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kathleenfix
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@kathleenfix-16649
Last seen 6.4 years ago
Hello,
I'm working on a newly updated Mac osx 10.11. I freshly updated R and XQuartz and then tried to install KEGGgraph using biocLite. When I list installed packages KEGGgraph is listed but when I try to use a function I get the error (for example):
Error in getKGMLurl("hsa00020") : could not find function "getKGMLurl"
Please help! Sample output is below
_______________________ R version 3.5.1 (2018-07-02) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help > ?biocLite starting httpd help server ... done > biocLite("KEGGgraph") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). Installing package(s) ‘KEGGgraph’ trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.5/KEGGgraph_1.40.0.tgz' Content type 'application/x-gzip' length 1783868 bytes (1.7 MB) ================================================== downloaded 1.7 MB The downloaded binary packages are in /var/folders/ls/sglxhr9s5yb0sr0f4sr7hbqr0000gn/T//RtmpWlv3qu/downloaded_packages > pkgs <- rownames(installed.packages()) > pkgs [1] "AnnotationDbi" "assertthat" "base" "BH" [5] "Biobase" "BiocGenerics" "BiocInstaller" "bit" [9] "bit64" "blob" "boot" "class" [13] "cluster" "codetools" "compiler" "datasets" [17] "DBI" "digest" "foreign" "graph" [21] "graphics" "grDevices" "grid" "IRanges" [25] "KEGGgraph" "KernSmooth" "lattice" "magrittr" [29] "MASS" "Matrix" "memoise" "methods" [33] "mgcv" "nlme" "nnet" "parallel" [37] "pkgconfig" "plogr" "prettyunits" "Rcpp" [41] "rpart" "RSQLite" "S4Vectors" "spatial" [45] "splines" "stats" "stats4" "survival" [49] "tcltk" "tools" "utils" "XML" > getKGMLurl("hsa00020") Error in getKGMLurl("hsa00020") : could not find function "getKGMLurl" > sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph") > sfile [1] "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/KEGGgraph/extdata/hsa04010.xml" > gR <- parseKGML2Graph(sfile,expandGenes=TRUE) Error in parseKGML2Graph(sfile, expandGenes = TRUE) : could not find function "parseKGML2Graph" > sessioninfo() Error in sessioninfo() : could not find function "sessioninfo"
Yes, finally figured that out. Thank you for helping a newb. :(