39/4c3d29d345c11e257f46f60d682bed191732f4d16584c34071
  Building wheel for pandoc (setup.py) ... done
  Created wheel for pandoc: filename=pandoc-2.3-py3-none-any.whl size=33261 sha256=d73bef2968663d8f628a2ff5fc682f0ec7acc54698dcd25cd4b6787d3874dcae
  Stored in directory: /home/sark/.cache/pip/wheels/1c/a9/c4/6254542c4e8202d52fcd69798d2507aaad1f2a4bb60f2f0fea
  Building wheel for pybedtools (setup.py) ... done
  Created wheel for pybedtools: filename=pybedtools-0.9.1-cp311-cp311-linux_x86_64.whl size=12771130 sha256=55918c840905ac68547e4aa1cea68b4aff615271207931830c314092fcb87bd2
  Stored in directory: /home/sark/.cache/pip/wheels/c4/f4/19/26c8d60799f04c0cd0167e9e823203eb4c8d16c41afe60f6d6
  Building wheel for pyfasta (setup.py) ... done
  Created wheel for pyfasta: filename=pyfasta-0.5.2-py3-none-any.whl size=14277 sha256=1eab6a3587d446d5521b1c3ac9187e97834cdc3f2d70f4fa9ee2a44448399434
  Stored in directory: /home/sark/.cache/pip/wheels/81/8f/3d/40f56b0c512fc87d84288e300cebb27493d91d6888293d5145
  Building wheel for easydev (setup.py) ... done
  Created wheel for easydev: filename=easydev-0.12.1-py3-none-any.whl size=64213 sha256=b6b885c1c6131caaabeb6cb421f2e351f5fa792dfdd039a46a1a05e19f15a872
  Stored in directory: /home/sark/.cache/pip/wheels/e3/a9/d2/88070b802bde8e7ec4da08ebd59dd1f6683f183ee9795cfacf
  Building wheel for fbpca (setup.py) ... done
  Created wheel for fbpca: filename=fbpca-1.0-py3-none-any.whl size=11373 sha256=b0949c184d9fcc2a455794d7f7273a86d142198dfdc24e0c1a688ce1b3265efa
  Stored in directory: /home/sark/.cache/pip/wheels/71/ae/f7/5b7e1e16a133d094431428169e9a8d9f750afe5459f0333c9b
  Building wheel for globre (setup.py) ... done
  Created wheel for globre: filename=globre-0.1.5-py3-none-any.whl size=19545 sha256=7dad6e5b251094b56d80e547321c36c5b2abdefd60578efdd2b17c068a6dc04c
  Stored in directory: /home/sark/.cache/pip/wheels/71/cf/b4/19548cbf0c2fdd913452d49948163ab9313a20fc454515d429
  Building wheel for gpustat (pyproject.toml) ... done
  Created wheel for gpustat: filename=gpustat-1.1-py3-none-any.whl size=26274 sha256=20c320037bc342a373cd7287041739eb78e76f3fe2d6c50dba0b18c4bcb6a7dd
  Stored in directory: /home/sark/.cache/pip/wheels/e0/e5/58/11741d67a9ca5b8f09be16e15b13a72e32acff1aacaea2d5d3
  Building wheel for intervaltree (setup.py) ... done
  Created wheel for intervaltree: filename=intervaltree-3.1.0-py2.py3-none-any.whl size=26098 sha256=8a2b2b69d68a07f67114576f59b5dbf5eba3224202400c4d395888b067a1d971
  Stored in directory: /home/sark/.cache/pip/wheels/31/d7/d9/eec6891f78cac19a693bd40ecb8365d2f4613318c145ec9816
  Building wheel for numpy-groupies (setup.py) ... done
  Created wheel for numpy-groupies: filename=numpy_groupies-0.9.22-py3-none-any.whl size=25845 sha256=9aed06ffe66cf2d4e33e3dc22a6b14799626c61b5e3e3536cc7200e0b8823d7f
  Stored in directory: /home/sark/.cache/pip/wheels/1e/af/f7/db34aa0b4e0f5715a9af58fcbf92d83c731ba40db10657a3ac
Successfully built loomxpy pyscenic MACS2 pycistarget pycisTopic statistics tspex typing loompy annoy bioservices bs4 future interlap multiprocessing_on_dill pandoc pybedtools pyfasta easydev fbpca globre gpustat intervaltree numpy-groupies
Failed to build lda
ERROR: Could not build wheels for lda, which is required to install pyproject.toml-based projects
SeppeDeWinter commented 10 months ago

Hi

This issue is related to your Python version (3.11), see https://stackoverflow.com/questions/74979674/gensim-install-in-python-3-11-fails-because-of-missing-longintrepr-h-file.

Try installing with python 3.8 instead.

Best,

Seppe

strawberry098 commented 4 months ago

I'm using python 3.8.15 in Jupyter notebook, and upon executing !pip3 install . , I get the following error:

Complete output from command python setup.py egg_info: Download error on https://pypi.org/simple/setuptools_scm/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:897) -- Some packages may not be found! Download error on https://pypi.org/simple/setuptools-scm/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:897) -- Some packages may not be found! Couldn't find index page for 'setuptools_scm' (maybe misspelled?) Download error on https://pypi.org/simple/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:897) -- Some packages may not be found! No local packages or working download links found for setuptools_scm Traceback (most recent call last): File "", line 1, in File "/tmp/pip-689h3nko-build/setup.py", line 48, in "Operating System :: OS Independent", File "/usr/lib/python3.6/site-packages/setuptools/init.py", line 128, in setup _install_setup_requires(attrs) File "/usr/lib/python3.6/site-packages/setuptools/init.py", line 123, in _install_setup_requires dist.fetch_build_eggs(dist.setup_requires) File "/usr/lib/python3.6/site-packages/setuptools/dist.py", line 514, in fetch_build_eggs replace_conflicting=True, File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 770, in resolve replace_conflicting=replace_conflicting File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 1053, in best_match return self.obtain(req, installer) File "/usr/lib/python3.6/site-packages/pkg_resources/init.py", line 1065, in obtain return installer(requirement) File "/usr/lib/python3.6/site-packages/setuptools/dist.py", line 581, in fetch_build_egg return cmd.easy_install(req) File "/usr/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 672, in easy_install raise DistutilsError(msg) distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('setuptools_scm')

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-689h3nko-build/

SeppeDeWinter commented 4 months ago

Hi @strawberry098

This does not seem to be a SCENIC+ specific issue, are you able to install other packages?

All the best,

Seppe

strawberry098 commented 3 months ago

Hi @SeppeDeWinter

I realized the install was calling an older version of python (e.g. 3.6), resulting in the above error. When I tried the same code, adding the path of the updated python version, the download started normally.

However, the installation stalls for >1 hr (without going to the next line of code) after: Successfully built scenicplus loomxpy pyscenic pycistarget pycisTopic Installing collected packages: virtualenv, openpyxl, docutils, dill, defusedxml, cytoolz, cython, cycler, contourpy, colorlog, colorama, cloudpickle, click, charset-normalizer, cffi, certifi, cachetools, blosc2, blessed, bleach, bidict, beautifulsoup4, Babel, attrs, async-timeout, array-api-compat, annotated-types, alabaster, aiosignal, accessible-pygments, tables, statistics, scikit-learn, scikit-image, rich, requests, referencing, python-Levenshtein, python-igraph, pydantic, progressbar2, pandas, multiprocessing_on_dill, matplotlib, MACS2, loompy, leidenalg, gpustat, google-auth, gevent, gensim, easydev, dataclasses-json, dask, cryptography, cattrs, bs4, aiohttp, tspex, tmtoolkit, statsmodels, sphinx, seaborn, rich-argparse, requests-cache, pyrle, pyranges, pyopenssl, pynndescent, pygam, mizani, jsonschema-specifications, harmonypy, grequests, google-api-core, geosketch, distributed, ctxcore, bokeh, anndata, aiohttp-cors, adjustText, umap-learn, sphinxcontrib-jquery, scatac-fragment-tools, scanorama, pyvis, pydata-sphinx-theme, pybiomart, plotnine, opencensus, numpydoc, mudata, jsonschema, ipywidgets, bioservices, sphinx_rtd_theme, sphinx_book_theme, scrublet, scanpy, ray, nbformat, ipympl, gseapy, bbknn, nbclient, arboreto, pyscenic, papermill, nbconvert, nbsphinx, loomxpy, nbsphinx_link, pycisTopic, pycistarget, scenicplus

Is this normal (e.g. just takes some time) or not?

Thanks.

SeppeDeWinter commented 3 months ago

Hi @strawberry098

1 hour is a very long time ... are you using conda by any chance?

All the best.

Seppe

strawberry098 commented 3 months ago

Hi @SeppeDeWinter

I'm using the regular installation method (without conda) since I'm not familiar with using conda.

Thanks.

SeppeDeWinter commented 3 months ago

Hi @strawberry098

I'm sorry, but I'm not sure why it is taking so long for you to install... Are you trying to install the package on your local machine or on a cluster?

All the best,

Seppe

strawberry098 commented 3 months ago

Hi @SeppeDeWinter

I'm installing the package onto a server.

I decided to give conda a try and installed miniconda3.

The beginning of the command line now says base. However, despite trying to activate scenicplus, it still says base.

Thank you

kakaisi commented 3 months ago

Hi @SeppeDeWinter I have a problem when installing the scenicplus package, pycistopic, just this one, the problem is described as follows, can you help me solve it?

(scenicplus) [fang@localhost ~]$ cd scenicplus (scenicplus) [fang@localhost scenicplus]$ pip install -e . Obtaining file:///home/fang/scenicplus Preparing metadata (setup.py) ... done Collecting pycisTopic@ git+https://github.com/aertslab/pycisTopic@master (from scenicplus==1.0.1.dev6+ge5ba6fc.d20240318) Cloning https://github.com/aertslab/pycisTopic (to revision master) to /tmp/pip-install-pdnam6rz/pycistopic_5076824fab544b069995e0a602d7abaa Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-pdnam6rz/pycistopic_5076824fab544b069995e0a602d7abaa fatal: unable to access 'https://github.com/aertslab/pycisTopic/': Failed to connect to github.com port 443 after 127246 ms: Couldn't connect to server error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-pdnam6rz/pycistopic_5076824fab544b069995e0a602d7abaa did not run successfully. │ exit code: 128 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-pdnam6rz/pycistopic_5076824fab544b069995e0a602d7abaa did not run successfully. │ exit code: 128 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. (scenicplus) [fang@localhost scenicplus]$ python Python 3.8.18 | packaged by conda-forge | (default, Dec 23 2023, 17:21:28) [GCC 12.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import scenicplus scenicplus.version '1.0.1.dev6+ge5ba6fc.d20240314' pycistopic.version Traceback (most recent call last): File "", line 1, in NameError: name 'pycistopic' is not defined

strawberry098 commented 3 months ago

Hi @SeppeDeWinter

I was able to activate the conda environment. At the last step pip install -e. I'm getting a similar error as before of python setup.py egg_info did not run successfully when I did the regular installation (without conda).

Here's the error message:

Preparing metadata (setup.py) ... error error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [56 lines of output] WARNING: Cannot look at git URL git+https://github.com/aertslab/pycisTopic@master#egg=pycisTopic because it does not support lookup as web pages. WARNING: Cannot look at git URL git+https://github.com/aertslab/pycistarget@master#egg=pycistarget because it does not support lookup as web pages. WARNING: Cannot look at git URL git+https://github.com/aertslab/pySCENIC@master#egg=pyscenic because it does not support lookup as web pages. WARNING: Cannot look at git URL git+https://github.com/aertslab/LoomXpy@main#egg=loomxpy because it does not support lookup as web pages. WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1131)'))': /simple/setuptools-scm/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1131)'))': /simple/setuptools-scm/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1131)'))': /simple/setuptools-scm/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1131)'))': /simple/setuptools-scm/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1131)'))': /simple/setuptools-scm/ ERROR: Could not find a version that satisfies the requirement setuptools_scm (from versions: none) ERROR: No matching distribution found for setuptools_scm /home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/setuptools/init.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !!

      ********************************************************************************
      Requirements should be satisfied by a PEP 517 installer.
      If you are using pip, you can try `pip install --use-pep517`.
      ********************************************************************************

!! dist.fetch_build_eggs(dist.setup_requires) Traceback (most recent call last): File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/setuptools/installer.py", line 101, in _fetch_build_egg_no_warn subprocess.check_call(cmd) File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/jtse02/miniconda3/envs/scenicplus/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmp4p04y3lj', '--quiet', '--find-links', 'git+https://github.com/aertslab/pycisTopic@master#egg=pycisTopic', '--find-links', 'git+https://github.com/aertslab/pycistarget@master#egg=pycistarget', '--find-links', 'git+https://github.com/aertslab/pySCENIC@master#egg=pyscenic', '--find-links', 'git+https://github.com/aertslab/LoomXpy@main#egg=loomxpy', 'setuptools_scm']' returned non-zero exit status 1.

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/home/jtse02/scenicplus/setup.py", line 31, in setuptools.setup( File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/setuptools/init.py", line 102, in setup _install_setup_requires(attrs) File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/setuptools/init.py", line 75, in _install_setup_requires _fetch_build_eggs(dist) File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/setuptools/init.py", line 80, in _fetch_build_eggs dist.fetch_build_eggs(dist.setup_requires) File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/setuptools/dist.py", line 662, in fetch_build_eggs return _fetch_build_eggs(self, requires) File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/setuptools/installer.py", line 38, in _fetch_build_eggs resolved_dists = pkg_resources.working_set.resolve( File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/pkg_resources/init.py", line 829, in resolve dist = self._resolve_dist( File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/pkg_resources/init.py", line 865, in _resolve_dist dist = best[req.key] = env.best_match( File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/pkg_resources/init.py", line 1135, in best_match return self.obtain(req, installer) File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/pkg_resources/init.py", line 1147, in obtain return installer(requirement) File "/home/jtse02/miniconda3/envs/scenicplus/lib/python3.8/site-packages/setuptools/installer.py", line 103, in _fetch_build_egg_no_warn raise DistutilsError(str(e)) from e distutils.errors.DistutilsError: Command '['/home/jtse02/miniconda3/envs/scenicplus/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmp4p04y3lj', '--quiet', '--find-links', 'git+https://github.com/aertslab/pycisTopic@master#egg=pycisTopic', '--find-links', 'git+https://github.com/aertslab/pycistarget@master#egg=pycistarget', '--find-links', 'git+https://github.com/aertslab/pySCENIC@master#egg=pyscenic', '--find-links', 'git+https://github.com/aertslab/LoomXpy@main#egg=loomxpy', 'setuptools_scm']' returned non-zero exit status 1. [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details. Could not fetch URL https://pypi.org/simple/pip/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/pip/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1131)'))) - skipping

Thank you

strawberry098 commented 3 months ago

I tried to install the development version of SCENIC+, but encountered an error 30 minutes into the installation:

Preparing metadata (pyproject.toml) ... error error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [6 lines of output]

  Cargo, the Rust package manager, is not installed or is not on PATH.
  This package requires Rust and Cargo to compile extensions. Install it through
  the system's package manager or via https://rustup.rs/

  Checking for Rust toolchain....
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details.

SeppeDeWinter commented 3 months ago

Hi @strawberry098

Like the error suggests, you need to have cargo installed (this is the Rust package manager). See https://rustup.rs/ for more info.

All the best,

Seppe

strawberry098 commented 3 months ago

@SeppeDeWinter Thanks for your reply.

I already installed rustup and cargo into the scenicplus folder, but this error persists. I wonder if the path is correct?

image

SeppeDeWinter commented 3 months ago

Hi @strawberry098

How did you install rust?

All the best, Seppe

strawberry098 commented 3 months ago

@SeppeDeWinter As recommended on https://rustup.rs/

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

SeppeDeWinter commented 3 months ago

Hi @strawberry098

Are you able to run?


cargo --version

Seppe

strawberry098 commented 3 months ago

@SeppeDeWinter

This is what I got:

$path/scenicplus/.cargo/bin/cargo --version error: rustup could not choose a version of cargo to run, because one wasn't specified explicitly, and no default is configured. help: run 'rustup default stable' to download the latest stable release of Rust and set it as your default toolchain.

I looked through the rustup folder and tried again with a different path in the rustup folder rather than the cargo folder: $path/scenicplus/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/bin/cargo --version and the version is cargo 1.77.1 (e52e36006 2024-03-26)

strawberry098 commented 2 months ago

@SeppeDeWinter

How do I ensure the right cargo (path) is installed during scenicplus installation?

SeppeDeWinter commented 2 months ago

Hi @strawberry098

Did you run?


rustup default stable

Best,

Seppe

kakaisi commented 2 months ago

yeah.thanks

---- Replied Message ---- | From | @.> | | Date | 04/23/2024 22:00 | | To | @.> | | Cc | @.>@.> | | Subject | Re: [aertslab/scenicplus] Linux installation Error (Issue #193) |

Hi @strawberry098

Did you run?

rustup default stable

Best,

Seppe

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

strawberry098 commented 2 months ago

I ran rustup default stable and was able to retrieve the version number of cargo.

Then, I resumed pip install . of the development scenicplus and get the following error at the pycistarget stage:

Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Collecting loomxpy@ git+https://github.com/aertslab/LoomXpy@main (from scenicplus==1.0a1) Cloning https://github.com/aertslab/LoomXpy (to revision main) to /tmp/pip-install-9ipa6tf_/loomxpy5a1424fde4ff4379973c0ed327ee5ec1 Running command git clone --quiet https://github.com/aertslab/LoomXpy /tmp/pip-install-9ipa6tf/loomxpy5a1424fde4ff4379973c0ed327ee5ec1 Resolved https://github.com/aertslab/LoomXpy to commit 61995ff10940968eac2cee8fe48300ab477a15d0 Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting pycistarget@ git+https://github.com/aertslab/pycistarget@development (from scenicplus==1.0a1) Cloning https://github.com/aertslab/pycistarget (to revision development) to /tmp/pip-install-9ipa6tf/pycistargetebded4a0ffcf4d36a53eddc8b312d183 Running command git clone --quiet https://github.com/aertslab/pycistarget /tmp/pip-install-9ipa6tf/pycistarget_ebded4a0ffcf4d36a53eddc8b312d183 WARNING: Did not find branch or tag 'development', assuming revision or ref. Running command git checkout -q development error: pathspec 'development' did not match any file(s) known to git. error: subprocess-exited-with-error

× git checkout -q development did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× git checkout -q development did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. WARNING: There was an error checking the latest version of pip.

SeppeDeWinter commented 2 months ago

Hi @strawberry098

The development branch of SCENIC+ has been renamed to "main". I would recommend to reclone the repository or rename te branch locally.


git branch -m development main
git fetch origin
git branch -u origin/main main
git remote set-head origin -a

Best,

Seppe