graphite functions missing, installed version is out of date
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Entering edit mode
mhlinder • 0
@mhlinder-8179
Last seen 7.3 years ago
United States

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, pathways() or 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:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] graphite_1.12.0      AnnotationDbi_1.28.2 GenomeInfoDb_1.2.5
[4] IRanges_2.0.1        S4Vectors_0.4.0      Biobase_2.26.0
[7] BiocGenerics_0.12.1  RSQLite_1.0.0        DBI_0.3.1

loaded via a namespace (and not attached):
[1] graph_1.44.1       org.Hs.eg.db_3.0.0 tools_3.1.0
> pathway()
Error: could not find function "pathway"
graphite bioclite • 1.2k views
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 23 months ago
United States

Use the current release version of R (3.2.0).

 

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mhlinder • 0
@mhlinder-8179
Last seen 7.3 years ago
United States

Dan: It's always the simple things, isn't it? Your suggestion worked like a charm; thanks so much!

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