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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=es_AR.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=es_AR.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=es_AR.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  GSEABase_1.37.0 graph_1.53.0 annotate_1.53.1  XML_3.98-1.5 AnnotationDbi_1.37.2 IRanges_2.9.18  S4Vectors_0.13.13 Biobase_2.35.0 BiocGenerics_0.21.3  BiocInstaller_1.25.3 loaded via a namespace (and not attached):  Rcpp_0.12.9 digest_0.6.12 bitops_1.0-6 xtable_1.8-2 DBI_0.5-1  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:
 AnnotationDbi_1.37.1 IRanges_2.9.14 S4Vectors_0.13.7
loaded via a namespace (and not attached):