[R] R 3.3.0 Crashing: Error in readRDS(nsInfoFilePath) : unknown input format

Jeff Newmiller jdnewmil at dcn.davis.ca.us
Tue May 17 15:55:20 CEST 2016 

A) I am not a Dr. I am just someone who has been using R for awhile. Since the install process usually works for me, I might not even be the best person to identify your problem, but I will help if I can. 

B) sessionInfo is a function.  You have to invoke functions by including argument parentheses,  like so:

sessionInfo()

Looking at how that function is implemented when you ask the interpreter to print the function definition doesn't help us differentiate your setup from anyone else's.

C) you have not addressed the question of what might be in your .Rprofile. That is a file by that name in your home directory (My Documents?) If it does not exist, it can't be a problem, but you need to confirm. 

D) You have not addressed what might be corrupted in your personal package library (typically My Documents\R\win-lib\3.3). Confirm that you have renamed or deleted it. 

E) It might be relevant to ask how you are installing the package. What was the exact URL of the installation file?  Did you make the mistake of using the "Run As Administrator" option when you started that install file? (If so,  that can make it quite difficult to clean up bad file permissions. I am not even sure how to fix that, so you would need someone else to help if so.)

F) What commands are you giving to R during your first run?
-- 
Sent from my phone. Please excuse my brevity.

On May 17, 2016 6:18:45 AM PDT, Amitava Mukherjee <amitmukh2 at gmail.com> wrote:
>Dear Dr. Jeff,
>
>Many thanks for your reply. Here is the output of session info.
>
>I uninstalled all versions of R from my PC and stored R files, then
>reinstall.
>
>First time, it works smoothly. But crashing once I shut down and
>reopen...
>
>Details appended below...
>
>Thanks and hope you will be able to help and support ...
>
>Best regards,
>Amitava
>
>Error in readRDS(nsInfoFilePath) : unknown input format
>
>R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
>Copyright (C) 2016 The R Foundation for Statistical Computing
>Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
>R is a collaborative project with many contributors.
>Type 'contributors()' for more information and
>'citation()' on how to cite R or R packages in publications.
>
>Type 'demo()' for some demos, 'help()' for on-line help, or
>'help.start()' for an HTML browser interface to help.
>Type 'q()' to quit R.
>
>Warning message:
>package "methods" in options("defaultPackages") was not found
>Error in readRDS(nsInfoFilePath) : unknown input format
>During startup - Warning message:
>package ‘methods’ in options("defaultPackages") was not found
>> 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()
>    if (.Platform$OS.type == "windows") {
>        z$running <- win.version()
>    }
>    else if (nzchar(Sys.which("uname"))) {
>        uname <- system("uname -a", intern = TRUE)
>        os <- sub(" .*", "", uname)
>    z$running <- switch(os, Linux = if (file.exists("/etc/os-release"))
>{
>            tmp <- readLines("/etc/os-release")
>            t2 <- if (any(startsWith(tmp, "PRETTY_NAME=")))
>sub("^PRETTY_NAME=",
>              "", grep("^PRETTY_NAME=", tmp, value = TRUE)[1L]) else if
>(any(startsWith(tmp,
>                "NAME"))) sub("^NAME=", "", grep("^NAME=", tmp,
>                value = TRUE)[1L]) else "Linux (unknown distro)"
>            sub("\"(.*)\"", "\\1", t2)
>        } else if (file.exists("/etc/system-release")) {
>            readLines("/etc/system-release")
>        }, Darwin = {
>            ver <-
>readLines("/System/Library/CoreServices/SystemVersion.plist")
>            ind <- grep("ProductUserVisibleVersion", ver)
>            ver <- ver[ind + 1L]
>            ver <- sub(".*<string>", "", ver)
>            ver <- sub("</string>$", "", ver)
>            ver1 <- strsplit(ver, ".", fixed = TRUE)[[1L]][2L]
>            sprintf("OS X %s (%s)", ver, switch(ver1, `4` = "Tiger",
>                `5` = "Leopard", `6` = "Snow Leopard", `7` = "Lion",
>                `8` = "Mountain Lion", `9` = "Mavericks", `10` =
>"Yosemite",
>                `11` = "El Capitan", "unknown"))
>        }, SunOS = {
>            ver <- system("uname -r", intern = TRUE)
>           paste("Solaris", strsplit(ver, ".", fixed = TRUE)[[1L]][2L])
>        }, uname)
>    }
>    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]
>    }
>    class(z) <- "sessionInfo"
>    z
>}
><bytecode: 0x0000000008a8a8c0>
><environment: namespace:utils>
>>
>
>
>On 16 May 2016 at 21:08, Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
>wrote:
>
>> I don't know why this is happening, but the nsInfo.rds file is part
>of
>> every installed package (see Section 4.1 of the R Internals
>documentation)
>> and it sounds like one or more of them are getting corrupted. This
>could be
>> because you or your .Rprofile or an .RData file are triggering a bug
>in one
>> of your packages.
>>
>> You might try
>> * posting the output of the sessionInfo function,
>> * looking in your .Rprofile file with a text editor,
>> * deleting/renaming any RData files in your working directory, and
>perhaps
>> * clearing/renaming your personal 3.3 package library and
>re-installing
>> one package at a time to see which one triggers the error.
>> --
>> Sent from my phone. Please excuse my brevity.
>>
>> On May 13, 2016 11:53:05 PM PDT, Amitava Mukherjee
><amitmukh2 at gmail.com>
>> wrote:
>>
>>> Dear All,
>>>
>>> Greetings. I hope you will be able to provide kind help with the
>following:
>>>
>>> I am facing a strange problem ever since I have started working with
>R
>>> 3.3.0.
>>>
>>> I download and work with it, it was fine. Then when I shut down and
>reopen,
>>> it is not working properly.
>>>
>>> I am getting following message:
>>>
>>> Error in readRDS(nsInfoFilePath) : unknown input format
>>>
>>> R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
>>> Copyright (C) 2016 The R Foundation for Statistical Computing
>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>>   Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more
>>> information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>> Warning message:
>>> package "methods" in options("defaultPackages") was not found
>>> [Previously saved workspace restored]
>>>
>>> Error in readRDS(nsInfoFilePath) : unknown input format
>>> During startup - Warning message:
>>> package ‘methods’ in options("defaultPackages") was not found
>>>
>>>>  ?mean
>>>>
>>> Error in readRDS(nsInfoFilePath) : unknown input format
>>>
>>>>
>>>>
>>>
>>> I have uninstall it three times and reinstall -- Every time after
>first
>>> installation it is working perfectly.
>>>
>>> Then when I am closing R window and reopening it, the problem
>starts.
>>>
>>> Kindly suggest what should I do. Looking forward to hear from you,
>>>
>>> Best regards,
>>> Amitava
>>>
>>>
>>>
>>>
>>>
>>> Dr. Amitava Mukherjee, Ph.D.
>>> Associate Professor,
>>> Production, Operations and Decision Sciences Area,
>>> XLRI-Xavier School of Management, India.
>>>
>>>  [[alternative HTML version deleted]]
>>>
>>> ------------------------------
>>>
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>

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