could not find function "dimRedMethodList" about dimred HOT 6 CLOSED

That is very strange, I export dimRedMethodList just as any other function and it isn't even a method.

From your error message I would think that this is unrelated, but try running:

names(completeClassDefinition("dimRedMethod", doExtends = FALSE)@subclasses)

from inside your package. You might need to import the classes dimRedMethod and all children (or maybe just the methods you are using) separately.

Have you tried calling dimRed::embed(...)?

from dimred.

I added a print statement for that line and get output before the error:

 [1] "DiffusionMaps"       "DRR"                 "FastICA"             "KamadaKawai"        
 [5] "DrL"                 "FruchtermanReingold" "HLLE"                "Isomap"             
 [9] "kPCA"                "LaplacianEigenmaps"  "LLE"                 "MDS"                
[13] "nMDS"                "PCA"                 "tSNE"               
Error in eval(expr, envir, enclos) : 
  could not find function "dimRedMethodList"

Calling as dimRed::embed had the same results.

It is weird... before loading dimRed I can access it via dimRed::dimRedMethodList and dimRed:::dimRedMethodList. Even more, I imported the whole dimRed package and still get the same error.

I'll figure out how to convert over to non-embed code. Can .mute be passed into the @fun and @apply functions?

from dimred.

that is strange, I will try this myself when I find some time.
You can look at the implementation of the embed function and simply copy the code I use for muting: https://github.com/gdkrmr/dimRed/blob/master/R/embed.R#L115

You are trying to use Isomap? I had some problems with the CVST package I use for the DRR method and had to import the whole thing because of namespace issues.

Another weird namespace hack I had to do is here, maybe it helps :
https://github.com/gdkrmr/dimRed/blob/master/R/kpca.R#L116

from dimred.

I can reproduce it without a package:

  dimRed::embed(dimRed::dimRedData(iris[1:4]),
                "Isomap", knn = 25,
                ndim = 2, .mute = "")

in a fresh R session gives the same error.

from dimred.

fixed with 36f4975

from dimred.

It works for me. Thanks

from dimred.