[Bioc-devel] Using BiocInstaller with R 3.4.0 beta

[Martin Morgan]

On 04/11/2017 05:01 AM, Gordon K Smyth wrote:
> The problem appears to be with installed.packages(). If I start a fresh R 3.4.0beta session, then I can run installed.packages() once with correct results, but running it a second time gives the error message:
>
>> installed.packages()
> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>   missing value where TRUE/FALSE needed

The test is in this code chunk, from utils/R/packages.R

     for(lib in lib.loc) {
         if(noCache) {
             ret0 <- .readPkgDesc(lib, fields)
             if(length(ret0)) retval <- rbind(retval, ret0)
         } else {
             ## Previously used URLencode for e.g. Windows paths with drives
             ## This version works for very long file names.
             base <- paste(c(lib, fields), collapse = ",")
             ## add length and 64-bit CRC in hex (in theory, seems
             ## it is actually 32-bit on some systems)
             enc <- sprintf("%d_%s", nchar(base), .Call(C_crc64, base))
             dest <- file.path(tempdir(), paste0("libloc_", enc, ".rds"))
             if(file.exists(dest) &&
                file.mtime(dest) > file.mtime(lib) &&
                (val <- readRDS(dest))$base == base)
                 ## use the cache file
                 retval <- rbind(retval, val$value)
             else {
                 ret0 <- .readPkgDesc(lib, fields)
                 if(length(ret0)) {
                     retval <- rbind(retval, ret0)
                     ## save the cache file
                     saveRDS(list(base = base, value = ret0), dest)
                 }
             }
         }


where 'lib' is one of .libPaths(), 'dest' is one of

   dir(tempdir(), pattern="libloc_", full=TRUE)

and 'base' should be a character(1)

I think the code chunk has tried to cache the packages installed in each 
directory of .libPaths() (the saveRDS() line), and these are somehow 
corrupted on the second time through (I guess evaluating the readRDS()??).

For instance I have two paths in .libPaths() and after the first 
install.packages() I have

 > str(readRDS(dir(tempdir(), full=TRUE)[1]))
List of 2
  $ base : chr 
"/home/mtmorgan/bin/R-3-4-branch/library,Version,Priority,Depends,Imports,LinkingTo,Suggests,Enhances,License,Li"| 
__truncated__
  $ value: chr [1:29, 1:17] "base" "boot" "class" "cluster" ...
 > str(readRDS(dir(tempdir(), full=TRUE)[2]))
List of 2
  $ base : chr 
"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5,Version,Priority,Depends,Imports,LinkingTo,Suggests,E"| 
__truncated__
  $ value: chr [1:513, 1:17] "abind" "acepack" "aCGH" "ADaCGH2" ...

I'm guessing that one of these files is corrupted somehow, but it's not 
obvious how. Can you use options(error=recover) and find the values that 
cause the conditional to fail?

Martin

>
>
>> -----Original Message-----
>> From: Gordon K Smyth
>> Sent: Tuesday, 11 April 2017 6:26 PM
>> To: bioc-devel at r-project.org
>> Subject: Using BiocInstaller with R 3.4.0 beta
>>
>> I thought I would test out R 3.4.0 beta (for Windows) but now I can't use the
>> BiocInstaller package. Attempts to use biocLite() or biocValid() lead to an error
>> message as shown below.
>>
>> What have I overlooked?
>>
>> Thanks
>> Gordon
>>
>>> sessionInfo()
>> R version 3.4.0 beta (2017-04-08 r72499)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 7 x64 (build 7601) Service Pack 1
>>
>> Matrix products: default
>>
>> locale:
>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>> LC_MONETARY=English_Australia.1252
>> [4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.4.0
>>> remove.packages("BiocInstaller")
>> Removing package from 'C:/lib/R/R-3.4.0beta/library'
>> (as 'lib' is unspecified)
>> Error in find.package(pkgs, lib) :
>>   there is no package called 'BiocInstaller'
>>> source("https://bioconductor.org/biocLite.R")
>> trying URL
>> 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocInst
>> aller_1.25.3.zip'
>> Content type 'application/zip' length 127489 bytes (124 KB)
>> downloaded 124 KB
>>
>> package 'BiocInstaller' successfully unpacked and MD5 sums checked
>>
>> The downloaded binary packages are in
>>
>> C:\Users\smyth\AppData\Local\Temp\RtmpOUhCbB\downloaded_packages
>> Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
>>> BiocInstaller::biocValid()
>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>>   missing value where TRUE/FALSE needed
>>
>>
>> ---------------------------------------------
>> Professor Gordon K Smyth,
>> Head, Bioinformatics Division,
>> Walter and Eliza Hall Institute of Medical Research,
>> http://www.statsci.org/smyth
>
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