search for: affyio

Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun root@bio...

...9-1 * checking for file 'nvNormalize/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'nvNormalize' version '1.0' * checking package name space information ... OK * checking package dependencies ... ERROR Namespace dependencies not required: affy affyio hgu133acdf hgu133plus2cdf simpleaffy See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. I've looked at the manual but cannot figure out if the problem is in the way I have specified dependencies in NAMESPACE or D...

...9 with R version 2.4.0 Your version of R requires version 1.9 of Bioconductor. Avis dans install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using /usr/local/lib/R/site-library also installing the dependencies 'affy', 'affyio' essai de l'URL ' http://bioconductor.org/packages/1.9/bioc/src/contrib/affy_1.12.1.tar.gz' Content type 'application/x-gzip' length 1370295 bytes URL ouverte ================================================== downloaded 1338Kb essai de l'URL ' http://bioconductor....

...t the package should be included in the Depends list, but this has not helped. https://stat.ethz.ch/pipermail/bioc-devel/2007-April/001079.html Thank you. The contents of my DESCRIPTION file are: Package: nvQC Type: Package ... Depends: R(>= 2.5.0), Biobase, qcc Imports: affy, RColorBrewer, affyio, nvNormalize Suggests: nvCELFiles LazyLoad: no LazyData: yes and those of the NAMESPACE file export(nv.evalQC, gridQC, control.plots) import(qcc, affy) importFrom(RColorBrewer, brewer.pal) importFrom(affyio, read.celfiles) importFrom(nvNormalize, norm.options) The output from R CMD check nvQC...

Hello, I follow the Bioconductor instruction (http://www.bioconductor.org/download <http://www.bioconductor.org/download> ) to install Biocoductor, there have some errors: /usr/lib/R/bin/SHLIB: line 115: make: command not found chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such file or directory ERROR: compilation failed for package 'affyio' ** Removing '/usr/local/lib/R/site-library/affyio' * Installing *source* package 'survival' ... ** libs /usr/lib/R/bin/SHLIB: line 115: make: command not found ERROR: compilation failed fo...

...2 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 [4] BiocInstaller_1.8.1 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.0 affyio_1.26.0 Biostrings_2.26.1 [4] bit_1.1-8 codetools_0.2-8 DBI_0.2-5 [7] ff_2.2-7 foreach_1.4.0 GenomicRanges_1.10.1 [10] IRanges_1.16.2 iterators_1.0.6 parallel_2.15.1 [13] preprocessCore_1.20.0 splines_2.15.1 stats4_2.15.1 [16] tool...

...EPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: affy affyio Biobase "1.14.0" "1.4.0" "1.14.0"

...=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: ?1? "stats" "graphics" "grDevices" "datasets" "utils" "tools" ?7? "methods" "base" other attached packages: limma affy affyio Biobase "2.9.13" "1.13.14" "1.3.3" "1.13.39" > -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine

...=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: ?1? "stats" "graphics" "grDevices" "datasets" "utils" "tools" ?7? "methods" "base" other attached packages: limma affy affyio Biobase "2.9.13" "1.13.14" "1.3.3" "1.13.39" > -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine

...GO graph Ruuid limma genefilter survival rat2302 "1.8.1" "1.11.5" "1.6.5" "1.11.13" "1.11.2" "2.7.9" "1.11.8" "2.28" "1.12.0" affy affyio Biobase "1.11.6" "1.1.8" "1.11.29" fileName<-paste(experiment, contrast, "FDR", FDR, "Graph", "ps", sep=".") postscript(file=fileName, paper="special",width=width, height=height) #set up graphics...

...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: affyio > getMethods("geneNames") An object of class ?MethodsList? Slot "methods": $ExpressionSet Method Definition: function (object) { .Deprecated("featureNames") featureNames(object) } <environment: namespace:Biobase> Signatures: object...

...-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12" "1.11.4" "1.13.6" "1.15.12" graph limma affy affyio Biobase "1.13.6" "2.9.13" "1.13.14" "1.3.3" "1.13.39" -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine

...-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12" "1.11.4" "1.13.6" "1.15.12" graph limma affy affyio Biobase "1.13.6" "2.9.13" "1.13.14" "1.3.3" "1.13.39" -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine

I have identical R.profiles and R_HOME directories set up on both my local machine and a remote linux cluster. To keep my libraries and R install separate, I use a site-library on both machines. The first line of my .Rprofile is: '.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is' Until R-2.6.0 this was working fine on both machines, but since I have been

...e to Bioconductor > > > Vignettes contain introductory material. > > To view, simply type 'openVignette()' or start with 'help(Biobase)'. > > For details on reading vignettes, see the openVignette help page. > > >Loading required package: affyio >Loading required package: affydata >Loading required package: Biobase >Loading required package: gcrma >Loading required package: matchprobes >Loading required package: reposTools >Loading required package: simpleaffy >Loading required package: genefilter >Loading required...

...IC=C;LC_TIME=English_United States.1252 attached base packages: [1] "stats" "graphics" "grDevices" "datasets" "utils" "tools" "methods" "base" other attached packages: DBI limma affy affyio Biobase "0.1-12" "2.9.8" "1.13.14" "1.3.3" "1.13.34" > Mark W. Kimpel MD (317) 490-5129 Work, & Mobile (317) 663-0513 Home (no voice mail please) 1-(317)-536-2730 FAX -----Original Message----- From: Steffen Durinck [mai...

...t;) It failed and I got the error, Error in read.celfile.header(as.character(filenames[[1]])) : Is CH1.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats Also, I tried the command read.celfile in package "affyio" and it works, > x<-read.celfile("CH1.CEL") > str(x) List of 6 $ HEADER :List of 9 ..$ cdfName : chr "Axiom_GW_ASI_SNP" ..$ CEL dimensions : int [1:2] 1190 1190 ..$ GridCornerUL : int [1:2] 0 0 ..$ GridCornerUR : int [1:2]...

...; ?Vignettes contain introductory material. To view, type >> ?'openVignette()'. To cite Bioconductor, see >> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: affy >> Loading required package: affyio >>> >>> sessionInfo() >> >> R version 2.10.0 (2009-10-26) >> x86_64-unknown-linux-gnu >> >> locale: >> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >> ?[5] LC_MONETARY=C ? ? ?...

Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty:

...o point with 0.25 inches warning: no point with 0.25 inches warning: no point with 0.25 inches Why does this happen. 2) Now I am trying to run EBAM: and when I type I get an error > find.out<-find.a0(datrmanhi,groupsnhi.cl,rand=123) Loading required package: affy Loading required package: affyio EBAM Analysis for the two class unpaired case. Warning: There are 1 genes which have variance Zero or no non-missing values. The d-value of these genes is set to NA. The following object(s) are masked _by_ .GlobalEnv : n The following object(s) are masked fro...