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Question: R crashes when calling readCelFile in Starr package
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gravatar for Koh, Fong Ming
4.3 years ago by
Koh, Fong Ming20 wrote:
Hi all, I am trying to run the sample code found in the vignette for the Starr package, but my R crashes upon calling the readCelFile function. This problem seemed to have appeared previously (Nov 2011), but there was no solution listed. I've appended my session below. R crashes on the very last line. I'll be happy to take any suggestions on what I may be doing wrong. Thanks! Fong Koh ================ Package vignette: http://www.bioconductor.org/packages/2.11/bioc/vigne ttes/Starr/inst/doc/Starr.pdf Previous mention of problem: https://stat.ethz.ch/pipermail/bioconductor/2011-November/042165.html ================ > sessionInfo() R version 2.15.3 (2013-03-01) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("Starr") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'Starr' trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/macosx/leop ard/contrib/2.15/Starr_1.14.1.tgz' Content type 'application/x-gzip' length 1814289 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb The downloaded binary packages are in /var/folders/tl/dm9b5srj1bqfqwx7fk4bllpc0000gn/T//Rtmp1VFAMD/d ownloaded_packages > library(Starr) Loading required package: Ringo Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: RColorBrewer Loading required package: limma Loading required package: Matrix Loading required package: lattice Loading required package: grid Loading required package: affy Attaching package: ?affy? The following object(s) are masked from ?package:Ringo?: probes Loading required package: affxparser Attaching package: ?Starr? The following object(s) are masked from ?package:affy?: plotDensity The following object(s) are masked from ?package:limma?: plotMA > dataPath <- system.file("extdata", package="Starr") > bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap")) > cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), file.path(dataPath,"Rpb3_IP2_chr1.cel")) > names <- c("rpb3_1", "wt_1","rpb3_2") > type <- c("IP", "CONTROL", "IP") ==== everything looks ok up to here, but crashes with the next line ======= > rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=T, log.it=T)
ADD COMMENTlink modified 4.3 years ago by Henrik Bengtsson2.4k • written 4.3 years ago by Koh, Fong Ming20
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gravatar for Henrik Bengtsson
4.3 years ago by
United States
Henrik Bengtsson2.4k wrote:
Workaround here: http://aroma-project.org/install Henrik On Mar 15, 2013 11:18 PM, "Koh, Fong Ming" <fongming.koh@ucsf.edu> wrote: > > Hi all, > > I am trying to run the sample code found in the vignette for the Starr package, but my R crashes upon calling the readCelFile function. This problem seemed to have appeared previously (Nov 2011), but there was no solution listed. I've appended my session below. R crashes on the very last line. I'll be happy to take any suggestions on what I may be doing wrong. > > Thanks! > Fong Koh > > ================ > > Package vignette: http://www.bioconductor.org/packages/2.11/bioc/vignettes/Starr/inst/do c/Starr.pdf > Previous mention of problem: https://stat.ethz.ch/pipermail/bioconductor/2011-November/042165.html > > ================ > > > sessionInfo() > R version 2.15.3 (2013-03-01) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > > biocLite("Starr") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'Starr' > trying URL ' http://bioconductor.org/packages/2.11/bioc/bin/macosx/leopard/contrib/ 2.15/Starr_1.14.1.tgz ' > Content type 'application/x-gzip' length 1814289 bytes (1.7 Mb) > opened URL > ================================================== > downloaded 1.7 Mb > > > The downloaded binary packages are in > /var/folders/tl/dm9b5srj1bqfqwx7fk4bllpc0000gn/T//Rtmp1VFAMD/downloade d_packages > > library(Starr) > Loading required package: Ringo > Loading required package: Biobase > 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 > > Welcome to Bioconductor > > Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, > see 'citation("Biobase")', and for packages 'citation("pkgname")'. > > Loading required package: RColorBrewer > Loading required package: limma > Loading required package: Matrix > Loading required package: lattice > Loading required package: grid > Loading required package: affy > > Attaching package: ‘affy’ > > The following object(s) are masked from ‘package:Ringo’: > > probes > > Loading required package: affxparser > > Attaching package: ‘Starr’ > > The following object(s) are masked from ‘package:affy’: > > plotDensity > > The following object(s) are masked from ‘package:limma’: > > plotMA > > > dataPath <- system.file("extdata", package="Starr") > > bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap")) > > cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), file.path(dataPath,"Rpb3_IP2_chr1.cel")) > > names <- c("rpb3_1", "wt_1","rpb3_2") > > type <- c("IP", "CONTROL", "IP") > > ==== everything looks ok up to here, but crashes with the next line ======= > > > rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=T, log.it=T) > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 4.3 years ago by Henrik Bengtsson2.4k
Thanks! Installing affxparser from the Aroma project solved the problem. (I'm on OS X 10.8.3 and running R v2.15.3.) Cheers, Fong On Mar 16, 2013, at 12:36 AM, Henrik Bengtsson <hb at="" biostat.ucsf.edu=""> wrote: > Workaround here: > > http://aroma-project.org/install > > Henrik > > On Mar 15, 2013 11:18 PM, "Koh, Fong Ming" <fongming.koh at="" ucsf.edu=""> wrote: > > > > Hi all, > > > > I am trying to run the sample code found in the vignette for the Starr package, but my R crashes upon calling the readCelFile function. This problem seemed to have appeared previously (Nov 2011), but there was no solution listed. I've appended my session below. R crashes on the very last line. I'll be happy to take any suggestions on what I may be doing wrong. > > > > Thanks! > > Fong Koh > > > > ================ > > > > Package vignette: http://www.bioconductor.org/packages/2.11/bioc/v ignettes/Starr/inst/doc/Starr.pdf > > Previous mention of problem: https://stat.ethz.ch/pipermail/bioconductor/2011-November/042165.html > > > > ================ > > > > > sessionInfo() > > R version 2.15.3 (2013-03-01) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > source("http://bioconductor.org/biocLite.R") > > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > > > biocLite("Starr") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > > Installing package(s) 'Starr' > > trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/macosx/ leopard/contrib/2.15/Starr_1.14.1.tgz' > > Content type 'application/x-gzip' length 1814289 bytes (1.7 Mb) > > opened URL > > ================================================== > > downloaded 1.7 Mb > > > > > > The downloaded binary packages are in > > /var/folders/tl/dm9b5srj1bqfqwx7fk4bllpc0000gn/T//Rtmp1VFA MD/downloaded_packages > > > library(Starr) > > Loading required package: Ringo > > Loading required package: Biobase > > 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 > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, > > see 'citation("Biobase")', and for packages 'citation("pkgname")'. > > > > Loading required package: RColorBrewer > > Loading required package: limma > > Loading required package: Matrix > > Loading required package: lattice > > Loading required package: grid > > Loading required package: affy > > > > Attaching package: ?affy? > > > > The following object(s) are masked from ?package:Ringo?: > > > > probes > > > > Loading required package: affxparser > > > > Attaching package: ?Starr? > > > > The following object(s) are masked from ?package:affy?: > > > > plotDensity > > > > The following object(s) are masked from ?package:limma?: > > > > plotMA > > > > > dataPath <- system.file("extdata", package="Starr") > > > bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap")) > > > cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), file.path(dataPath,"Rpb3_IP2_chr1.cel")) > > > names <- c("rpb3_1", "wt_1","rpb3_2") > > > type <- c("IP", "CONTROL", "IP") > > > > ==== everything looks ok up to here, but crashes with the next line ======= > > > > > rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=T, log.it=T) > > _______________________________________________ > > 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
ADD REPLYlink written 4.3 years ago by Koh, Fong Ming20
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