Hi Wolfgang, Your suggestion does work for me, and so provides a functional work-around. Thanks very much for the information. Best Steve McKinney Original question: >> Hi Wolfgang, >> >> I'm currently having a problem while analysing >> gene chip data using snapCGH. >> >> snapCGH loads tilingArray. >> >> After I process some data and either >> - quit with save = "yes" >> - use save.image() >> I am unable to reload the .Rdata contents on subsequent >> invocations of R. I get an error message >> >> >> Error: object 'breakpoints' not found whilst loading namespace 'tilingArray' >> Fatal error: unable to restore saved data in .RData >> >> >> I can reproduce this error by just starting up R, >> loading library(tilingArray), saving some simple variable >>> foo <- 7 >> then quitting R with save = "yes". >> >> If I try to restart R, R crashes with the error message above. >> >> I'm using the latest Developer version of tilingArray >> Package: tilingArray >> Version: 1.11.8 >> Date: 3 Aug 2006 >> >> Any information/assistance on how to patch this issue would >> be appreciated. I need to be able to save data to avoid lengthly >> reruns of time consuming algorithms on these big gene data >> sets. >> >> Copies of R output showing this issue are included below. >> >> Best regards >> >> >> >> Steven McKinney >> >> Statistician >> Molecular Oncology and Breast Cancer Program >> British Columbia Cancer Research Centre >> >> email: smckinney at bccrc.ca >> >> tel: 604-675-8000 x7561 >> >> BCCRC >> Molecular Oncology >> 675 West 10th Ave, Floor 4 >> Vancouver B.C. >> V5Z 1L3 >> Canada >> >> Reply: >Hi Steven, > >best to send this kind of questions to the bioc mailing list, rather >than to myself privately, because other people might (a) also have >answers or (b) benefit from the questions & answers. > >There is a problem / inconsistency with name spaces, a feature of R >which is currently rapidly evolving and which I (and others) need to >follow with our package code. > >Try loading the "tilingArray" (and in particular the "strucchange") >package before loading the .Rdata file, e.g. > >In the shell: >$ mv .Rdata myData.Rdata >$ R > >In R: > > library("tilingArray") > > load("myData.Rdata") > >Let me know if this helps, > Bw >Wolfgang > Output of original email illustrating problem: > Package: tilingArray > Version: 1.11.8 > Date: 3 Aug 2006 > Title: Analysis of high-density oligonucleotide tiling arrays > Author: Wolfgang Huber, Matt Ritchie, Joern Toedling > Maintainer: W. Huber <huber at="" ebi.ac.uk=""> > > > > > > ##------------------------------------------------------------------ --------------------------------- > ## Running R from Emacs 22.0.50.1 with ESS 5.2.12 on Apple PowerPC G5 > ## with OS X (Tiger 10.4.7) > > > R : Copyright 2006, The R Foundation for Statistical Computing > Version 2.3.1 (2006-06-01) > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> if(!exists("baseenv", mode="function")) baseenv <- function() NULL > options(STERM='iESS', editor='emacsclient') >>> library(tilingArray) > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > Loading required package: affy > Loading required package: affyio > Loading required package: RColorBrewer > Loading required package: grid > Loading required package: strucchange > Loading required package: zoo > Loading required package: sandwich > Loading required package: colorspace > > Attaching package: 'colorspace' > > > The following object(s) are masked from package:grDevices : > > hcl > > Loading required package: vsn > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: geneplotter > Loading required package: annotate > KernSmooth 2.22 installed > Copyright M. P. Wand 1997 > Loading required package: pixmap > Warning message: > found an S4 version of 'barplot' so it has not been imported correctly >> foo <- 7 >> q() > Save workspace image? [y/n/c]: y > > Process R:2 finished at Mon Aug 28 12:02:34 2006 > > > R : Copyright 2006, The R Foundation for Statistical Computing > Version 2.3.1 (2006-06-01) > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Error: object 'breakpoints' not found whilst loading namespace 'tilingArray' > Fatal error: unable to restore saved data in .RData > > > Process R:2 exited abnormally with code 2 at Mon Aug 28 12:02:52 2006 > > ##------------------------------------------------------------------ --------------------------------- > ## Running R from a *nix Terminal console window on Apple PowerPC G5 > ## with OS X (Tiger 10.4.7) > > > > steven-mckinneys-power-mac-g5:/Volumes/KilroyHD/kilroy/Projects/foo stevenmckinney$ rm .Rdata > steven-mckinneys-power-mac-g5:/Volumes/KilroyHD/kilroy/Projects/foo stevenmckinney$ R > > R : Copyright 2006, The R Foundation for Statistical Computing > Version 2.3.1 (2006-06-01) > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(tilingArray) > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > Loading required package: affy > Loading required package: affyio > Loading required package: RColorBrewer > Loading required package: grid > Loading required package: strucchange > Loading required package: zoo > Loading required package: sandwich > Loading required package: colorspace > > Attaching package: 'colorspace' > > > The following object(s) are masked from package:grDevices : > > hcl > > Loading required package: vsn > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: geneplotter > Loading required package: annotate > KernSmooth 2.22 installed > Copyright M. P. Wand 1997 > Loading required package: pixmap > Warning message: > found an S4 version of 'barplot' so it has not been imported correctly >> foo <- 7 >> q() > Save workspace image? [y/n/c]: y > steven-mckinneys-power-mac-g5:/Volumes/KilroyHD/kilroy/Projects/foo stevenmckinney$ ls -alF > total 152 > drwxr-xr-x 6 stevenmc stevenmc 204 Aug 28 12:06 ./ > drwxr-xr-x 13 stevenmc stevenmc 442 Jul 27 12:53 ../ > -rw-r--r-- 1 stevenmc stevenmc 16971 Aug 28 12:06 .RData > -rw-r--r-- 1 stevenmc stevenmc 70 Aug 28 12:06 .Rhistory > -rw-r--r-- 1 stevenmc stevenmc 875 Jun 22 18:05 ORDER_ID3051_SampleKey.txt > -rw-r--r-- 1 stevenmc stevenmc 48640 Jun 22 15:06 smiris.xls > steven-mckinneys-power-mac-g5:/Volumes/KilroyHD/kilroy/Projects/foo stevenmckinney$ R > > R : Copyright 2006, The R Foundation for Statistical Computing > Version 2.3.1 (2006-06-01) > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Error: object 'breakpoints' not found whilst loading namespace 'tilingArray' > Fatal error: unable to restore saved data in .RData > > steven-mckinneys-power-mac-g5:/Volumes/KilroyHD/kilroy/Projects/foo stevenmckinney$ > > Output showing success of work-around: steven-mckinneys-power-mac-g5:/Volumes/KilroyHD/kilroy/Projects/foo stevenmckinney$ mv .Rdata my.Rdata steven-mckinneys-power-mac-g5:/Volumes/KilroyHD/kilroy/Projects/foo stevenmckinney$ ls -alF total 152 drwxr-xr-x 6 stevenmc stevenmc 204 Aug 28 14:46 ./ drwxr-xr-x 14 stevenmc stevenmc 476 Aug 28 12:30 ../ -rw-r--r-- 1 stevenmc stevenmc 70 Aug 28 12:06 .Rhistory -rw-r--r-- 1 stevenmc stevenmc 875 Jun 22 18:05 ORDER_ID3051_SampleKey.txt -rw-r--r-- 1 stevenmc stevenmc 16971 Aug 28 12:06 my.Rdata -rw-r--r-- 1 stevenmc stevenmc 48640 Jun 22 15:06 smiris.xls steven-mckinneys-power-mac-g5:/Volumes/KilroyHD/kilroy/Projects/foo stevenmckinney$ R R : Copyright 2006, The R Foundation for Statistical Computing Version 2.3.1 (2006-06-01) ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(tilingArray) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: affy Loading required package: affyio Loading required package: RColorBrewer Loading required package: grid Loading required package: strucchange Loading required package: zoo Loading required package: sandwich Loading required package: colorspace Attaching package: 'colorspace' The following object(s) are masked from package:grDevices : hcl Loading required package: vsn Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: geneplotter Loading required package: annotate KernSmooth 2.22 installed Copyright M. P. Wand 1997 Loading required package: pixmap Warning message: found an S4 version of 'barplot' so it has not been imported correctly > load("my.Rdata") > foo [1] 7 >

Hi Steven, One more, I'd recommend using "save" explicitely for the objects you care about. Best wishes Wolfgang Steven McKinney wrote: > > Hi Wolfgang, > > Your suggestion does work for me, and so > provides a functional work-around. > > Thanks very much for the information. > > >

Hi Steven, using a more recent devel version of R and the other packages, the problem seems to have gone away, I can 1. rm .RData 2. Start R 3. (in R:) library(tilingArray); example(segment); q("yes") ## this will create an object 'res' of class segmentation 4. Start R again: [Previously saved workspace restored] 5. typing "res" will load the dependencies and print a summary of the object. So - your problem results from a feature in R, name spaces, that has recently undergone and is currently undergoing some changes. We package developers are trying to keep up with it, but some hickups may be expected: http://www.bioconductor.org/checkResults/1.9/gopher5-tilingArray- checksrc.html Best wishes Wolfgang > sessionInfo() R version 2.4.0 Under development (unstable) (2006-08-25 r38982) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;L C_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] "splines" "grid" "tools" "methods" "stats" "graphics" [7] "grDevices" "utils" "datasets" "base" other attached packages: tilingArray pixmap geneplotter annotate genefilter survival "1.11.9" "0.4-4" "1.11.8" "1.11.4" "1.11.8" "2.28" vsn colorspace strucchange sandwich zoo RColorBrewer "1.11.2" "0.9" "1.3-0" "2.0-0" "1.2-0" "0.2-3" affy affyio Biobase fortunes "1.11.6" "1.1.7" "1.11.28" "1.2-1" >