Hi Martin,
 
Thanks a lot for the help! I believe it's due to some virus on my computer as I just found out that my computer's antivirus programs all got turned off and could not be turned back on. I am re-installing Windows now and will try to re-install R and googleVis later.
 
Thanks,
 
Ying
 
> Date: Thu, 24 Apr 2014 18:19:40 -0700
> From: mtmorgan@fhcrc.org
> To: ying_chen@live.com; bioconductor@r-project.org
> Subject: Re: [BioC]  googleVis installation error
> 
> On 04/23/2014 08:43 PM, ying chen wrote:
> > Hi guys,
> >
> > I have this weird error when I tried to install googleVis package. I installed it in my other PC with no problem and both runs Win7 Enterprise 64x. I tired to install from biocLite("googleVis"), install.packages("googleVis"), install.packages() from downloaded source, and had the same error.
> >
> >> biocLite("googleVis")
> > BioC_mirror: http://bioconductor.org
> > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.1.0.
> > Installing package(s) 'googleVis'
> > trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.1/googleVis_0.5.1.zip'
> > Content type 'application/zip' length 962989 bytes (940 Kb)
> > opened URL
> > downloaded 940 Kb
> > Error in if (any(diff)) { : missing value where TRUE/FALSE needed
> >> utils:::menuInstallLocal()
> > Error in if (any(diff)) { : missing value where TRUE/FALSE needed
> 
> This is unusual. The code being evaluated is tools::checkMD5sums, and the idea 
> is that the MD5 sums included in the zip archive are compared with the MD5 sums 
> calculated from the installed (in a temporary location) package.
> 
> I think what happens is that some of the installed files are not readable by the 
> process that wrote them and md5sums() returns 'NA'; later, this is compared with 
> the true md5sum from the zip archive and the test -- 'diff' -- contains an 'NA'. 
> any(diff) then reports NA, and the 'if' statement fails
> 
>     if (NA) "foo"
> 
>  > any(c(FALSE, NA))
> [1] NA
>  > if (NA) "foo"
> Error in if (NA) "foo" : missing value where TRUE/FALSE needed
> 
> I don't really know why your files might not be readable; maybe some other 
> process (a virus checker?) has marked one or more files as not readable, or the 
> your temporary directory itself is write-only (likely other packages would fail 
> to install, too), or .... You could discover the problematic file by
> 
>    options(error=recover)
>    biocLite("googleVis")
> 
> and when the error occurs choosing Selection: 5 (so that you end up inside 
> tools::checkMD5sums) and look at
> 
>      xx[is.na(nmxx)]
> 
> (the md5 sums from the package) or x[is.na(nmxx)] (the md5 sums from the 
> installed directory). The variable 'dir' is the directory where all the action 
> is taking place.
> 
> It would be good to hear back about what your investigation indicates.
> 
> Martin
> 
> >> traceback()
> > 5: tools::checkMD5sums(pkgname, file.path(tmpDir, pkgname))
> > 4: unpackPkgZip(pkgs[i], pkgnames[i], lib, libs_only, lock, quiet)
> > 3: .install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
> >         method = method, available = available, destdir = destdir,
> >         dependencies = dependencies, libs_only = libs_only, quiet = quiet,
> >         ...)
> > 2: install.packages(choose.files("", filters = Filters[c("zip",
> >         "All"), ]), .libPaths()[1L], repos = NULL)
> > 1: utils:::menuInstallLocal()
> >> sessionInfo()
> > R version 3.1.0 (2014-04-10)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> > locale:
> > [1] LC_COLLATE=English_United States.1252
> > [2] LC_CTYPE=English_United States.1252
> > [3] LC_MONETARY=English_United States.1252
> > [4] LC_NUMERIC=C
> > [5] LC_TIME=English_United States.1252
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> > other attached packages:
> > [1] BiocInstaller_1.12.1
> > loaded via a namespace (and not attached):
> > [1] tools_3.1.0
> >>
> >
> > Thanks a lot for the help!
> >
> > Ying
> >
> >
> >    		 	   		
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> >
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> >
> 
> 
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