Closed timothyjlaurent closed 10 years ago
when I run fab -f fabfile.py -H localhost install_libraries:r
fab -f fabfile.py -H localhost install_libraries:r
I get :
DBG [config.py]: Using config file /install/cloudbiolinux/cloudbio/../config/r-libs.yaml Error in value[[3L]](cond) : could not find function "is" Calls: source ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted Fatal error: local() encountered an error (return code 1) while executing 'sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "Rscript install_packages.R"' Aborting. [localhost] Executing task 'install_libraries' [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = [localhost] local: echo $HOME [localhost] local: uname -m [localhost] local: touch install_packages.R [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /usr/local/lib/R/site-library" [localhost] local: echo ' .libPaths(c("/usr/local/lib/R/site-library")) cran.repos <- getOption("repos") cran.repos["CRAN" ] <- "http://cran.fhcrc.org/" options(repos=cran.repos) source("http://bioconductor.org/biocLite.R") ' >> "$(echo install_packages.R)" [localhost] local: echo ' repo.installer <- function(repos, install.fn) { update.packages(lib.loc="/usr/local/lib/R/site-library", repos=repos, ask=FALSE) maybe.install <- function(pname) { if (!(pname %in% installed.packages())) install.fn(pname) } } ' >> "$(echo install_packages.R)" [localhost] local: echo ' std.pkgs <- c("abind", "ape", "aplpack", "biglm", "BiodiversityR", "bitops", "boot", "car", "caret", "caTools", "chron", "class", "cluster", "codetools", "coin", "colorspace", "date", "DBI", "devtools", "digest", "effect s", "FactoMineR", "flashClust", "foreign", "gdata", "gee", "graph", "ggplot2", "gplots", "gsalib", "gtools", "hdf5", "hexbin", "hmisc", "HH", "hwriter", "kernlab", "kernsmooth", "knitr", "lattice", "latticeExtra", "leaps", " lmtest", "maptree", "markdown", "mass", "matrix", "mclust", "mgcv", "modeltools", "multcomp", "multicore", "nlme", "NMF", "nnet", "pamr", "pi0", "plotrix", "plyr", "proto", "qvalue", "rcmdr", "relimp", "reshape", "reshape2", "rgl", "RColorBrewer", "RCurl", "rpart", "rjson", "Rmpi", "RMySQL", "RSQLite", "sandwich", "sm", "snowfall", "spatial", "sqldf", "statmod", "stringr", "strucchange", "survival", "testthat", "vegan", "vgam", "VennDiagram", " vr", "XML", "xtable", "yacca", "yaml", "zoo") std.installer = repo.installer(cran.repos, install.packages) lapply(std.pkgs, std.installer) ' >> "$(echo install_packages.R)" [localhost] local: echo ' bioc.pkgs <- c("affxparser", "affy", "affydata", "affyio", "affyPLM", "affyQCReport", "annaffy", "annotate", "AnnotationDbi", "aroma.light", "ArrayExpress", "arrayQualityMetrics", "ArrayTools", "BayesPeak", "baySeq", "beadarray", "Biobase", "BiocInstaller", "bioDist", "biomaRt", "Biostrings", "BSgenome", "ChIPpeakAnno", "chipseq", "ChIPseqR", "ChIPsim", "CNAnorm", "cn.mops", "CSAR", "cummeRbund", "DEGseq", "DESeq", "DEXSeq", "DiffBind", "DNAcopy", "DynDoc", "edgeR", "EDASeq", "exomeCopy", "gage", "gcrma", "genefilter", "geneplotter", "GenomeGraphs", "genomeIntervals", "GenomicFeatures", "GenomicRanges", "Genominator", "GEOquery", "GGBase", "GGtools", "ggbi o", "girafe", "globaltest", "GOFunction", "goseq", "GOstats", "GSEABase", "GWASTools", "hgu95av2.db", "HilbertVis", "htSeqTools", "impute", "IRanges", "KEGG.db", "limma", "lumi", "makecdfenv", "marray", "MEDIPS", "multtest", "MotIV", "mzR", "oneChannelGUI", "PAnnBuilder", "preprocessCore", "PICS", "qpgraph", "qrqc", "rGADEM", "R453Plus1Toolbox", "RBGL", "Repitools", "rGADEM", "Rgraphviz", "Ringo", "rnaSeqMap", "Rolexa", "Rsamtools", "Rsubread", "rtracklayer", "segmentSeq", "seqbias", "seqLogo", "ShortRead", "siggenes", "simpleaffy", "snpMatrix", "snpStats", "splots", "SRAdb", "tkWidgets", "VariantAnnotation", "vsn", "widgetTools", "xcms", "zlibbioc") bioc.installer = repo.installer(biocinstallRepos(), biocLite) lapply(bioc.pkgs, bioc.installer) ' >> "$(echo install_packages.R)" [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "Rscript install_packages.R" 2014/04/25 15:13:30 The command [/bin/sh -c fab -f fabfile.py -H localhost install_libraries:r] returned a non-zero code: 1
Not sure what is going on here
Fixed with #165
chapmanb
commented
10 years ago chapmanb
commented
10 years ago
when I run
fab -f fabfile.py -H localhost install_libraries:rI get :
Not sure what is going on here