Patrick Wijchers wrote: > I guess my saved session is problematic... > To confirm this, I started a new folder and made new objects and there, > everything works like a charm. > > However, I can still access all my objects, so it appears all my work > and data is not lost.... thank god for that as a start to the weekend! > > Is there a easy way to access these objects in a different folder, e.g. > by copying or editing them into a new R session? The problem, as you experience it, seems to be that loading your earlier session compromises a number of things. You could just try saving individual objects of importance into files (with the command "save"), and then import them one by one in a fresh R session (where attaching library seems to be working). > Or does this mean I > will have to spend some time to reproduce all my data in new session > (which should be a lot quicker second time around)? If you have a file in which all operations are recorded, this should be no major issue (beside possibly the computation time). Hoping this helps, L. > Again, thank you very much for your help, > > Patrick > > Laurent Gautier wrote: >> >> Try then >> >> R --no-site-file --no-init-file --no-environ >> >> If you experience trouble again, that means that your saved session is >> problematic. Let's hope not for now. >> >> >> L. >> >> >> Patrick Wijchers wrote: >>> Thanks for your quick response. If I use R --vanilla I can load the >>> affyPLM package without problems: >>> /*> library(affyPLM) >>> Loading required package: affy >>> Loading required package: Biobase >>> Loading required package: tools >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>> Loading required package: gcrma >>> Loading required package: matchprobes >>> Loading required package: splines >>> Loading required package: preprocessCore*/ >>> >>> However, now, my objects seem to be gone: >>> /*> ls() >>> character(0) >>> > objects() >>> character(0)*/ >>> >>> Any idea why? >>> >>> Thanks again, >>> >>> Patrick >>> >>> Laurent Gautier wrote: >>>> >>>> >>>> Is this this happening when starting R like: >>>> >>>> R --vanilla >>>> >>>> ? >>>> >>>> Patrick Wijchers wrote: >>>>> Dear all, >>>>> >>>>> I encountered a problem while working on R that I do not know how >>>>> to solve. >>>>> It started when I wanted to load the affyPLM package: >>>>> */> library(affyPLM) >>>>> Loading required package: gcrma >>>>> Loading required package: matchprobes >>>>> Loading required package: splines >>>>> Loading required package: preprocessCore >>>>> Error in ls(where) : unused argument(s) (2) >>>>> Error in library(affyPLM) : .First.lib failed for 'affyPLM'/* >>>>> >>>>> As packages such as 'affy', 'genefilter' and 'limma' load fine, I >>>>> thought it might be something related to the affyPLM package. >>>>> However, upon trying to re-install the package, I got a similar error: >>>>> /*> source("http://bioconductor.org/biocLite.R") >>>>> Error in ls(all.names = TRUE) : unused argument(s) (all.names = >>>>> TRUE)*/ >>>>> >>>>> Now, I think it may be related to the 'ls' function. Strangely >>>>> enough, when using the 'ls' command I get this: >>>>> /*> ls() >>>>> Quality control information for mouse4302: >>>>> This package has the following mappings: >>>>> Error in get(mapname) : variable "mouse4302ACCNUM" was not found*/ >>>>> >>>>> I can now only access my objects using 'objects()'. >>>>> Strangely, I have been using all week without problems. I have >>>>> tried restarting R, even reinstalling R, but to no avail. I hope it >>>>> is something stupid I do not see.... Does anyone have a suggestion >>>>> how I can solve this? >>>>> >>>>> Any help would be greatly appreciated, >>>>> >>>>> Patrick >>>>> >>>>> /*> sessionInfo() >>>>> R version 2.8.1 (2008-12-22) >>>>> x86_64-redhat-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_ IDENTIFICATION=C >>>>> >>>>> >>>>> attached base packages: >>>>> [1] splines tools stats graphics grDevices utils >>>>> datasets >>>>> [8] methods base other attached packages: >>>>> [1] preprocessCore_1.4.0 gcrma_2.14.1 matchprobes_1.14.1 >>>>> [4] affy_1.20.0 Biobase_2.2.1 RSQLite_0.7-1 >>>>> [7] DBI_0.2-4 loaded via a namespace (and not attached): >>>>> [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2 >>>>> [4] genefilter_1.22.0 mouse4302.db_2.2.5 survival_2.34-1 */ >>>>> >>>> >>> >> >