[Solved] GSEAlm: failed importing gsealmPerm function
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kmezhoud ▴ 10
@kmezhoud-6841
Last seen 2.5 years ago
Tunisia

Dear All,

I would like to import gsealmPerm function from GSEAlm package:

I added to DESCRIPTION file  :    imports: GSEAlm

I added to NAMESPACE file:       importFrom (GSEAlm, gsealmPerm)

And I used the function as:       GSEAlm::gsealmPerm(arguments.....)

but it yet failed to run function. When I load GSEAlm package it works.

When is there a NON-exportable function from package how can I use it without to load all functionalities of package?

This post seems talk about this. The use of ::: is not recommended.

Thanks

Karim

 

loadnamespace importing • 777 views
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@martin-morgan-1513
Last seen 3 months ago
United States

When I look at the source code for the GSEAlm package, I see a function called gsealmPerm. Is this the function you mean? If so, your problem is simple typo. DESCRIPTION

Imports: GSEAlm

NAMESPACE:

importFrom(GSEAlm, gsealmPerm)

.R:

gsealmPerm(...)

Or is there another problem, e.g., the function fails in your own code? If so, then please add to your question by including the exact error message.

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kmezhoud ▴ 10
@kmezhoud-6841
Last seen 2.5 years ago
Tunisia

Dear Dr Morgan,

Yes I did that           gseaPerm

The error message was:

Error in match(x, table, nomatch = 0L) :   could not find function "varLabels"

Finally the prblm comes from an other function

Biobase::varLabels

which was silenced by

if(inherits(try(pVals<-GSEAlm::gsealmPerm(eSet,coVariables,mSigDB_forGeneList,nperm= permutVal, na.rm=TRUE), silent=TRUE),"try-error"))
{tkmessage(message="ERROR"}.

Thanks

Karim

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