Question: Question regarding Installation of annotation package which was built using SQLforge
0
gravatar for Suyog Pol
9.9 years ago by
Suyog Pol40
Suyog Pol40 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="illu mina_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_ensemb le_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) *Warning in install.packages("illuminaHumanv3_ensemble_beta.db", repos = NULL) : argument 'lib' is missing: using 'C:\Default/location/of/library/R/win-library/2.10' * ##I checked in my default library directory and a new folder for the package had been made #But when I attempted to load the package using the library command :- >library("illuminaHumanv3_ensemble_beta.db") *Error in library("illuminaHumanv3_ensemble_beta.db") : 'illuminaHumanv3_ensemble_beta.db' is not a valid installed package * ##I repeated the process using the lengthier method described in same guide #manual. This approach landed me in the same situation as the above. Can someone help me to know if there is a mistake in my approach used for making or installing the annotation package. Thanks in advance 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] RSQLite_0.8-1 DBI_0.2-5 human.db0_2.3.6 [4] AnnotationDbi_1.8.1 Biobase_2.6.1 loaded via a namespace (and not attached): [1] tools_2.10.1 -- Masters Student Department of Chemical and Biological Eng, University at Buffalo, Buffalo, NY . Ph: 801 814 3893 [[alternative HTML version deleted]]
ADD COMMENTlink modified 9.9 years ago by Seth Falcon7.4k • written 9.9 years ago by Suyog Pol40
Answer: Question regarding Installation of annotation package which was built using SQLf
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gravatar for Seth Falcon
9.9 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
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="il lumina_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_ense mble_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
ADD COMMENTlink written 9.9 years ago by Seth Falcon7.4k
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