Question

could not find function "champ.load"

0

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david.ch • 0

@davidch-14061

Last seen 6.5 years ago

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.

ChAMP champ 2.9.10 methylationepic • 2.4k views

ADD COMMENT • link 6.8 years ago • updated 6.7 years ago david.ch • 0

score 2 · Answer 1 · 2018-03-23

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Martin Morgan 25k

@martin-morgan-1513

Last seen 5 months ago

United States

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 COMMENT • link 6.8 years ago Martin Morgan 25k

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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 REPLY • link 6.8 years ago david.ch • 0

1

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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 REPLY • link 6.8 years ago Yuan Tian ▴ 290

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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 REPLY • link 6.8 years ago Martin Morgan 25k

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Hello Yuan,

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

ADD REPLY • link 6.7 years ago david.ch • 0

score 0 · Answer 2 · 2018-03-28

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david.ch • 0

@davidch-14061

Last seen 6.5 years ago

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 COMMENT • link 6.7 years ago david.ch • 0