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Question: "Error in readRDS(file) : unknown input format" appearing every time starting Rstudio after BiocUpgrade
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gravatar for svlachavas
2.0 years ago by
svlachavas570
Greece/Athens/National Hellenic Research Foundation
svlachavas570 wrote:

Dear All,

after using BiocUpgrade to update my Bioconductor version to the latest one--having already installed the latest R version, when i started again Rstudio, the following message appears and appears again every time i start Rstudio:

Error in readRDS(file) : unknown input format

I also tried to clear my environment and also used update.packages() but the same thing appears again every time i start again Rstudio.

How severe is that error and how i could fix it ??

source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help

sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253    LC_MONETARY=Greek_Greece.1253
[4] LC_NUMERIC=C                  LC_TIME=Greek_Greece.1253    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_3.2.2

ADD COMMENTlink written 2.0 years ago by svlachavas570

Any help or suggestion ??

ADD REPLYlink written 2.0 years ago by svlachavas570

It sounds like you have an .RData file in your home or root directory that is corrupt, or that you have start-up instructions in an .Rprofile file that are incorrect, or that Rstudio is doing something unexpected. See ?Startup, eliminate Rstudio as a problem (by starting R from the command line) and use traceback() after the error occurs to understand the sequence of calls that are causing problems.

ADD REPLYlink written 2.0 years ago by Martin Morgan ♦♦ 20k

Dear Martin,

thank you for your comments !!!---after i started Rstudio and the error appeared i used traceback:

Error in readRDS(file) : unknown input format
> traceback()
6: readRDS(file)
5: utils:::packageDescription(packageName, fields = "Version")
4: package_version(utils:::packageDescription(packageName, fields = "Version"))
3: .rs.getPackageVersion(pkgName)
2: updateIfNecessary("manipulate")
1: (function (libDir, pkgSrcDir, rsVersion, force) 
   {
       if (getRversion() >= "3.0.0") {
           .rs.ensureWriteableUserLibrary()
           updateIfNecessary <- function(pkgName) {
               isInstalled <- .rs.isPackageInstalled(pkgName, .rs.defaultLibraryPath())
               if (force || !isInstalled || (.rs.getPackageVersion(pkgName) != 
                   rsVersion)) {
                   if (isInstalled) 
                     utils::remove.packages(pkgName, .rs.defaultLibraryPath())
                   .Call("rs_installPackage", file.path(pkgSrcDir, 
                     pkgName), .rs.defaultLibraryPath())
               }
           }
           updateIfNecessary("rstudio")
           updateIfNecessary("manipulate")
       }
       else {
           .rs.libPathsAppend(libDir)
       }
   })("C:/Program Files/RStudio/R/library", "C:/Program Files/RStudio/R/packages", 
       "0.98.1103", FALSE)

So you meant something different to try ??

ADD REPLYlink modified 2.0 years ago by Martin Morgan ♦♦ 20k • written 2.0 years ago by svlachavas570
1

This looks like something Rstudio is trying to do -- get the package version of the 'manipulate' package to see whether it needs to be updated. I guess your installation of this package is somehow corrupted, and you should remove the package remove.packages("manipulate"). If that fails, then look for the directory 'manipulate' in .libPaths(), and remove the directory manually.

ADD REPLYlink written 2.0 years ago by Martin Morgan ♦♦ 20k

Dear Martin,

the function remove.packages("manipulate") 

didnt worked, so i followed your advice and deleted the file directory of the package manually from its location. But, possibly there is elsewhere /or additionally another problem.  I restarted Rstudio, then the following happened:

Error in readRDS(file) : unknown input format
Error in readRDS(pfile) : unknown input format
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
> biocLite("manipulate")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.0), R 3.2.2 (2015-08-14).
Installing package(s) ‘manipulate’
Error in readRDS(file) : unknown input format
Error in readRDS(file) : unknown input format
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.2/manipulate_1.0.1.zip'
Content type 'application/zip' length 35812 bytes (34 KB)
downloaded 34 KB

package ‘manipulate’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Efstathios\AppData\Local\Temp\RtmpSyDOqi\downloaded_packages
Old packages: 'BiocInstaller'
Update all/some/none? [a/s/n]: 
a
Warning: package ‘BiocInstaller’ is in use and will not be installed

But, i didnt load any other package or function() and i also have previously clear my Rhistory and enviroment.

Thus, i should also try to remove and reinstall BiocInstaller ??

ADD REPLYlink modified 2.0 years ago by Martin Morgan ♦♦ 20k • written 2.0 years ago by svlachavas570

Dear Martin,

one last but crusial update---i restarted my computer and started again Rstudio---and this time the previous error did not appeared. Also, i loaded the package manipulate without problem:

> library(manipulate)
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253    LC_MONETARY=Greek_Greece.1253
[4] LC_NUMERIC=C                  LC_TIME=Greek_Greece.1253    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.0 manipulate_0.98.1103

loaded via a namespace (and not attached):
[1] tools_3.2.2

I also then updated manipulate from the option Update in section packages of Rstudio with install.packages

The only thing now that bothers me is about the issue with BiocInstaller from my previous message ??

Can i somehow check again if the specific package needs update ? Because in the above section, only the manipulate package appeared and updated !!

Best,

Efstathios

ADD REPLYlink written 2.0 years ago by svlachavas570
2

My guess is that you have more than one version of BiocInstaller installed -- one in each of your .libPaths(). If so, I'd resolve this by removing both (via remove.packages("BiocInstaller"), repeated until it reports that "there is no package called 'BiocInstaller'"; if it reports something else, like that it does not have permission to remove the BiocInstaller package, then you should manually remove the BiocInstaller directory as you did with manipulate.

Restart R, confirm that there is no BiocInstaller (e.g., library("BiocInstaller"), which should fail) and run source("http://bioconductor.org/biocLIte.R") to install the current version of BiocInstaller.

I don't know how you updated you 'installed the latest R version'; my guess is that you re-used a previously installed R library, whereas a 'best practice' would be to ensure that the new R version only uses newly installed packages.

ADD REPLYlink written 2.0 years ago by Martin Morgan ♦♦ 20k

Dear Martin,

thank you again for your valuable confirmation !!  The latest R version i installed through the package installr via updateR funcrion(+copy and updating old packages to the new R installation)--but i have also kept the file with the previous R version(3.2.0). So, i will follow your advice with the above issue and hope to solve it--although now it does not trigger any warnings--

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by svlachavas570
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