error while using oligo to build a custom affy cdf
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Mark W Kimpel ▴ 830
@mark-w-kimpel-2027
Last seen 10.2 years ago
I need to build a custom cdf for Affy Rat Gene ST 1.0 chipset and am attempting to follow Jim's helpful suggestions which can be found at http://article.gmane.org/gmane.science.biology.informatics.conductor/1 8963/match=oligo+st I get the error '"AffyGenePDInfoPkgSeed" is not a defined class'. My script, debugging info and sessionInfo is below. Any help is much appreciated. Mark > require(oligo) Loading required package: oligo Loading required package: splines Loading required package: RSQLite Loading required package: DBI Loading required package: preprocessCore Loading required package: AnnotationDbi Loading required package: affxparser Loading required package: oligoClasses oligo Package - Series 1.5.x > setwd("~/R.functions/Annotation_builds/Rat_ST_1.0_lib_files") > pgfFile <- "RaGene-1_0-st-v1.r3.pgf" > clfFile <- "MoGene-1_0-st-v1.r3.clf" > transFile <- "RaGene-1_0-st-v1.na26.rn4.transcript.csv" > probeFile <- "RaGene-1_0-st-v1.probe.tab" > pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email = + "mwkimpel@gmail.com", version = "0.0.1", genomebuild = "July,2008", + biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, + transFile = transFile, probeFile = probeFile) Error in getClass(Class, where = topenv(parent.frame())) : "AffyGenePDInfoPkgSeed" is not a defined class Enter a frame number, or 0 to exit 1: new("AffyGenePDInfoPkgSeed", author = "authorname", email = "mwkimpel@gmail 2: getClass(Class, where = topenv(parent.frame())) Selection: 2 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "Class" "value" "where" Browse[1]> Class [1] "AffyGenePDInfoPkgSeed" Browse[1]> value NULL Browse[1]> where where 1: eval(expr, envir, enclos) where 2: eval(quote(browser()), envir = sys.frame(which)) where 3: function () { if (.isMethodsDispatchOn()) { tState <- tracingState(FALSE) on.exit(tracingState(tState)) } calls <- sys.calls() from <- 0 n <- length(calls) if (identical(sys.function(n), recover)) n <- n - 1 for (i in rev(seq_len(n))) { calli <- calls[[i]] fname <- calli[[1]] if (!is.na(match(deparse(fname)[1], c("methods::.doTrace", ".doTrace")))) { from <- i - 1 break } } if (from == 0) for (i in rev(seq_len(n))) { calli <- calls[[i]] fname <- calli[[1]] if (!is.name(fname) || is.na(match(as.character(fname), c("recover", "stop", "Stop")))) { from <- i break } } if (from > 0) { if (!interactive()) { try(dump.frames()) cat(gettext("recover called non-interactively; frames dumped, use debugger() to view\n")) return(NULL) } else if (identical(getOption("show.error.messages"), FALSE)) return(NULL) calls <- limitedLabels(calls[1:from]) repeat { which <- menu(calls, title = "\nEnter a frame number, or 0 to exit ") if (which > 0) eval(quote(browser()), envir = sys.frame(which)) else break } } else cat(gettext("No suitable frames for recover()\n")) }() where 4: stop(gettextf("\"%s\" is not a defined class", Class), domain = NA) where 5: getClass(Class, where = topenv(parent.frame())) where 6: new("AffyGenePDInfoPkgSeed", author = "authorname", email = " mwkimpel@gmail.com", version = "0.0.1", genomebuild = "July,2008", biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, transFile = transFile, probeFile = probeFile) Browse[1]> c Enter a frame number, or 0 to exit 1: new("AffyGenePDInfoPkgSeed", author = "authorname", email = "mwkimpel@gmail 2: getClass(Class, where = topenv(parent.frame())) Selection: 0 > sessionInfo() R version 2.8.0 Under development (unstable) (2008-08-30 r46465) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] oligo_1.5.9 oligoClasses_1.3.6 affxparser_1.13.8 [4] AnnotationDbi_1.3.12 preprocessCore_1.3.4 RSQLite_0.7-0 [7] DBI_0.2-4 Biobase_2.1.7 graph_1.19.6 loaded via a namespace (and not attached): [1] cluster_1.11.11 ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]
BiocViews cdf affy biocViews BiocViews BiocViews cdf affy biocViews • 1.1k views
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@james-w-macdonald-5106
Last seen 15 hours ago
United States
Hi Mark, Mark Kimpel wrote: > I need to build a custom cdf for Affy Rat Gene ST 1.0 chipset and am > attempting to follow Jim's helpful suggestions which can be found at > http://article.gmane.org/gmane.science.biology.informatics.conductor /18963/match=oligo+st > I get the error '"AffyGenePDInfoPkgSeed" is not a defined class'. My script, > debugging info and sessionInfo is below. Any help is much appreciated. > > Mark > >> require(oligo) You need to load the pdInfoBuilder package to build pdInfoPackages ;-D Best, Jim > Loading required package: oligo > Loading required package: splines > Loading required package: RSQLite > Loading required package: DBI > Loading required package: preprocessCore > Loading required package: AnnotationDbi > Loading required package: affxparser > Loading required package: oligoClasses > oligo Package - Series 1.5.x >> setwd("~/R.functions/Annotation_builds/Rat_ST_1.0_lib_files") >> pgfFile <- "RaGene-1_0-st-v1.r3.pgf" >> clfFile <- "MoGene-1_0-st-v1.r3.clf" >> transFile <- "RaGene-1_0-st-v1.na26.rn4.transcript.csv" >> probeFile <- "RaGene-1_0-st-v1.probe.tab" >> pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email = > + "mwkimpel at gmail.com", version = "0.0.1", genomebuild = "July,2008", > + biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, > + transFile = transFile, probeFile = probeFile) > Error in getClass(Class, where = topenv(parent.frame())) : > "AffyGenePDInfoPkgSeed" is not a defined class > > Enter a frame number, or 0 to exit > > 1: new("AffyGenePDInfoPkgSeed", author = "authorname", email = > "mwkimpel at gmail > 2: getClass(Class, where = topenv(parent.frame())) > > Selection: 2 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "Class" "value" "where" > Browse[1]> Class > [1] "AffyGenePDInfoPkgSeed" > Browse[1]> value > NULL > Browse[1]> where > where 1: eval(expr, envir, enclos) > where 2: eval(quote(browser()), envir = sys.frame(which)) > where 3: function () > { > if (.isMethodsDispatchOn()) { > tState <- tracingState(FALSE) > on.exit(tracingState(tState)) > } > calls <- sys.calls() > from <- 0 > n <- length(calls) > if (identical(sys.function(n), recover)) > n <- n - 1 > for (i in rev(seq_len(n))) { > calli <- calls[[i]] > fname <- calli[[1]] > if (!is.na(match(deparse(fname)[1], c("methods::.doTrace", > ".doTrace")))) { > from <- i - 1 > break > } > } > if (from == 0) > for (i in rev(seq_len(n))) { > calli <- calls[[i]] > fname <- calli[[1]] > if (!is.name(fname) || is.na(match(as.character(fname), > c("recover", "stop", "Stop")))) { > from <- i > break > } > } > if (from > 0) { > if (!interactive()) { > try(dump.frames()) > cat(gettext("recover called non-interactively; frames dumped, > use debugger() to view\n")) > return(NULL) > } > else if (identical(getOption("show.error.messages"), > FALSE)) > return(NULL) > calls <- limitedLabels(calls[1:from]) > repeat { > which <- menu(calls, title = "\nEnter a frame number, or 0 to > exit ") > if (which > 0) > eval(quote(browser()), envir = sys.frame(which)) > else break > } > } > else cat(gettext("No suitable frames for recover()\n")) > }() > where 4: stop(gettextf("\"%s\" is not a defined class", Class), domain = NA) > where 5: getClass(Class, where = topenv(parent.frame())) > where 6: new("AffyGenePDInfoPkgSeed", author = "authorname", email = " > mwkimpel at gmail.com", > version = "0.0.1", genomebuild = "July,2008", biocViews = > "AnnotationData", > pgfFile = pgfFile, clfFile = clfFile, transFile = transFile, > probeFile = probeFile) > > Browse[1]> c > > Enter a frame number, or 0 to exit > > 1: new("AffyGenePDInfoPkgSeed", author = "authorname", email = > "mwkimpel at gmail > 2: getClass(Class, where = topenv(parent.frame())) > > Selection: 0 >> sessionInfo() > R version 2.8.0 Under development (unstable) (2008-08-30 r46465) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] oligo_1.5.9 oligoClasses_1.3.6 affxparser_1.13.8 > [4] AnnotationDbi_1.3.12 preprocessCore_1.3.4 RSQLite_0.7-0 > [7] DBI_0.2-4 Biobase_2.1.7 graph_1.19.6 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." -- B. > F. Skinner > ****************************************************************** > -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
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