Problem with GeneSetCollection after updating R devel packages.
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Entering edit mode
jcrodriguez ▴ 20
@jcrodriguez-12079
Last seen 7.7 years ago

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

bug gseabase example • 2.0k views
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@martin-morgan-1513
Last seen 3 months ago
United States

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.

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Entering edit mode
jcrodriguez ▴ 20
@jcrodriguez-12079
Last seen 7.7 years ago

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

Rodriguez, Juan C.

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