search for: oligoclass

...ucture package that works fine (I can build, check and load it successfully) on revision r53950. The very same package fails on r54591 with the error below: Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : cyclic name space dependency detected when loading ?oligoClasses?, already loading ?oligoClasses? I don't see anything obvious in the name space that would indicate cyclic dependency and I wonder: a) if there were changes that were meant to affect this; b) what is the recommended strategy to solve this issue. Thank you very much for any suggestion, be...

Hi, ExonFeatureSet I have an object of the above class. The following document mentioned it. http://www.bioconductor.org/packages/2.5/bioc/vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf But I would like to see its defintion. I'm wondering if there is a way in R to give me the definition of any class? Regards, Peng

...> $ signature: Named chr [1:4] "TilingFeatureSet" "ANY" "ANY" "array" >> ..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value" >> ..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods" >> $ mnames : chr [1:2] "object" "value" >> $ fnames : chr [1:4] "object" "subset" "target" "value" >> [1] "f" "fdef"...

...12,4,3,2 List of 3 $ signature: Named chr [1:4] "TilingFeatureSet" "ANY" "ANY" "array" ..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value" ..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods" $ mnames : chr [1:2] "object" "value" $ fnames : chr [1:4] "object" "subset" "target" "value" [1] "f" "fdef" "fnames"...

...of 3 > $ signature: Named chr [1:4] "TilingFeatureSet" "ANY" "ANY" "array" > ..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value" > ..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods" > $ mnames : chr [1:2] "object" "value" > $ fnames : chr [1:4] "object" "subset" "target" "value" > [1] "f" "fdef" &quot...

...ry(pdInfoBuilder) Loading required package: RSQLite Loading required package: DBI Loading required package: affxparser Loading required package: oligo Loading required package: splines Loading required package: preprocessCore Loading required package: AnnotationDbi Loading required package: oligoClasses oligo Package - Series 1.5.x > setwd("D:/Anne-Marie/Doctorat/puces ADN macrophages/puces rat/Annie Dube/Analyse") > transFile <- "RaGene-1_0-st-v1.na27.rn4.transcript.csv1/RaGene-1_0-st-v1.na27.rn4.transcr ipt.csv" > probeFile <- "RaGene-1_0-st-v1.probe...

...nature: Named chr [1:4] "TilingFeatureSet" "ANY" "ANY" "array" > >> ..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value" > >> ..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods" > >> $ mnames : chr [1:2] "object" "value" > >> $ fnames : chr [1:4] "object" "subset" "target" "value" > >> [1] "f" &quo...

...ge rawData$v1 and rawData$v1.1 since they are consistent each other. I was trying to use "merge" function as merge(rawData$v1, rawData$v1.1) but it failed with error as Error in as.data.frame.default(x) : cannot coerce class 'structure("TilingFeatureSet", package = "oligoClasses")' into a data.frame Calls: merge ... merge.default -> merge -> as.data.frame -> as.data.frame.default Can you please help with some advices? Thanks, Best regards, Seungyeul Yoo Postdoc Fellow, Institute of Genomics and Multiscale Biology Department of Genetics and Genomic...

...r [1:4] "TilingFeatureSet" "ANY" "ANY" "array" >> >> ..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value" >> >> ..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods" >> >> $ mnames : chr [1:2] "object" "value" >> >> $ fnames : chr [1:4] "object" "subset" "target" "value" >> >> [1] &qu...

..."TilingFeatureSet" "ANY" "ANY" "array" ? ? >>> >>? ..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value" ? ? >>> >>? ..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods" ? ? >>> >> $ mnames? : chr [1:2] "object" "value" ? ? >>> >> $ fnames? : chr [1:4] "object" "subset" "target" "value" ? ? >>> >...

..."TilingFeatureSet" "ANY" "ANY" "array" >>> >> ..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value" >>> >> ..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods" >>> >> $ mnames : chr [1:2] "object" "value" >>> >> $ fnames : chr [1:4] "object" "subset" "target" "value" >>> >...

..."TilingFeatureSet" "ANY" "ANY" "array" >>> >> ..- attr(*, "names")= chr [1:4] "object" "subset" "target" "value" >>> >> ..- attr(*, "package")= chr [1:4] "oligoClasses" "methods" "methods" "methods" >>> >> $ mnames : chr [1:2] "object" "value" >>> >> $ fnames : chr [1:4] "object" "subset" "target" "value" >>> >...

Henrik, If a minimal reprex is hard to construct, could you perhaps instrument your version of R to include a browser() call at the start of the else if(!all(signature[omittedSig] == "missing")) { branch, run the code that triggers the issue for you (and must hit that branch) and tell us what the "signature" and "omittedSig" objects look like at that point?

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is