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Question: could not find function "champ.load"
0
gravatar for david.ch
4 months ago by
david.ch0
david.ch0 wrote:

Hi,

I Have installed the most recent Champ version 2.9.10

ChAMP.load gives me the error message:

Error in champ.load(directory = getwd(), method = "ChAMP", methValue = "B",  : 
  could not find function "champ.load"

And library(ChAMP):

Error: package or namespace load failed for 'ChAMP' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/mvtnorm/libs/mvtnorm.so':
  `maximal number of DLLs reached...
In addition: Warning messages:
1: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP' 
2: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP' 
3: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP' 
4: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'

 

Any ideas or help is appreciated.

ADD COMMENTlink modified 4 months ago • written 4 months ago by david.ch0
2
gravatar for Martin Morgan
4 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Make sure that you have a valid and current installation of Bioconductor

BiocInstaller::biocValid()

Depending on your version of R, you may be able to increase the number of DLLs that can be loaded. See ?R_MAX_NUM_DLLS.

ADD COMMENTlink written 4 months ago by Martin Morgan ♦♦ 22k

Hello Martin,

Thank you for your response. I have the most recent R version 3.4.4.

How I can see the number of DLLs I use and how I can increase it?

Thanks!

ADD REPLYlink written 4 months ago by david.ch0
1

Hello David:

You can reset your Renviron file and add one line: R_MAX_NUM_DLLS=512, then this error should be no more.

The Renviron file should be at /usr/local/lib64/R/3.4.4/lib64/R/etc (on my computer).

I am now fixing the package, deciding to cut down some packages. I have detected that if I remove some large packages like DMRcate or missMethyl. ChAMP's loading DLL numbers would decrease significantly.

Best

Yuan Tian

ADD REPLYlink written 4 months ago by Yuan Tian40

Usually one would set this on a user or project level, rather than at the system level. From ?.Renviron

the files searched for are '.Renviron' in the current or in the user's home directory (in that order)
ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 22k

Hello Yuan,

I can not locate Renviron file. I am using Mac.

ADD REPLYlink written 4 months ago by david.ch0
0
gravatar for david.ch
4 months ago by
david.ch0
david.ch0 wrote:

Thanks for all replies. The "renviron" file in Mac is located at:

/Library/Frameworks/R.framework/Versions/3.4/Resources/etc

 

I even couldn't start RStudio  when set R_MAX_NUM_DLLS=512 

R_MAX_NUM_DLLS=150 worked fine.

ChAMP works.

ADD COMMENTlink modified 4 months ago • written 4 months ago by david.ch0
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