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conda-forge / miniforge

A conda-forge distribution.
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Can't install large packages in Termux-proot #568

Open SHLEM666 opened 8 months ago

SHLEM666 commented 8 months ago

Solution to issue cannot be found in the documentation.

Issue

When I try to install SageMath package on Android device with conda or mamba the following error occurs

ERROR conda.core.link:_execute(945): An error occurred while installing package 'conda-forge::ipykernel-6.29.3-pyhd33586a_0'.

[Errno 2] No such file or directory: '/root/miniforge3/pkgs/ipykernel-6.29.3-pyhd33586a_0/site-packages/ipykernel/inprocess/__init__.py'

Moreover, at several installation attempts, this error occurs with different packages. E.g. ipython, sagelib, python, giac, nbconvert, pythran, sphinx, notebook, rpy2 and many-many others.

Additionally, I tried splitting the SageMath package installation into parts, but result was the same. The error always has the same form: No such file or directory: '/root/miniforge3/pkgs/package_name-version-build/some/path/__init__.py

Commands to reproduce

# in termux
yes | pkg update
yes | pkg install proot-distro
proot-distro install debian
proot-distro login debian

# in proot debian
apt update
yes | apt upgrade
curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh
bash Miniforge3-Linux-aarch64.sh

# relogin
exit
proot-distro login debian

conda create -n sage sage=10.2

Detailed information

The full installation output is too large to post here output.txt

Environment info active environment : base active env location : /root/miniforge3 shell level : 1 user config file : /root/.condarc populated config files : /root/miniforge3/.condarc conda version : 23.11.0 conda-build version : not installed python version : 3.10.13.final.0 solver : libmamba (default) virtual packages : __archspec=1=aarch64 __conda=23.11.0=0 __glibc=2.36=0 __linux=6.2.1=0 __unix=0=0 base environment : /root/miniforge3 (writable) conda av data dir : /root/miniforge3/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/linux-aarch64 https://conda.anaconda.org/conda-forge/noarch package cache : /root/miniforge3/pkgs /root/.conda/pkgs envs directories : /root/miniforge3/envs /root/.conda/envs platform : linux-aarch64 user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Linux/6.2.1-PRoot-Distro debian/12.5 glibc/2.36 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5 UID:GID : 0:0 netrc file : None offline mode : False

Hardware

Software

[!NOTE] On Raspberry Pi 3 Model B (aarch64, 1Gb ram) + Raspberry OS lite 64 bit Installation with the same commands completes successfully

hmaarrfk commented 8 months ago

I think there might have been a bug in conda and libmamba's solver in the previous version.

Try the latest version of miniforge's installer (it updates the default package).

Apparently the next version should be even better in terms of memory limitations.

PS. not many of us use Termux so that is why we are all hesitant to reply

SHLEM666 commented 8 months ago

Thank you, I didn’t expect a quick response)).

Miniforge3 v24.1.2-0 test showed that the error still occurs.

mistune commented 2 months ago

@SHLEM666 were you able to resolve this error? I am still seeing it in 24.7.1

mistune commented 2 months ago

@hmaarrfk I would like to help solve this issue by testing. What logs do I need to collect and how do I enable those logs?

hmaarrfk commented 2 months ago

the best thing to do would be to help create some kind of docker image that recreates the issue so we all be on the same page.

without that, we are going to be very slow at iterating.

SHLEM666 commented 2 months ago

@SHLEM666 were you able to resolve this error? I am still seeing it in 24.7.1

No, I faild to solve this problem.

SHLEM666 commented 2 months ago

the best thing to do would be to help create some kind of docker image that recreates the issue so we all be on the same page.

without that, we are going to be very slow at iterating.

According to your idea, I tried to use termux-docker aarch64 image.

docker pull termux/termux-docker:aarch64
docker run -it termux/termux-docker:aarch64
# default mirror is not works for me
echo "deb https://packages.termux.dev/apt/termux-main stable main" > $PREFIX/etc/apt/sources.list
yes | apt update
yes | apt upgrade
yes | pkg install proot-distro
proot-distro install debian

This attempt fails at proot-distro install step with the following error:

Error: the rootfs of distribution 'daebian' has unexpected structure (no /etc directory). Make sure that variable TARBALL_STRIP_OPT specified in distribution plug-in is correct.

I've found topic with similar problem. But in my case, the reason is not in the wrong PATH value.

According to the result of the next two commands, the error reason may be related to bad linking. (There is only 636 - 658 lines of log.txt under the first spoiler)

bash -x proot-distro install debian |& tee log.txt ```... [*] Extracting rootfs, please wait... + set +e + grep -v /linkerconfig/ + proot --link2symlink tar -C /data/data/com.termux/files/usr/var/lib/proot-distro/installed-rootfs/debian --warning=no-unknown-keyword --delay-directory-restore --preserve-permissions --strip=1 -xf /data/data/com.termux/files/usr/var/lib/proot-distro/dlcache/debian-bookworm-aarch64-pd-v4.7.0.tar.xz --exclude=dev proot error: ptrace(TRACEME): Function not implemented proot error: execve("/data/data/com.termux/files/usr/bin/tar"): Function not implemented proot info: possible causes: * the program is a script but its interpreter (eg. /bin/sh) was not found; * the program is an ELF but its interpreter (eg. ld-linux.so) was not found; * the program is a foreign binary but qemu was not specified; * qemu does not work correctly (if specified); * the loader was not found or doesn't work. fatal error: see `proot --help`. + set -e + '[' '!' -e /data/data/com.termux/files/usr/var/lib/proot-distro/installed-rootfs/debian/etc ']' + msg + echo -e + msg 'Error: the rootfs of distribution '\''debian'\'' has unexpected structure (no /etc directory). Make sure that variable TARBALL_STRIP_OPT specified in distribution plug-in is correct.' + echo -e 'Error: the rootfs of distribution '\''debian'\'' has unexpected structure (no /etc directory). Make sure that variable TARBALL_STRIP_OPT specified in distribution plug-in is correct.' Error: the rootfs of distribution 'debian' has unexpected structure (no /etc directory). Make sure that variable TARBALL_STRIP_OPT specified in distribution plug-in is correct. + msg + echo -e ... ```
proot --link2symlink tar --version ``` proot error: ptrace(TRACEME): Function not implemented proot error: execve("/data/data/com.termux/files/usr/bin/tar"): Function not implemented proot info: possible causes: * the program is a script but its interpreter (eg. /bin/sh) was not found; * the program is an ELF but its interpreter (eg. ld-linux.so) was not found; * the program is a foreign binary but qemu was not specified; * qemu does not work correctly (if specified); * the loader was not found or doesn't work. fatal error: see `proot --help`. ```

That's all for now. Research continues.

[!NOTE] I use Win10 + Docker Desktop 4.34.2 (167172).