Question: error in ls() unused arguments
0
gravatar for Wijchers, Patrick
10.7 years ago by
Wijchers, Patrick40 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_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] 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 */ -- Patrick Wijchers, PhD MRC Clinical Sciences Centre Imperial College London Hammersmith Campus Du Cane Road London W12 0NN Phone: +44 (0)20 8383 8500 (office) +44 (0)20 8383 8317 (lab) Fax: +44 (0)20 8383 8306 Email: patrick.wijchers at csc.mrc.ac.uk
mouse4302 affyplm • 1.4k views
ADD COMMENTlink modified 10.7 years ago by Laurent Gautier2.2k • written 10.7 years ago by Wijchers, Patrick40
Answer: error in ls() unused arguments
0
gravatar for Laurent Gautier
10.7 years ago by
Laurent Gautier2.2k
Laurent Gautier2.2k 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_IDEN TIFICATION=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 */ >
ADD COMMENTlink written 10.7 years ago by Laurent Gautier2.2k
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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=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 */ >> > -- Patrick Wijchers, PhD MRC Clinical Sciences Centre Imperial College London Hammersmith Campus Du Cane Road London W12 0NN Phone: +44 (0)20 8383 8500 (office) +44 (0)20 8383 8317 (lab) Fax: +44 (0)20 8383 8306 Email: patrick.wijchers at csc.mrc.ac.uk
ADD REPLYlink written 10.7 years ago by Wijchers, Patrick40
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=e n_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_ID ENTIFICATION=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 */ >>> >> >
ADD REPLYlink written 10.7 years ago by Laurent Gautier2.2k
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? 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)? 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_I DENTIFICATION=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 */ >>>> >>> >> > -- Patrick Wijchers, PhD MRC Clinical Sciences Centre Imperial College London Hammersmith Campus Du Cane Road London W12 0NN Phone: +44 (0)20 8383 8500 (office) +44 (0)20 8383 8317 (lab) Fax: +44 (0)20 8383 8306 Email: patrick.wijchers at csc.mrc.ac.uk
ADD REPLYlink written 10.7 years ago by Wijchers, Patrick40
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 */ >>>>> >>>> >>> >> >
ADD REPLYlink written 10.7 years ago by Laurent Gautier2.2k
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