[BioC] Question regarding Installation of annotation package which was built using SQLforge

[Seth Falcon]

On 1/29/10 10:45 AM, Suyog Pol wrote:
> Hi
>
> I have built an annotation package with the help of guidlines set in the
> vignette/document
> "SQLforge by Marc Carlson et al." I am having problem installing it.
> The following code was used for building the  package:-
>
> if(interactive()){
> mart<- useMart("ensembl")
> datasets<- listDatasets(mart)
> mart<-useDataset("hsapiens_
> gene_ensembl",mart)
> ensemble.illumina<-
> getBM(attributes=c("illumina_humanwg_6_v3","entrezgene"),filters="illumina_humanwg_6_v3",
> values=illumina.humanv3.probeset, mart=mart,na.value = NA)
>
> }
>
> ##ensemble.Illumina was written into a file and modified to satisfy the
> requisites of the input vector
> ##required for the function makeDBPackage.  The following code was used for
> making the final
> ##package:-
>
>> tmpout<- "Y:/path/to/annotation/package"
>> library("human.db0")
> Loading required package: AnnotationDbi
> Loading .......
>
>> library("AnnotationDbi")
>> makeDBPackage("HUMANCHIP_DB",
> + affy=FALSE,
> + prefix="illuminaHumanv3_ensemble_beta",
> + fileName=filename,
> + baseMapType="eg",
> + outputDir = tmpout,
> + version="1.0.0",
> + manufacturer = "Illumina",
> + chipName = "HT-12",
> + manufacturerUrl = "http://www.illumina.com")
> Loading required package: RSQLite
> Loading required package: DBI
> baseMapType is eg
> Prepending Metadata
> Creating Genes table
> Appending Probes
> Found 0 Probe Accessions
> Appending Gene Info
> Found 24758 Gene Names
> Found 24758 Gene Symbols
> Appending Chromosomes
> Appending Cytogenetic Locations
> Appending Omim
> Appending RefSeq
> Appending Pubmed
> Appending Unigene
> Appending ChrLengths
> Appending 3 GO tables
> Appending 3 GO ALL tables
> Appending KEGG
> Appending EC
> Appending Chromosome Locations
> Appending Pfam
> Appending Prosite
> Appending Alias
> Appending Ensembl
> Appending Uniprot
> Appending Metadata
>
>
> simplifying probes table
> dropping redundant data
> Creating package in
> Y:/path/to/annotation/package/illuminaHumanv3_ensemble_beta.db
>
> #To install the above package : -
>
>>
> install.packages("Y:/path/to/annotation/package/illuminaHumanv3_ensemble_beta.db",
> +                  repos = NULL)
> *Warning in install.packages("Y:/Genomics/ArrayData/Jan 2010 - CD140aO4
> sorts/annotation/anno2/illuminaHumanv3_ensemble_beta.db",  :
>    argument 'lib' is missing: using
> 'C:\Users\suyogpol\Documents/R/win-library/2.10'
> Error in gzfile(file, "r") : cannot open the connection
> In addition: Warning messages:
> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
> 2: In gzfile(file, "r") :
>    cannot open compressed file
> 'illuminaHumanv3_ensemble_beta.db/DESCRIPTION', probable reason 'No such
> file or directory*
>
> # I assumed that install.packages by default attempts to unzip the requested
> package file
> #To fix this I zipped the package directory and re used the install.packages
> function:-
>
>
>> setwd("Y:/path/to/annotation/package" )
>> install.packages("illuminaHumanv3_ensemble_beta.db",
> +                  repos = NULL)

Can you please try again with:


install.packages("illuminaHumanv3_ensemble_beta.db", 
repos = NULL, type = "source")

I think that adding the type = "source" argument will get things going 
for you.  If you want to be able to build package archives (.tar.gz as 
well as Windows binary packages .zip) you need to install Rtools (see R 
admin manual).

+ seth


-- 
Seth Falcon
Bioconductor Core Team | FHCRC