[BioC] Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)

[Martin Morgan]

On 10/11/2011 10:02 AM, Tim Triche, Jr. wrote:
> This is after trying to reinstall snpStats, which was the first thing I
> tried.  That fails with the same error message ("error: argument "lib.loc"
> is missing, with no default")

Hi Tim --

This is a bleeding-edge issue, associated with using R-devel. The 
maintainer will undoubtedly address this, but if you're desperate to 
make progress either use R-2-14 alpha (where the 'error' is just a 
warning) or download the source code and edit it as:

- remove zzz.R -- these paradigms aren't needed any more
- edit DESCRIPTION Collate: to exclude zzz.R
- edit NAMESPACE to useDynLib("snpStats")

then R CMD build snpStats && R CMD INSTALL snpStats_*gz

Martin

>    I didn't have this problem previously... should I rebuild R and see if it
> was some sort of a transient issue with HEAD?
>
> BiocInstaller version 1.1.28, ?biocLite for help
> * installing *source* package ‘VariantAnnotation’ ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Warning: replacing previous import ‘ls’ when loading ‘AnnotationDbi’
> Error : .onLoad failed in loadNamespace() for 'snpStats', details:
>    call: library.dynam("snpStats", package)
>    error: argument "lib.loc" is missing, with no default
> ERROR: lazy loading failed for package ‘VariantAnnotation’
> * removing ‘/usr/lib/R/library/VariantAnnotation’
> * restoring previous ‘/usr/lib/R/library/VariantAnnotation’
>
> Session info:
>
>> sessionInfo()
> R Under development (unstable) (2011-10-04 r57169)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices datasets  utils     methods
> [8] base
>
> other attached packages:
>   [1] Rsubread_1.2.1
>   [2] methylumi_1.9.12
>   [3] matrixStats_0.2.2
>   [4] R.methodsS3_1.2.1
>   [5] MASS_7.3-15
>   [6] ggplot2_0.8.9
>   [7] proto_0.3-9.2
>   [8] reshape_0.8.4
>   [9] plyr_1.6
> [10] IlluminaHumanMethylation450kprobe_1.9.12
> [11] IlluminaHumanMethylation450k.db_1.4.9
> [12] org.Hs.eg.db_2.6.2
> [13] RSQLite_0.10.0
> [14] DBI_0.2-5
> [15] AnnotationDbi_1.15.29
> [16] Biobase_2.13.10
> [17] BiocInstaller_1.1.28
> [18] gtools_2.6.2
>
> loaded via a namespace (and not attached):
> [1] annotate_1.31.1    digest_0.5.1       IRanges_1.11.30    lattice_0.19-33
>
> [5] RColorBrewer_1.0-5 tools_2.15.0       xtable_1.5-6
>
>
>
>
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