Question: problems installing VariantFiltering package
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gravatar for Robert Castelo
5.3 years ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k wrote:
hi Daniel, i hope you don't mind i carbon copy the Bioconductor mailing list, as this problem you have may occur to other people who want to use VariantFiltering and in this way they'll find the answer if they google for this same question. the problem you are reporting below comes from the fact that you are using Bioconductor 2.13 bound to R version 3.0.2 while VariantFiltering only entered the latest release of Bioconductor 2.14 which is bound to R version 3.1.0, and therefore, it does not exist in previous releases of Bioconductor. you have to upgrade your installation of R to the latest one (3.1.0) and then install VariantFiltering. best regards, robert. On 05/19/2014 04:19 PM, Daniel Benitez Rivera wrote: > Dear Robert, > > I' m having problems installing VariantFiltering package. I don't > understand much of the error, but I copy the R-console log here: > >> install.packages("~/Escritorio/VariantFiltering_1.1.3.tar.gz", repos = NULL, type ="source") > Installing package into ?/home/daniel/R/x86_64-pc-linux-gnu- library/3.0? > (as ?lib? is unspecified) > ERROR: dependencies ?S4Vectors?, ?GenomeInfoDb?, ?BSgenome.Hsapiens.UCSC.hg19?, ?shiny? are not available for package ?VariantFiltering? > * removing ?/home/daniel/R/x86_64-pc-linux-gnu- library/3.0/VariantFiltering? > Warning in install.packages : > installation of package ?/home/daniel/Escritorio/VariantFiltering_1.1.3.tar.gz? had non-zero exit status > > > that's when I try to install it from source (a tar.gz file downloaded frombioconductor.org <http: bioconductor.org="">). When I try to install with > > source("http://bioconductor.org/biocLite.R") > biocLite("VariantFiltering") > > > I got this: > >> source("http://bioconductor.org/biocLite.R") > > Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help > A newer version of Bioconductor is available after installing a new version of R, > ?BiocUpgrade for help >> biocLite("VariantFiltering") > BioC_mirror:http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2. > Installing package(s)'VariantFiltering' > Mensajes de aviso perdidos > 1: package ?VariantFiltering? is not available (for R version 3.0.2) > 2: installed directory not writable, cannot update packages'annotate', > 'aroma.affymetrix','aroma.apd','aroma.core','BiocInstaller','caTo ols','gdata', > 'gplots','gtools','IRanges','limma','matrixStats','optparse','PSCBS', > 'R.devices','R.filesets','R.huge','R.methodsS3','R.oo','R.rsp','R samtools', > 'rtracklayer','R.utils','truncnorm','xtable','boot','class','cluster', > 'foreign','KernSmooth','lattice','MASS','Matrix','mgcv','nlme','nnet', > 'rpart','spatial','survival' > > > maybe the version of R or Bioconductor isn't right? > > thanks a lot!!! > > > -- > *Daniel Benitez Rivera* > /Asistente de Investigaci?n/ > /Bioinform?tica/ > *Centro de Biotecnolog?a* > *Universidad de Concepci?n* > Fono: (56)9-62207479 -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550
variantfiltering • 1.1k views
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