Question: ChAMP Methylation analysis error code "could not find function champ.load"
0
gravatar for sinha.puja
10 months ago by
sinha.puja0
sinha.puja0 wrote:

Hi..I tried to use ChAMP for my EPIC methylation array data and I use the following commands but it's not working,

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("ChAMP", version = "3.8")
a
BiocManager::install("ChAMPdata", version = "3.8")

library(ChAMPdata)
library(ChAMP)
BiocManager::install("DMRcate")
BiocManager::install("ChAMP", dependencies=TRUE)
baseDir2 <- "C:/Users/sinha.puja/Desktop/idats"
myLoad <- champ.load("C:/Users/sinha.puja/Desktop/baseDir2")

It gives me error: Error in champ.load("C:/Users/sinha.puja/Desktop/baseDir2") : 
  could not find function "champ.load"

I tried very hard by uninstalling and the re-installing the same but every time I am stuck at the same step. Has anyone else experienced this, or has any idea what I can do to solve this problem, as I seem to be going round in circles, which is incredibly frustrating!

Thank you in advance for your suggestions!

champ • 213 views
ADD COMMENTlink written 10 months ago by sinha.puja0

Hi, could you try to type and use tab key in R to show how many "champ.XXX" function do you have now?

Also, during your way of installing ChAMP, did you encounter any errors?

Best

Yuan Tian

ADD REPLYlink written 10 months ago by Yuan Tian120

I tried to use tab key in R and it shows no matches. Also while installing ChAMP I got the following warning messages:

ERROR: failed to lock directory 'C:/Users/sinha.puja/Documents/R/win-library/3.5' for modifying
Try removing 'C:/Users/sinha.puja/Documents/R/win-library/3.5/00LOCK-IlluminaHumanMethylationEPICanno.ilm10b2.hg19'
In R CMD INSTALL

Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’ had non-zero exit status.

Please help.

ADD REPLYlink written 10 months ago by sinha.puja0

Good, that's an error I have seen before. The message inform your that you have a bloken package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19. 

Do as the message suggested: Go to folder  C:/Users/sinha.puja/Documents/R/win-library/3.5/, then remove the whole "00LOCK-IlluminaHumanMethylationEPICanno.ilm10b2.hg19'" folder. Then try reinstall this package.

Personally, I think when you install ChAMP without any error, then it should work.

Best

Yuan Tian

ADD REPLYlink written 10 months ago by Yuan Tian120
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