Question: ChAMP Methylation analysis error code "could not find function champ.load"
gravatar for sinha.puja
5 weeks ago by
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))
BiocManager::install("ChAMP", version = "3.8")
BiocManager::install("ChAMPdata", version = "3.8")

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 • 89 views
ADD COMMENTlink written 5 weeks 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?


Yuan Tian

ADD REPLYlink written 5 weeks ago by Yuan Tian40

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'

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 5 weeks 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.


Yuan Tian

ADD REPLYlink written 5 weeks ago by Yuan Tian40
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