[BioC] googleVis installation error

[Martin Morgan]

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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