Hi Steve-

Thanks for the help. I deleted the development and corrupted release versions of R from my computer. Then, I downloaded the release version. Next, I renamed the release version in my Applications folder to R_3.0. Then I downloaded the installer package from att.com<http://att.com> for the development version. I opened up a terminal and in my / directory I typed in sudo pkgutil —forget org.r-project.R.x86_64.fw.pkg.

parsons-three-sixty:/ fontanez$ sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg
Forgot package 'org.r-project.R.x86_64.fw.pkg' on '/'.

Then, I proceeded to install the development version from the R development installer package. It installed correctly and I was able to download the development version of DESeq and my other packages. However, this is where I ran into a problem.

I shut down R and opened up the R_3.0 app from my Applications. It opened, which was good but it drops a ton of warnings. Anytime I try to type something (as I’m typing) that “anyNA” is not a builtin function error pops up. It looks like my R 3.0 is still corrupted. I didn’t change anything in /Library/Frameworks - should I have done that as well, like Dan suggested?

Thanks,
Kristina



R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
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Platform: x86_64-apple-darwin10.8.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: package ‘methods’ was built under R version 3.1.0
2: package "methods" in options("defaultPackages") was not found
3: package ‘datasets’ was built under R version 3.1.0
4: package ‘datasets’ in options("defaultPackages") was not found
5: package ‘utils’ was built under R version 3.1.0
6: package ‘utils’ in options("defaultPackages") was not found
7: package ‘grDevices’ was built under R version 3.1.0
Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: package ‘grDevices’ in options("defaultPackages") was not found
2: package ‘graphics’ was built under R version 3.1.0
Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: package ‘graphics’ in options("defaultPackages") was not found
2: package ‘stats’ was built under R version 3.1.0
During startup - Warning messages:
1: package ‘stats’ in options("defaultPackages") was not found
2: package ‘methods’ was built under R version 3.1.0
3: package ‘methods’ in options("defaultPackages") was not found
Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function
[History restored from /Users/fontanez/.Rapp.history]
Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function

> library(DESeq2)
Loading required package: GenomicRanges
Loading required package: methods
Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function
In addition: Warning messages:
1: package ‘DESeq2’ was built under R version 3.1.0
2: package ‘GenomicRanges’ was built under R version 3.1.0
3: In get(".__S3MethodsTable__.", envir = env, inherits = FALSE) :
  internal error -3 in R_decompress1
Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function
> traceback()
11: .deparseOpts(control)
10: deparse(x[[1L]])
9: mode(expr)
8: match(x, table, nomatch = 0L)
7: mode(expr) %in% c("call", "expression", "(", "function")
6: deparse(call)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch(expr, error = function(e) {
       call <- conditionCall(e)
       if (!is.null(call)) {
           if (identical(call[[1L]], quote(doTryCatch)))
               call <- sys.call(-4L)
           dcall <- deparse(call)[1L]
           prefix <- paste("Error in", dcall, ": ")
           LONG <- 75L
           msg <- conditionMessage(e)
           sm <- strsplit(msg, "\n")[[1L]]
           w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
           if (is.na(w))
               w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
                   type = "b")
           if (w > LONG)
               prefix <- paste0(prefix, "\n  ")
       }
       else prefix <- "Error : "
       msg <- paste0(prefix, conditionMessage(e), "\n")
       .Internal(seterrmessage(msg[1L]))
       if (!silent && identical(getOption("show.error.messages"),
           TRUE)) {
           cat(msg, file = stderr())
           .Internal(printDeferredWarnings())
       }
       invisible(structure(msg, class = "try-error", condition = e))
   })
1: try(gsub("\\s+<smb://s+>", " ", paste(capture.output(print(args(traceback))),
       collapse = "")), silent = TRUE)


------------------------------------------------------------------
Kristina Fontanez, Postdoctoral Fellow
fontanez@mit.edu<mailto:fontanez@mit.edu>
Massachusetts Institute of Technology
Department of Civil and Environmental Engineering
48-120E
15 Vassar Street
Cambridge, MA 02139



On Jan 17, 2014, at 5:37 PM, Steve Lianoglou <lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>> wrote:

The good news is that it's not too onerous to recover from scratch.
Just download the latest R-release installer pkg from CRAN. The
installer will (should) contain the same warning telling you what the
command is to perform a "non-destructive" isntall. For what it's
worth, you simply have to open up a terminal and type in the following
command:

sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg

Then continue with the installation and all will be Feng Shui.

After doing so, launching "R" from the terminal should now open
R-3.0.2 (no need to use RSwitch). Just do the usual biocinstall (ie.
source the biocLite script then re-install the packages you need).
Being at MIT, the bandwidth available to you should make this a quick
process, especially since the packages for the mac do not need to be
compiled for installation.


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