Hello everyone,

I am having problems installing the VariantAnnotation library of Bioconductor in R version 3.0.1.

I have tried installing the library using RSQLite new version 1.0.0 and old version 0.11.4 but I still got a message error (its content depending on the version of the installed RSQLite version).

Here are the commands used:

• install.packages("RSQLite")
  install.packages("~/Téléchargements/RSQLite_0.11.4.tar.gz", repos = NULL, type = "source")
  source("http://bioconductor.org/biocLite.R")
  biocLite("VariantAnnotation")

The message error using the RSQLite version 1.0.0:

• ** preparing package for lazy loading
  Error : the object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
  ERROR: lazy loading failed for package ‘VariantAnnotation’
  * removing ‘/home/tournebi/R/x86_64-pc-linux-gnu-library/3.0/VariantAnnotation’
  * restoring previous ‘/home/tournebi/R/x86_64-pc-linux-gnu-library/3.0/VariantAnnotation’
  
  The downloaded source packages are in
      ‘/tmp/RtmpjgWMN4/downloaded_packages’
  Warning message :
  1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
    installation of package ‘VariantAnnotation’ had non-zero exit status
  2: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'codetools', 'foreign',
    'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival'

Here is the message error when using the RSQLite version 0.11.4:

• BioC_mirror: http://bioconductor.org
  Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.1.
  Installing package(s) 'VariantAnnotation'
  essai de l'URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/VariantAnnotation_1.8.13.tar.gz'
  Content type 'application/x-gzip' length 1280329 bytes (1.2 Mb)
  
  [...]
  
  Warning message :
  installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival'

When trying to install the above-specified packages in an admin R session (via terminal and sudo R), I get the following error message:

• installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'foreign',
  'KernSmooth', 'lattice', 'MASS',
    'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial' 
  
  Would you like to use a personal library instead?  (y/n) y
  Error in if (libs_only) args0 <- c(args0, "--libs-only") :
    argument is not interpretable as logical

If you have also encountered and/or solved the issue, I would be glad to here more about it!

Many thanks in advance,

RT.

sessionInfo()

• R version 3.0.1 (2013-05-16)
  Platform: x86_64-pc-linux-gnu (64-bit)
  
  locale:
   [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
   [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8    LC_PAPER=C                 LC_NAME=C                 
   [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
  
  attached base packages:
  [1] parallel  stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
  [1] Rsamtools_1.14.3     Biostrings_2.30.1    GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.7      
  [6] BiocGenerics_0.8.0   BiocInstaller_1.12.1
  
  loaded via a namespace (and not attached):
  [1] Biobase_2.22.0 bitops_1.0-6   DBI_0.3.1      RSQLite_0.11.4  stats4_3.0.1   tools_3.0.1    zlibbioc_1.8.0

Dear James,

Yes, the RSQLite package works well for the old version 0.11.4.

It seems the youngest version of R (3.2.1) can fix the problem... at least on Windows.

Best regards,

Rémi