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Question: Question about locked environments
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gravatar for Jenny Drnevich
6.5 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
Hi Michael, I'm sorry you are having trouble with the RemoveProbes() function I posted the BioC mailing list many years ago. I have not had to use that function myself in years, and did not know it wasn't working with newer versions of R. I didn't write the original code, Ariel Chernomoretz did. I only modified it, and I'm not sure I know enough to solve the problem. I'm posting this to the BioC mailing list to see if anyone can help. Below is my reproducible code (link to download the "RemoveProbes.RData" file is below ), showing where the problem occurs. It appears that the environments containing the Affymetrix probe and probe set information that the code is trying to change in now locked. I have no idea if there is a way to overcome this. Thanks in advance to anyone for any help, Jenny https://netfiles.uiuc.edu/xythoswfs/webui/_xy-42144579_2-t_YuabdiYC (link expires 7/7/12) > library(affy) Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object(s) are masked from 'package:stats': xtabs The following object(s) are masked from 'package:base': anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > load("RemoveProbes.RData") > ls() [1] "nonsoygenes" "RemoveProbes" "ResetEnvir" "soygenes" > > cleancdf <- "soybean" > > ResetEnvir(cleancdf) Loading required package: soybeancdf Loading required package: AnnotationDbi Loading required package: soybeanprobe > > RemoveProbes(listOutProbeSets=nonsoygenes, cleancdf=cleancdf) Error in assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) : cannot change value of locked binding for 'soybeanprobe' > > debug(RemoveProbes) > RemoveProbes(listOutProbeSets=nonsoygenes, cleancdf=cleancdf) debugging in: RemoveProbes(listOutProbeSets = nonsoygenes, cleancdf = cleancdf) debug: { cdfpackagename <- paste(cleancdf, "cdf", sep = "") probepackagename <- paste(cleancdf, "probe", sep = "") require(cdfpackagename, character.only = TRUE) require(probepackagename, character.only = TRUE) probe.env.orig <- get(probepackagename) if (!is.null(listOutProbes)) { probes <- unlist(lapply(listOutProbes, function(x) { a <- strsplit(x, "at") aux1 <- paste(a[[1]][1], "at", sep = "") aux2 <- as.integer(a[[1]][2]) c(aux1, aux2) })) n1 <- as.character(probes[seq(1, (length(probes)/2)) * 2 - 1]) n2 <- as.integer(probes[seq(1, (length(probes)/2)) * 2]) probes <- data.frame(I(n1), n2) probes[, 1] <- as.character(probes[, 1]) probes[, 2] <- as.integer(probes[, 2]) pset <- unique(probes[, 1]) for (i in seq(along = pset)) { ii <- grep(pset[i], probes[, 1]) iout <- probes[ii, 2] a <- get(pset[i], env = get(cdfpackagename)) a <- a[-iout, ] assign(pset[i], a, env = get(cdfpackagename)) } } if (!is.null(listOutProbeSets)) { rm(list = listOutProbeSets, envir = get(cdfpackagename)) } tmp <- get("xy2indices", paste("package:", cdfpackagename, sep = "")) newAB <- new("AffyBatch", cdfName = cleancdf) pmIndex <- unlist(indexProbes(newAB, "pm")) subIndex <- match(tmp(probe.env.orig$x, probe.env.orig$y, cdf = cdfpackagename), pmIndex) rm(newAB) iNA <- whichis.na(subIndex)) if (length(iNA) > 0) { ipos <- grep(probepackagename, search()) assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) } } Browse[2]> debug: cdfpackagename <- paste(cleancdf, "cdf", sep = "") Browse[2]> debug: probepackagename <- paste(cleancdf, "probe", sep = "") Browse[2]> debug: require(cdfpackagename, character.only = TRUE) Browse[2]> debug: require(probepackagename, character.only = TRUE) Browse[2]> debug: probe.env.orig <- get(probepackagename) Browse[2]> debug: if (!is.null(listOutProbes)) { probes <- unlist(lapply(listOutProbes, function(x) { a <- strsplit(x, "at") aux1 <- paste(a[[1]][1], "at", sep = "") aux2 <- as.integer(a[[1]][2]) c(aux1, aux2) })) n1 <- as.character(probes[seq(1, (length(probes)/2)) * 2 - 1]) n2 <- as.integer(probes[seq(1, (length(probes)/2)) * 2]) probes <- data.frame(I(n1), n2) probes[, 1] <- as.character(probes[, 1]) probes[, 2] <- as.integer(probes[, 2]) pset <- unique(probes[, 1]) for (i in seq(along = pset)) { ii <- grep(pset[i], probes[, 1]) iout <- probes[ii, 2] a <- get(pset[i], env = get(cdfpackagename)) a <- a[-iout, ] assign(pset[i], a, env = get(cdfpackagename)) } } Browse[2]> debug: NULL Browse[2]> debug: if (!is.null(listOutProbeSets)) { rm(list = listOutProbeSets, envir = get(cdfpackagename)) } Browse[2]> debug: rm(list = listOutProbeSets, envir = get(cdfpackagename)) Browse[2]> debug: tmp <- get("xy2indices", paste("package:", cdfpackagename, sep = "")) Browse[2]> debug: newAB <- new("AffyBatch", cdfName = cleancdf) Browse[2]> debug: pmIndex <- unlist(indexProbes(newAB, "pm")) Browse[2]> debug: subIndex <- match(tmp(probe.env.orig$x, probe.env.orig$y, cdf = cdfpackagename), pmIndex) Browse[2]> debug: rm(newAB) Browse[2]> debug: iNA <- whichis.na(subIndex)) Browse[2]> debug: if (length(iNA) > 0) { ipos <- grep(probepackagename, search()) assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) } Browse[2]> debug: ipos <- grep(probepackagename, search()) Browse[2]> debug: assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) #The line above is what causes the error Browse[2]> probepackagename [1] "soybeanprobe" There were 50 or more warnings (use warnings() to see the first 50) Browse[2]> warnings()[1:3] $`object 'AFFX-BioB-3_at' not found` rm(list = listOutProbeSets, envir = get(cdfpackagename)) $`object 'AFFX-BioB-5_at' not found` rm(list = listOutProbeSets, envir = get(cdfpackagename)) $`object 'AFFX-BioB-M_at' not found` rm(list = listOutProbeSets, envir = get(cdfpackagename)) #Not sure what the above warnings mean or if they are related Browse[2]> ?assign starting httpd help server ... done Browse[2]> ?lockBinding Browse[2]> environmentIsLocked(as.environment(ipos)) [1] TRUE Browse[2]> assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) Error in assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) : cannot change value of locked binding for 'soybeanprobe' In addition: There were 50 or more warnings (use warnings() to see the first 50) > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 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] soybeanprobe_2.10.0 soybeancdf_2.10.0 AnnotationDbi_1.18.1 affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.6 DBI_0.2-5 IRanges_1.14.3 preprocessCore_1.18.0 RSQLite_0.11.1 stats4_2.15.0 [8] tools_2.15.0 zlibbioc_1.2.0 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center High Performance Biological Computing Program University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA NOTE NEW PHONE NUMBER ph: 217-300-6543 fax: 217-265-5066 e-mail: drnevich@illinois.edu [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.5 years ago by Martin Morgan ♦♦ 22k • written 6.5 years ago by Jenny Drnevich1.9k
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gravatar for Martin Morgan
6.5 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
On 06/07/2012 07:20 AM, Zadeh, Jenny Drnevich wrote: > Hi Michael, > > I'm sorry you are having trouble with the RemoveProbes() function I posted the BioC mailing list many years ago. I have not had to use that function myself in years, and did not know it wasn't working with newer versions of R. I didn't write the original code, Ariel Chernomoretz did. I only modified it, and I'm not sure I know enough to solve the problem. I'm posting this to the BioC mailing list to see if anyone can help. Below is my reproducible code (link to download the "RemoveProbes.RData" file is below ), showing where the problem occurs. It appears that the environments containing the Affymetrix probe and probe set information that the code is trying to change in now locked. I have no idea if there is a way to overcome this. > > Thanks in advance to anyone for any help, > Jenny > > https://netfiles.uiuc.edu/xythoswfs/webui/_xy-42144579_2-t_YuabdiYC (link expires 7/7/12) > >> library(affy) > Loading required package: BiocGenerics > > Attaching package: 'BiocGenerics' > > The following object(s) are masked from 'package:stats': > > xtabs > > The following object(s) are masked from 'package:base': > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, > pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique > > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages > 'citation("pkgname")'. > >> load("RemoveProbes.RData") >> ls() > [1] "nonsoygenes" "RemoveProbes" "ResetEnvir" "soygenes" >> >> cleancdf<- "soybean" >> >> ResetEnvir(cleancdf) > Loading required package: soybeancdf > Loading required package: AnnotationDbi > > Loading required package: soybeanprobe >> >> RemoveProbes(listOutProbeSets=nonsoygenes, cleancdf=cleancdf) > Error in assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) : > cannot change value of locked binding for 'soybeanprobe' >> >> debug(RemoveProbes) >> RemoveProbes(listOutProbeSets=nonsoygenes, cleancdf=cleancdf) > debugging in: RemoveProbes(listOutProbeSets = nonsoygenes, cleancdf = cleancdf) > debug: { > cdfpackagename<- paste(cleancdf, "cdf", sep = "") > probepackagename<- paste(cleancdf, "probe", sep = "") > require(cdfpackagename, character.only = TRUE) > require(probepackagename, character.only = TRUE) > probe.env.orig<- get(probepackagename) > if (!is.null(listOutProbes)) { > probes<- unlist(lapply(listOutProbes, function(x) { > a<- strsplit(x, "at") > aux1<- paste(a[[1]][1], "at", sep = "") > aux2<- as.integer(a[[1]][2]) > c(aux1, aux2) > })) > n1<- as.character(probes[seq(1, (length(probes)/2)) * > 2 - 1]) > n2<- as.integer(probes[seq(1, (length(probes)/2)) * > 2]) > probes<- data.frame(I(n1), n2) > probes[, 1]<- as.character(probes[, 1]) > probes[, 2]<- as.integer(probes[, 2]) > pset<- unique(probes[, 1]) > for (i in seq(along = pset)) { > ii<- grep(pset[i], probes[, 1]) > iout<- probes[ii, 2] > a<- get(pset[i], env = get(cdfpackagename)) > a<- a[-iout, ] > assign(pset[i], a, env = get(cdfpackagename)) > } > } > if (!is.null(listOutProbeSets)) { > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > } > tmp<- get("xy2indices", paste("package:", cdfpackagename, > sep = "")) > newAB<- new("AffyBatch", cdfName = cleancdf) > pmIndex<- unlist(indexProbes(newAB, "pm")) > subIndex<- match(tmp(probe.env.orig$x, probe.env.orig$y, > cdf = cdfpackagename), pmIndex) > rm(newAB) > iNA<- whichis.na(subIndex)) > if (length(iNA)> 0) { > ipos<- grep(probepackagename, search()) > assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) I think you can replace assign() with assignInNamespace(). I don't know whether that is a good idea or not... From ?assignInNamespace They should not be used in production code. but I don't think this is any more dire than what the original code was doing, before the introduction of package name spaces. Martin > } > } > Browse[2]> > debug: cdfpackagename<- paste(cleancdf, "cdf", sep = "") > Browse[2]> > debug: probepackagename<- paste(cleancdf, "probe", sep = "") > Browse[2]> > debug: require(cdfpackagename, character.only = TRUE) > Browse[2]> > debug: require(probepackagename, character.only = TRUE) > Browse[2]> > debug: probe.env.orig<- get(probepackagename) > Browse[2]> > debug: if (!is.null(listOutProbes)) { > probes<- unlist(lapply(listOutProbes, function(x) { > a<- strsplit(x, "at") > aux1<- paste(a[[1]][1], "at", sep = "") > aux2<- as.integer(a[[1]][2]) > c(aux1, aux2) > })) > n1<- as.character(probes[seq(1, (length(probes)/2)) * 2 - > 1]) > n2<- as.integer(probes[seq(1, (length(probes)/2)) * 2]) > probes<- data.frame(I(n1), n2) > probes[, 1]<- as.character(probes[, 1]) > probes[, 2]<- as.integer(probes[, 2]) > pset<- unique(probes[, 1]) > for (i in seq(along = pset)) { > ii<- grep(pset[i], probes[, 1]) > iout<- probes[ii, 2] > a<- get(pset[i], env = get(cdfpackagename)) > a<- a[-iout, ] > assign(pset[i], a, env = get(cdfpackagename)) > } > } > Browse[2]> > debug: NULL > Browse[2]> > debug: if (!is.null(listOutProbeSets)) { > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > } > Browse[2]> > debug: rm(list = listOutProbeSets, envir = get(cdfpackagename)) > Browse[2]> > debug: tmp<- get("xy2indices", paste("package:", cdfpackagename, sep = "")) > Browse[2]> > debug: newAB<- new("AffyBatch", cdfName = cleancdf) > Browse[2]> > debug: pmIndex<- unlist(indexProbes(newAB, "pm")) > Browse[2]> > debug: subIndex<- match(tmp(probe.env.orig$x, probe.env.orig$y, cdf = cdfpackagename), > pmIndex) > Browse[2]> > debug: rm(newAB) > Browse[2]> > debug: iNA<- whichis.na(subIndex)) > Browse[2]> > debug: if (length(iNA)> 0) { > ipos<- grep(probepackagename, search()) > assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) > } > Browse[2]> > debug: ipos<- grep(probepackagename, search()) > Browse[2]> > debug: assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) > > #The line above is what causes the error > > Browse[2]> probepackagename > [1] "soybeanprobe" > There were 50 or more warnings (use warnings() to see the first 50) > Browse[2]> warnings()[1:3] > $`object 'AFFX-BioB-3_at' not found` > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > > $`object 'AFFX-BioB-5_at' not found` > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > > $`object 'AFFX-BioB-M_at' not found` > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > > #Not sure what the above warnings mean or if they are related > > Browse[2]> ?assign > starting httpd help server ... done > Browse[2]> ?lockBinding > Browse[2]> environmentIsLocked(as.environment(ipos)) > [1] TRUE > > Browse[2]> assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) > Error in assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) : > cannot change value of locked binding for 'soybeanprobe' > In addition: There were 50 or more warnings (use warnings() to see the first 50) >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 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] soybeanprobe_2.10.0 soybeancdf_2.10.0 AnnotationDbi_1.18.1 affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 BiocInstaller_1.4.6 DBI_0.2-5 IRanges_1.14.3 preprocessCore_1.18.0 RSQLite_0.11.1 stats4_2.15.0 > [8] tools_2.15.0 zlibbioc_1.2.0 > > > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > High Performance Biological Computing Program > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > NOTE NEW PHONE NUMBER > ph: 217-300-6543 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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
ADD COMMENTlink written 6.5 years ago by Martin Morgan ♦♦ 22k
Hi Martin, Thanks for your suggestion about using assignInNamespace() instead of assign(). That seems to work, except the ResetEnvir() function no longer restores the original probes and probe sets in that R session. However, just quitting and re-starting R will restore the original probes/sets, so just use that if you need it, Michael. A text file with the revised code for RemoveProbes is attached. Thanks again, Jenny -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Thursday, June 07, 2012 7:22 PM To: Zadeh, Jenny Drnevich Cc: Seidl, M.F. (Michael); bioconductor at r-project.org; Ariel Chernomoretz Subject: Re: [BioC] Question about locked environments On 06/07/2012 07:20 AM, Zadeh, Jenny Drnevich wrote: > Hi Michael, > > I'm sorry you are having trouble with the RemoveProbes() function I posted the BioC mailing list many years ago. I have not had to use that function myself in years, and did not know it wasn't working with newer versions of R. I didn't write the original code, Ariel Chernomoretz did. I only modified it, and I'm not sure I know enough to solve the problem. I'm posting this to the BioC mailing list to see if anyone can help. Below is my reproducible code (link to download the "RemoveProbes.RData" file is below ), showing where the problem occurs. It appears that the environments containing the Affymetrix probe and probe set information that the code is trying to change in now locked. I have no idea if there is a way to overcome this. > > Thanks in advance to anyone for any help, Jenny > > https://netfiles.uiuc.edu/xythoswfs/webui/_xy-42144579_2-t_YuabdiYC > (link expires 7/7/12) > >> library(affy) > Loading required package: BiocGenerics > > Attaching package: 'BiocGenerics' > > The following object(s) are masked from 'package:stats': > > xtabs > > The following object(s) are masked from 'package:base': > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, > pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, > sapply, setdiff, table, tapply, union, unique > > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages > 'citation("pkgname")'. > >> load("RemoveProbes.RData") >> ls() > [1] "nonsoygenes" "RemoveProbes" "ResetEnvir" "soygenes" >> >> cleancdf<- "soybean" >> >> ResetEnvir(cleancdf) > Loading required package: soybeancdf > Loading required package: AnnotationDbi > > Loading required package: soybeanprobe >> >> RemoveProbes(listOutProbeSets=nonsoygenes, cleancdf=cleancdf) > Error in assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) : > cannot change value of locked binding for 'soybeanprobe' >> >> debug(RemoveProbes) >> RemoveProbes(listOutProbeSets=nonsoygenes, cleancdf=cleancdf) > debugging in: RemoveProbes(listOutProbeSets = nonsoygenes, cleancdf = > cleancdf) > debug: { > cdfpackagename<- paste(cleancdf, "cdf", sep = "") > probepackagename<- paste(cleancdf, "probe", sep = "") > require(cdfpackagename, character.only = TRUE) > require(probepackagename, character.only = TRUE) > probe.env.orig<- get(probepackagename) > if (!is.null(listOutProbes)) { > probes<- unlist(lapply(listOutProbes, function(x) { > a<- strsplit(x, "at") > aux1<- paste(a[[1]][1], "at", sep = "") > aux2<- as.integer(a[[1]][2]) > c(aux1, aux2) > })) > n1<- as.character(probes[seq(1, (length(probes)/2)) * > 2 - 1]) > n2<- as.integer(probes[seq(1, (length(probes)/2)) * > 2]) > probes<- data.frame(I(n1), n2) > probes[, 1]<- as.character(probes[, 1]) > probes[, 2]<- as.integer(probes[, 2]) > pset<- unique(probes[, 1]) > for (i in seq(along = pset)) { > ii<- grep(pset[i], probes[, 1]) > iout<- probes[ii, 2] > a<- get(pset[i], env = get(cdfpackagename)) > a<- a[-iout, ] > assign(pset[i], a, env = get(cdfpackagename)) > } > } > if (!is.null(listOutProbeSets)) { > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > } > tmp<- get("xy2indices", paste("package:", cdfpackagename, > sep = "")) > newAB<- new("AffyBatch", cdfName = cleancdf) > pmIndex<- unlist(indexProbes(newAB, "pm")) > subIndex<- match(tmp(probe.env.orig$x, probe.env.orig$y, > cdf = cdfpackagename), pmIndex) > rm(newAB) > iNA<- whichis.na(subIndex)) > if (length(iNA)> 0) { > ipos<- grep(probepackagename, search()) > assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) I think you can replace assign() with assignInNamespace(). I don't know whether that is a good idea or not... From ?assignInNamespace They should not be used in production code. but I don't think this is any more dire than what the original code was doing, before the introduction of package name spaces. Martin > } > } > Browse[2]> > debug: cdfpackagename<- paste(cleancdf, "cdf", sep = "") Browse[2]> > debug: probepackagename<- paste(cleancdf, "probe", sep = "") > Browse[2]> > debug: require(cdfpackagename, character.only = TRUE) Browse[2]> > debug: require(probepackagename, character.only = TRUE) Browse[2]> > debug: probe.env.orig<- get(probepackagename) Browse[2]> > debug: if (!is.null(listOutProbes)) { > probes<- unlist(lapply(listOutProbes, function(x) { > a<- strsplit(x, "at") > aux1<- paste(a[[1]][1], "at", sep = "") > aux2<- as.integer(a[[1]][2]) > c(aux1, aux2) > })) > n1<- as.character(probes[seq(1, (length(probes)/2)) * 2 - > 1]) > n2<- as.integer(probes[seq(1, (length(probes)/2)) * 2]) > probes<- data.frame(I(n1), n2) > probes[, 1]<- as.character(probes[, 1]) > probes[, 2]<- as.integer(probes[, 2]) > pset<- unique(probes[, 1]) > for (i in seq(along = pset)) { > ii<- grep(pset[i], probes[, 1]) > iout<- probes[ii, 2] > a<- get(pset[i], env = get(cdfpackagename)) > a<- a[-iout, ] > assign(pset[i], a, env = get(cdfpackagename)) > } > } > Browse[2]> > debug: NULL > Browse[2]> > debug: if (!is.null(listOutProbeSets)) { > rm(list = listOutProbeSets, envir = get(cdfpackagename)) } > Browse[2]> > debug: rm(list = listOutProbeSets, envir = get(cdfpackagename)) > Browse[2]> > debug: tmp<- get("xy2indices", paste("package:", cdfpackagename, sep = > "")) Browse[2]> > debug: newAB<- new("AffyBatch", cdfName = cleancdf) Browse[2]> > debug: pmIndex<- unlist(indexProbes(newAB, "pm")) Browse[2]> > debug: subIndex<- match(tmp(probe.env.orig$x, probe.env.orig$y, cdf = cdfpackagename), > pmIndex) > Browse[2]> > debug: rm(newAB) > Browse[2]> > debug: iNA<- whichis.na(subIndex)) > Browse[2]> > debug: if (length(iNA)> 0) { > ipos<- grep(probepackagename, search()) > assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) } > Browse[2]> > debug: ipos<- grep(probepackagename, search()) Browse[2]> > debug: assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) > > #The line above is what causes the error > > Browse[2]> probepackagename > [1] "soybeanprobe" > There were 50 or more warnings (use warnings() to see the first 50) > Browse[2]> warnings()[1:3] $`object 'AFFX-BioB-3_at' not found` > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > > $`object 'AFFX-BioB-5_at' not found` > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > > $`object 'AFFX-BioB-M_at' not found` > rm(list = listOutProbeSets, envir = get(cdfpackagename)) > > #Not sure what the above warnings mean or if they are related > > Browse[2]> ?assign > starting httpd help server ... done > Browse[2]> ?lockBinding > Browse[2]> environmentIsLocked(as.environment(ipos)) > [1] TRUE > > Browse[2]> assign(probepackagename, probe.env.orig[-iNA, ], pos = > ipos) Error in assign(probepackagename, probe.env.orig[-iNA, ], pos = ipos) : > cannot change value of locked binding for 'soybeanprobe' > In addition: There were 50 or more warnings (use warnings() to see the > first 50) >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 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] soybeanprobe_2.10.0 soybeancdf_2.10.0 AnnotationDbi_1.18.1 affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 BiocInstaller_1.4.6 DBI_0.2-5 IRanges_1.14.3 preprocessCore_1.18.0 RSQLite_0.11.1 stats4_2.15.0 > [8] tools_2.15.0 zlibbioc_1.2.0 > > > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist W.M. Keck Center for > Comparative and Functional Genomics Roy J. Carver Biotechnology Center > High Performance Biological Computing Program University of Illinois, > Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > NOTE NEW PHONE NUMBER > ph: 217-300-6543 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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
ADD REPLYlink written 6.4 years ago by Jenny Drnevich1.9k
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