search for: annotationdbi

Hi All, I tried to install AnnotationDBI like so: source("http://bioconductor.org/biocLite.R") biocLite("AnnotationDbi") and got this error: .... Loading required package: RSQLite Error in dyn.load(file, ...) : unable to load shared library '/RHEL3/local/lib64/R/library/ RSQLite/libs/RSQLite.so': /RHEL3...

Hi All, I tried to install AnnotationDBI like so: source("http://bioconductor.org/biocLite.R") biocLite("AnnotationDbi") and got this error: .... Loading required package: RSQLite Error in dyn.load(file, ...) : unable to load shared library '/RHEL3/local/lib64/R/library/ RSQLite/libs/RSQLite.so': /RHEL3...

...ped our own Affymetrix chip (Custom Express Array, PM-only with two species). I want to analyse the data with the limma package, but for that I need to built my own CDF package, probe package and built the filters to analyse one specie or another. I'm using the makeProbePackage available in the AnnotationDbi (for a R-2.13.0) but I got the following error message: Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument I already tried an old version of R-2.9.1 with a package matchprobes (that is no longer update for R-2.13.0) but the same error occurs. Does anyone knows how could...

...rch() In R-devel it seems like func --> NAMESPACE, including Imports: (and other details) --> ?? but not pkgs in Depends: Is this correct or as intended, or is there a better conception to have? This model is from the following: In 2.7.0: > library(KEGG.db) # Imports, Depends AnnotationDbi; KEGG.db is data-only > head(ls(KEGGPATHID2EXTID)) [1] "hsa00232" "hsa00230" "hsa04514" "hsa04010" "hsa04012" "hsa04150" vs. in a package tmpA with a NAMESPACE with Depend: and Imports: KEGG.db and in a new session of R > library(t...

...rg.Hs.eg.db") get("A GO TERM", org.Hs.egGO2ALLEGS) } > foo() Error in as.environment(pos) : invalid object for 'as.environment' ##================================================================= I fixed the problem by changing "get" explicitly to "AnnotationDbi::get". I'm just wondering what was the final decision on the problem and if there are more elegant ways of handling this. Thanks, ...Tao _________________________________________________________________ 50F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008

...in R-devel since 'both' has become the default pkgType for binary platforms. update.packages() fails when you set options(repos). Looks like it is trying to download a tgz file from the src/contrib section of a repository (on a mac). To reproduce this you need to have an older version of AnnotationDbi installed, which I accomplished by faking it, installing pkgKitten and then doing: library(pkgKitten) kitten("AnnotationDbi") Then exiting R and doing R CMD INSTALL AnnotationDbi. Here's the problem: > packageVersion("AnnotationDbi") [1] ?1.0? > options(repos=stru...

...ew 2: annotate - Basic GO Usage 3: annotate - HowTo: Get HTML Output 4: annotate - HowTo: use chromosomal information 5: annotate - HOWTO: Use the online query tools 6: annotate - Using Affymetrix Probe Level Data 7: annotate - Using Data Packages 8: annotate - Using the homology package 9: AnnotationDbi - AnnotationDbi 10: AnnotationDbi - SQLForge 11: Biobase - An introduction to Biobase and ExpressionSets 12: Biobase - Bioconductor Overview 13: Biobase - esApply Introduction 14: Biobase - Notes for eSet developers 15: Biobase - Notes for writing introductory 'how to' documents 16: Biobase...

mogene10stprobeset.db is generated with AnnotationDbi for mouse gene array. I don't find a package that seems generated by AnnotationDbi for exon arrays on the webpage you mentioned. Is it correct? On Tue, Oct 27, 2009 at 7:00 PM, Marc Carlson <mcarlson at fhcrc.org> wrote: > Hi Peng, > > I am not completely clear from your post wh...

...a character vector Browse[1]> gN[1:3] [1] "1005_at" "1007_s_at" "1008_f_at" ## Input 2, an object of class AtomicAnnMap (subclass of AnnMap) Browse[1]> class(LLe) [1] "AtomicAnnMap" attr(,"package") [1] "AnnotationDbi" ## See what selectMethod has to say (it finds the method I'm expecting) Browse[1]> selectMethod("mget", signature(x="character", envir=class(LLe))) Method Definition: function (x, envir, mode = "any", ifnotfound = list(function(x)...

...nstalled all the packages it asked for. It went all succesfull: "package 'IlluminaHumanMethylation27k.db' successfully unpacked and MD5 sums checked" But when I am trying to load this library I get an error: > library(IlluminaHumanMethylation27k.db) Loading required package: AnnotationDbi 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: org.Hs.eg.db...

This bug appears intermittently in R CMD check when reference classes have finalize methods. The problem is that garbage collection can be run after the methods package is no longer available. It affects (periodically) the Bioconductor AnnotationDbi package as well as packages that contain Rcpp classes. To reproduce: library(methods) a = setRefClass("A", methods=list(finalize=function() cat("A\n"))) b = setRefClass("B", contains="A") repeat b = setRefClass("B", contains="A&quot...

...have some tools to automatically generate annotation packages and those tools are implemented in software packages that use templates for the annotation packages to be generated. Those package templates are stored under the inst/ folder of the software package. One of those software packages is the AnnotationDbi package: it contains 41 package templates under inst/: [hpages at latitude Rpacks]$ ls AnnotationDbi/inst/AnnDbPkg-templates/ AFFYHUEX.DB CHIMP.DB MALARIA.DB WORM.DB ANOPHELES.DB COELICOLOR.DB MOUSECHIP.DB XENOPUSCHIP.DB ARABIDOPSISCHIP.DB ECOLICHIP.DB MOUSE.DB XE...

...)'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. registering new summary method 'pdnn'. registering new pmcorrect method 'pdnn' and 'pdnnpredict'. > library(hgu133atagprobe) Loading required package: AnnotationDbi > energy.file <- system.file("exampleData", "pdnn-energy-parameter_hg-u133a.txt", package = "affypdnn") > params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack = "hgu133aprobe") Calculating chip type specific parameters, (may take some...

...file. i get the following output. > library(hgu133a2.db) Error in library(hgu133a2.db) : there is no package called 'hgu133a2.db' > utils:::menuInstallLocal() package 'hgu133a2.db' successfully unpacked and MD5 sums checked > library(hgu133a2.db) Loading required package: AnnotationDbi 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: DBI Error in fun...

...datasets methods base other attached packages: [1] hgu95av2.db_2.2.12 ALL_1.4.4 ExpressionView_0.1 [4] caTools_1.9 bitops_1.0-4.1 KEGG.db_2.2.5 [7] GO.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 [10] eisa_0.1 genefilter_1.24.2 Category_2.10.0 [13] AnnotationDbi_1.6.0 Biobase_2.4.1 isa2_0.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 graph_1.22.2 GSEABase_1.6.0 RBGL_1.20.0 [5] splines_2.9.0 survival_2.35-4 tools_2.9.0 XML_2.6-0 [9] xtable_1.5-5 > Thanks, Gabor -- Gabor Csardi <Gabor.Csardi at unil.ch> UNI...

Hello, Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array) Im useing this script: library(matchprobes) library(affy) library(AnnotationDbi) library(hgu133plus2probe) library(hgu133aprobe) library(hgu133a.db) u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch u133a1 = ReadAffy() # reading hgu133a cel file into affybatch u133a2 = ReadAffy() # reading hgu133a cel file into affybatch data<-combineAffyBatch(list(u133p2,u1...

...reproducible case that I wanted to share. Also, please note the Bioconductor scenario which is potentially seriously impacted by this. The issue arises when a binary version of a package (like my example package below) is built under R 2.15.0 Patched but then installed under R 2.15.0. Our package AnnotationDbi (which hundreds of other packages depend on) is impacted by this issue to the extent that calling virtually any function in it will return something like this: Error in ls(2) : 7 arguments passed to .Internal(identical) which requires 6 My concern is that when R 2.15.1 is released and Bioconduct...

...ackage: Biobase Loading required package: tools 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: AnnotationDbi Loading required package: DBI Loading required package: RSQLite An object of class "GeneSetCollection" [[1]] setName: NA geneIds: X (total: 1) geneIdType: Null collectionType: Null details: use 'details(object)' Actually, the behavior is more complicate than appears; in a new...

...ll ready to go when Fedora infrastructure is working reliably again (the great datacenter migration has started and I can no longer git push). I'll also push R 4.0.1 into the tag when that's possible. There are two new packages that I created that are needed for R-biomaRt to be updated: R-AnnotationDbi https://bugzilla.redhat.com/show_bug.cgi?id=1845360 R-BiocFileCache https://bugzilla.redhat.com/show_bug.cgi?id=1845362 They are relatively simple noarch packages and should be quick reviews. Help in getting these reviewed quickly would be appreciated. Given the huge amount of builds (and rebuil...

...king reliably again (the great datacenter migration > has started and I can no longer git push). I'll also push R 4.0.1 into the > tag when that's possible. Much appreciated. > There are two new packages that I created that are needed for R-biomaRt to > be updated: > > R-AnnotationDbi > https://bugzilla.redhat.com/show_bug.cgi?id=1845360 > > R-BiocFileCache > https://bugzilla.redhat.com/show_bug.cgi?id=1845362 > > They are relatively simple noarch packages and should be quick reviews. > Help in getting these reviewed quickly would be appreciated. I took the...