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 <dtene...@fhcrc.org> wrote: > On Fri, Apr 15, 2011 at 8:10 AM, Ivan Gregoretti <ivang...@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 <dtene...@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@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >> > _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
