This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - April 03, 2003: tkWidgets - a widget - importWizard is under development to provide an interactive interface to import data to R (e.g. CEL files). JZ April 03, 2003: AnnBuilder - major modifications made so that the package does not need any database support and the process of making data packages is simplified. A pdf file (AnnBuilder.pdf) in the doc directory of the developmental version contains examples of using the new version to build data packages. JZ April 03, 2003: graph - added lots of functionality for manipulating nodes and edges. RG April 03, 2003: getBioC - Option 'prog' for package download now will obtain the Ruuid package. JG April 02, 2003: graph - added a method to the graph class 'isConnected', which will return a boolean indicating if a graph is fully connected. This is just a convenience wrapper around 'connComp'. JG April 02, 2003: Rgraphviz - Nodes are now forced to be a fixed size. Also, GraphViz version requirements (listed in SystemRequirements: of the DESCRIPTION file) will be enforced programattically. JG April 02, 2003: affy - (as the 1st was a tricky date to make an annoucement). Autoload of missing cdfenvs packages from the website (user prompted before). Can be configured through the options. LG March 31, 2003: Rgraphviz - added in support for twopi layouts. JG March 31, 2003: Biobase - openVignette() has been modified to no longer use the vignette functionality from DynDoc. DynDoc is no longer depended on by Biobase. JG March 31, 2003: Biobase - added a function getPkgPDFs(), which will return a vector of all PDF files stored in a package's 'doc' directory. March 31, 2003: Massive editing of RBGL, so that it works with graph library objects (only graphNELs at this time). A vignette is present.

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - April 11, 2003 - Major efforts are being made to simplify data package building using AnnBuilder by providing a single API. Code has been modified a lot. The Rnw files do not build right now but will be fine soon. JZ April 11, 2003 - Rgraphviz: The graphNEL plot method now allows for the argument 'rankDir', which with dot layouts will allow the user to specify a top-to-bottom (TB) or left-to-right (LR) orientation - JG April 10, 2003 - Rgraphviz: Package now includes a dataset, 'graphExamples', which contains a variety of graphNEL objects to test plotting on. JG April 9, 2003 - Rgraphviz: now generating the plots slightly differently, which will provide some graphical errors on the start/end of edges (generally stop short of the node itself, sometimes slightly overrun), but should provide for better plots overall. Also, trying some things to provide a bit more stahbility ... -JG April 8, 2003 - affycompp: added the package to repository. - RI April 7, 2003 - reposTools: syncLocalLibList() now will update all changes, and not just new packages beign added. It will also report what updates it is making. sLLLL() will be run when reposTools is loaded - JG April 7, 2003 - significant extensions to RBGL: dfsBGL, bfsBGL, vignette. - VJC April 7, 2003 - NELhandler of graph now handles edgeless graphs in GXL - VJC

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - April 18, 2003 - Rgraphviz: Rgraphviz will now use validGraph() to check the validity of graphs that are to be plotted. JG April 18, 2003 - AnnBuilder: function - ABPkgBuilder - was improved so that users are able to call that single function to build a data package or XML documents. The HowTo vignette in inst/doc describes how (pdf version available). JZ April 18, 2003 - Ruuid: Removed the iniRuuid classes routine and instead the package is now relying on the installl.R structure. This is considered a test case for this process in other packages. JG April 18, 2003 - reposTools - fixed a bug where it was not properly honoring the previous repository information on updates. JG April 17, 2003 - tkWidgets: importWizard imporved to enable users to import a data file (e.g. a Affymetrix CEL file) to R. It works reasonablely well. JZ

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - Apr 26 2003: limma - imported version 1.0. GKS Apr 25 2003: data packages - new data packages (1.2.1) constructed with several changes: 1. Any occurrence of AFFY has been replaced by PROBE to make the term generic. 2. Mappings to GO ids become a named vector with the name(s) being the evidence code(s) provided by NCBI. 3. Values of GOXXPARENTS in GO package also become named vectors with the names being either isa or partof to indicate the relations of GO ids to their parents. 4. GO package includes GOXXCHILDREN to allow for search for direct children and GOCATEGORY for grouping (to MF, BP, and CC) 5. Dependance of Biobase removed. JZ Apr 25 2003: reposTools - pathed the release 1.1 branch version of reposTools to account for the bug fixes and updates to the package from the development branch over the last month. JG Apr 24 2003: Iyer517 -- new package 0.1 ... time course experiment from Science 1999 paper of Iyer in Eisen lab. Includes vignette. May be ready for release VJC Apr 24 2003: affy - The default background adjustment given by the rma() function has been changed so that it agrees with the results of expresso. If you wish to enable the previous behaviour use bgversion=1 in your rma() call. The function just.rma() has also been adjusted accordingly. BMB Apr 25 2003: limma 0.9.7 - new package - Linear Models for Microarray Data. Data analysis, linear models and differential expression for spotted and oligonucleotide microarrays. GKS Apr 24 2003: reposTools - Fixed several bugs, primarily one in which the system was not always checking that the version of the package available was newer than the current installation of a package. JG Apr 23 2003: reposTools - Fixed a bug in the dependency checking routines, which would appear if a user maintained multiple libraries of R packages. The system would only check for dependency resolution in the same library directory that the package was being installed to. It now checks .libPaths(). JG Apr 22 2003: Rgraphviz - Graphs can be plotted w/ twopi layout method even if not fully connected. JG Apr 22 2003: tkWidgets - a new function - DPExplorer - added. The function allow users to explore a Bioconductor data package using an interactive widget. JZ Apr 22 2003: Rgraphviz - set up Rgraphviz to use stored images for generic and method code via install.R much like the Ruuid package. JG Apr 22 2003: reposTools - The default action when one specifies repositories manually is to no longer attach any repositories from the R options. This can be forced via 'searchOptions=TRUE'. Furthermore, when repositories are manually specified, the system will *not* honor previous repository information during updates. JG Apr 20 2003: ROC no longer requires Biobase