Arch Linux User Repository

Important note: This is the way how to upgrade.

Suppose that we have this line in ~/.bashrc or ~/.zshrc or etc.

[ -f /opt/miniconda3/etc/profile.d/conda.sh ] && source /opt/miniconda3/etc/profile.d/conda.sh

1. Before to upgrade I comment this line.
2. Upgrade the package as usual.
3. Uncomment the line.

I have packaged micromamba in AUR. Try it if you are looking for a lightweight, barebones alternative to miniconda.

New release: 4.7.10 (2019-07-19). Please update

hidebu, Thank you ! I looked for hours and can confirm that the symbolik link workaround seems to work.

jat255, I face the same issue, and solved it by overwriting ld in compailer_compat. e.g. ln -snf /bin/ld ~/.conda/envs/py365/compiler_compat/ld

it seems binutils 2.32 is required, but ld in compailer_compat is 2.31.1. I found the hint at https://bbs.archlinux.org/viewtopic.php?id=242682

Has anyone using this package (together with PyCharm) been able to install the Cython debugging extensions in a project that is using a conda environment as the Python interpreter? The extensions compile fine when using the system-wide python, but fail when using miniconda's python. I receive the following error when trying to compile the extensions manually:

$ sudo /path/to/miniconda/python /opt/pycharm-professional/helpers/pydev/setup_cython.py build_ext --inplace

running build_ext
building '_pydevd_bundle.pydevd_cython' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/_pydevd_bundle
gcc -pthread -B /home/xxx/.conda/envs/xxx/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/xxx/.conda/envs/xxx/include/python3.6m -c _pydevd_bundle/pydevd_cython.c -o build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/_pydevd_bundle
gcc -pthread -shared -B /home/xxx/.conda/envs/xxx/compiler_compat -L/home/xxx/.conda/envs/xxx/lib -Wl,-rpath=/home/xxx/.conda/envs/xxx/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o -o build/lib.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.cpython-36m-x86_64-linux-gnu.so
/home/xxx/.conda/envs/xxx/compiler_compat/ld: build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: unable to initialize decompress status for section .debug_info
/home/xxx/.conda/envs/xxx/compiler_compat/ld: build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: unable to initialize decompress status for section .debug_info
/home/xxx/.conda/envs/xxx/compiler_compat/ld: build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: unable to initialize decompress status for section .debug_info
/home/xxx/.conda/envs/xxx/compiler_compat/ld: build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.6/_pydevd_bundle/pydevd_cython.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

(x-posting this comment to the pycharm-professional AUR page)

nikatar, I don't think this is related to miniconda3 packaging, so this is not the right support channel. Still, I could give you some directions:

Consider moving / deleting the following directory

~/.ipython/profile_default/

Check your environment variables for remnants from your previous installation.

env | grep conda
env | grep CONDA

Hello. Could you help me please? At the beginning I installed anaconda from AUR. After I removed it(including files and directories in HOME manually) and installed miniconda, but now I can't run jupyter-notebook due to kernel errors: for some reasons jupyter-notebook tries to run command ~/anoconda3/bin/python

['/home/nikatar/anaconda3/bin/python', '-m', 'ipykernel_launcher', '-f', '/run/user/1000/jupyter/kernel-7cbb9d30-cfc3-4ecd-b067-adbcfb36eb29.json'] PATH='/home/nikatar/.conda/envs/myenv/bin:/home/nikatar/.rvm/gems/ruby-2.5.1/bin:/home/nikatar/.rvm/gems/ruby-2.5.1@global/bin:/home/nikatar/.rvm/rubies/ruby-2.5.1/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/nikatar/.rvm/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/nikatar/.rvm/bin' with kwargs: {'stdin': -1, 'stdout': None, 'stderr': None, 'cwd': '/home/nikatar/Документы/dev/omm/1-28', 'start_new_session': True}

@simonp Done :)