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tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
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returns numpy error while intsalling nanocompore on Ubuntu 22.04 #214

Closed annapopova-scripps closed 1 year ago

annapopova-scripps commented 1 year ago

Hi,

I am facing an installation error while running pip3 install nanocompore. Would appreciate any help. Tried to install on a local python3 environment and got same error type.

error: Command "x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=1 -DHAVE_CBLAS -I/usr/local/include -I/usr/include -I/home/anna/nanocompore-env/my_env1/include -Ibuild/src.linux-x86_64-3.1/numpy/core/src/umath -Ibuild/src.linux-x86_64-3.1/numpy/core/src/npymath -Ibuild/src.linux-x86_64-3.1/numpy/core/src/common -Inumpy/core/include -Ibuild/src.linux-x86_64-3.1/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/home/anna/nanocompore-env/my_env1/include -I/usr/include/python3.10 -Ibuild/src.linux-x86_64-3.1/numpy/core/src/common -Ibuild/src.linux-x86_64-3.1/numpy/core/src/npymath -Ibuild/src.linux-x86_64-3.1/numpy/core/src/common -Ibuild/src.linux-x86_64-3.1/numpy/core/src/npymath -c build/src.linux-x86_64-3.1/numpy/core/src/multiarray/scalartypes.c -o build/temp.linux-x86_64-3.10/build/src.linux-x86_64-3.1/numpy/core/src/multiarray/scalartypes.o -MMD -MF build/temp.linux-x86_64-3.10/build/src.linux-x86_64-3.1/numpy/core/src/multiarray/scalartypes.o.d" failed with exit status 1 [end of output]

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

  × Encountered error while trying to install package.
  ╰─> numpy

  note: This is an issue with the package mentioned above, not pip.
  hint: See above for output from the failure.
  [end of output]

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

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

lmulroney commented 1 year ago

Hi @annapopova-scripps,

Sorry you're having issues installing Nanocompore with pip3. I haven't been able to replicate your installation error on two different computers. However, it seems from the error message that there is a conflict with numpy versions. Did you create a clean virtual environment prior to installing Nanocompore?

Thanks, Logan

annapopova-scripps commented 1 year ago

Thank you, Logan.

Agree, that it looks like a conflict of versions. Yes, I made a new python 3.10.6 environment on the Linux machine and got the error, than realized that python 3.7 was recommended. I succeeded to install Nanocompore on Windows lap top computer using Anaconda with python 3.7 (which is not my proffered location ), and I hope to accomplish so on Linux.

Anna