Yikun / BBS

The Bioconductor Build System
0 stars 0 forks source link

Basilisk.build fails due to old (?!) version of conda #33

Open martin-g opened 1 year ago

martin-g commented 1 year ago

https://yikun.github.io/bioconductor-0301/report/basilisk/kunpeng1-buildsrc.html

R CMD build basilisk fails with:

==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.1.0

Please update conda by running

    $ conda update -n base -c defaults conda

Quitting from lines 294-313 (motivation.Rmd) 
Error: processing vignette 'motivation.Rmd' failed with diagnostics:
one node produced an error: '/tmp/RtmpCFB0iC/Rbuild65fce678e0ba4/basilisk/vignettes/basilisk-vignette-test2/bin/python' was not built with a shared library.
reticulate can only bind to copies of Python built with '--enable-shared'.
--- failed re-building ‘motivation.Rmd’

SUMMARY: processing the following file failed:
  ‘motivation.Rmd’

Error: Vignette re-building failed.
martin-g commented 1 year ago

I've added export BASILISK_MINICONDA_VERSION="py38_23.1.0" to ~/BBS/3.17/bioc/kunpeng1/config.sh hoping that this will make it use a newer version of (Mini)conda that installs Python with --enable-shared config flag.

martin-g commented 1 year ago

Some more info:

> library(reticulate)  
>  reticulate::py_discover_config()
python:         /usr/bin/python3
libpython:      /usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so
pythonhome:     //usr://usr
version:        3.10.6 (main, Nov 14 2022, 16:10:14) [GCC 11.3.0]
numpy:          /usr/local/lib/python3.10/dist-packages/numpy
numpy_version:  1.24.1

NOTE: Python version was forced by RETICULATE_PYTHON
$ python3
Python 3.10.6 (main, Nov 14 2022, 16:10:14) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sysconfig
>>> sysconfig.get_config_var('Py_ENABLE_SHARED')
1

1 should mean enabled, I guess.

martin-g commented 1 year ago

Asked for help with https://github.com/LTLA/basilisk/issues/22