Question

Error, could not find function"file.edit", the install problem

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JXG1819 • 0

@jxg1819-21059

Last seen 5.4 years ago

Description: Error: could not find function "file.edit" Warning message: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘illuminaHumanv2.db’ had non-zero exit status

Can you help me to solve the problem? Thank you so much.

illuminaHumanv2.db • 2.2k views

ADD COMMENT • link 5.4 years ago JXG1819 • 0

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Nobody can help you with that little snippet of code. How could they?

You need to supply a self-contained example of what you tried, including what happened. Also, file.edit is part of the utils package, which is loaded when you start R, so you must be somehow detaching utils? That is definitely non-standard.

ADD REPLY • link 5.4 years ago James W. MacDonald 67k

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Thank you so much. I just install the package followed by bioconductor:

> if (!requireNamespace("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install("illuminaHumanv2.db")
Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'illuminaHumanv2.db'
also installing the dependency ‘org.Hs.eg.db’

installing the source packages ‘org.Hs.eg.db’, ‘illuminaHumanv2.db’

trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/org.Hs.eg.db_3.8.2.tar.gz'
Content type 'application/x-gzip' length 74892843 bytes (71.4 MB)
downloaded 71.4 MB

trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/illuminaHumanv2.db_1.26.0.tar.gz'
Content type 'application/x-gzip' length 6168132 bytes (5.9 MB)
downloaded 5.9 MB

Error: could not find function "file.edit"
Execution halted
Error: could not find function "file.edit"
Execution halted

The downloaded source packages are in
    ‘C:\Users\jxg1819\AppData\Local\Temp\RtmpOas6tF\downloaded_packages’
installation path not writeable, unable to update packages: cluster, nlme
Update old packages: 'affy', 'Biobase', 'BiocGenerics', 'BiocParallel', 'DelayedArray', 'edgeR', 'fgsea', 'GenomicRanges', 'IRanges', 'limma',
  'mvtnorm', 'S4Vectors'
Update all/some/none? [a/s/n]: 
Update all/some/none? [a/s/n]: 
n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘illuminaHumanv2.db’ had non-zero exit status

Also I have tried to install "AnnotationDbi",it does work. But I still can not install the package of illuminaHumanv2.db, also "rgu34a.db". I am sure that my computer firewall is disabled.

ADD REPLY • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by JXG1819 • 0

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What do you get if you run sessionInfo after that?

ADD REPLY • link 5.4 years ago James W. MacDonald 67k

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Thanks a lot. After install the package, I ran sessionInfo as you told me, The details as below:

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘illuminaHumanv2.db’ had non-zero exit status
> sessionInfo
function (package = NULL) 
{
    z <- list()
    z$R.version <- R.Version()
    z$platform <- z$R.version$platform
    if (nzchar(.Platform$r_arch)) 
        z$platform <- paste(z$platform, .Platform$r_arch, sep = "/")
    z$platform <- paste0(z$platform, " (", 8 * .Machine$sizeof.pointer, 
        "-bit)")
    z$locale <- Sys.getlocale()
    z$running <- osVersion
    z$RNGkind <- RNGkind()
    if (is.null(package)) {
        package <- grep("^package:", search(), value = TRUE)
        keep <- vapply(package, function(x) x == "package:base" || 
            !is.null(attr(as.environment(x), "path")), 
            NA)
        package <- .rmpkg(package[keep])
    }
    pkgDesc <- lapply(package, packageDescription, encoding = NA)
    if (length(package) == 0) 
        stop("no valid packages were specified")
    basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && 
        x$Priority == "base")
    z$basePkgs <- package[basePkgs]
    if (any(!basePkgs)) {
        z$otherPkgs <- pkgDesc[!basePkgs]
        names(z$otherPkgs) <- package[!basePkgs]
    }
    loadedOnly <- loadedNamespaces()
    loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
    if (length(loadedOnly)) {
        names(loadedOnly) <- loadedOnly
        pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
        z$loadedOnly <- pkgDesc[loadedOnly]
    }
    z$matprod <- as.character(options("matprod"))
    es <- extSoftVersion()
    z$BLAS <- as.character(es["BLAS"])
    z$LAPACK <- La_library()
    class(z) <- "sessionInfo"
    z
}
<bytecode: 0x0000016074278690>
<environment: namespace:utils>

Thanks again. I have uninstalled R and Rstudio(with all packages), and re-installed them, but it still show me the same error.

ADD REPLY • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by JXG1819 • 0