When I use identifySignatures from somaticsignatures package it throws me out this error. What do I need to change ?
identifySignatures(sca_mm,5,nmfDecomposition)
Error in (new("standardGeneric", .Data = function (x) :
unused arguments (model = list("NMFstd", 5, 0), method = "random")
Hi Aslam,
I guess there should be some unknown library conflicts. Detaching and reloading NMF package may work.
There is an incompatibility here between NMF and SumarizedExperiment. If I start R without attaching any packages and run
library(NMF)
m = matrix(runif(100),nrow=10)
rank = 10
res = nmf(m,rank)
This runs fine and gives me an object of class NMF fit as expected. However, if I start up R without attaching anything and run
library(NMF)
library(SummarizedExperiment)
m = matrix(runif(100),nrow=10)
rank = 10
res = nmf(m,rank)
This reproduces the error:
Error in (new("standardGeneric", .Data = function (x) :
unused arguments (model = list("NMFstd", 10, 0), method = "random")
For completeness, I am appending my sessionInfo():
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SummarizedExperiment_1.14.0 DelayedArray_0.10.0
[3] BiocParallel_1.18.0 matrixStats_0.54.0
[5] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0
[7] IRanges_2.18.1 S4Vectors_0.22.0
[9] NMF_0.21.0 Biobase_2.44.0
[11] BiocGenerics_0.30.0 cluster_2.0.8
[13] rngtools_1.4 pkgmaker_0.27
[15] registry_0.5-1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 XVector_0.24.0 compiler_3.6.0
[4] pillar_1.4.2 RColorBrewer_1.1-2 plyr_1.8.4
[7] zlibbioc_1.30.0 bitops_1.0-6 iterators_1.0.10
[10] tools_3.6.0 digest_0.6.19 lattice_0.20-38
[13] tibble_2.1.3 gtable_0.3.0 gridBase_0.4-7
[16] pkgconfig_2.0.2 rlang_0.4.0 Matrix_1.2-17
[19] foreach_1.4.4 bibtex_0.4.2 GenomeInfoDbData_1.2.1
[22] withr_2.1.2 stringr_1.4.0 grid_3.6.0
[25] ggplot2_3.2.0 reshape2_1.4.3 magrittr_1.5
[28] scales_1.0.0 codetools_0.2-16 xtable_1.8-4
[31] colorspace_1.4-1 stringi_1.4.3 RCurl_1.95-4.12
[34] lazyeval_0.2.2 doParallel_1.0.14 munsell_0.5.0
[37] crayon_1.3.4
Both NMF and SummarizedExperiment (through a package it Depends: on, DelayedArray) have implemented a seed generic. Usually a package can be confident that, when it references functions defined in it's own package, it gets only those functions. Here we have
> nmf(m, rank)
Error in (new("standardGeneric", .Data = function (x) :
unused arguments (model = list("NMFstd", 10, 0), method = "random")
> traceback()
11: do.call(getGeneric("seed"), c(list(x = x, model = init, method = seed.method),
parameters.seed))
10: .local(x, rank, method, ...)
9: nmf(x, rank, method = strategy, ...)
8: nmf(x, rank, method = strategy, ...)
7: nmf(x, rank, method, seed = seed, model = model, ...)
6: nmf(x, rank, method, seed = seed, model = model, ...)
5: .local(x, rank, method, ...)
4: nmf(x, rank, NULL, ...)
3: nmf(x, rank, NULL, ...)
2: nmf(m, rank)
1: nmf(m, rank)
Note the getGeneric() call that causes the problem -- it does not have a package= argument, and appears to use the search() path to find the generic. Since SummarizedExperiment was loaded after NMF, it finds the wrong generic.
I think this is a bug in the NMF implementation, and will try to contact the maintainer.
A work-around, which may not be satisfactory if you also want to use DelayedArray::seed(), is to use the new function conflictRules() defined in base R to exclude DelayedArray::seed() from being seen.
conflictRules("DelayedArray", exclude = "seed")
library(NMF)
library(SummarizedExperiment)
UPDATE This issue had already been reported to NMF, and is fixed in the devel version of the package. You can install the devel version of the package with
BiocManager::install("renozao/NMF", ref = "devel")
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Hi, Aslam
I have encountered an exactly same problem. My code was working but I recently updated NMF packages (following biocLite suggestion). Then, when I ran the command, I had the error:
sigs_nmf = identifySignatures(sca_mm, n_sigs, nmfDecomposition)
Error in (new("standardGeneric", .Data = function (x) :
unused arguments (model = list("NMFstd", 5, 0), method = "random")
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Version of pacakges:
NMF_0.21.0
SomaticSignatures_2.16.0
VariantAnnotation_1.26.1
Thank you for the report. I have not been able to reproduce this issue with the same package versions as you have. Could you please post a complete example that I can rerun (from the starting of the R session until the error occurs) together with a complete output of the sessionInfo command?