error in rank comparison computations

[Frank73]

nmf was called with the following arguments, where tdm is a term-document matrix with 3133 rows and 5837 columns:

nmf(tdm, rank=2:10, seed = "random", nrun = 100, .options = "v")

The output was as follows:

Compute NMF rank= 2 ... + measures ... OK
Compute NMF rank= 3 ... + measures ... OK
Compute NMF rank= 4 ... + measures ... OK
Compute NMF rank= 5 ... + measures ... OK
Compute NMF rank= 6 ... + measures ... OK
Compute NMF rank= 7 ... + measures ... OK
Compute NMF rank= 8 ... + measures ... OK
Compute NMF rank= 9 ... ERROR
Timing stopped at: 3442 134.6 1907
ERROR
Compute NMF rank= 10 ... + measures ... OK
nmfPlotQuality: nmf from tdm: 27360.324758
Warning messages:
1: In (function (...) :
NAs were produced due to errors in some of the runs:
-#8[r=9] -> NMF::nmf - Unexpected error: no partial result seem to have been saved.
2: Removed 10 rows containing missing values (geom_point).

---

And I did not get results for rank=9.

How can this be avoided?

[renozao]

Can you please try reproducing the error using a fixed seed and just the rank=9 run, so that I can also debug it on my side?
You can either send me the data by email (if it is ok) or code to generate a toy data that produces the same error.
Thanks

[Frank73]

Hi Renozao,

While the above example is running with your requested changes, I played around to get an easier example and came up with this error:

> goodM
     [,1] [,2] [,3]
[1,]    1    1    1
[2,]    0    0    1
> badM
     [,1] [,2] [,3]
[1,]    1    1    0
[2,]    0    0    1
> r <- nmf(goodM, 2)                                                            
> fitted(r)                                                                     
             [,1]         [,2] [,3]
[1,] 1.000000e+00 1.000000e+00    1
[2,] 2.756248e-16 2.756248e-16    1
> r <- nmf(badM, 2)
Error in cons != .consold : non-conformable arrays
Timing stopped at: 0.012 0 0.012
>

Why isn't this working?

[renozao]

I don't think this is the same error, but this one was reported and fixed (issue #89) The fix is on the devel branch.

[Frank73]

OK, great.
The example at the beginning of this thread is impractical, since it is taking to much time to finish. I'll try to find a smaller example.

[renozao]

Maybe work from your data, limit to rank 9, with fewer runs (20). If it breaks then start skimming the data to a reduced set of rows for which it still breaks.

[pogacsa]

Hi, I'm running into all sorts of errors described here and in issue #89. I installed the devel branch therefore, but the exact same errors occur with the same parameters. :( Sometimes it runs through with the same matrix, if the number of runs is only 1, but not, if higher.
"Error in cons != .consold : non-conformable arrays" is my latest error mit devel.
Sessioninfo says NMF_0.23.6, my R version is 3.4.1.
Any ideas?

[pogacsa]

If I run it with a range of ranks, all produce an error:
Error in (function (...) : All the runs produced one of these two errors:
comparison of these types is not implemented [in call to '==']
non-conformable arrays [in call to '!=']

[KafeelBasha]

I am trying to work in NMF package in R for recommendations, so I am using 'lee' method in nmf().

Which minimizes squared error, ||V-WH||^2. With "model_nmf=nmf(as(rating,"matrix"),15,'lee')", getting error as "Error in cons != .consold : non-conformable arrays. Timing stopped at: 37.25 0.25 37.75"
The object "rating" has NAs, how can I resolve this error.