Cool, solved the problems.  Thanks!


On Tue, Oct 11, 2011 at 11:35 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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] IlluminaHumanMethylation450kpr**obe_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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>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
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>



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