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Thank you for developing such useful tool. I used lefse galaxy service but gut the following error:
/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Error in (function (file = "", n = NULL, text = NULL, prompt = "?", keep.source = getOption("keep.source"), :
<text>:1:71: unexpected input
1: z <- suppressWarnings(lda(as.formula(class ~ Streptococcus_infantis + _
^
warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
File "/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/run_lefse.py", line 89, in <module>
if params['rank_tec'] == 'lda': lda_res,lda_res_th = test_lda_r(cls,feats,class_sl,params['n_boots'],params['f_boots'],params['lda_abs_th'],0.0000000001,params['nlogs'])
File "/export/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/lefse.py", line 189, in test_lda_r
z = robjects.r('z <- suppressWarnings(lda(as.formula('+f+'),data=sub_d,tol='+str(tol_min)+'))')
File "/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 358, in __call__
p = _rparse(text=StrSexpVector((string,)))
rpy2.rinterface.RRuntimeError: Error in (function (file = "", n = NULL, text = NULL, prompt = "?", keep.source = getOption("keep.source"), :
<text>:1:71: unexpected input
1: z <- suppressWarnings(lda(as.formula(class ~ Streptococcus_infantis + _
^
And I checked the taxa names there are no special chars. And the abundance values are in normal float value notation (not scientific notation). Could you help me out?
The text was updated successfully, but these errors were encountered:
Thank you for developing such useful tool. I used lefse galaxy service but gut the following error:
And I checked the taxa names there are no special chars. And the abundance values are in normal float value notation (not scientific notation). Could you help me out?
The text was updated successfully, but these errors were encountered: