rpy2 may need a specified version about 2020plus HOT 4 CLOSED

This is actually a bug in rpy2 itself (see conda-forge/rpy2-feedstock#28). Apparently, rpy2 2.9.x does not work with numpy 1.17.

Here are some version numbers that worked in a clean install environment:
scipy-0.19.1
pandas-0.25.2
python-3.6.9
matplotlib-3.1.1
numpy-1.15.4
pysam-0.15.3

from 2020plus.

I was unaware of this problem as continuous integration (CI) hasn't yet indicated this error. My CI testing suggests rpy2 version 2.9.4 should be fine. My guess is that api changes from rpy2 version 2 to version 3 broke the code.

from 2020plus.

Thanks for reply. I install rpy2 v2.9.4, however, there still was something wrong. I used 2020plus v1.2.3. The command line is "python 2020plus.py --out-dir=result_compare classify -f test.features.txt" . The error is as follows:

Running Random forest . . .

AN ERROR HAS OCCURRED: check the log file

Type: <class 'ValueError'>
Exception: Buffer for this type not yet supported.
Traceback:
File "2020plus.py", line 275, in
args.func() # run function corresponding to user's command
File "2020plus.py", line 37, in _classify
src.classify.python.classifier.main(opts) # run code
....
....

The python modules I used were :
numpy==1.17.2
pandas==0.25.2
scipy==1.3.1
scikit-learn==0.19.2
matplotlib==3.1.1
PyYAML==5.1.2
pysam==0.15.3
rpy2==2.9.4
tzlocal==2.0.0
probabilistic2020==1.2.3
snakemake==5.7.4

from 2020plus.

Many thanks! Finally it worked for me. I reinstalled scipy-0.19.1 and numpy-1.15.4.

from 2020plus.