[BioC] Mac OS X Tiger builds now available (was Re: BioC 2.2 now available)

Patrick Aboyoun paboyoun at fhcrc.org
Fri May 2 16:58:57 CEST 2008


Last night we replaced the Mac OS X binary packages from Leopard (OS X 10.5) to Tiger (OS X 10.4) at the BioC 2.2 repository. Mac users on Tiger can now migrate to BioC 2.2 using biocLite with the default settings (i.e. type = "mac.binary").

For those users on Mac OS X Leopard, we are still building the Leopard binary packages but are not making them available since the standard CRAN-style repository does not support two types of Mac OS X universal binary packages. If there is a sufficient demand from the Bioconductor user-base, we can create a parallel repository for the Leopard binary packages that will be made available to Leopard users through biocLite.



Patrick




Martin Morgan wrote:
> Bioconductors:
>
> We are pleased to announce the release of Bioconductor 2.2. This
> release includes 35 new packages, and many improvements to existing
> packages.  There are now 260 package in Bioconductor 2.2. These
> packages are compatible with R 2.7.0.
>
> IMPORTANT: MAC OS USERS: the 'binary' builds currently available with
> biocLite are not suitable for Tiger (OS X 10.4). We expect to have
> Tiger-compatible builds within the next week. If you are using Tiger,
> please refrain from migrating to R-2.7.0 until these binaries become
> available, or use the 'type="source"' option to biocLite.
>
> As a member of the Bioconductor community, you have contributed
> greatly to this release. Perhaps you are a perplexed newcomer asking
> for help on the Bioc mailing list. Perhaps you are an experienced user
> seeking reproducible and advanced functionality. Or perhaps you are a
> package developer helping others to make sound sense of their
> data. Whatever your role, you've made Bioconductor the resource it is
> today. We are especially grateful to package developers, to members of
> the Bioconductor team in Seattle, and to those participants on the
> Bioc mailing list who knowledgeably and patiently answer questions
> large and small.
>
> High-throughput genomic research is a dynamic and exciting field. It
> is hard to predict what surprising packages are in store for future
> Bioconductor releases. We anticipate continued integration with
> diverse data sources, use of R's advanced graphics abilities, and
> implementation of cutting edge research algorithms for the benefit of
> all Bioconductor users. Short-read DNA resequencing technologies are
> one area where growth seems almost certain.
>
> We look forward to a vibrant release cycle!
>
> Contents
> ========
>
> * Getting Started With Bioconductor 2.2
>
> * New and Re-introduced Packages
>
> * Significant Changes to Annotation Packages
>
>
>
>
> Getting Started With Bioconductor 2.2
> =====================================
>
> IMPORTANT: MAC USERS: see the important note above.
>
> To install Bioconductor 2.2
>
> 1. Install R 2.7.0.  Bioconductor 2.2 has been designed expressly for
>    this version of R.
>
> 2. Follow the instructions here:
>
>    http://bioconductor.org/download
>
> Please visit http://bioconductor.org for details and downloads.
>
>
> New and Re-introduced Packages
> ==============================
>
> The following packages are new in this release of Bioconductor; visit
>
>   http://bioconductor.org/packages/release/Software.html
>
> for links to all package descriptions.
>
>
> AffyCompatible
>   Affymetrix GeneChip software compatibility
>
> BAC
>   Bayesian Analysis of Chip-chip experiment
>
> BCRANK
>   Predicting binding site consensus from ranked DNA sequences
>
> BGmix
>   Bayesian models for differential gene expression
>
> BiocCaseStudies
>   Support for the Bioconductor Case Studies Monograph
>
> GEOmetadb
>   A compilation of metadata from NCBI GEO
>
> GGBase
>   Infrastructure for genetics of gene expression (c) 2008 VJ Carey
>
> GSEAlm
>   Linear Model Toolset for Gene Set Enrichment Analysis
>
> GeneRfold
>   R for genes and sequences, using viennaRNA package (fold)
>
> GeneSelector
>   GeneSelector
>
> GenomeGraphs
>   Plotting genomic information from Ensembl
>
> GraphAlignment
>   GraphAlignment
>
> PCpheno
>   Phenotypes and cellular organizational units
>
> RBioinf
>   Support for R for Bioinformatics Monograph
>
> Rdisop
>   Decomposition of Isotopic Patterns
>
> Rtreemix
>   Mutagenetic trees mixture models.
>
> SLGI
>   Synthetic Lethal Genetic Interaction
>
> XDE
>   A Bayesian hierarchical model for cross-study analysis of
>   differential gene expression
>
> affyPara
>   Parallelized preprocessing methods for Affymetrix Oligonucleotide
>   Arrays
>
> flowClust
>   Clustering for Flow Cytometry
>
> flowQ
>   Qualitiy control for flow cytometry
>
> flowUtils
>   Utilities for flow cytometry
>
> gaga
>   GaGa hierarchical model for microarray data analysis
>
> goProfiles
>   An R package for the statistical analysis of functional profiles
>
> mdqc
>   Mahalanobis Distance Quality Control for microarrays
>
> occugene
>   Functions for Multinomial Occupancy Distribution
>
> plw
>   Probe level Locally moderated Weighted t-tests.
>
> rtracklayer
>   R interface to genome browsers and their annotation tracks
>
> snpMatrix
>   The snp.matrix and X.snp.matrix classes
>
> xps
>   Methods for Processing and Analysis of Affymetrix Oligonucleotide
>   Arrays
>
> yaqcaffy
>   Affymetrix expression data quality control and reproducibility analysis
>
>
> Additional packages have been re-introduced to the release branch:
>
> GeneticsPed
>   Pedigree and genetic relationship functions
>
> Rredland
>   Interface to redland RDF utilities
>
> externalVector
>   Vector objects for R with external storage
>
> stam
>   Structured Analysis of Microarray Data
>
>
> Packages still present in the 'development' branch, but no longer in
> the release, include BeadExplorer, GeneRfold, MCRestimate, and
> SAGElyzer. Packages retired from Bioconductor include arrayMagic,
> ChromoViz, GeneTS, iSNetwork, iSPlot, and RMAPPER.
>
>
> Significant Changes to Annotation Packages
> ==========================================
>
> Bioconductor 2.2 includes a large number of annotation
> packages. Descriptions are available here:
>
>   http://bioconductor.org/packages/release/AnnotationData.html
>
> New 'db' annotation packages replace their predecessors, e.g.,
> hgu95av2.db replaces hgu95av2 . Both 'db' and original packages are
> available in this release, but we anticipate that future releases will
> only contain 'db' packages.  Most db packages now contain Ensembl
> accessions,
>
> New 'organism' packages are available for several model organisms: human,
> org.Hs.eg.db; mouse, org.Mm.eg.db; rat, org.Rn.eg.db; yeast,
> org.Sc.sgd.db; fly, org.Dm.eg.db; malaria, org.Pf.plasmo.db.  Many of
> these packages contain additional organism-specific annotations, e.g.,
> flybase (Drosophila) or Jackson Laboratories (mouse) IDs.
>
> New 'homology' packages summarize InParanoid homology data. Use these
> and the organism packages to map between InParanoid and other IDS
> IDs. Available homology packages include: human, hom.Hs.inp.db; mouse,
> hom.Mm.inp.db; rat, hom.Rn.inp.db; yeast, hom.Sc.inp.db; fly,
> hom.Dm.inp.db.
>
> The PFAM package is available as PFAM.db
>
> Custom CDF packages provided by Manhong Dai are not currently
> available, but should be shortly.
>
>
> Martin
>



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