error in extractSignatures: (list) object cannot be coerced to type 'double' [in call to 'which.min']

[solovictor]

Hi,
most of tested procedures worked perfectly (such as
plotApobecDiff(tnm = laml.tnm, maf = laml) , for example, just I have problem with extractSignatures.
Please look at the output and resolve.
Best Regards, Victor

laml.sign = extractSignatures(mat = laml.tnm, nTry = 3, plotBestFitRes = FALSE)
Estimating best rank..
Timing stopped at: 16.39 6.268 3.847
Timing stopped at: 19.64 7.504 5.454
Error in (function (...) : All the runs produced an error:
-#1 [r=2] -> (list) object cannot be coerced to type 'double' [in call to 'which.min']
-#2 [r=3] -> (list) object cannot be coerced to type 'double' [in call to 'which.min']

[PoisonAlien]

Hi,
Can you load NMF library and try again ?

[solovictor]

Hi, I did and it is not helping:

require("NMF") laml.sign = extractSignatures(mat = laml.tnm, nTry = 6, plotBestFitRes =

FALSE) Estimating best rank.. Timing stopped at: 15.55 6.024 3.676 Timing stopped at: 18.22 13.99 9.147 Timing stopped at: 25.8 9.721 6.922 Timing stopped at: 39.45 12.5 8.235 Timing stopped at: 41.16 12.22 8.611 Error in (function (...) : All the runs produced an error: -#1 [r=2] -> (list) object cannot be coerced to type 'double' [in call to 'which.min'] -#2 [r=3] -> (list) object cannot be coerced to type 'double' [in call to 'which.min'] -#3 [r=4] -> (list) object cannot be coerced to type 'double' [in call to 'which.min'] -#4 [r=5] -> (list) object cannot be coerced to type 'double' [in call to 'which.min'] -#5 [r=6] -> (list) object cannot be coerced to type 'double' [in call to 'which.min'] Unless some warning important when I first request NMF:

require("NMF")

Loading required package: NMF Loading required package: pkgmaker Loading required package: registry Attaching package: ‘pkgmaker’ The following object is masked from ‘package:base’: isNamespaceLoaded Loading required package: rngtools Loading required package: cluster NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 7/8 To enable shared memory capabilities, try: install.extras(' NMF ')

…

On Wed, Apr 18, 2018 at 11:43 PM PoisonAlien ***@***.***> wrote: Hi, Can you load NMF library and try again ? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#138 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AXl9Piw6A4IAkbuF1mBO0Gxos8FX15aIks5tqDIPgaJpZM4Ta-nW> .

[PoisonAlien]

This is weird. Could you try install NMF from GitHub and see if it helps.

devtools::install_github("renozao/NMF")

[solovictor]

unfortunately not helping. In R console even produce *segfault* *(while pdlotapobecdiff and others are working OK)*

require("NMF")

*Loading required package: NMF* *Loading required package: pkgmaker* *Loading required package: registry* *Loading required package: rngtools* *Loading required package: cluster* *NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 7/8* * To enable shared memory capabilities, try: install.extras('* *NMF* *')*

laml.sign = extractSignatures(mat = laml.tnm, nTry = 6, plotBestFitRes =

FALSE) *Estimating best rank..* * *** caught segfault **** *address 0x110, cause 'memory not mapped'* *Traceback:* * 1: .local(object, ...)* * 2: fitted(x)* * 3: fitted(x)* * 4: .KL(y, fitted(x))* * 5: obj.fun(x, y, ...)* * 6: .local(object, ...)* * 7: deviance(strategy, nmfFit, v, ...)* * 8: deviance(strategy, nmfFit, v, ...)* * 9: trackError(nmfData, deviance(strategy, nmfFit, v, ...), niter = i, force = TRUE)* *10: .local(object, y, x, ...)* *11: run(strategyX, y, x, maxIter = maxIter, ...)* *12: run(strategyX, y, x, maxIter = maxIter, ...)* *13: .local(object, y, x, ...)* *14: run(object = <S4 object of class "NMFStrategyIterative">, y = c(0, 1, 1, 1, 1, 1, 0, 0, 2, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 2, 1, 0, 2, 3, 2, 2, 3, 0, 2, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 2, 0, 0, 0, 0, 2, 0, 1, 2, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 2, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 2, 0, 1, 0, 0, 0*

…

On Thu, Apr 19, 2018 at 1:20 PM PoisonAlien ***@***.***> wrote: This is weird. Could you try install NMF from GitHub and see if it helps. devtools::install_github("renozao/NMF") — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#138 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AXl9PoDHjPz38-bkKJpnT0w-4D0rhBhBks5tqPFugaJpZM4Ta-nW> .

[PoisonAlien]

Hi,
Its hard for me to suggest anything without a reproducible data. Is it possible for you to share the matrix ? Also can you post your sessioninfo after loading maftools and maf ?