Question: Problem with GeneSetCollection after updating R devel packages.
0
gravatar for jcrodriguez
2.7 years ago by
jcrodriguez20
jcrodriguez20 wrote:

Hi everyone!
I have updated my R devel packages, and suddenly my library (under development) stopped working.
I've found my error was with GSEABase's GeneSetCollection constructor. In this sense I am not being able to run their simple example, but I see GSEABase's check report is passing (so their examples are working). I do not have any idea what could be happening, any help?
I copy the error log:

> library(GSEABase);
> gs1 <- GeneSet(setName="set1", setIdentifier="101")
> gs2 <- GeneSet(setName="set2", setIdentifier="102")
>      
> ## construct from indivdiual elements...
> gsc <- GeneSetCollection(gs1, gs2)
Error in validObject(.Object) : 
  invalid class “GeneSetCollection” object: superclass "vectorORfactor" not defined in the environment of the object's class
> ## or from a list
> gsc <- GeneSetCollection(list(gs1, gs2))
Error in validObject(.Object) : 
  invalid class “GeneSetCollection” object: superclass "vectorORfactor" not defined in the environment of the object's class
> sessionInfo();
R Under development (unstable) (2017-01-04 r71888)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 13.04

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_AR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=es_AR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=es_AR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] GSEABase_1.37.0      graph_1.53.0         annotate_1.53.1     
 [4] XML_3.98-1.5         AnnotationDbi_1.37.2 IRanges_2.9.18      
 [7] S4Vectors_0.13.13    Biobase_2.35.0       BiocGenerics_0.21.3 
[10] BiocInstaller_1.25.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9    digest_0.6.12  bitops_1.0-6   xtable_1.8-2   DBI_0.5-1     
 [6] RSQLite_1.1-2  tools_3.4.0    RCurl_1.95-4.8 compiler_3.4.0 memoise_1.0.0

The packages which got updated since my last working version were:

other attached packages:
[1] AnnotationDbi_1.37.1                IRanges_2.9.14           S4Vectors_0.13.7

loaded via a namespace (and not attached):
[1] digest_0.6.11

gseabase bug example • 693 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by jcrodriguez20
Answer: Problem with GeneSetCollection after updating R devel packages.
0
gravatar for Martin Morgan
2.7 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

This affects users of the devel branch only. It is solved by re-installing GSEABase

biocLite("GSEABase")

The problem is that class definitions are cached when a package is installed. GeneSetCollection's class definition is indirectly influenced by S4Vectors. S4Vectors changed the name of the class vectorORfactor to vector_OR_factor. The indirect nature of the class relationship meant that the person making the change in S4Vectors did not realize the consequence for GeneSetCollection.

ADD COMMENTlink written 2.7 years ago by Martin Morgan ♦♦ 23k
Answer: Problem with GeneSetCollection after updating R devel packages.
0
gravatar for jcrodriguez
2.7 years ago by
jcrodriguez20
jcrodriguez20 wrote:

Martin, thanks!
Actually it is working with your help.
I did not know class definitions were cached, thanks for knowledge.

Rodriguez, Juan C.

ADD COMMENTlink written 2.7 years ago by jcrodriguez20
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