Search
Question: [Solved] GSEAlm: failed importing gsealmPerm function
0
3.8 years ago by
kmezhoud10
Tunisia
kmezhoud10 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 3.8 years ago • written 3.8 years ago by kmezhoud10
0
3.8 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k 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 3.8 years ago • written 3.8 years ago by Martin Morgan ♦♦ 22k
0
3.8 years ago by
kmezhoud10
Tunisia
kmezhoud10 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 3.8 years ago • written 3.8 years ago by kmezhoud10
Please log in to add an answer.

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 291 users visited in the last hour