Hi Jo?o, Your suggestion works as advertised. Just to keep it handy on the record, this is an example source("http://bioconductor.org/biocLite.R") chooseBioCmirror("http://watson.nci.nih.gov/bioc_mirror") biocLite("BSgenome.Hsapiens.UCSC.hg19") Thank you, Ivan On Fri, Apr 15, 2011 at 12:18 PM, Jo?o Moura <palerma at="" gmail.com=""> wrote: > Hi Ivan, > Just look at the output of the source() >> source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). > Cheers > On Fri, Apr 15, 2011 at 5:41 PM, Ivan Gregoretti <ivangreg at="" gmail.com=""> wrote: >> >> Great. >> >> Would you mind showing how you can update the packages using any of >> those mirrors? >> >> Thank you, >> >> Ivan >> >> >> >> On Fri, Apr 15, 2011 at 11:34 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> wrote: >> > On Fri, Apr 15, 2011 at 8:10 AM, Ivan Gregoretti <ivangreg at="" gmail.com=""> >> > wrote: >> >> Hello Dan, >> >> >> >> Updating Bioconductor devel packages as instructed in >> >> >> >> http://bioconductor.org/install/ >> >> >> >> usually leads to stalled downloads when it retrieves large packages. >> >> The BSgenome packages are notorious for this. >> >> >> >> Can you or anybody recommend a solution that does not involve manually >> >> downloading the tar balls one by one? (Perhaps the is a mirror for >> >> devel.) >> > >> > Hi Ivan, >> > >> > There are mirrors for release and devel here: >> > >> > http://bioconductor.org/about/mirrors/ >> > >> > Dan >> > >> > >> >> >> >> Thank you, >> >> >> >> Ivan >> >> >> >> >> >> >> >> On Thu, Apr 14, 2011 at 5:33 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> wrote: >> >>> Bioconductors: >> >>> >> >>> We are pleased to announce Bioconductor 2.8, consisting of 466 >> >>> software packages and more than 500 up-to-date annotation packages. >> >>> There are 48 new software packages, and many updates and improvements >> >>> to existing packages. Two software packages that were in the previous >> >>> version have been removed. Bioconductor 2.8 is compatible with >> >>> R 2.13.0, and is supported on Linux, 32- and 64-bit Windows, and Mac >> >>> OS. ?Visit >> >>> >> >>> http://bioconductor.org >> >>> >> >>> for details and downloads. >> >>> >> >>> Contents >> >>> ======== >> >>> >> >>> * Getting Started with Bioconductor 2.8 >> >>> * New Software Packages >> >>> * Using Bioconductor in the cloud >> >>> >> >>> Getting Started with Bioconductor 2.8 >> >>> ===================================== >> >>> >> >>> To install Bioconductor 2.8: >> >>> >> >>> 1. Install R 2.13.0. ?Bioconductor 2.8 has been designed expressly for >> >>> this version of R. >> >>> >> >>> 2. Follow the instructions here: >> >>> >> >>> http://bioconductor.org/install/ >> >>> >> >>> Please visit http://bioconductor.org for details and downloads. >> >>> >> >>> New Software Packages >> >>> ===================== >> >>> >> >>> There are 48 new packages in this release of Bioconductor. >> >>> >> >>> a4 >> >>> >> >>> ?Automated Affymetrix Array Analysis Umbrella Package >> >>> >> >>> a4Base >> >>> >> >>> ?Automated Affymetrix Array Analysis Base Package >> >>> >> >>> a4Classif >> >>> >> >>> ?Automated Affymetrix Array Analysis Classification Package >> >>> >> >>> a4Core >> >>> >> >>> ?Automated Affymetrix Array Analysis Core Package >> >>> >> >>> a4Preproc >> >>> >> >>> ?Automated Affymetrix Array Analysis Preprocessing Package >> >>> >> >>> a4Reporting >> >>> >> >>> ?Automated Affymetrix Array Analysis Reporting Package >> >>> >> >>> AnnotationFuncs >> >>> >> >>> ?Annotation translation functions >> >>> >> >>> anota >> >>> >> >>> ?ANalysis Of Translational Activity >> >>> >> >>> chopsticks >> >>> >> >>> ?The snp.matrix and X.snp.matrix classes >> >>> >> >>> Clonality >> >>> >> >>> ?Clonality testing >> >>> >> >>> clst >> >>> >> >>> ?Classification by local similarity threshold >> >>> >> >>> clstutils >> >>> >> >>> ?Tools for performing taxonomic assignment >> >>> >> >>> clusterProfiler >> >>> >> >>> ?statistical analysis and visulization of >> >>> ?functional profiles for genes and gene clusters >> >>> >> >>> cn.farms >> >>> >> >>> ?Factor Analysis for copy number estimation >> >>> >> >>> ENVISIONQuery >> >>> >> >>> ?Retrieval from the ENVISION bioinformatics data portal into R >> >>> >> >>> ExiMiR >> >>> >> >>> ?R functions for the normalization of Exiqon miRNA array data >> >>> >> >>> flowPhyto >> >>> >> >>> ?Methods for Continuous Flow Cytometry >> >>> >> >>> flowPlots >> >>> >> >>> ?analysis plots and data class for gated flow cytometry data >> >>> >> >>> gaia >> >>> >> >>> ?An R package for genomic analysis of significant >> >>> ?chromosomal aberrations >> >>> >> >>> genefu >> >>> >> >>> ?Relevant Functions for Gene Expression Analysis, >> >>> ?Especially in Breast Cancer >> >>> >> >>> genoset >> >>> >> >>> ?Provides classes similar to ExpressionSet for copy number analysis >> >>> >> >>> GSVA >> >>> >> >>> ?Gene Set Variation Analysis >> >>> >> >>> ibh >> >>> >> >>> ?Interaction Based Homogeneity for Evaluating Gene Lists >> >>> >> >>> inveRsion >> >>> >> >>> ?Inversions in genotype data >> >>> >> >>> IPPD >> >>> >> >>> ?Isotopic peak pattern deconvolution for Protein Mass >> >>> ?Spectrometry by template matching >> >>> >> >>> joda >> >>> >> >>> ?JODA algorithm for quantifying gene deregulation using knowledge >> >>> >> >>> lol >> >>> >> >>> ?Lots Of Lasso >> >>> >> >>> mcaGUI >> >>> >> >>> ?Microbial Community Analysis GUI >> >>> >> >>> mgsa >> >>> >> >>> ?Model-based gene set analysis >> >>> >> >>> MLP >> >>> >> >>> ?Mean Log P Analysis >> >>> >> >>> mosaics >> >>> >> >>> ?MOdel-based one and two Sample Analysis and Inference for ChIP-Seq >> >>> >> >>> MSnbase >> >>> >> >>> ?Base Functions and Classes for MS-based Proteomics >> >>> >> >>> NCIgraph >> >>> >> >>> ?Pathways from the NCI Pathways Database >> >>> >> >>> phenoDist >> >>> >> >>> ?Phenotypic distance measures >> >>> >> >>> phenoTest >> >>> >> >>> ?Tools to test correlation between gene expression and phenotype >> >>> >> >>> procoil >> >>> >> >>> ?Prediction of Oligomerization of Coiled Coil Proteins >> >>> >> >>> pvac >> >>> >> >>> ?PCA-based gene filtering for Affymetrix arrays >> >>> >> >>> qrqc >> >>> >> >>> ?Quick Read Quality Control >> >>> >> >>> RNAinteract >> >>> >> >>> ?Estimate Pairwise Interactions from multidimensional features >> >>> >> >>> Rsubread >> >>> >> >>> ?a super fast, sensitive and accurate read aligner for mapping >> >>> ?next-generation sequencing reads >> >>> >> >>> seqbias >> >>> >> >>> ?Estimation of per-position bias in high-throughput sequencing data >> >>> >> >>> snm >> >>> >> >>> ?Supervised Normalization of Microarrays >> >>> >> >>> snpStats >> >>> >> >>> ?SnpMatrix and XSnpMatrix classes and methods >> >>> >> >>> survcomp >> >>> >> >>> ?Performance Assessment and Comparison for Survival Analysis >> >>> >> >>> TDARACNE >> >>> >> >>> ?Network reverse engineering from time course data >> >>> >> >>> TEQC >> >>> >> >>> ?Quality control for target capture experiments >> >>> >> >>> TurboNorm >> >>> >> >>> ?A fast scatterplot smoother suitable for microarray normalization >> >>> >> >>> Vega >> >>> >> >>> ?An R package for copy number data segmentation >> >>> >> >>> >> >>> Using Bioconductor in the cloud >> >>> =============================== >> >>> >> >>> This release features the Bioconductor Amazon Machine >> >>> Image (AMI), which allows easy access to R and Bioconductor >> >>> within the Elastic Compute Cloud (EC2). It's easy to run >> >>> parallelizable tasks on MPI clusters, run R from within >> >>> your web browser using RStudio Server, and more. No >> >>> installation required. Information available at: >> >>> >> >>> http://bioconductor.org/help/bioconductor-cloud-ami/ >> >>> >> >>> _______________________________________________ >> >>> Bioc-sig-sequencing mailing list >> >>> Bioc-sig-sequencing at r-project.org >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >>> >> >> >> > >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> Bioc-sig-sequencing at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > -- > Jo?o Moura >