error in ls() unused arguments
1
0
Entering edit mode
@wijchers-patrick-2973
Last seen 10.2 years ago
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 mouse4302 affyPLM • 2.6k views
ADD COMMENT
0
Entering edit mode
Laurent Gautier ★ 2.3k
@laurent-gautier-29
Last seen 10.2 years ago
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 COMMENT
0
Entering edit mode
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 REPLY
0
Entering edit mode
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 REPLY
0
Entering edit mode
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 REPLY
0
Entering edit mode
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 REPLY

Login before adding your answer.

Traffic: 815 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6