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Question: [Solved] GSEAlm: failed importing gsealmPerm function
0
gravatar for kmezhoud
3.0 years ago by
kmezhoud0
Tunisia
kmezhoud0 wrote:

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

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by kmezhoud0
0
gravatar for Martin Morgan
3.0 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

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.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Martin Morgan ♦♦ 20k
0
gravatar for kmezhoud
3.0 years ago by
kmezhoud0
Tunisia
kmezhoud0 wrote:

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

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by kmezhoud0
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