[BioC] GGtools and GGBase installation problems

[Vincent Carey]

This problem was addressed on Feb 7.  Let us know if the solution does
not work for you.  The problem concerns a dependency of Ruuid
infrastructure on glib2, which is not uniformly available on MacOSX
machines.  Quoting below from the Feb 7 exchange

Dear Vincent,

Thanks a lot. I have got GGtools installed in my Mac book pro (with
updated Mac OS and Xcode).

What I have done:
(1). install fink in order to let all unix program run in Mac,
following the manual in fink website (http://www.finkproject.org/).

(2). then, run "sudo fink install glib glib2-dev".

(3). next, log in R, and
source("http://bioconductor.org/biocLite.R")
biocLite("Ruuid", type="source") # you must install Ruuid from source.
biocLite("GGtools")

(4). invoke GGtools
library(GGtools)

I need to mention that all my progresses were got under helps of Mr.
Vincent and Martin, especially Vincent has given me much.

Thanks a lot.

Best,

On Sat, Feb 26, 2011 at 6:42 AM, Neel Aluru <naluru at whoi.edu> wrote:
> Hello,
>
> I have installed GGtools and GGBase and when I try to load them, I keep getting the following error messages. I really appreciate if someone can help me in sorting this problem.
>
> Thank you,
> Neel
>
>
> [R.app GUI 1.35 (5665) x86_64-apple-darwin9.8.0]
>
> [Workspace restored from /Users/naluru/.RData]
> [History restored from /Users/naluru/.Rapp.history]
>
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: snpMatrix
> Loading required package: survival
> Loading required package: splines
> Loading required package: RSQLite
> Loading required package: DBI
> Error in as.environment(pos) :
>  no item called "newtable" on the search list
> In addition: Warning message:
> In objects(newtable, all.names = TRUE) :
>  ‘newtable’ converted to character string
> Error: package/namespace load failed for 'GGBase'
> Loading required package: GGBase
> Error in as.environment(pos) :
>  no item called "newtable" on the search list
> In addition: Warning message:
> In objects(newtable, all.names = TRUE) :
>  ‘newtable’ converted to character string
> Error: package 'GGBase' could not be loaded
>
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RSQLite_0.9-4    DBI_0.2-5        snpMatrix_1.14.1 survival_2.36-2  Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.28.0      AnnotationDbi_1.12.0 graph_1.28.0         GSEABase_1.12.2      tools_2.12.1
> [6] XML_3.2-0            xtable_1.5-6
>>
>
>
> Neel Aluru
> Visiting Investigator
> Biology Department
> Redfield Building 3-04
> Woods Hole Oceanographic Institution
> 45, Water Street
> Woods Hole, MA
>
> naluru at whoi.edu
> 508-289-3607
>
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