Unknown format code 'd' for object of type 'float'

[dlippold]

After I installed genipe (on a fully updated Fedora 25 system) as described in the documentation I executed the test and get an error message.

In detail I did the following as root:

dnf install python3 python3-devel python3-numpy python3-jinja2 python3-pandas python3-setuptools

And then I did the following as a user:

pyvenv $HOME/genipe_pyvenv
source $HOME/genipe_pyvenv/bin/activate
pip install genipe
pip install pyfaidx
python
import genipe
genipe.test()

After that I get the following error message:

ERROR: test_read_phenotype (genipe.tests.test_imputed_stats.TestImputedStats)
Tests the 'read_phenotype' function.

Traceback (most recent call last):
File "/home/user/genipe_pyvenv/lib64/python3.5/site-packages/genipe/tests/test_imputed_stats.py", line 248, in test_read_phenotype
filename, args,
File "/home/user/genipe_pyvenv/lib64/python3.5/site-packages/genipe/tools/imputed_stats.py", line 251, in read_phenotype
(sex_counts.index == 2))].sum()
ValueError: Unknown format code 'd' for object of type 'float'

I get one more error message which is described in another ticket.

It seems to me that the character 'd' in line 247 of the file genipe/tools/imputed_stats.py has to be replaced by the character 'f'.

The output of the command source $HOME/genipe_pyvenv/bin/activate; python --version; deactivate is: Python 3.5.4

[lemieuxl]

The failed test looks like it's related to pandas version 0.21.

$ pip list
Package         Version
--------------- -------
genipe          1.3.3  
Jinja2          2.10   
MarkupSafe      1.0    
numpy           1.13.3 
pandas          0.21.0 
pip             9.0.1  
pyfaidx         0.5.1  
python-dateutil 2.6.1  
pytz            2017.3 
setuptools      36.6.0 
six             1.11.0 
$ python -m unittest genipe.tests.test_imputed_stats.TestImputedStats.test_read_phenotype
E
======================================================================
ERROR: test_read_phenotype (genipe.tests.test_imputed_stats.TestImputedStats)
Tests the 'read_phenotype' function.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/lemieuxl/genipe_pyvenv/lib64/python3.6/site-packages/genipe/tests/test_imputed_stats.py", line 248, in test_read_phenotype
    filename, args,
  File "/home/lemieuxl/genipe_pyvenv/lib64/python3.6/site-packages/genipe/tools/imputed_stats.py", line 251, in read_phenotype
    (sex_counts.index == 2))].sum()
ValueError: Unknown format code 'd' for object of type 'float'

----------------------------------------------------------------------
Ran 1 test in 0.008s

FAILED (errors=1)

If you downgrade to pandas version 0.20, the test should pass.

pip uninstall pandas
pip install pandas==0.20

$ pip list
Package         Version
--------------- -------
genipe          1.3.3  
Jinja2          2.10   
MarkupSafe      1.0    
numpy           1.13.3 
pandas          0.20.0 
pip             9.0.1  
pyfaidx         0.5.1  
python-dateutil 2.6.1  
pytz            2017.3 
setuptools      36.6.0 
six             1.11.0 
$ python -m unittest genipe.tests.test_imputed_stats.TestImputedStats.test_read_phenotype
.
----------------------------------------------------------------------
Ran 1 test in 0.114s

OK

I will fix this in a future release, but, for now, I suggest downgrading to pandas version 0.20.

[dlippold]

Thanks for your immediate answer.

I first had to install the RPM packages redhat-rpm-config and gcc-c++ (by dnf install redhat-rpm-config gcc-c++). Then the two pip commands run successful and the error was gone.

[lemieuxl]

Yes, to downgrade pandas, you need to compile from the source code.
I'll keep the ticket opened until I fix the code for the newest version of pandas.