[BioC] Installation of hmyriB36

[Patrick Aboyoun]

David,
Could you send your session info? I find no evidence that Ruuid is 
required to load the experiment data package you specified. (I would 
like to sort out any unspecified dependencies if there are any.)


 > library(hmyriB36)
Loading required package: GGBase
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: GSEABase
Loading required package: AnnotationDbi
Loading required package: annotate
Loading required package: graph
Loading required package: snpMatrix
Loading required package: survival
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
 > data(hmyriB36)
 > search()
 [1] ".GlobalEnv"            "package:hmyriB36"      "package:GGBase"      
 [4] "package:RSQLite"       "package:DBI"           "package:snpMatrix"   
 [7] "package:survival"      "package:splines"       "package:GSEABase"    
[10] "package:graph"         "package:annotate"      "package:AnnotationDbi"
[13] "package:Biobase"       "package:stats"         "package:graphics"    
[16] "package:grDevices"     "package:utils"         "package:datasets"    
[19] "package:methods"       "Autoloads"             "package:base"        
 > library(Ruuid)
Error in library(Ruuid) : there is no package called 'Ruuid'
 > sessionInfo()
R version 2.9.0 Patched (2009-04-25 r48402)
i386-apple-darwin9.6.0

locale:
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 
[8] base    

other attached packages:
 [1] hmyriB36_0.99.0     GGBase_3.4.0        RSQLite_0.7-1     
 [4] DBI_0.2-4           snpMatrix_1.8.0     survival_2.35-4   
 [7] GSEABase_1.6.0      graph_1.22.0        annotate_1.22.0   
[10] AnnotationDbi_1.6.0 Biobase_2.4.1     

loaded via a namespace (and not attached):
[1] cluster_1.11.13 tools_2.9.0     XML_2.3-0       xtable_1.5-5  



Vincent Carey wrote:
> try biocLite("Ruuid") -- there must be a dependency missing somewhere that
> prevents
> automatic success, and we will try to fix it, but for now a manual install
> of Ruuid should
> do it.
>
> On Thu, Apr 30, 2009 at 6:49 AM, David Edwards <David.Edwards at agrsci.dk>wrote:
>
>   
>> Dear list
>>
>> I am attempting to install the library hmyriB36 on a windows XP machine.
>> The following occurs
>>
>>     
>>> source("http://bioconductor.org/biocLite.R")
>>>       
>> Warning messages:
>> 1: In safeSource() : Redefining 'biocinstall'
>> 2: In safeSource() : Redefining 'biocinstallPkgGroups'
>> 3: In safeSource() : Redefining 'biocinstallRepos'
>>     
>>>     biocLite("hmyriB36")
>>>       
>> Running biocinstall version 2.4.10 with R version 2.9.0
>> Your version of R requires version 2.4 of Bioconductor.
>> Warning: unable to access index for repository
>> http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.9
>> trying URL '
>> http://bioconductor.org/packages/2.4/data/experiment/bin/windows/contrib/2.9/hmyriB36_0.99.0.zip
>> '
>> Content type 'application/zip' length 93084013 bytes (88.8 Mb)
>> opened URL
>> downloaded 88.8 Mb
>>
>> package 'hmyriB36' successfully unpacked and MD5 sums checked
>>
>> The downloaded packages are in
>>        C:\Documents and Settings\daed\Local
>> Settings\Temp\RtmpbiJFRg\downloaded_packages
>> updating HTML package descriptions
>>     
>>> library(hmyriB36)
>>>       
>> Loading required package: GGBase
>> 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: GSEABase
>> Loading required package: AnnotationDbi
>> Loading required package: annotate
>> Loading required package: graph
>> Loading required package: snpMatrix
>> Loading required package: survival
>> Loading required package: splines
>> Loading required package: RSQLite
>> Loading required package: DBI
>> Error in loadNamespace(name) : there is no package called 'Ruuid'
>> Error in as.environment(pos) :
>>  no item called "newtable" on the search list
>> Error: package 'GGBase' could not be loaded
>>     
>>> data(hmyriB36)
>>>       
>> Warning message:
>> In data(hmyriB36) : data set 'hmyriB36' not found
>>
>> What should I do? Any help would be gratefully received.
>>
>> BR David Edwards
>>
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>>
>>     
>
>
>
>