I have installed the graphite package according to the instructions---namely, by running
biocLite("graphite")---and it installs and I can load it. However, basic functions (eg,
pathwayDatabases()) are not available, and
sessionInfo() indicates that the installed version of graphite is 1.12.0, not 1.14.0 (the most recent version, according to the above link). How do I update my version of graphite and gain access to these functions? Thanks very much!
> library(graphite) Loading required package: DBI Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: GenomeInfoDb Loading required package: S4Vectors Loading required package: IRanges Attaching package: ‘AnnotationDbi’ The following object is masked from ‘package:GenomeInfoDb’: species > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin13.2.0 (64-bit) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  parallel stats4 stats graphics grDevices utils datasets  methods base other attached packages:  graphite_1.12.0 AnnotationDbi_1.28.2 GenomeInfoDb_1.2.5  IRanges_2.0.1 S4Vectors_0.4.0 Biobase_2.26.0  BiocGenerics_0.12.1 RSQLite_1.0.0 DBI_0.3.1 loaded via a namespace (and not attached):  graph_1.44.1 org.Hs.eg.db_3.0.0 tools_3.1.0 > pathway() Error: could not find function "pathway"