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 30 2003: reposTools - Fixed several bugs in syncLocalLibList() that caused problems when dealing with multiple package library directories. This also caused problems down the line w/ getBioC and *.packages2() (REL1.1 and Devel) - JG Apr 29 2003: annotate - references to data package hgu95a have been changed to hgu95av2. JG Apr 29 2003: limma - imported version 1.0.2 - fixed bug in ebayes when more than two coefficients (bug introduced on Apr 25). Added new normalization method, robust splines. Changes to plotPrintTipLoess. Several changes to .Rd files. Apr 28 2003: reposTools - Fixed a bug in save.locLib (called mainly by syncLocalLibList() where the system would not check that write access exists for liblisting.Rda before attempting to write. Also wrapped a call to installed.packages() in a try() due to a bug in the way it handles empty dirs. (Rel1.1 and Devel) JG Apr 28 2003: getBioC - Replaced the 'isDevel' and 'version' parameters with 'relLevel' which can take one of 'release', 'devel', 'contrib', and 'release1.0' as arguments. Default is 'release' (1.1) JG Apr 27 2003: limma - imported version 1.0.1 - Several new help topics and consolidation of a couple of old ones. Correction of a couple of small code bugs concerning creation of classed objects by MA.RG and backgroundCorrect. Other minor changes to help topics entries. GKS

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. ---------------------------------------------------------------------- - May 9 2003: Rgraphviz - Finalizers were being called on the graphviz pointer prematurely. Fixed this, but the negative is that there is now a bit of a memory leak. Still working on that. JG May 7 2003: limma - imported version 1.0.4 - basically a file permission change. May 6 2003: affy - The large datasets moved to a new (and *required*) package 'aFfYDaTA' (erh, I meant 'affydata'). The version number is still increasing as we fix minor things... LG May 5 2003: getBioC - If no destdir is supplied, instead of assuming .libPaths()[1], it will present the user with a menu of choices for installation directories if there is more then one directory in .libPaths(). JG May 4 2003: limma - imported version 1.0.3 - New function printorder. Correct typo in DESCRIPTION. Alias for merge method to reflect dispatching on two arguments.

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. ---------------------------------------------------------------------- - 15 May, 2003: annotate/geneplotter - These packages now make use of the 1.2.6 version of the data packages (and will not work on any version less then 1.2.6). JG 15 May, 2003: A new version (1.2.6) of the data packages are available for download. JZ 14 May, 2003: geneplotter - Cleaned up cPlot/cColor/alongChrom and friends to utilize the new chromLocation class structure, and to be portable across any organism. 12 May, 2003: Ruuid - Fixed a memory bug in Ruuid. JG 12 May, 2003: annotate - Fixed a bug in locuslinkByID where if multiple locuslink IDs were chosen, only the page for the first was shown. JG 12 May, 2003: Rgraphviz - More properly fixed the stability problems in Rgraphviz, in a way that solves the problem at its root. Also does not have the memory leak side effect of the previous fix. JG 10 May, 2003: limma - imported version 1.0.5 - new function 'printorder', added sma to dependencies in DESCRIPTION, updates and corrections to User's Guide. GKS

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 of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - May 23, 2003: limma - version 1.0.8 - corrected bug in read.maimages for quantarray data. Added wtIgnore.Filter function for quantarray data. GKS May 21, 2003: data package - a data package for yeast (YG) is available for downloading. A total of 6262 ORFs are included in the package. JZ May 20, 2003: reposTools - changed the structure of the local package management file. Automatic conversion tools are now integrated. JG May 19 2003: limma - imported version 1.0.7 - printable pdf version of User's Guide, use of chol pivot in classifyTests.vector, plus a couple of typos corrected. GKS May 18 2003: limma - imported version 1.0.6 - minor cleaning up of documentation files and vignette ready for BioC release. GKS

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 of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - May 25 2003: edd -- completely revised; old functionality available in eddObsolete function which will be eliminated. HOWTO-edd and eddDetails vignettes - VJC