[BioC] Question regarding Installation of annotation package which was built using SQLforge (Suyog Pol)
Martin Morgan
mtmorgan at fhcrc.org
Sun Jan 31 23:50:36 CET 2010
Hi Suyong --
I'm replying on-list, in case this is helpful to others.
On 01/31/2010 11:05 AM, Martin Morgan wrote:
> Hi Suyong --
>
> On 01/30/2010 03:49 PM, Suyog Pol wrote:
>> HI
>>
>> Thank You Seth for your suggestion. I was able to install the Package
>> using the following command.
>>
>> install.packages("illuminaHumanv3_ensemble_beta.db",
>> repos = NULL, type = "source")
>> However I am still unable to use the installed package. Although
>> this time I am facing a different error
>>
>> I was applying the nsFilter from the genefilter library to filter my
>> Expression set object eset. The eset was generated and used as follows:-
>>
>> dataMatrix <- exprs(eset.generated_using_lumi_package)
>>
>> #setting the rownames to the values which can be used by standard
>> #package illuminaHumanv3
>>
>> rownames(dataMatrix) <- corrected.Probe_ID[1:48795]
>>
>> annotation <- 'illuminaHumanv3.ensemble.beta.db'
>>
>> eset <- new("ExpressionSet", exprs = dataMatrix ,
>> annotation = 'illuminaHumanv3.ensemble.beta.db'
>>
>> library(genefilter)
>> library("illuminaHumanv3.ensemble.beta.db") #The code for making and
>> installing this package was discussed in my previous mail
>> nsF <- nsFilter(eset, var.filter = FALSE)$eset
>>
>> I am getting the following error:-
>>
>>> nsF <- nsFilter(eset, var.filter = FALSE)$eset
>> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>> object 'illuminaHumanv3.ensemble.beta_dbconn' not found
>
> Are your names consistent, for instance below you use an underscore '_'
> rather than a '.' to separate 'illuminaHumanv3' and 'ensemble'. It would
> help to see, after loading your database, the output of
>
>> search()
>
> and
>
>> ls("package:illuminaHumanv3.ensemble.beta.db")
Here the package name is '.' separated
> search()
[1] ".GlobalEnv"
[2] "package:illuminaHumanv3.db"
[3] "package:illuminaHumanv3.ensemble.beta.db"
[4] "package:org.Hs.eg.db"
but here the package has variables with '_' separation
> ls("package:illuminaHumanv3.ensemble.beta.db")
[1] "illuminaHumanv3_ensemble_beta"
[2] "illuminaHumanv3_ensemble_beta_dbconn"
[3] "illuminaHumanv3_ensemble_beta_dbfile"
[4] "illuminaHumanv3_ensemble_beta_dbInfo"
[5] "illuminaHumanv3_ensemble_beta_dbschema"
[6] "illuminaHumanv3_ensemble_betaACCNUM"
[7] "illuminaHumanv3_ensemble_betaALIAS2PROBE"
You mentioned in an off-list email that you changed the DESCRIPTION file
when you were trying to install the package (because R did not allow _
in a package name). Unfortunately, you need to start with the correct
name earlier in the package build process, I think when you say
>>>> makeDBPackage("HUMANCHIP_DB",
>>> + affy=FALSE,
>>> + prefix="illuminaHumanv3_ensemble_beta",
>>> + fileName=filename,
>>> + baseMapType="eg",
>>> + outputDir = tmpout,
>>> + version="1.0.0",
>>> + manufacturer = "Illumina",
>>> + chipName = "HT-12",
g>>> + manufacturerUrl = "http://www.illumina.com")
it should be with
prefix="illuminaHumanv3.ensemble.beta"
Martin
>
> Martin
>
>>
>> I was unable to figure out if this issue is related to procedure used for
>> making the object or code for its installation.
>>
>> Your help will be much appreciated
>>
>> Suyog P
>>
>>
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] illuminaHumanv3.db_1.4.1
>> [2] illuminaHumanv3.ensemble.beta.db_1.0.0
>> [3] org.Hs.eg.db_2.3.6
>> [4] genefilter_1.28.2
>> [5] lumi_1.12.2
>> [6] MASS_7.3-4
>> [7] RSQLite_0.8-1
>> [8] DBI_0.2-5
>> [9] preprocessCore_1.8.0
>> [10] mgcv_1.6-1
>> [11] affy_1.24.2
>> [12] annotate_1.24.1
>> [13] AnnotationDbi_1.8.1
>> [14] Biobase_2.6.1
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.14.0 grid_2.10.1 lattice_0.17-26
>> Matrix_0.999375-33
>> [5] nlme_3.1-96 splines_2.10.1 survival_2.35-7
>> tools_2.10.1
>> [9] xtable_1.5-6
>>
>>
>>
>>> 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
>>
>> [[alternative HTML version deleted]]
>>
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>
>
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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