champ.norm task 1 failed - "could not find function "blc""

Question

[zkun8638]

When using champ.norm to process the data, the following error occurred. And it doesn‘t work and shows the same error after I load the RPMM package:

library(RPMM)
Loading required package: cluster

myNorm <- champ.norm(beta=myLoad$beta,arraytype="450K",cores=5)
[===========================]
[>>>>> ChAMP.NORM START <<<<<<]
-----------------------------
champ.norm Results will be saved in ./CHAMP_Normalization/
[ SWAN method call for BOTH rgSet and mset input, FunctionalNormalization call for rgset only , while PBC and BMIQ only needs beta value. Please set parameter correctly. ]
<< Normalizing data with BMIQ Method >>
Note that,BMIQ function may fail for bad quality samples (Samples did not even show beta distribution).
5 cores will be used to do parallel BMIQ computing.
Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x],  :
  task 1 failed - "could not find function "blc""

[Carlo Yague]

Hello kun8638,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[Carlo Yague]

Hello kun8638!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/p133866/

This is typically not recommended as it runs the risk of annoying people in both communities.

[zkun8638]

sorry，I already deleted the other post

[Carlo Yague]

Thank you. In the future, if you feel that there is some value in cross-posting (some of us are not in both forums after all), you can do it, but make sure to add a disclaimer in your post with a direct link to the other site. That way we do not duplicate efforts to provide answers.

Answer 1

[Carlo Yague]

Have you tried re-installing the RPMM and ChAMP packages ?

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChAMP")
install.packages("RPMM", dependencies=T)

[zkun8638]

I am operating on a rented server, therefore I don't have the authoritation to install packages. Can you tell me what are the dependencies of RPMM packages?

[Carlo Yague]

Can you tell me what are the dependencies of RPMM packages?

ENmix, MEAT, MethylMix

I don't have the authoritation to install packages.

Can you contact an administrator to help you with the issue ? Because if you can't install anything, not even a R package, then there is not much you can do about your issue.

[zkun8638]

I have contacted the administrator，Thank you for the suggestions. The problem was fixed after re-installation of the RPMM and ChAMP packages